2023

Jump to: 2022, 2021, 2020

19 pages, 4262 KiB

Open AccessArticle

Hepatic Transcriptome Analysis Reveals Genes, Polymorphisms, and Molecules Related to Lamb Tenderness

by Kasita Listyarini, Cece Sumantri, Sri Rahayu, Md. Aminul Islam, Syeda Hasina Akter, Muhammad Jasim Uddin and Asep Gunawan

Animals 2023, 13(4), 674; https://doi.org/10.3390/ani13040674 - 15 Feb 2023

Cited by 4 | Viewed by 1953

Abstract

Tenderness is a key meat quality trait that determines the public acceptance of lamb consumption, so genetic improvement toward lamb with higher tenderness is pivotal for a sustainable sheep industry. However, unravelling the genomics controlling the tenderness is the first step. Therefore, this [...] Read more.

Tenderness is a key meat quality trait that determines the public acceptance of lamb consumption, so genetic improvement toward lamb with higher tenderness is pivotal for a sustainable sheep industry. However, unravelling the genomics controlling the tenderness is the first step. Therefore, this study aimed to identify the transcriptome signatures and polymorphisms related to divergent lamb tenderness using RNA deep sequencing. Since the molecules and enzymes that control muscle growth and tenderness are metabolized and synthesized in the liver, hepatic tissues of ten sheep with divergent phenotypes: five high- and five low-lamb tenderness samples were applied for deep sequencing. Sequence analysis identified the number of reads ranged from 21.37 to 25.37 million bases with a mean value of 22.90 million bases. In total, 328 genes are detected as differentially expressed (DEGs) including 110 and 218 genes that were up- and down-regulated, respectively. Pathway analysis showed steroid hormone biosynthesis as the dominant pathway behind the lamb tenderness. Gene expression analysis identified the top high (such as TP53INP1, CYP2E1, HSD17B13, ADH1C, and LPIN1) and low (such as ANGPTL2, IGFBP7, FABP5, OLFML3, and THOC5) expressed candidate genes. Polymorphism and association analysis revealed that mutation in OLFML3, ANGPTL2, and THOC5 genes could be potential candidate markers for tenderness in sheep. The genes and pathways identified in this study cause variation in tenderness, thus could be potential genetic markers to improve meat quality in sheep. However, further validation is needed to confirm the effect of these markers in different sheep populations so that these could be used in a selection program for lamb with high tenderness. Full article

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12 pages, 2166 KiB

Open AccessArticle

Insights into Transcriptomic Differences in Ovaries between Lambs and Adult Sheep after Superovulation Treatment

by Qingwei Wang, Xiaofei Guo, Dawei Yao, Biao Wang, Yupeng Li, Jinlong Zhang and Xiaosheng Zhang

Animals 2023, 13(4), 665; https://doi.org/10.3390/ani13040665 - 14 Feb 2023

Cited by 1 | Viewed by 1481

Abstract

Superovulation technology shows a great potential for shortening breeding time. Using the juvenile superovulation technology, juvenile animals can generate more follicles than adult animals. By sequencing using high-throughput methods, we studied and described differentially expressed (DE) long non-coding RNA (lncRNAs) and messenger RNAs [...] Read more.

Superovulation technology shows a great potential for shortening breeding time. Using the juvenile superovulation technology, juvenile animals can generate more follicles than adult animals. By sequencing using high-throughput methods, we studied and described differentially expressed (DE) long non-coding RNA (lncRNAs) and messenger RNAs (mRNAs) in the ovaries of young and adult sheep. Herein, 242 DE lncRNAs and 3150 DE mRNAs were screened. Through GO and KEGG analyses, we obtained genes related to ovarian/follicle development and ovulation in DE mRNAs, including OaFSHR, OaLHCGR, OaLDLR, OaZP3, OaSCARB1, and OaPDGFRA; through lncRNA-mRNA correlation analysis, we found that genes associated with ovarian/follicle development or ovulation include: XR_003585520.1, MSTRG.15652.1, XR_003588840.1, and their paired genes PDGFC, LRP5, and LRP1. We observed a synergistic effect between PDGFR and LRP1. PDGFR may play a leading role compared with LRP1. The induced LHCGR in lambs is higher than in adult sheep, showing more sensitivity to LH. The release of the oocytes was stimulated. Among the three lncRNAs, we found that XR_003588840.1 was significantly different and might perform a regulatory role in ovarian/follicle growth or ovulation. Full article

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17 pages, 3327 KiB

Open AccessArticle

Transcriptome Analysis of Marbled Rockfish Sebastiscus marmoratus under Salinity Stress

by Zhiqi He, Chenyan Shou and Zhiqiang Han

Animals 2023, 13(3), 400; https://doi.org/10.3390/ani13030400 - 24 Jan 2023

Viewed by 1624

Abstract

The marbled rockfish, Sebastiscus marmoratus, belongs to the euryhaline fish and is an oviparous scleractinian fish. There are few studies on the adaptation mechanism, functional genes, and related pathways of S. marmoratus and salinity. The results showed that a total of 72.1 [...] Read more.

The marbled rockfish, Sebastiscus marmoratus, belongs to the euryhaline fish and is an oviparous scleractinian fish. There are few studies on the adaptation mechanism, functional genes, and related pathways of S. marmoratus and salinity. The results showed that a total of 72.1 GB of clean reads were obtained and all clean reads annotated a total of 25,278 Unigenes, of which 2,160 were novel genes. Compared to 20‰, 479 and 520 differential genes were obtained for 35‰ and 10‰, respectively. Gene ontology (GO) enrichment analysis revealed significant enrichment in protein binding, ion binding, ATP binding, and catalytic activity. Kyoto Encyclopedia of Genes and Genomes (KEGG) showed that differentially expressed genes significantly expressed under salinity stress were mainly involved in the pathways of the cytochrome P450 metabolism of xenobiotics, tryptophan metabolism, cellular senescence, and calcium signaling pathways. Among them, pik3r6b, cPLA2γ-like, and WSB1 were differentially expressed in all three groups, and they were associated with apoptosis, inflammation, DNA damage, immune regulation, and other physiological processes. Six differentially expressed genes were randomly selected for qRT-PCR validation, and the results showed that the transcriptomic data were of high confidence. Full article

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2022

Jump to: 2023, 2021, 2020

17 pages, 1508 KiB

Open AccessArticle

Identification of Key Genes and Biological Pathways Associated with Skeletal Muscle Maturation and Hypertrophy in Bos taurus, Ovis aries, and Sus scrofa

by Fatemeh Mohammadinejad, Mohammadreza Mohammadabadi, Zahra Roudbari and Tomasz Sadkowski

Animals 2022, 12(24), 3471; https://doi.org/10.3390/ani12243471 - 08 Dec 2022

Cited by 14 | Viewed by 1706

Abstract

The aim of the current study was to identify the major genes and pathways involved in the process of hypertrophy and skeletal muscle maturation that is common for Bos taurus, Ovis aries, and Sus scrofa species. Gene expression profiles related to [...] Read more.

The aim of the current study was to identify the major genes and pathways involved in the process of hypertrophy and skeletal muscle maturation that is common for Bos taurus, Ovis aries, and Sus scrofa species. Gene expression profiles related to Bos taurus, Ovis aries, and Sus scrofa muscle, with accession numbers GSE44030, GSE23563, and GSE38518, respectively, were downloaded from the GEO database. Differentially expressed genes (DEGs) were screened out using the Limma package of R software. Genes with Fold Change > 2 and an adjusted p-value < 0.05 were identified as significantly different between two treatments in each species. Subsequently, gene ontology and pathway enrichment analyses were performed. Moreover, hub genes were detected by creating a protein–protein interaction network (PPI). The results of the analysis in Bos taurus showed that in the period of 280 dpc–3-months old, a total of 1839 genes showed a significant difference. In Ovis aries, however, during the period of 135dpc–2-months old, a total of 486 genes were significantly different. Additionally, in the 91 dpc–adult period, a total of 2949 genes were significantly different in Sus scrofa. The results of the KEGG pathway enrichment analysis and GO function annotation in each species separately revealed that in Bos taurus, DEGs were mainly enriched through skeletal muscle fiber development and skeletal muscle contraction, and the positive regulation of fibroblast proliferation, positive regulation of skeletal muscle fiber development, PPAR signaling pathway, and HIF-1 signaling pathway. In Ovis aries, DEGs were mainly enriched through regulating cell growth, skeletal muscle fiber development, the positive regulation of fibroblast proliferation, skeletal muscle cell differentiation, and the PI3K-Akt signaling, HIF-1 signaling, and Rap1 signaling pathways. In Sus scrofa, DEGs were mainly enriched through regulating striated muscle tissue development, the negative regulation of fibroblast proliferation and myoblast differentiation, and the HIF-1 signaling, AMPK signaling, and PI3K-Akt signaling pathways. Using a Venn diagram, 36 common DEGs were identified between Bos taurus, Ovis aries, and Sus scrofa. A biological pathways analysis of 36 common DEGs in Bos taurus, Ovis aries, and Sus scrofa allowed for the identification of common pathways/biological processes, such as myoblast differentiation, the regulation of muscle cell differentiation, and positive regulation of skeletal muscle fiber development, that orchestrated the development and maturation of skeletal muscle. As a result, hub genes were identified, including PPARGC1A, MYOD1, EPAS1, IGF2, CXCR4, and APOA1, in all examined species. This study provided a better understanding of the relationships between genes and their biological pathways in the skeletal muscle maturation process. Full article

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12 pages, 2192 KiB

Open AccessArticle

Genome-Wide DNA Methylation Patterns of Muscle and Tail-Fat in DairyMeade Sheep and Mongolian Sheep

by Rongsong Luo, Xuelei Dai, Li Zhang, Guangpeng Li and Zhong Zheng

Animals 2022, 12(11), 1399; https://doi.org/10.3390/ani12111399 - 29 May 2022

Cited by 6 | Viewed by 1904

Abstract

This study aimed to explore the genome-wide DNA methylation differences between muscle and tail-fat tissues of DairyMeade sheep (thin-tailed, lean carcass) and Mongolian sheep (fat-tailed, fat-deposited carcass). Whole-genome bisulfite sequencing (WGBS) was conducted and the global DNA methylation dynamics were mapped. Generally, CGs [...] Read more.

This study aimed to explore the genome-wide DNA methylation differences between muscle and tail-fat tissues of DairyMeade sheep (thin-tailed, lean carcass) and Mongolian sheep (fat-tailed, fat-deposited carcass). Whole-genome bisulfite sequencing (WGBS) was conducted and the global DNA methylation dynamics were mapped. Generally, CGs had a higher DNA methylation level than CHHs and CHGs, and tail-fat tissues had higher CG methylation levels than muscle tissues. For DNA repeat elements, SINE had the highest methylation level, while Simple had the lowest. When dividing the gene promoter region into small bins (200 bp per bin), the bins near the transcription start site (±200 bp) had the highest CG count per bin but the lowest DNA methylation levels. A series of DMRs were identified in muscle and tail-fat tissues between the two breeds. Among them, the introns of gene CAMK2D (calcium/calmodulin-dependent protein kinase II δ) demonstrated significant DNA methylation level differences between the two breeds in both muscle and tail-fat tissues, and it may play a crucial role in fat metabolism and meat quality traits. This study may provide basic datasets and references for further epigenetic modification studies during sheep genetic improvement. Full article

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20 pages, 5099 KiB

Open AccessArticle

Transcriptome Analysis of Breast Muscle Reveals Pathways Related to Protein Deposition in High Feed Efficiency of Native Turkeys

by Zahra Pezeshkian, Seyed Ziaeddin Mirhoseini, Shahrokh Ghovvati and Esmaeil Ebrahimie

Animals 2022, 12(10), 1240; https://doi.org/10.3390/ani12101240 - 11 May 2022

Cited by 3 | Viewed by 2148

Abstract

Feed efficiency is important due to the high cost of food, which accounts for about 70% of the total cost of a turkey breeding system. Native poultry are an important genetic resource in poultry breeding programs. This study aimed to conduct a global [...] Read more.

Feed efficiency is important due to the high cost of food, which accounts for about 70% of the total cost of a turkey breeding system. Native poultry are an important genetic resource in poultry breeding programs. This study aimed to conduct a global transcriptome analysis of native male turkeys which have been phenotyped for high and low feed efficiency. Feed efficiency traits were recorded during the experimental period. After slaughter, the three most efficient and three least efficient male turkeys were selected for RNA-Seq analysis. A total of 365 genes with different expressions in muscle tissue were identified between turkeys with a high feed efficiency compared to turkeys with a low feed efficiency. In the pathway analysis of up-regulated genes, major pathways included the “metabolism of glycine, serine, and threonine”; the “adipocytokine signaling pathway” and the “biosynthesis of amino acids”. In the pathway analysis of down-regulated genes, the major pathways included “dorso-ventral axis formation” and “actin cytoskeleton regulation”. In addition, gene set enrichment analyses were performed, which showed that high feed efficiency birds exhibit an increased expression of genes related to the biosynthesis of amino acids and low feed efficiency birds an increased expression of genes related to the immune response. Furthermore, functional analysis and protein network interaction analysis revealed that genes including GATM, PSAT1, PSPH, PHGDH, VCAM1, CD44, KRAS, SRC, CAV3, NEDD9, and PTPRQ were key genes for feed efficiency. These key genes may be good potential candidates for biomarkers of feed efficiency in genetic selection in turkeys. Full article

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18 pages, 5834 KiB

Open AccessArticle

Morphological Characteristics and Transcriptome Landscapes of Chicken Follicles during Selective Development

by Ruixue Nie, Xiaotong Zheng, Wenhui Zhang, Bo Zhang, Yao Ling, Hao Zhang and Changxin Wu

Animals 2022, 12(6), 713; https://doi.org/10.3390/ani12060713 - 11 Mar 2022

Cited by 15 | Viewed by 3309

Abstract

Ovarian follicle selection largely depends on the transition of granulosa cells from an undifferentiated to a fully differentiated state, which is accompanied by morphological and functional changes in follicles. The processes and transcriptional regulation of follicles during follicle selection are unclear; we thus [...] Read more.

Ovarian follicle selection largely depends on the transition of granulosa cells from an undifferentiated to a fully differentiated state, which is accompanied by morphological and functional changes in follicles. The processes and transcriptional regulation of follicles during follicle selection are unclear; we thus used follicles from the prehierarchal to the hierarchal stage to investigate histology, reproductive endocrinology, and transcription. The morphology of follicles changed markedly during follicle selection. The numbers of large white, small yellow, and large yellow follicles (LWF, SYF, and LYF, respectively) were 11.83 ± 2.79, 6.83 ± 2.23, and 1.00, respectively, per ovary. LYF showed thicker granulosa cell layers than those of other prehierarchal follicles. Progesterone concentrations were significantly higher in LYF than that in LWF and SYF. In total, 16,823 genes were positively expressed in LWF, SYF, and LYF. Among follicle types, 1290 differentially expressed genes were enriched regarding cell differentiation, blood vessel morphogenesis, and response to steroid hormones. Candidate genes associated with follicle selection participated in the Wnt signaling pathway, steroid hormone biosynthesis, and the TGF-β signaling pathway. We produced insights into crucial morphological characteristics of transcriptional regulation in follicle development. Our results provide an important basis for revealing the mechanism of follicle selection and potential impact on the poultry industry. Full article

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14 pages, 2897 KiB

Open AccessArticle

Analysis Polyadenylation Signal Usage in Sus scrofa

by Yuting Zhang, Jingwen Song, Min Zhang and Zhongyuan Deng

Animals 2022, 12(2), 194; https://doi.org/10.3390/ani12020194 - 13 Jan 2022

Cited by 1 | Viewed by 1994

Abstract

RNA polyadenylation is an important step in the messenger RNA (mRNA) maturation process, and the first step is recognizing the polyadenylation signal (PAS). The PAS type and distribution is a key determinant of post-transcriptional mRNA modification and gene expression. However, little is known [...] Read more.

RNA polyadenylation is an important step in the messenger RNA (mRNA) maturation process, and the first step is recognizing the polyadenylation signal (PAS). The PAS type and distribution is a key determinant of post-transcriptional mRNA modification and gene expression. However, little is known about PAS usage and alternative polyadenylation (APA) regulation in livestock species. Recently, sequencing technology has enabled the generation of a large amount of sequencing data revealing variation in poly(A) signals and APA regulation in Sus scrofa. We identified 62,491 polyadenylation signals in Sus scrofa using expressed sequence tag (EST) sequences combined with RNA-seq analysis. The composition and usage frequency of polyadenylation signal in Sus scrofa is similar with that of human and mouse. The most highly conserved polyadenylation signals are AAUAAA and AUUAAA, used for over 63.35% of genes. In addition, we also analyzed the U/GU-rich downstream sequence (DSE) element, located downstream of the cleavage site. Our results indicate that APA regulation was widely occurred in Sus scrofa, as in other organisms. Our result was useful for the accurate annotation of RNA 3′ ends in Sus scrofa and the analysis of polyadenylation signal usage in Sus scrofa would give the new insights into the mechanisms of transcriptional regulation. Full article

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12 pages, 1671 KiB

Open AccessArticle

ACSL4 Directs Intramuscular Adipogenesis and Fatty Acid Composition in Pigs

by Hongyan Ren, Haoyuan Zhang, Zaidong Hua, Zhe Zhu, Jiashu Tao, Hongwei Xiao, Liping Zhang, Yanzhen Bi and Heng Wang

Animals 2022, 12(1), 119; https://doi.org/10.3390/ani12010119 - 04 Jan 2022

Cited by 6 | Viewed by 2401

Abstract

The intramuscular fat is a major quality trait of meat, affecting sensory attributes such as flavor and texture. Several previous GWAS studies identified Acyl-CoA Synthetase Long Chain Family Member 4 (ACSL4) gene as the candidate gene to regulate intramuscular fat content in different [...] Read more.

The intramuscular fat is a major quality trait of meat, affecting sensory attributes such as flavor and texture. Several previous GWAS studies identified Acyl-CoA Synthetase Long Chain Family Member 4 (ACSL4) gene as the candidate gene to regulate intramuscular fat content in different pig populations, but the underlying molecular function of ACSL4 in adipogenesis within pig skeletal muscle is not fully investigated. In this study, we isolated porcine endogenous intramuscular adipocyte progenitors and performed ACSL4 loss- and gain-of-function experiments during adipogenic differentiation. Our data showed that ACSL4 is a positive regulator of adipogenesis in intramuscular fat cells isolated from pigs. More interestingly, the enhanced expression of ACSL4 in pig intramuscular adipocytes could increase the cellular content of monounsaturated and polyunsaturated fatty acids, such as gamma-L eicosapentaenoic acid (EPA), docosahexaenoic acid (DHA). The above results not only confirmed the function of ACSL4 in pig intramuscular adipogenesis and meat quality attributes, but also provided new clues for the improvement of the nutritional value of pork for human health. Full article

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2021

Jump to: 2023, 2022, 2020

16 pages, 3214 KiB

Open AccessArticle

Integrated Analysis of lncRNA and mRNA Reveals Novel Insights into Wool Bending in Zhongwei Goat

by Xiaobo Li, Zhanfa Liu, Shaohui Ye, Yue Liu, Qian Chen, Weijun Guan, Yabin Pu, Lin Jiang, Xiaohong He, Yuehui Ma and Qianjun Zhao

Animals 2021, 11(11), 3326; https://doi.org/10.3390/ani11113326 - 22 Nov 2021

Cited by 6 | Viewed by 2243

Abstract

Chinese Zhongwei goat is a rare and precious fur breed as its lamb fur is a well-known fur product. Wool bending of lamb fur of the Zhongwei goat is its most striking feature. However, the curvature of the wool decreases gradually with growth, [...] Read more.

Chinese Zhongwei goat is a rare and precious fur breed as its lamb fur is a well-known fur product. Wool bending of lamb fur of the Zhongwei goat is its most striking feature. However, the curvature of the wool decreases gradually with growth, which significantly affects its quality and economic value. The mechanism regulating the phenotypic changes of hair bending is still unclear. In the present study, the skin tissues of Zhongwei goats at 45 days (curving wool) and 108 days (slight-curving wool) after birth were taken as the research objects, and the expression profiling of long non-coding RNAs (lncRNAs) and mRNAs were analyzed based on the Ribo Zero RNA sequencing (RNA-seq) method. In total, 46,013 mRNAs and 13,549 lncRNAs were identified, of which 352 were differentially expressed mRNAs and 60 were. lncRNAs. Functional enrichment analysis of the target genes of lncRNAs were mainly enriched in PI3K-Akt, Arachidonic acid metabolic, cAMP, Wnt, and other signaling pathways. The qRT-PCR results of eight selected lncRNAs and target genes were consistent with the sequencing result, which indicated our data were reliable. Through the analysis of the weighted gene co-expression network, 13 co-expression modules were identified. The turquoise module contained a large number of differential expressed lncRNAs, which were mainly enriched in the PI3K-Akt signaling pathway and cAMP signaling pathway. The predicted LOC102172600 and LOC102191729 might affect the development of hair follicles and the curvature of wool by regulating the target genes. Our study provides novel insights into the potential roles of lncRNAs in the regulation of wool bending. In addition, the study offers a theoretical basis for further study of goat wool growth, so as to be a guidance and reference for breeding and improvement in the future. Full article

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13 pages, 1993 KiB

Open AccessArticle

Revealing Pathways Associated with Feed Efficiency and Meat Quality Traits in Slow-Growing Chickens

by Chotima Poompramun, Christelle Hennequet-Antier, Kanjana Thumanu, Panpradub Sinpru, Saknarin Pengsanthia, Wittawat Molee, Amonrat Molee, Elisabeth Le Bihan-Duval and Amélie Juanchich

Animals 2021, 11(10), 2977; https://doi.org/10.3390/ani11102977 - 15 Oct 2021

Cited by 7 | Viewed by 2107

Abstract

Here, molecular pathways and genes involved in the feed efficiency (FE) and thigh-meat quality of slow-growing Korat chickens were investigated. Individual feed intake values and body weights were collected weekly to the calculate feed conversion ratios (FCR) and residual feed intake. The biochemical [...] Read more.

Here, molecular pathways and genes involved in the feed efficiency (FE) and thigh-meat quality of slow-growing Korat chickens were investigated. Individual feed intake values and body weights were collected weekly to the calculate feed conversion ratios (FCR) and residual feed intake. The biochemical composition and meat quality parameters were also measured. On the basis of extreme FCR values at 10 weeks of age, 9 and 12 birds from the high and the low FCR groups, respectively, were selected, and their transcriptomes were investigated using the 8 × 60 K Agilent chicken microarray. A weighted gene co-expression network analysis was performed to determine the correlations between co-expressed gene modules and FE, thigh-meat quality, or both. Groups of birds with different FE values also had different nucleotide, lipid, and protein contents in their thigh muscles. In total, 38 modules of co-expressed genes were identified, and 12 were correlated with FE and some meat quality traits. A functional analysis highlighted several enriched functions, such as biological processes, metabolic processes, nucleotide metabolism, and immune responses. Several molecular factors were involved in the interactions between FE and meat quality, including the assembly competence domain, baculoviral IAP repeat containing 5, cytochrome c oxidase assembly factor 3, and myosin light chain 9 genes. Full article

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24 pages, 2775 KiB

Open AccessArticle

Jejunal Transcriptomic Profiling for Differences in Feed Conversion Ratio in Slow-Growing Chickens

by Panpradub Sinpru, Cindy Riou, Satoshi Kubota, Chotima Poompramun, Wittawat Molee and Amonrat Molee

Animals 2021, 11(9), 2606; https://doi.org/10.3390/ani11092606 - 05 Sep 2021

Cited by 3 | Viewed by 3356

Abstract

Improving feed efficiency is an important breeding target for the poultry industry; to achieve this, it is necessary to understand the molecular basis of feed efficiency. We compared the jejunal transcriptomes of low- and high-feed conversion ratio (FCR) slow-growing Korat chickens (KRs). Using [...] Read more.

Improving feed efficiency is an important breeding target for the poultry industry; to achieve this, it is necessary to understand the molecular basis of feed efficiency. We compared the jejunal transcriptomes of low- and high-feed conversion ratio (FCR) slow-growing Korat chickens (KRs). Using an original sample of 75 isolated 10-week-old KR males, we took jejunal samples from six individuals in two groups: those with extremely low FCR (n = 3; FCR = 1.93 ± 0.05) and those with extremely high FCR (n = 3; FCR = 3.29 ± 0.06). Jejunal transcriptome profiling via RNA sequencing revealed 56 genes that were differentially expressed (p < 0.01, FC > 2): 31 were upregulated, and 25 were downregulated, in the low-FCR group relative to the high-FCR group. Functional annotation revealed that these differentially expressed genes were enriched in biological processes related to immune response, glutathione metabolism, vitamin transport and metabolism, lipid metabolism, and neuronal and cardiac maturation, development, and growth, suggesting that these are important mechanisms governing jejunal feed conversion. These findings provide an important molecular basis for future breeding strategies to improve slow-growing chicken feed efficiency. Full article

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15 pages, 3153 KiB

Open AccessArticle

Identification of Novel lncRNA and Differentially Expressed Genes (DEGs) of Testicular Tissues among Cattle, Yak, and Cattle-Yak Associated with Male Infertility

by Shaokang Zhao, Tingting Chen, Xinmao Luo, Shiyi Chen, Jie Wang, Songjia Lai and Xianbo Jia

Animals 2021, 11(8), 2420; https://doi.org/10.3390/ani11082420 - 17 Aug 2021

Cited by 11 | Viewed by 3188

Abstract

Cattle-yak is an excellent hybrid of cattle and yak; they are characterized by better meat quality and stronger adaptability of harsh environments than their parents. However, male sterility of cattle-yak lay restraints on the transmission of heterosis. In this study, next generation sequence [...] Read more.

Cattle-yak is an excellent hybrid of cattle and yak; they are characterized by better meat quality and stronger adaptability of harsh environments than their parents. However, male sterility of cattle-yak lay restraints on the transmission of heterosis. In this study, next generation sequence technology was performed to profile the testicular tissues transcriptome (lncRNA and mRNA) of cattle, yak, and cattle-yak. We analyzed the features and functions of significant differentially expressed genes among the three breeds. There are 9 DE lncRNAs and 46 DE mRNAs with comparisons of cattle, yak, and cattle-yak. Among them, the upregulated targeting genes, such as IGF1 and VGLL3 of cattle-yak lncRNA, may be related to the derangement of spermatocyte maturation and cell proliferation. Similarly, we found that the LDOC1 gene, which is related to the process of cellular apoptosis, is overexpressed in cattle-yak. GO enrichment analysis demonstrated that the cattle-yak is lacking the regulation of fertilization (GO: 0009566), spermatogenesis process (GO: 0007283), male gamete generation process (GO: 0048232), sexual reproduction (GO: 0019953), and multi-organism reproductive process (GO: 0044703), such processes may play important and positive roles in spermatogenesis and fertilization. Furthermore, the KEGG enrichment analysis showed that the upregulated DEGs of cattle-yak most enriched in Apoptosis (ko04210) and Hippo signaling pathway (ko04390), may lead to excessively dead of cell and inhibit cell growth, resulting in obstruction of meiosis and spermatogenesis processes. This study will enable us to deeper understand the mechanism of male cattle-yak infertility. Full article

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15 pages, 4756 KiB

Open AccessArticle

Comparative Analysis for Genetic Characterization in Korean Native Jeju Horse

by Wooseok Lee, Seyoung Mun, Song-Yi Choi, Dong-Yep Oh, Yong-Soo Park and Kyudong Han

Animals 2021, 11(7), 1924; https://doi.org/10.3390/ani11071924 - 28 Jun 2021

Viewed by 2414

Abstract

The Jeju horse is a native Korean species that has been breeding on Jeju Island since the 13th century. Their shape has a distinct appearance from the representative species, Thoroughbred. Here, we performed a comparison of the Jeju horse and Thoroughbred horse for [...] Read more.

The Jeju horse is a native Korean species that has been breeding on Jeju Island since the 13th century. Their shape has a distinct appearance from the representative species, Thoroughbred. Here, we performed a comparison of the Jeju horse and Thoroughbred horse for the identification of genome-wide structure variation by using the next-generation sequencing (NGS) technique. We generated an average of 95.59 Gb of the DNA sequence, resulting in an average of 33.74 X sequence coverage from five Jeju horses. In addition, reads obtained from WGRS data almost covered the horse reference genome (mapped reads 98.4%). Based on our results, we identified 1,244,064 single nucleotide polymorphisms (SNPs), 113,498 genomic insertions, and 114,751 deletions through bioinformatics analysis. Interestingly, the results of the WGRS comparison indicated that the eqCD1a6 gene contains signatures of positive natural selection in Jeju horses. The eqCD1a6 gene is known to be involved in immunity. The eqCD1a6 gene of Jeju horses commonly contained 296 variants (275 SNPs and 21 INDELs) that were compared with its counterpart of two Thoroughbred horses. In addition, we used LOAA, digital PCR, to confirm the possibility of developing a molecular marker for species identification using variant sites. As a result, it was possible to confirm the result of the molecular marker with high accuracy. Nevertheless, eqCD1a6 was shown to be functionally intact. Taken together, we have found significant genomic variation in these two different horse species. Full article

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18 pages, 3146 KiB

Open AccessArticle

Genotyping of Two Mediterranean Trout Populations in Central-Southern Italy for Conservation Purposes Using a Rainbow-Trout-Derived SNP Array

by Valentino Palombo, Elena De Zio, Giovanna Salvatore, Stefano Esposito, Nicolaia Iaffaldano and Mariasilvia D’Andrea

Animals 2021, 11(6), 1803; https://doi.org/10.3390/ani11061803 - 17 Jun 2021

Cited by 7 | Viewed by 2133

Abstract

Mediterranean trout is a freshwater fish of particular interest with economic significance for fishery management, aquaculture and conservation biology. Unfortunately, native trout populations’ abundance is significantly threatened by anthropogenic disturbance. The introduction of commercial hatchery strains for recreation activities has compromised the genetic [...] Read more.

Mediterranean trout is a freshwater fish of particular interest with economic significance for fishery management, aquaculture and conservation biology. Unfortunately, native trout populations’ abundance is significantly threatened by anthropogenic disturbance. The introduction of commercial hatchery strains for recreation activities has compromised the genetic integrity status of native populations. This work assessed the fine-scale genetic structure of Mediterranean trout in the two main rivers of Molise region (Italy) to support conservation actions. In total, 288 specimens were caught in 28 different sites (14 per basins) and genotyped using the Affymetrix 57 K rainbow-trout-derived SNP array. Population differentiation was analyzed using pairwise weighted F_ST and overall F-statistic estimated by locus-by-locus analysis of molecular variance. Furthermore, an SNP data set was processed through principal coordinates analysis, discriminant analysis of principal components and admixture Bayesian clustering analysis. Firstly, our results demonstrated that rainbow trout SNP array can be successfully used for Mediterranean trout genotyping. In fact, despite an overwhelming number of loci that resulted as monomorphic in our populations, it must be emphasized that the resulted number of polymorphic loci (i.e., ~900 SNPs) has been sufficient to reveal a fine-scale genetic structure in the investigated populations, which is useful in supporting conservation and management actions. In particular, our findings allowed us to select candidate sites for the collection of adults, needed for the production of genetically pure juvenile trout, and sites to carry out the eradication of alien trout and successive re-introduction of native trout. Full article

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13 pages, 2761 KiB

Open AccessArticle

Oryzias curvinotus in Sanya Does Not Contain the Male Sex-Determining Gene dmy

by Zhongdian Dong, Xueyou Li, Zebin Yao, Chun Wang, Yusong Guo, Qian Wang, Changwei Shao and Zhongduo Wang

Animals 2021, 11(5), 1327; https://doi.org/10.3390/ani11051327 - 06 May 2021

Cited by 6 | Viewed by 2032

Abstract

Hainan medaka (Oryzias curvinotus) is distributed in the coastal waters of the South China Sea and is able to adapt to a wide range of salinities. In this study, we characterized O. curvinotus in Sanya River (SY-medaka), which lacks dmy [...] Read more.

Hainan medaka (Oryzias curvinotus) is distributed in the coastal waters of the South China Sea and is able to adapt to a wide range of salinities. In this study, we characterized O. curvinotus in Sanya River (SY-medaka), which lacks dmy (a male sex-determining gene in O. latipes and O. curvinotus). In a comparison of SY-medaka and Gaoqiao medaka (GQ-medaka), the morphological difference between the two populations does not reach the subspecies level and they can be considered two geographic populations of O. curvinotus. A mitochondrial cytochrome oxidase subunit I (CoI) sequence alignment showed that the sequence identities between SY-medaka and other geographic populations of O. curvinotus are as high as 95%. A phylogenetic analysis of the mitochondrial genome also indicated that SY-medaka belongs to O. curvinotus. Molecular marker-based genetic sex assays and whole genome re-sequencing showed that SY-medaka does not contain dmy. Further, in RNA-Seq analyses of the testis and ovaries of sexually mature SY-medaka, dmy expression was not detected. We speculate that high temperatures resulted in the loss of dmy in SY-medaka during evolution, or the lineage has another sex-determining gene. This study provides a valuable dataset for elucidating the mechanism underlying sex determination in Oryzias genus and advances research on functional genomics or reproduction biology in O. curvinotus. Full article

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18 pages, 1555 KiB

Open AccessArticle

Dissecting the Gene Expression Networks Associated with Variations in the Major Components of the Fatty Acid Semimembranosus Muscle Profile in Large White Heavy Pigs

by Martina Zappaterra, Silvia Gioiosa, Giovanni Chillemi, Paolo Zambonelli and Roberta Davoli

Animals 2021, 11(3), 628; https://doi.org/10.3390/ani11030628 - 27 Feb 2021

Cited by 9 | Viewed by 2395

Abstract

To date, high-throughput technology such as RNA-sequencing has been successfully applied in livestock sciences to investigate molecular networks involved in complex traits, such as meat quality. Pork quality depends on several organoleptic, technological, and nutritional characteristics, and it is also influenced by the [...] Read more.

To date, high-throughput technology such as RNA-sequencing has been successfully applied in livestock sciences to investigate molecular networks involved in complex traits, such as meat quality. Pork quality depends on several organoleptic, technological, and nutritional characteristics, and it is also influenced by the fatty acid (FA) composition of intramuscular fat (IMF). To explore the molecular networks associated with different IMF FA compositions, the Semimembranosus muscle (SM) from two groups of Italian Large White (ILW) heavy pigs divergent for SM IMF content was investigated using transcriptome analysis. After alignment and normalization, the obtained gene counts were used to perform the Weighted Correlation Network Analysis (WGCNA package in R environment). Palmitic and palmitoleic contents showed association with the same gene modules, comprising genes significantly enriched in autophagy, mitochondrial fusion, and mitochondrial activity. Among the key genes related to these FAs, we found TEAD4, a gene regulating mitochondrial activity that seems to be a promising candidate for further studies. On the other hand, the genes comprised in the modules associated with the IMF contents of oleic, n-6, and n-3 polyunsaturated FAs (PUFAs) were significantly enriched in Mitogen-Activated Protein Kinase (MAPK) signaling, in agreement with previous studies suggesting that several MAPK players may have a primary role in regulating lipid deposition. These results give an insight into the molecular cascade associated with different IMF FA composition in ILW heavy pigs. Further studies are needed to validate the results and confirm whether some of the identified key genes may be effective candidates for pork quality. Full article

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2020

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19 pages, 1507 KiB

Open AccessFeature PaperReview

Emerging Genetic Tools to Investigate Molecular Pathways Related to Heat Stress in Chickens: A Review

by Francesco Perini, Filippo Cendron, Giacomo Rovelli, Cesare Castellini, Martino Cassandro and Emiliano Lasagna

Animals 2021, 11(1), 46; https://doi.org/10.3390/ani11010046 - 29 Dec 2020

Cited by 34 | Viewed by 5776

Abstract

Chicken products are the most consumed animal-sourced foods at a global level across greatly diverse cultures, traditions, and religions. The consumption of chicken meat has increased rapidly in the past few decades and chicken meat is the main animal protein source in developing [...] Read more.

Chicken products are the most consumed animal-sourced foods at a global level across greatly diverse cultures, traditions, and religions. The consumption of chicken meat has increased rapidly in the past few decades and chicken meat is the main animal protein source in developing countries. Heat stress is one of the environmental factors which decreases the productive performance of poultry and meat quality. Heat stress produces the over-expression of heat shock factors and heat shock proteins in chicken tissues. Heat shock proteins regulate several molecular pathways in cells in response to stress conditions, changing the homeostasis of cells and tissues. These changes can affect the physiology of the tissue and hence the production ability of chickens. Indeed, commercial chicken strains can reach a high production level, but their body metabolism, being comparatively accelerated, has poor thermoregulation. In contrast, native backyard chickens are more adapted to the environments in which they live, with a robustness that allows them to survive and reproduce constantly. In the past few years, new molecular tools have been developed, such as RNA-Seq, Single Nucleotide Polymorphisms (SNPs), and bioinformatics approaches such as Genome-Wide Association Study (GWAS). Based on these genetic tools, many studies have detected the main pathways involved in cellular response mechanisms. In this context, it is necessary to clarify all the genetic and molecular mechanisms involved in heat stress response. Hence, this paper aims to review the ability of the new generation of genetic tools to clarify the molecular pathways associated with heat stress in chickens, offering new perspectives for the use of these findings in the animal breeding field. Full article

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13 pages, 1266 KiB

Open AccessArticle

Advantage of including Genomic Information to Predict Breeding Values for Lactation Yields of Milk, Fat, and Protein or Somatic Cell Score in a New Zealand Dairy Goat Herd

by Megan Scholtens, Nicolas Lopez-Villalobos, Klaus Lehnert, Russell Snell, Dorian Garrick and Hugh T. Blair

Animals 2021, 11(1), 24; https://doi.org/10.3390/ani11010024 - 25 Dec 2020

Cited by 4 | Viewed by 2369

Abstract

Selection on genomic breeding values (GBVs) is now readily available for ranking candidates in improvement schemes. Our objective was to quantify benefits in terms of accuracy of prediction from including genomic information in the single-trait estimation of breeding values (BVs) for a New [...] Read more.

Selection on genomic breeding values (GBVs) is now readily available for ranking candidates in improvement schemes. Our objective was to quantify benefits in terms of accuracy of prediction from including genomic information in the single-trait estimation of breeding values (BVs) for a New Zealand mixed breed dairy goat herd. The dataset comprised phenotypic and pedigree records of 839 does. The phenotypes comprised estimates of 305-day lactation yields of milk, fat, and protein and average somatic cell score from the 2016 production season. Only 388 of the goats were genotyped with a Caprine 50K SNP chip and 41,981 of the single nucleotide polymorphisms (SNPs) passed quality control. Pedigree-based best linear unbiased prediction (PBLUP) was used to obtain across-breed breeding values (EBVs), whereas a single-step BayesC model (ssBC) was used to estimate across-breed GBVs. The average prediction accuracies ranged from 0.20 to 0.22 for EBVs and 0.34 to 0.43 for GBVs. Accuracies of GBVs were up to 103% greater than EBVs. Breed effects were more reliably estimated in the ssBC model compared with the PBLUP model. The greatest benefit of genomic prediction was for individuals with no pedigree or phenotypic records. Including genomic information improved the prediction accuracy of BVs compared with the current pedigree-based BLUP method currently implemented in the New Zealand dairy goat population. Full article

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23 pages, 10579 KiB

Open AccessArticle

Transcriptomic and Morphological Analysis of Cells Derived from Porcine Buccal Mucosa—Studies on an In Vitro Model

by Artur Bryja, Grzegorz Latosiński, Maurycy Jankowski, Ana Angelova Volponi, Paul Mozdziak, Jamil A. Shibli, Rut Bryl, Julia Spaczyńska, Hanna Piotrowska-Kempisty, Krzysztof Krawiec, Bartosz Kempisty and Marta Dyszkiewicz-Konwińska

Animals 2021, 11(1), 15; https://doi.org/10.3390/ani11010015 - 24 Dec 2020

Viewed by 2562

Abstract

Transcriptional analysis and live-cell imaging are a powerful tool to investigate the dynamics of complex biological systems. In vitro expanded porcine oral mucosal cells, consisting of populations of epithelial and connective lineages, are interesting and complex systems for study via microarray transcriptomic assays [...] Read more.

Transcriptional analysis and live-cell imaging are a powerful tool to investigate the dynamics of complex biological systems. In vitro expanded porcine oral mucosal cells, consisting of populations of epithelial and connective lineages, are interesting and complex systems for study via microarray transcriptomic assays to analyze gene expression profile. The transcriptomic analysis included 56 ontological groups with particular focus on 7 gene ontology groups that are related to the processes of differentiation and development. Most analyzed genes were upregulated after 7 days and downregulated after 15 and 30 days of in vitro culture. The performed transcriptomic analysis was then extended to include automated analysis of differential interference contrast microscopy (DIC) images obtained during in vitro culture. The analysis of DIC imaging allowed to identify the different populations of keratinocytes and fibroblasts during seven days of in vitro culture, and it was possible to evaluate the proportion of these two populations of cells. Porcine mucosa may be a suitable model for reference research on human tissues. In addition, it can provide a reference point for research on the use of cells, scaffolds, or tissues derived from transgenic animals for applications in human tissues reconstruction. Full article

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14 pages, 994 KiB

Open AccessArticle

Analysis of Hindgut Microbiome of Sheep and Effect of Different Husbandry Conditions

by Giulietta Minozzi, Filippo Biscarini, Emanuela Dalla Costa, Matteo Chincarini, Nicola Ferri, Clara Palestrini, Michela Minero, Silvia Mazzola, Renata Piccinini, Giorgio Vignola and Simona Cannas

Animals 2021, 11(1), 4; https://doi.org/10.3390/ani11010004 - 22 Dec 2020

Cited by 2 | Viewed by 2381

Abstract

The microbiome is now seen as an important resource to understand animal health and welfare in many species. However, there are few studies aiming at identifying the association between fecal microbiome composition and husbandry conditions in sheep. A wide range of stressors associated [...] Read more.

The microbiome is now seen as an important resource to understand animal health and welfare in many species. However, there are few studies aiming at identifying the association between fecal microbiome composition and husbandry conditions in sheep. A wide range of stressors associated with management and housing of animals increases the hypothalamic–pituitary axis activity, with growing evidence that the microbiome composition can be modified. Therefore, the purpose of the present study was to describe the core microbiome in sheep, characterized using 16S rRNA gene sequencing, and to explore whether exposure to stressful husbandry conditions changed sheep hindgut microbiome composition. Sheep (n = 10) were divided in two groups: isolated group (individually separated for 3 h/day) and control group (housed in the home pen for the entire trial period). Sheep core microbiome was dominated by Firmicutes (43.6%), Bacteroidetes (30.38%), Proteobacteria (10.14%), and Verrucomicrobia (7.55%). Comparative results revealed few operational taxonomic units (OTUs) with significantly different relative abundance between groups. Chao1, abundance-based coverage estimator (ACE), and Fisher’s alpha indices did not show differences between groups. OTU-based Bray–Curtis distances between groups were not significant (p-value = 0.07). In conclusion, these results describing the core microbiome of sheep do not suggest a strong effect of stressful husbandry conditions on microbial composition. Full article

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15 pages, 4027 KiB

Open AccessArticle

Identification of Candidate Genes and Pathways Associated with Obesity-Related Traits in Canines via Gene-Set Enrichment and Pathway-Based GWAS Analysis

by Sunirmal Sheet, Srikanth Krishnamoorthy, Jihye Cha, Soyoung Choi and Bong-Hwan Choi

Animals 2020, 10(11), 2071; https://doi.org/10.3390/ani10112071 - 09 Nov 2020

Cited by 7 | Viewed by 3378

Abstract

The present study aimed to identify causative loci and genes enriched in pathways associated with canine obesity using a genome-wide association study (GWAS). The GWAS was first performed to identify candidate single-nucleotide polymorphisms (SNPs) associated with obesity and obesity-related traits including body weight [...] Read more.

The present study aimed to identify causative loci and genes enriched in pathways associated with canine obesity using a genome-wide association study (GWAS). The GWAS was first performed to identify candidate single-nucleotide polymorphisms (SNPs) associated with obesity and obesity-related traits including body weight and blood sugar in 18 different breeds of 153 dogs. A total of 10 and 2 SNPs were found to be significantly (p < 3.74 × 10⁻⁷) associated with body weight and blood sugar, respectively. None of the SNPs were identified to be significantly associated with obesity trait. We subsequently followed up the GWAS analysis with gene-set enrichment and pathway analyses. A gene-set with 1057, 1409, and 1243 SNPs annotated to 449, 933 and 820 genes for obesity, body weight, and blood sugar, respectively was created by sub-setting the GWAS result at a threshold of p < 0.01 for the gene-set enrichment analysis. In total, 84 GO and 21 KEGG pathways for obesity, 114 GO and 44 KEGG pathways for blood sugar, 120 GO and 24 KEGG pathways for body weight were found to be enriched. Among the pathways and GO terms, we highlighted five enriched pathways (Wnt signaling pathway, adherens junction, pathways in cancer, axon guidance, and insulin secretion) and seven GO terms (fat cell differentiation, calcium ion binding, cytoplasm, nucleus, phospholipid transport, central nervous system development, and cell surface) that were found to be shared among all the traits. Our data provide insights into the genes and pathways associated with obesity and obesity-related traits. Full article

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14 pages, 2115 KiB

Open AccessArticle

ssc-miR-451 Regulates Porcine Primary Adipocyte Differentiation by Targeting ACACA

by Mailin Gan, Linyuan Shen, Yuan Fan, Ya Tan, Lin Liu, Lei Chen, Ye Zhao, Lili Niu, Guoqing Tang, Qiang Li, Xu Xu, Tinghuan Zhang, Xuewei Li, Shunhua Zhang and Li Zhu

Animals 2020, 10(10), 1891; https://doi.org/10.3390/ani10101891 - 16 Oct 2020

Cited by 7 | Viewed by 2195

Abstract

miRNA is a small non-coding RNA, which plays an important role in diverse biological processes. In the present study, we explore the effect of ssc-miR-451 on porcine adipose development and meat quality. We observed that ssc-miR-451 was downregulated during porcine primary adipocyte differentiation. [...] Read more.

miRNA is a small non-coding RNA, which plays an important role in diverse biological processes. In the present study, we explore the effect of ssc-miR-451 on porcine adipose development and meat quality. We observed that ssc-miR-451 was downregulated during porcine primary adipocyte differentiation. Overexpression of ssc-miR-451 inhibited adipogenic differentiation, while inhibition of ssc-miR-451 promoted adipogenic differentiation. The dual luciferase reporter system indicated Acetyl-CoA carboxylase alpha (ACACA) as a target gene of ssc-miR-451. Correlation analysis negatively correlated miR-451 expression with intramuscular fat content (IMF) and positively correlated ACACA expression with IMF. Further analysis of fatty acid composition revealed that pigs with high expression of ssc-miR-451 had higher monounsaturated fatty acid (MUFA) and lower polyunsaturated fatty acid (PUFA). Taken together, our study suggests that ssc-miR-451 regulates lipid deposition and fatty acid composition by targeting ACACA, and ssc-miR-451 may serve as a potential genetic marker to improve pork quality. Full article

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19 pages, 582 KiB

Open AccessArticle

Bayesian Analysis of the Association between Casein Complex Haplotype Variants and Milk Yield, Composition, and Curve Shape Parameters in Murciano-Granadina Goats

by María Gabriela Pizarro Inostroza, Francisco Javier Navas González, Vincenzo Landi, Jose Manuel León Jurado, Juan Vicente Delgado Bermejo, Javier Fernández Álvarez and María del Amparo Martínez Martínez

Animals 2020, 10(10), 1845; https://doi.org/10.3390/ani10101845 - 10 Oct 2020

Cited by 13 | Viewed by 2265

Abstract

Considering casein haplotype variants rather than SNPs may maximize the understanding of heritable mechanisms and their implication on the expression of functional traits related to milk production. Effects of casein complex haplotypes on milk yield, milk composition, and curve shape parameters were used [...] Read more.

Considering casein haplotype variants rather than SNPs may maximize the understanding of heritable mechanisms and their implication on the expression of functional traits related to milk production. Effects of casein complex haplotypes on milk yield, milk composition, and curve shape parameters were used using a Bayesian inference for ANOVA. We identified 48 single nucleotide polymorphisms (SNPs) present in the casein complex of 159 unrelated individuals of diverse ancestry, which were organized into 86 haplotypes. The Ali and Schaeffer model was chosen as the best fitting model for milk yield (Kg), protein, fat, dry matter, and lactose (%), while parabolic yield-density was chosen as the best fitting model for somatic cells count (SCC × 103 sc/mL). Peak and persistence for all traits were computed respectively. Statistically significant differences (p < 0.05) were found for milk yield and components. However, no significant difference was found for any curve shape parameter except for protein percentage peak. Those haplotypes for which higher milk yields were reported were the ones that had higher percentages for protein, fat, dry matter, and lactose, while the opposite trend was described by somatic cells counts. Conclusively, casein complex haplotypes can be considered in selection strategies for economically important traits in dairy goats. Full article

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18 pages, 2807 KiB

Open AccessArticle

Characterization of microRNAs during Embryonic Skeletal Muscle Development in the Shan Ma Duck

by Chuan Li, Ting Xiong, Mingfang Zhou, Lei Wan, Suwang Xi, Qiuhong Liu, Yi Chen, Huirong Mao, Sanfeng Liu and Biao Chen

Animals 2020, 10(8), 1417; https://doi.org/10.3390/ani10081417 - 14 Aug 2020

Cited by 10 | Viewed by 2637

Abstract

Poultry skeletal muscle provides high quality protein for humans. Study of the genetic mechanisms during duck skeletal muscle development contribute to future duck breeding and meat production. In the current study, three breast muscle samples from Shan Ma ducks at embryonic day 13 [...] Read more.

Poultry skeletal muscle provides high quality protein for humans. Study of the genetic mechanisms during duck skeletal muscle development contribute to future duck breeding and meat production. In the current study, three breast muscle samples from Shan Ma ducks at embryonic day 13 (E13) and E19 were collected, respectively. We detected microRNA (miRNA) expression using high throughput sequencing following bioinformatic analysis. qRT-PCR validated the reliability of sequencing results. We also identified target prediction results using the luciferase reporter assay. A total of 812 known miRNAs and 279 novel miRNAs were detected in six samples; as a result, 61 up-regulated and 48 down-regulated differentially expressed miRNAs were identified between E13 and E19 (|log2 fold change| ≥ 1 and p ≤ 0.05). Enrichment analysis showed that target genes of the differentially expressed miRNAs were enriched on many muscle development-related gene ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, especially mitogen-activated protein kinase (MAPK) signaling pathways. An interaction network was constructed using the target genes of the differentially expressed miRNAs. These results complement the current duck miRNA database and offer several miRNA candidates for future studies of skeletal muscle development in the duck. Full article

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18 pages, 2287 KiB

Open AccessArticle

Insight into the Current Genetic Diversity and Population Structure of Domestic Reindeer (Rangifer tarandus) in Russia

by Veronika Kharzinova, Arsen Dotsev, Anastasiya Solovieva, Olga Sergeeva, Georgiy Bryzgalov, Henry Reyer, Klaus Wimmers, Gottfried Brem and Natalia Zinovieva

Animals 2020, 10(8), 1309; https://doi.org/10.3390/ani10081309 - 30 Jul 2020

Cited by 8 | Viewed by 3285

Abstract

To examine the genetic diversity and population structure of domestic reindeer, using the BovineHD BeadChip, we genotyped reindeer individuals belonging to the Nenets breed of the five main breeding regions, the Even breed of the Republic of Sakha, the Evenk breed of the [...] Read more.

To examine the genetic diversity and population structure of domestic reindeer, using the BovineHD BeadChip, we genotyped reindeer individuals belonging to the Nenets breed of the five main breeding regions, the Even breed of the Republic of Sakha, the Evenk breed of the Krasnoyarsk and Yakutia regions, and the Chukotka breed of the Chukotka region and its within-breed ecotype, namely, the Chukotka–Khargin, which is bred in Yakutia. The Chukotka reindeer was shown to have the lowest genetic diversity in terms of the allelic richness and heterozygosity indicators. The principal component analysis (PCA) results are consistent with the neighbor-net tree topology, dividing the reindeer into groups according to their habitat location and origin of the breed. Admixture analysis indicated a genetic structuring of two groups of Chukotka origin, the Even breed and most of the geographical groups of the Nenets breed, with the exception of the Murmansk reindeer, the gene pool of which was comprised of the Nenets and apparently the native Sami reindeer. The presence of a genetic component of the Nenets breed in some reindeer inhabiting the Krasnoyarsk region was detected. Our results provide a deeper insight into the current intra-breeding reindeer genetic diversity, which is an important requirement for future reindeer herding strategies and for animal adaptation to environmental changes. Full article

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14 pages, 1195 KiB

Open AccessArticle

Use of the Multivariate Discriminant Analysis for Genome-Wide Association Studies in Cattle

by Elisabetta Manca, Alberto Cesarani, Giustino Gaspa, Silvia Sorbolini, Nicolò P.P. Macciotta and Corrado Dimauro

Animals 2020, 10(8), 1300; https://doi.org/10.3390/ani10081300 - 29 Jul 2020

Cited by 10 | Viewed by 2329

Abstract

Genome-wide association studies (GWAS) are traditionally carried out by using the single marker regression model that, if a small number of individuals is involved, often lead to very few associations. The Bayesian methods, such as BayesR, have obtained encouraging results when they are [...] Read more.

Genome-wide association studies (GWAS) are traditionally carried out by using the single marker regression model that, if a small number of individuals is involved, often lead to very few associations. The Bayesian methods, such as BayesR, have obtained encouraging results when they are applied to the GWAS. However, these approaches, require that an a priori posterior inclusion probability threshold be fixed, thus arbitrarily affecting the obtained associations. To partially overcome these problems, a multivariate statistical algorithm was proposed. The basic idea was that animals with different phenotypic values of a specific trait share different allelic combinations for genes involved in its determinism. Three multivariate techniques were used to highlight the differences between the individuals assembled in high and low phenotype groups: the canonical discriminant analysis, the discriminant analysis and the stepwise discriminant analysis. The multivariate method was tested both on simulated and on real data. The results from the simulation study highlighted that the multivariate GWAS detected a greater number of true associated single nucleotide polymorphisms (SNPs) and Quantitative trait loci (QTLs) than the single marker model and the Bayesian approach. For example, with 3000 animals, the traditional GWAS highlighted only 29 significantly associated markers and 13 QTLs, whereas the multivariate method found 127 associated SNPs and 65 QTLs. The gap between the two approaches slowly decreased as the number of animals increased. The Bayesian method gave worse results than the other two. On average, with the real data, the multivariate GWAS found 108 associated markers for each trait under study and among them, around 63% SNPs were also found in the single marker approach. Among the top 118 associated markers, 76 SNPs harbored putative candidate genes. Full article

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9 pages, 1097 KiB

Open AccessArticle

Transcriptome Profiling Associated with Carcass Quality of Loin Muscles in Crossbred Pigs

by Sang-Mo Kim, Kesavan Markkandan, Jong-Young Lee, Gye-Woong Kim and Jae Young Yoo

Animals 2020, 10(8), 1279; https://doi.org/10.3390/ani10081279 - 27 Jul 2020

Cited by 5 | Viewed by 2239

Abstract

Carcass quality traits, such as lean depth and loin depth, are of extreme economic importance for the swine industry. This study aimed to identify the gene expression pattern related to carcass quality in crossbred pigs ((Landrace × Yorkshire) × Duroc). In total, 20 [...] Read more.

Carcass quality traits, such as lean depth and loin depth, are of extreme economic importance for the swine industry. This study aimed to identify the gene expression pattern related to carcass quality in crossbred pigs ((Landrace × Yorkshire) × Duroc). In total, 20 crossbred pigs were used in this study and they were divided into two groups (class I grade, n = 10; class II grade, n = 10) based on the carcass grades. Total RNA samples extracted from the loin muscles of both groups were submitted for RNA-seq. The quality assessment of the sequencing reads resulted in 25,458 unigenes and found 12,795 candidate coding unigenes with homology to other species after annotation. Differentially expressed gene (DEG) analysis of the two groups revealed 282 up-regulated and 189 down-regulated genes (p ≤ 0.01), linked to tissue development, striated muscle tissue development, tissue morphogenesis, and lipid metabolic process gene ontology (GO) terms. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis highlighted genes related to the calcium signaling pathway, melanogenesis, the sphingolipid signaling pathway, the apelin signaling pathway, and the mTOR signaling pathway. We constructed an expressed gene profile, which may serve as a resource for genomic studies focused on uncovering the molecular mechanisms underlying carcass quality in crossbred pigs. Full article

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19 pages, 1677 KiB

Open AccessReview

MicroRNA Milk Exosomes: From Cellular Regulator to Genomic Marker

by Michela Cintio, Giulia Polacchini, Elisa Scarsella, Tommaso Montanari, Bruno Stefanon and Monica Colitti

Animals 2020, 10(7), 1126; https://doi.org/10.3390/ani10071126 - 02 Jul 2020

Cited by 23 | Viewed by 4253

Abstract

Recent advances in ruminants’ milk-derived exosomes (EXO) have indicated a role of microRNAs (miRNAs) in cell-to-cell communication in dairy ruminants. The miRNAs EXO retain peculiar mechanisms of uptake from recipient cells, which enables the selective delivery of cargos, with a specific regulation of [...] Read more.

Recent advances in ruminants’ milk-derived exosomes (EXO) have indicated a role of microRNAs (miRNAs) in cell-to-cell communication in dairy ruminants. The miRNAs EXO retain peculiar mechanisms of uptake from recipient cells, which enables the selective delivery of cargos, with a specific regulation of target genes. Although many studies have been published on the miRNAs contained in milk, less information is available on the role of miRNAs EXO, which are considered stable over time and resistant to digestion and milk processing. Several miRNAs EXO have been implicated in the cellular signaling pathway, as in the regulation of immune response. Moreover, they exert epigenetic control, as extenuating the expression of DNA methyltransferase 1. However, the study of miRNAs EXO is still challenging due to the difficulty of isolating EXO. In fact, there are not agreed protocols, and different methods, often time-consuming, are used, making it difficult to routinely process a large number of samples. The regulation of cell functions in mammary glands by miRNAs EXO, and their applications as genomic markers in livestock, is presented. Full article

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16 pages, 3958 KiB

Open AccessArticle

Effect of Nutritional Restriction on the Hair Follicles Development and Skin Transcriptome of Chinese Merino Sheep

by Xuefeng Lv, Lei Chen, Sangang He, Chenxi Liu, Bin Han, Zhilong Liu, Mayila Yusupu, Hugh Blair, Paul Kenyon, Stephen Morris, Wenrong Li and Mingjun Liu

Animals 2020, 10(6), 1058; https://doi.org/10.3390/ani10061058 - 19 Jun 2020

Cited by 18 | Viewed by 2687

Abstract

The high concentration of secondary branched wool follicles is a distinctive feature of the Merino sheep. At present, the molecular control of the development and branching of secondary wool follicles (SF) remains elusive. To reveal the potential genes associated with the development of [...] Read more.

The high concentration of secondary branched wool follicles is a distinctive feature of the Merino sheep. At present, the molecular control of the development and branching of secondary wool follicles (SF) remains elusive. To reveal the potential genes associated with the development of hair follicles, we investigated the characteristics of prenatal and postnatal development of wool follicles, and the transcriptional expression profile in fetuses/lambs from dams under either maternal maintenance or sub-maintenance (75% maintenance) nutrition. The density of SF and the ratio of SF to primary wool follicles (PF) were reduced (p < 0.05) in fetuses from day 105 to 135 of gestation under sub-maintenance nutrition. Differentially expressed genes were enriched in the binding, single-organism process, cellular process, cell and cell part Gene Ontology (GO) functional categories and metabolism, apoptosis, and ribosome pathways. Four candidate genes, SFRP4, PITX1, BAMBI, and KRT16, which were involved in secondary wool follicles branching and development, were identified. Our results indicate that nutritional intervention imposed on pregnant ewes by short-term sub-maintenance nutrition could provide a strategy for the study of wool follicle development. Overall insight into the global gene expression associated with SF development can be used to investigate the underlying mechanisms of SF branching in Merino sheep. Full article

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12 pages, 757 KiB

Open AccessArticle

Genomic Structural Diversity in Local Goats: Analysis of Copy-Number Variations

by Rosalia Di Gerlando, Salvatore Mastrangelo, Angelo Moscarelli, Marco Tolone, Anna Maria Sutera, Baldassare Portolano and Maria Teresa Sardina

Animals 2020, 10(6), 1040; https://doi.org/10.3390/ani10061040 - 16 Jun 2020

Cited by 7 | Viewed by 2834

Abstract

Copy-number variations (CNVs) are one of the widely dispersed forms of structural variations in mammalian genomes, and are present as deletions, insertions, or duplications. Only few studies have been conducted in goats on CNVs derived from SNP array data, and many local breeds [...] Read more.

Copy-number variations (CNVs) are one of the widely dispersed forms of structural variations in mammalian genomes, and are present as deletions, insertions, or duplications. Only few studies have been conducted in goats on CNVs derived from SNP array data, and many local breeds still remain uncharacterized, e.g., the Sicilian goat dairy breeds. In this study, CNV detection was performed, starting from the genotypic data of 120 individuals, belonging to four local breeds (Argentata dell’Etna, Derivata di Siria, Girgentana, and Messinese), genotyped with the Illumina GoatSNP50 BeadChip array. Overall, 702 CNVs were identified in 107 individuals using PennCNV software based on the hidden Markov model algorithm. These were merged in 75 CNV regions (CNVRs), i.e., regions containing CNVs overlapped by at least 1 base pair, while 85 CNVs remained unique. The part of the genome covered by CNV events was 35.21 Mb (1.2% of the goat genome length). Functional annotation of the CNVRs allowed the identification of 139 genes/loci within the most frequent CNVRs that are involved in local adaptations, such as coat colour (ADAMTS20 and EDNRA), mild behaviour (NR3C2), immune response (EXOC3L4 and TNFAIP2), reproduction (GBP1 and GBP6), and olfactory receptors (OR7E24). This study provides insights into the genomic variations for these Sicilian dairy goat breeds and should be of value for future studies to identify the relationships between this type of genetic variation and phenotypic traits. Full article

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14 pages, 1480 KiB

Open AccessArticle

Estimation of Linkage Disequilibrium and Effective Population Size in Three Italian Autochthonous Beef Breeds

by Maria Chiara Fabbri, Christos Dadousis and Riccardo Bozzi

Animals 2020, 10(6), 1034; https://doi.org/10.3390/ani10061034 - 14 Jun 2020

Cited by 7 | Viewed by 3418

Abstract

The objective was to investigate the pattern of linkage disequilibrium (LD) in three local beef breeds, namely, Calvana (n = 174), Mucca Pisana (n = 270), and Pontremolese (n = 44). As a control group, samples of the Italian Limousin breed (n = [...] Read more.

The objective was to investigate the pattern of linkage disequilibrium (LD) in three local beef breeds, namely, Calvana (n = 174), Mucca Pisana (n = 270), and Pontremolese (n = 44). As a control group, samples of the Italian Limousin breed (n = 100) were used. All cattle were genotyped with the GeneSeek GGP-LDv4 33k SNP chip containing 30,111 SNPs. The genotype quality control for each breed was conducted separately, and SNPs with call rate < 0.95 and minor allele frequency (MAF) > 1% were used for the analysis. LD extent was estimated in PLINK v1.9 using the squared correlation between pairs of loci (r²) across autosomes. Moreover, r² values were used to calculate historical and contemporary effective population size (N_e) in each breed. Average r² was similar in Calvana and Mucca Pisana (~0.14) and higher in Pontremolese (0.17); Limousin presented the lowest LD extent (0.07). LD up to 0.11–0.15 was persistent in the local breeds up to 0.75 Mbp, while in Limousin, it showed a more rapid decay. Variation of different LD levels across autosomes was observed in all the breeds. The results demonstrated a rapid decrease in N_e across generations for local breeds, and the contemporary population size observed in the local breeds, ranging from 41.7 in Calvana to 17 in Pontremolese, underlined the demographic alarming situation. Full article

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13 pages, 276 KiB

Open AccessArticle

Influence of the Casein Composite Genotype on Milk Quality and Coagulation Properties in the Endangered Agerolese Cattle Breed

by Sara Albarella, Maria Selvaggi, Emanuele D’Anza, Gianfranco Cosenza, Simonetta Caira, Andrea Scaloni, Annunziata Fontana, Vincenzo Peretti and Francesca Ciotola

Animals 2020, 10(5), 892; https://doi.org/10.3390/ani10050892 - 20 May 2020

Cited by 12 | Viewed by 3104

Abstract

The aim of this study was the characterization of CSN1S1, CSN2 and CSN3 genetic variability in Agerolese cattle, and the investigation of the effect of casein composite genotypes (CSN1S1, CSN2 and CSN3) on quality and coagulation traits of the corresponding milk. To these [...] Read more.

The aim of this study was the characterization of CSN1S1, CSN2 and CSN3 genetic variability in Agerolese cattle, and the investigation of the effect of casein composite genotypes (CSN1S1, CSN2 and CSN3) on quality and coagulation traits of the corresponding milk. To these purposes, blood and milk from 84 cows were sampled and analysed. Allele frequencies at CSN2 and CSN3 revealed no Hardy–Weinberg equilibrium in the population with a prevalence of allele A² for CSN2 and allele B for CSN3. BBA¹A²AB and BBA²A²AB composite genotypes were the most common in the population. BBA¹A²AB showed a higher total solids and fat content (12.70 ± 0.16 and 3.93 ± 0.10, respectively), while BBA²A²BB showed the best coagulation properties (RCT 12.62 ± 0.81; k₂₀ 5.84 ± 0.37; a₃₀ 23.72 ± 1.10). Interestingly, the A² allele of CSN2 was very widespread in the population; thus, it will be intriguing to verify if A²A² Agerolese cattle milk and the derived cheese may have better nutraceutical characteristics. Full article

11 pages, 1260 KiB

Open AccessArticle

Identification of Differentially Expressed MicroRNAs and Their Potential Target Genes in Adipose Tissue from Pigs with Highly Divergent Backfat Thickness

by Kai Xing, Xitong Zhao, Yibing Liu, Fengxia Zhang, Zhen Tan, Xiaolong Qi, Xiangguo Wang, Hemin Ni, Yong Guo, Xihui Sheng and Chuduan Wang

Animals 2020, 10(4), 624; https://doi.org/10.3390/ani10040624 - 05 Apr 2020

Cited by 11 | Viewed by 2732

Abstract

Fatty traits are very important in pig production. However, the role of microRNAs (miRNAs) in fat deposition is not clearly understood. In this study, we compared adipose miRNAs from three full-sibling pairs of female Landrace pigs, with high and low backfat thickness, to [...] Read more.

Fatty traits are very important in pig production. However, the role of microRNAs (miRNAs) in fat deposition is not clearly understood. In this study, we compared adipose miRNAs from three full-sibling pairs of female Landrace pigs, with high and low backfat thickness, to investigate the associated regulatory network. We obtained an average of 17.29 million raw reads from six libraries, 62.27% of which mapped to the pig reference genome. A total of 318 pig miRNAs were detected among the samples. Among them, 18 miRNAs were differentially expressed (p-value < 0.05, |log₂fold change| ≥ 1) between the high and low backfat groups; 6 were up-regulated and 12 were down-regulated. Functional enrichment of the predicted target genes of the differentially expressed miRNAs, indicated that these miRNAs were involved mainly in lipid and carbohydrate metabolism, and glycan biosynthesis and metabolism. Comprehensive analysis of the mRNA and miRNA transcriptomes revealed possible regulatory relationships for fat deposition. Negatively correlated mRNA–miRNA pairs included miR-137–PPARGC1A, miR-141–FASN, and miR-122-5p–PKM, indicating these interactions may be key regulators of fat deposition. Our findings provide important insights into miRNA expression patterns in the backfat tissue of pig and new insights into the regulatory mechanisms of fat deposition in pig. Full article

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9 pages, 1822 KiB

Open AccessArticle

Genome-Wide Analyses Identifies Known and New Markers Responsible of Chicken Plumage Color

by Salvatore Mastrangelo, Filippo Cendron, Gianluca Sottile, Giovanni Niero, Baldassare Portolano, Filippo Biscarini and Martino Cassandro

Animals 2020, 10(3), 493; https://doi.org/10.3390/ani10030493 - 15 Mar 2020

Cited by 13 | Viewed by 4241

Abstract

Through the development of the high-throughput genotyping arrays, molecular markers and genes related to phenotypic traits have been identified in livestock species. In poultry, plumage color is an important qualitative trait that can be used as phenotypic marker for breed identification. In order [...] Read more.

Through the development of the high-throughput genotyping arrays, molecular markers and genes related to phenotypic traits have been identified in livestock species. In poultry, plumage color is an important qualitative trait that can be used as phenotypic marker for breed identification. In order to assess sources of genetic variation related to the Polverara chicken breed plumage colour (black vs. white), we carried out a genome-wide association study (GWAS) and a genome-wide fixation index (F_ST) scan to uncover the genomic regions involved. A total of 37 animals (17 white and 20 black) were genotyped with the Affymetrix 600 K Chicken single nucleotide polymorphism (SNP) Array. The combination of results from GWAS and F_ST revealed a total of 40 significant markers distributed on GGA 01, 03, 08, 12 and 21, and located within or near known genes. In addition to the well-known TYR, other candidate genes have been identified in this study, such as GRM5, RAB38 and NOTCH2. All these genes could explain the difference between the two Polverara breeds. Therefore, this study provides the basis for further investigation of the genetic mechanisms involved in plumage color in chicken. Full article

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19 pages, 5979 KiB

Open AccessArticle

Integrated Analysis of miRNA-mRNA Network Reveals Different Regulatory Patterns in the Endometrium of Meishan and Duroc Sows during Mid-Late Gestation

by Kaijie Yang, Jue Wang, Kejun Wang, Yabiao Luo, Qiguo Tang, Ximing Liu and Meiying Fang

Animals 2020, 10(3), 420; https://doi.org/10.3390/ani10030420 - 03 Mar 2020

Cited by 10 | Viewed by 2779

Abstract

Embryo loss is a major factor affecting profitability in the pig industry. Embryonic mortality occurs during peri-implantation and mid-late gestation in pigs. Previous investigations have shown that the embryo loss rate in Meishan pigs is significantly lower than in commercial breeds. Most studies [...] Read more.

Embryo loss is a major factor affecting profitability in the pig industry. Embryonic mortality occurs during peri-implantation and mid-late gestation in pigs. Previous investigations have shown that the embryo loss rate in Meishan pigs is significantly lower than in commercial breeds. Most studies have focused on embryonic mortality during early gestation, but little is known about losses during mid-late gestation. In this study, we performed a transcriptome analysis of endometrial tissue in mid-late gestation sows (gestation days 49 and 72) sampled from two breeds (Meishan (MS) and Duroc (DU)) that have different embryo loss rates. We identified 411, 1113, 697, and 327 differentially expressed genes, and 14, 36, 57, and 43 differentially expressed miRNAs in four comparisons (DU49 vs. DU72, DU49 vs. MS49, DU72 vs. MS72, and MS49 vs. MS72), respectively. Subsequently; seven differentially expressed mRNAs and miRNAs were validated using qPCR. Functional analysis suggested the differentially expressed genes and miRNAs target genes mainly involved in regulation of hormone levels, blood vessel development, developmental process involved in reproduction, embryonic placenta development, and the immune system. A network analysis of potential miRNA-gene interactions revealed that differentially expressed miRNAs in Meishan pigs are involved in the response to estradiol and oxygen levels, and affect angiogenesis and blood vessel development. The binding site on ssc-miR-503 for epidermal growth factor (EGF) and the binding site on ssc-miR-671-5p for estrogen receptor α (ESR1) were identified using a dual luciferase assay. The results of this study will enable further exploration of miRNA-mRNA interactions important in pig pregnancy and will help to uncover molecular mechanisms affecting embryonic mortality in pigs during mid-late gestation. Full article

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15 pages, 2840 KiB

Open AccessArticle

Gene Expression Profiling in Ovaries and Association Analyses Reveal HEP21 as a Candidate Gene for Sexual Maturity in Chickens

by Biao Chen, Guitao Liang, Xuenong Zhu, Yuwen Tan, Jiguo Xu, Hongxiang Wu, Huirong Mao, Yutao Zhang, Jiakun Chen, Yousheng Rao, Min Zhou and Sanfeng Liu

Animals 2020, 10(2), 181; https://doi.org/10.3390/ani10020181 - 21 Jan 2020

Cited by 10 | Viewed by 3253

Abstract

The age of onset of sexual maturity is an important reproductive trait in chickens. In this study, we explored candidate genes associated with sexual maturity and ovary development in chickens. We performed DGE RNA-sequencing analyses of ovaries of pre-laying (P-F-O1, L-F-O1) and laying [...] Read more.

The age of onset of sexual maturity is an important reproductive trait in chickens. In this study, we explored candidate genes associated with sexual maturity and ovary development in chickens. We performed DGE RNA-sequencing analyses of ovaries of pre-laying (P-F-O1, L-F-O1) and laying (P-F-O2, L-F-O2) hens of two sub-breeds of Ningdu Yellow chicken. A total of 3197 genes were identified in the two comparisons, and 966 and 1860 genes were detected exclusively in comparisons of P-F-O1 vs. P-F-O2 and L-F-O1 vs. L-F-O2, respectively. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses showed that genes involved in transmembrane signaling receptor activity, cell adhesion, developmental processes, the neuroactive ligand–receptor interaction pathway, and the calcium signaling pathway were enriched in both comparisons. Genes on these pathways, including growth hormone (GH), integrin subunit beta 3 (ITGB3), thyroid stimulating hormone subunit beta (TSHB), prolactin (PRL), and transforming growth factor beta 3 (TGFB3), play indispensable roles in sexual maturity. As a gene unique to poultry, hen egg protein 21 kDa (HEP21) was chosen as the candidate gene. Differential expression and association analyses were performed. RNA-seq data and qPCR showed that HEP21 was significantly differentially expressed in pre-pubertal and pubertal ovaries. A total of 23 variations were detected in HEP21. Association analyses of single nucleotide polymorphisms (SNPs) in HEP21 and reproductive traits showed that rs315156783 was significantly related to comb height at 84 and 91 days. These results indicate that HEP21 is a candidate gene for sexual maturity in chickens. Our results contribute to a more comprehensive understanding of sexual maturity and reproduction in chickens. Full article

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9 pages, 1037 KiB

Open AccessArticle

Myostatin (MSTN) Gene Indel Variation and Its Associations with Body Traits in Shaanbei White Cashmere Goat

by Yi Bi, Bo Feng, Zhen Wang, Haijing Zhu, Lei Qu, Xianyong Lan, Chuanying Pan and Xiaoyue Song

Animals 2020, 10(1), 168; https://doi.org/10.3390/ani10010168 - 19 Jan 2020

Cited by 22 | Viewed by 3901

Abstract

Myostatin (MSTN) gene, also known as growth differentiation factor 8 (GDF8), is a member of the transforming growth factor-beta super-family and plays a negative role in muscle development. It acts as key points during pre- and post-natal life of [...] Read more.

Myostatin (MSTN) gene, also known as growth differentiation factor 8 (GDF8), is a member of the transforming growth factor-beta super-family and plays a negative role in muscle development. It acts as key points during pre- and post-natal life of amniotes that ultimately determine the overall muscle mass of animals. There are several studies that concentrate on the effect of a 5 bp insertion/deletion (indel) within the 5’ untranslated region (5’ UTR) of goat MSTN gene in goats. However, almost all sample sizes were below 150 individuals. Only in Boer goats, the sample sizes reached 482. Hence, whether the 5 bp indel was still associated with the growth traits of goats in large sample sizes which were more reliable is not clear. To find an effective and dependable DNA marker for goat rearing, we first enlarged the sample sizes (n = 1074, Shaanbei White Cashmere goat) which would enhance the robustness of the analysis and did the association analyses between the 5 bp indel and growth traits. Results uncovered that the 5 bp indel was significantly related to body height, height at hip cross, and chest width index (p < 0.05). In addition, individuals with DD genotype had a superior growing performance than those with the ID genotype. These findings suggested that the 5 bp indel in MSTN gene are significantly associated with growth traits and the specific genotype might be promising for maker-assisted selection (MAS) of goats. Full article

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