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Genes of value: Individual genes that currently contribute, or might...
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Genes of value: Individual genes that currently contribute, or might soon contribute, to sheep and goat production systems

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Animal Genetics and Genomics".

Deadline for manuscript submissions: closed (30 December 2019) | Viewed by 30851

Special Issue Editors

Prof. Dr. Jonathan Hickford

E-Mail Website
Guest Editor
Department of Agricultural Sciences, Lincoln University, Lincoln 7647, New Zealand
Interests: PCR; DNA sequencing; animal science; animal breeding; cattle; animal genetics; meat; lamb; bovine
Dr. Huitong Zhou

E-Mail Website
Guest Editor
Department of Agricultural Sciences, Lincoln University, Lincoln 7647, New Zealand
Interests: animal genetics; sheep; genetic variation; gene-marker technology; PCR-based diagnostics

Special Issue Information

Dear Colleagues,

In the context of the large body of literature now focused on finding important sheep anf goat genes, and the various technologies being applied to selecting whole sheep and goat genomes for a given production system, the role that individual genes play can be overlooked. How then is our knowledge of individual sheep and goat genes and their effect being used currently, or how will it be used in the near future, to improve sheep and goat production. Is there a large disconnect between the science and technology and its practical applications in sheep anf goat farming?

Prof. Jonathan Hickford
Dr. Huitong Zhou
Guest Editors

Manuscript Submission Information

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Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Sheep and Goat Production
  • Genes
  • Gene-markers
  • Genetic Gain

Published Papers (7 papers)

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Research

19 pages, 6534 KiB  
Article
Comprehensive Analysis of Differentially Expressed Profiles of mRNA, lncRNA, and circRNA in the Uterus of Seasonal Reproduction Sheep
by Yongfu La, Xiaoyun He, Liping Zhang, Ran Di, Xiangyu Wang, Shangquan Gan, Xiaosheng Zhang, Jinlong Zhang, Wenping Hu and Mingxing Chu
Genes 2020, 11(3), 301; https://doi.org/10.3390/genes11030301 - 12 Mar 2020
Cited by 25 | Viewed by 4180
Abstract
Photoperiod is one of the important factors leading to seasonal reproduction of sheep. However, the molecular mechanisms underlying the photoperiod regulation of seasonal reproduction remain poorly understood. In this study, we compared the expression profiles of mRNAs, lncRNAs, and circRNAs in uterine tissues [...] Read more.
Photoperiod is one of the important factors leading to seasonal reproduction of sheep. However, the molecular mechanisms underlying the photoperiod regulation of seasonal reproduction remain poorly understood. In this study, we compared the expression profiles of mRNAs, lncRNAs, and circRNAs in uterine tissues from Sunite sheep during three different photoperiods, namely, the short photoperiod (SP), short transfer to long photoperiod (SLP), and long photoperiod (LP). The results showed that 298, 403, and 378 differentially expressed (DE) mRNAs, 171, 491, and 499 DE lncRNAs, and 124, 270, and 400 DE circRNAs were identified between SP and LP, between SP and SLP, and between LP and SLP, respectively. Furthermore, functional enrichment analysis showed that the differentially expressed RNAs were mainly involved in the GnRH signaling pathway, thyroid hormone synthesis, and thyroid hormone signaling pathway. In addition, co-expression networks of lncRNA–mRNA were constructed based on the correlation analysis between the differentially expressed RNAs. Our study provides new insights into the expression changes of RNAs in different photoperiods, which might contribute to understanding the molecular mechanisms of seasonal reproduction in sheep. Full article
(This article belongs to the Special Issue Genes of value: Individual genes that currently contribute, or might soon contribute, to sheep and goat production systems)
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14 pages, 4917 KiB  
Article
Comparative Transcriptome Analysis Identifying the Different Molecular Genetic Markers Related to Production Performance and Meat Quality in Longissimus Dorsi Tissues of MG × STH and STH Sheep
by Shuru Cheng, Xueying Wang, Quanwei Zhang, Yuqin He, Xia Zhang, Lei Yang and Jinping Shi
Genes 2020, 11(2), 183; https://doi.org/10.3390/genes11020183 - 10 Feb 2020
Cited by 23 | Viewed by 3008
Abstract
Crossbred sheep have many prominent traits, such as excellent production performance and high-quality meat, when compared to local sheep breeds. However, the genetic molecular markers related to these characteristics remain unclear. The crossbred MG × STH (small-tailed Han sheep (STH) × Mongolian sheep [...] Read more.
Crossbred sheep have many prominent traits, such as excellent production performance and high-quality meat, when compared to local sheep breeds. However, the genetic molecular markers related to these characteristics remain unclear. The crossbred MG × STH (small-tailed Han sheep (STH) × Mongolian sheep (MG)) breed and the STH breed were selected to measure production performance and meat quality. We used 14 indexes of production performance and meat quality, which in the MG × STH population showed significant differences compared to the STH breed. Subsequently, the longissimus dorsi from the two sheep were subjected to comparative transcriptomic analyses to identify differentially expressed genes (DEGs) related to production performance and meat quality. A total of 874 DEGs were identified between the two sheep groups. A total of 110 unique DEGs related to sheep production performance and meat quality were selected as the candidate DEGs. We found 6 production-performance-related and 30 meat-quality-related DEGs through a correlation analysis, including SPARC, ACVRL1, FNDC5, and FREM1. The expression levels of 11 DEGs were validated by real-time PCR, and the results were in accordance with the results of the comparative transcriptomic and correlation analyses. These results will assist in understanding sheep heterosis and molecular marker-assisted selection. Full article
(This article belongs to the Special Issue Genes of value: Individual genes that currently contribute, or might soon contribute, to sheep and goat production systems)
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10 pages, 1945 KiB  
Article
The LCORL Locus Is under Selection in Large-Sized Pakistani Goat Breeds
by Rashid Saif, Jan Henkel, Vidhya Jagannathan, Cord Drögemüller, Christine Flury and Tosso Leeb
Genes 2020, 11(2), 168; https://doi.org/10.3390/genes11020168 - 05 Feb 2020
Cited by 20 | Viewed by 10598
Abstract
Goat domestication and human selection for valued traits have formed diverse breeds with characteristic phenotypes. This process led to the fixation of causative genetic variants controlling breed-specific traits within regions of reduced genetic diversity—so-called “selection signatures”. We previously reported an analysis of selection [...] Read more.
Goat domestication and human selection for valued traits have formed diverse breeds with characteristic phenotypes. This process led to the fixation of causative genetic variants controlling breed-specific traits within regions of reduced genetic diversity—so-called “selection signatures”. We previously reported an analysis of selection signatures based on pooled whole-genome sequencing data of 20 goat breeds and bezoar goats. In the present study, we reanalyzed the data and focused on a subset of eight Pakistani goat breeds (Angora, Barbari, Beetal, Dera Din Panah, Kamori, Nachi, Pahari, Teddy). We identified 749 selection signatures based on reduced heterozygosity in these breeds. A search for signatures that are shared across large-sized goat breeds revealed that five medium-to-large-sized Pakistani goat breeds had a common selection signature on chromosome 6 in a region harboring the LCORL gene, which has been shown to modulate height or body size in several mammalian species. Fine-mapping of the region confirmed that all five goat breeds with the selection signature were nearly fixed for the same haplotype in a ~191 kb region spanning positions 37,747,447–37,938,449. From the pool sequencing data, we identified a frame-shifting single base insertion into an isoform-specific exon of LCORL as a potential candidate causal variant mediating the size-increasing effect. If this preliminary result can be confirmed in independent replication studies, genotyping of this variant might be used to improve breeding programs and the selection for stature in goats. Full article
(This article belongs to the Special Issue Genes of value: Individual genes that currently contribute, or might soon contribute, to sheep and goat production systems)
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10 pages, 823 KiB  
Article
The Mean Staple Length of Wool Fibre Is Associated with Variation in the Ovine Keratin-Associated Protein 21-2 Gene
by Shaobin Li, Huitong Zhou, Hua Gong, Fangfang Zhao, Jiqing Wang, Xiu Liu, Jiang Hu, Yuzhu Luo and Jon G.H. Hickford
Genes 2020, 11(2), 148; https://doi.org/10.3390/genes11020148 - 30 Jan 2020
Cited by 19 | Viewed by 2757
Abstract
Wool and hair fibres consist of a variety of proteins, including the keratin-associated proteins (KAPs). In this study, a putative ovine homologue of the human KAP21-2 gene (KRTAP21-2) was identified. It was located on chromosome 1 as a 201-bp open reading [...] Read more.
Wool and hair fibres consist of a variety of proteins, including the keratin-associated proteins (KAPs). In this study, a putative ovine homologue of the human KAP21-2 gene (KRTAP21-2) was identified. It was located on chromosome 1 as a 201-bp open reading frame (ORF) in the ovine genome assembly from a Texel sheep (v.4 NC_019458.2: nt122932727 to 122932927). A polymerase chain reaction- single strand conformation polymorphism (PCR-SSCP) analysis of this ORF, and subsequent DNA sequencing, identified five sequences (named A-E). The putative amino acid sequences that would be produced, shared some identity with each other and with other KAPs, but they were most similar to ovine KAP21-1, and phylogenetically related to human KAP21-2. The location of the ovine KRTAP21-2 sequence was consistent with the location of human KRTAP21-2, and this suggests they represent different variant forms of ovine KRTAP21-2. Variation in this gene was investigated in 389 Merino (sire) × Southdown-cross (ewe) lambs. These were derived from four independent sire-lines. The sequence variation was found to be associated with variation in five wool traits: including mean staple length (MSL), mean fibre diameter (MFD), fibre diameter standard deviation (FDSD), prickle factor (PF), and greasy fleece weight (GFW). The most persistent effect of KRTAP21-2 variation was with variation in MSL; with the MSL of sheep of genotype AC being 12.5% greater than those of genotype CE. A similar effect was observed from individual variant absence/presence models. This suggests that KRTAP21-2 should be further investigated as a possible gene-marker for improving MSL. Full article
(This article belongs to the Special Issue Genes of value: Individual genes that currently contribute, or might soon contribute, to sheep and goat production systems)
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12 pages, 3205 KiB  
Article
Identification of Caprine KRTAP28-1 and Its Effect on Cashmere Fiber Diameter
by Jiqing Wang, Huitong Zhou, Jon G. H. Hickford, Mengli Zhao, Hua Gong, Zhiyun Hao, Jiyuan Shen, Jiang Hu, Xiu Liu, Shaobin Li and Yuzhu Luo
Genes 2020, 11(2), 121; https://doi.org/10.3390/genes11020121 - 22 Jan 2020
Cited by 6 | Viewed by 2055
Abstract
The keratin-associated proteins (KAPs) are constituents of cashmere fibers and variation in many KAP genes (KRTAPs) has been found to be associated with fiber traits. The gene encoding the high-sulphur KAP28-1 has been described in sheep, but it has not been [...] Read more.
The keratin-associated proteins (KAPs) are constituents of cashmere fibers and variation in many KAP genes (KRTAPs) has been found to be associated with fiber traits. The gene encoding the high-sulphur KAP28-1 has been described in sheep, but it has not been identified in the goat genome. In this study, a 255-bp open reading frame on goat chromosome 1 was identified using a search of similar sequence to ovine KRTAP28-1, and that would if transcribed and translated encode a high sulphur KAP. Based on the analysis of polymerase chain reaction amplicons for the goat nucleotide sequences in 385 Longdong cashmere goats in China, five unique banding patterns were detected using single strand conformation polymorphism analysis. These represented five DNA sequences (named variants A to E) and they had the highest resemblance to KRTAP28-1 sequences from sheep, suggesting A–E are variants of caprine KRTAP28-1. DNA sequencing revealed a 2 or 4-bp deletion and eleven nucleotide sequence differences, including four non-synonymous substitutions. Of the four common variants (A, B, C and D) found in these goats, the presence of variant A was associated with decreased mean fiber diameter and this effect appeared to be additive. These results indicate that caprine KRTAP28-1 variation might have value as a molecular marker for reducing cashmere mean fiber diameter. Full article
(This article belongs to the Special Issue Genes of value: Individual genes that currently contribute, or might soon contribute, to sheep and goat production systems)
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18 pages, 927 KiB  
Article
Effects of Intronic SNPs in the Myostatin Gene on Growth and Carcass Traits in Colored Polish Merino Sheep
by Ewa Grochowska, Bronisław Borys and Sławomir Mroczkowski
Genes 2020, 11(1), 2; https://doi.org/10.3390/genes11010002 - 18 Dec 2019
Cited by 14 | Viewed by 3239
Abstract
Myostatin acts as a negative regulator of muscle growth; therefore, its role is important with regard to animal growth and meat production. This study was undertaken with the objective to detect polymorphisms in the first intron and c.*1232 position of the MSTN gene [...] Read more.
Myostatin acts as a negative regulator of muscle growth; therefore, its role is important with regard to animal growth and meat production. This study was undertaken with the objective to detect polymorphisms in the first intron and c.*1232 position of the MSTN gene and to analyze effects of the detected alleles/genotypes on growth and carcass traits in Colored Polish Merino sheep. In total, 23 traits were analyzed, i.e., seven describing lamb growth and 16 carcass traits. Single nucleotide polymorphisms (SNPs) in the first intron and the c.*1232 position were identified using polymerase chain reaction single-strand conformation polymorphism (PCR-SSCP) and PCR-restriction fragment length polymorphism (PCR-RFLP) methods, respectively. The MIXED procedure of the SAS software package was used to analyze allelic and genotypic effects of the MSTN gene on growth and carcass traits. Polymorphisms were only detected in the first intron of the MSTN gene. All investigated sheep were monomorphic G in the c.*1232 position. The MSTN genotype was found to have significant effect on body weight at 2nd day of life (BW2) and loin and fore shank weights. Significant allelic effects were detected with respect to BW2, scrag, leg, fore, and hind shank weights. These results suggest that polymorphisms in the first intron of the MSTN gene are relevant with respect to several carcass traits and BW2 in Colored Polish Merino sheep. Full article
(This article belongs to the Special Issue Genes of value: Individual genes that currently contribute, or might soon contribute, to sheep and goat production systems)
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11 pages, 2473 KiB  
Article
Molecular Characterization and Expression of SPP1, LAP3 and LCORL and Their Association with Growth Traits in Sheep
by Yongfu La, Xiaoxue Zhang, Fadi Li, Deyin Zhang, Chong Li, Futao Mo and Weimin Wang
Genes 2019, 10(8), 616; https://doi.org/10.3390/genes10080616 - 14 Aug 2019
Cited by 16 | Viewed by 4384
Abstract
The SPP1, LAP3, and LCORL are located on chromosome 6 of sheep and a domain of 36.15-38.56 Mb, which plays an essential role in tissue and embryonic growth. In this study, we cloned the complete coding sequences of SPP1 and partial [...] Read more.
The SPP1, LAP3, and LCORL are located on chromosome 6 of sheep and a domain of 36.15-38.56 Mb, which plays an essential role in tissue and embryonic growth. In this study, we cloned the complete coding sequences of SPP1 and partial coding regions of LAP3 and LCORL from Hu sheep (Gansu Province, China) and analyzed their genomic structures. The RT-qPCR showed that the three genes were expressed widely in the different tissues of Hu sheep. The SPP1 expression was significantly higher in the kidney (p < 0.01) and LAP3 expression was significantly higher in the spleen, lung, kidney, and duodenum than in the other tissues (heart, liver, rumen, muscle, fat, and ovary; p < 0.05). The LCORL was preferentially expressed in the spleen, duodenum, and lung (p < 0.05). In addition, the nucleotide substitution NM_001009224.1:c.132A>C was found in SPP1; an association analysis showed that it was associated with birth weight and yearling weight (p < 0.05), and NM_001009224.1:c.132C was the dominant allele. Two mutations XM_012179698.3:c.232C>G and XM_012179698.3:c.1154C>T were identified in LAP3. The nucleotide substitution XM_012179698.3:c.232C>G was confirmed to be associated with birth weight, 1-month weight, 3-month weight (p < 0.05), and 2-month weight (p < 0.01). The nucleotide substitution XM_012179698.3:c.1154C>T was associated with birth weight (p < 0.01), 1-month weight, and 2-month weight (p < 0.05). The LAP3 gene XM_012179698.3:c.232C>G mutation with the C allele has higher body weight than other sheep, and CC genotype individuals show higher birth weight, 1-month weight, and weaning weight than the GG genotype individuals (p < 0.05). Our results support the conclusion that the mutations on ovine SPP1 and LAP3 successfully track functional alleles that affect growth in sheep, and these genes could be used as candidate genes for improving the growth traits of sheep during breeding. Full article
(This article belongs to the Special Issue Genes of value: Individual genes that currently contribute, or might soon contribute, to sheep and goat production systems)
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