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Animal Genetics and Livestock Production: The Biodiversity Challenge

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A special issue of Animals (ISSN 2076-2615). This special issue belongs to the section "Animal Genetics and Genomics".

Deadline for manuscript submissions: closed (31 December 2021) | Viewed by 34360

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Dr. Maria Selvaggi

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Department of Agricultural and Environmental Science, University of Bari Aldo Moro, 70126 Bari, Italy
Interests: animal genetics; milk quality; animal production
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Dr. Maria Antonietta Colonna

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Department of Agricultural and Environmental Science, University of Bari Aldo Moro, 70126 Bari, Italy
Interests: animal feeding; nutrition; meat quality; sheep; goat; beef production
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Dear Colleagues,

Animal breeding strategies, commonly used to improve domestic animal production traits, have led to genetic gain for cosmopolitan breeds for many important performance traits. As a consequence, a great loss of genetic diversity has been observed and, in some cases, an increase of inbreeding rate has also been reported. In the past 25 years a lot of indigenous breeds have become extinct or are considered at risk of extinction and knowledge and information on these breeds are often lacking.

To date, domestic animal genetic resources are facing different challenges; the erosion of genetic diversity and the need to increase livestock production in developing countries. Moreover, biodiversity investigation could be an important opportunity also to face climate change: many local breeds are more resistant to high temperature being able to provide food in difficult environmental conditions and with low planes of nutrition.

Finally, local breeds may be a great opportunity also for a more sustainable livestock production system in developed countries in order to avoid the abandonment of marginal areas.

For this special issue, original manuscripts covering all aspects of animal genetics, such as population genetics, local breed investigation, quantitative genetics, genetic variability, crossbreeding strategies, gene polymorphisms, indigenous breed valorization opportunities are invited.

We invite original research papers on animal breeding, population genetics, genetic association studies, transcriptomics and quantitative genomics in livestock, which address the biological mechanisms underlying the expression of complex (quantitative) traits, to give insight into the origin and impact of genetic variation and population stratification at the genome scale, so as to explore genomics opportunities for long-term selection strategies.

Prof. Dr. Maria Selvaggi
Dr. Maria Antonietta Colonna
Guest Editors

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Keywords

Population genetics
Gene polymorphism
Sustainable livestock production
Genetic variability
Farm animal biodiversity
Breed characterization
Animal breeding

Published Papers (11 papers)

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Research

12 pages, 984 KiB

Open AccessArticle

Estimates of Effective Population Size in Commercial and Hatchery Strains of Coho Salmon (Oncorhynchus kisutch (Walbaum, 1792))

by Victor Martinez, Phillip J. Dettleff, Nicolás Galarce, Cristian Bravo, Jessica Dorner, Robert N. Iwamoto and Kerry Naish

Animals 2022, 12(5), 647; https://doi.org/10.3390/ani12050647 - 03 Mar 2022

Cited by 5 | Viewed by 2571

Abstract

Understanding the genetic status of aquaculture strains is essential for developing management guidelines aimed at sustaining the rates of genetic gain for economically important traits, as well as securing populations that will be robust to climate change. Coho salmon was the first salmonid introduced to Chile for commercial purposes and now comprises an essential component of the country’s aquaculture industry. Several events, such as admixture, genetic bottlenecks, and rapid domestication, appear to be determinants in shaping the genome of commercial strains representing this species. To determine the impact of such events on the genetic diversity of these strains, we sought to estimate the effective population size (Ne) of several of these strains using genome-wide approaches. We compared these estimates to commercial strains from North America and Japan, as well as a hatchery strain used for supportive breeding of wild populations. The estimates of Ne were based on a method robust to assumptions about changes in population history, and ranged from low (Ne = 34) to relatively high (Ne = 80) in the Chilean strains. These estimates were higher than those obtained from the commercial North American strain but lower than those observed in the hatchery population and the Japanese strain (with Ne over 150). Our results suggest that some populations require measures to control the rates of inbreeding, possibly by using genomic information and incorporating new genetic material to ensure the long-term sustainability of these populations. Full article

(This article belongs to the Special Issue Animal Genetics and Livestock Production: The Biodiversity Challenge)

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14 pages, 849 KiB

Open AccessCommunication

Carcass Quality Profiles and Associated Genomic Regions of South African Goat Populations Investigated Using Goat SNP50K Genotypes

by Keabetswe Tebogo Ncube, Edgar Farai Dzomba, Khanyisile Hadebe, Pranisha Soma, Lorinda Frylinck and Farai Catherine Muchadeyi

Animals 2022, 12(3), 364; https://doi.org/10.3390/ani12030364 - 02 Feb 2022

Cited by 4 | Viewed by 2020

Abstract

Carcass quality includes a battery of essential economic meat traits that play a significant role in influencing farmer breed preferences. A preliminary study was undertaken to investigate the carcass quality and the associated genomic regions in a small nucleus of animals that are representative of South African goat genetic resources. Samples of the South African Boer (n = 14), Northern Cape Speckled (n = 14), Eastern Cape Xhosa Lob ear (n = 12), Nguni/Mbuzi (n = 13), and Village (n = 20) were genotyped using the Illumina goat SNP50K and were phenotyped for carcass quality traits. SA Boer goats had heavier warm and cold carcass weights (17.2 ± 2.3 kg and 16.3 ± 2.3 kg). Pella village goats raised under an intensive system had significantly (p < 0.05) heavier warm and cold carcass weights (9.9 ± 1.1 kg and 9.2 ± 1.2 kg) compared to the village goats that are raised extensively (9.1 ± 2.0 kg and 8.4 ± 1.9). A total of 40 SNPs located on chromosomes 6, 10, 12, 13, 19, and 21 were significantly associated with carcass traits at (−log10 [p < 0.05]). Candidate genes that were associated with carcass characteristics (GADD45G, IGF2R, GAS1, VAV3, CAPN8, CAPN7, CAPN2, GHSR, COLQ, MRAS, and POU1F1) were also observed. Results from this study will inform larger future studies that will ultimately find use in breed improvement programs. Full article

(This article belongs to the Special Issue Animal Genetics and Livestock Production: The Biodiversity Challenge)

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10 pages, 1462 KiB

Open AccessArticle

Lamb Meat Quality and Carcass Evaluation of Five Autochthonous Sheep Breeds: Towards Biodiversity Protection

by Maria Giovanna Ciliberti, Antonella Santillo, Rosaria Marino, Elena Ciani, Mariangela Caroprese, Luigina Rillo, Donato Matassino, Agostino Sevi and Marzia Albenzio

Animals 2021, 11(11), 3222; https://doi.org/10.3390/ani11113222 - 11 Nov 2021

Cited by 4 | Viewed by 1977

Abstract

In the present study, the evaluation of the carcasses and meat quality, in terms of chemical composition and fatty acid profile, of lambs from five autochthonous sheep breeds (Altamurana, Bagnolese, Gentile di Puglia, Laticauda, and Leccese) reared in continental Southern Italy, were studied. All the carcasses were evaluated according to the EU Mediterranean classification system for carcasses weighing less than 13 kg. Meat chemical composition and fatty acids profile were assessed on both loin and leg commercial cuts. Fatty acid composition of loin resulted in differences among breeds, displaying lower values of saturated fatty acid in Altamurana, Bagnolese, and Leccese breeds and the highest content of polyunsaturated fatty acid in the Altamurana breed. Principal component analysis grouped lamb according to fatty acid content and to conjugated linoleic acid (CLA), omega n-3 and n-6 fatty acids; thus, Altamurana, Bagnolese, and Leccese breeds are characterized by the highest values of CLA content. Our data demonstrated that lamb meat from autochthonous breed has good carcass quality and the content of CLA, n-3, and n-6 was valuable for human consumption; therefore, the valorisation of local meat quality can help to avoid the extinction of the autochthonous breed offering to the market and consumer’s high nutritive products. Full article

(This article belongs to the Special Issue Animal Genetics and Livestock Production: The Biodiversity Challenge)

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8 pages, 318 KiB

Open AccessCommunication

Variation in the Ovine Glycogen Synthase Kinase 3 Beta-Interaction Protein Gene (GSKIP) Affects Carcass and Growth Traits in Romney Sheep

by Fangfang Zhao, Huitong Zhou, Shaobin Li, Qingming An, Qian Fang, Yuzhu Luo and Jon G. H. Hickford

Animals 2021, 11(9), 2690; https://doi.org/10.3390/ani11092690 - 14 Sep 2021

Cited by 1 | Viewed by 2336

Abstract

The glycogen synthase kinase 3 beta (GSK3β)-interacting protein (encoded by the gene GSKIP) is a small A-kinase anchoring protein, which complexes with GSK3βand protein kinase A (PKA) and acts synergistically with cAMP/PKA signaling to inhibit GSK3β activity. The protein plays a role in regulating glycogen metabolism, protein synthesis, the cell cycle, and in regulating gene expression. In this study, PCR-single strand conformation polymorphism (PCR-SSCP) analyses were used to screen for variation in exon 1 and exon 2 of GSKIP in 840 New Zealand (NZ) Romney sheep. Two SSCP banding patterns representing two different nucleotide variants (A and B) were detected in an exon 1 region, whereas in an exon 2 region only one pattern was detected. Variants A and B of exon 1 had one non-synonymous nucleotide difference c.37A/G (p.Met13Val). The birthweight of sheep of genotype AA (5.9 ± 0.06 kg) was different (p = 0.023) to sheep of genotype AB (5.7 ± 0.06 kg) and BB (5.7 ± 0.06 kg). The hot carcass weight (HCW) of sheep of genotype AA (17.2 ± 0.22 kg) was different (p = 0.012) to sheep of genotype AB (17.6 ± 0.22 kg) and BB (18.0 ± 0.29 kg), and the fat depth at the 12th rib (V-GR) of sheep of genotype AA (7.7 ± 0.31 mm) was different (p = 0.016) to sheep of genotype AB (8.3 ± 0.30 mm) and BB (8.5 ± 0.39 mm). The results suggest that the c.37A/G substitution in ovine GSKIP may affect sheep growth and carcass traits. Full article

(This article belongs to the Special Issue Animal Genetics and Livestock Production: The Biodiversity Challenge)

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11 pages, 262 KiB

Open AccessArticle

Genetic Parameters of Workability Traits in the Population of Polish Holstein-Friesian Cows Based on Conventional and Genomic Data

by Bartosz Szymik, Piotr Topolski and Wojciech Jagusiak

Animals 2021, 11(8), 2443; https://doi.org/10.3390/ani11082443 - 19 Aug 2021

Cited by 2 | Viewed by 1940

Abstract

Heritabilities of workability (WT) traits—milking speed (MS) and temperament (MT)—as well as genetic and phenotypic correlations between these traits in the population of Polish Holstein-Friesian (PHF) cows were estimated. The estimation of genetic parameters was performed twice: first with the use of pedigree data; and second with the use of pedigree and genomic data. Phenotypic data from routinely conducted MS and MT evaluations for 1,045,511 cows born from 2004 to 2013 were available; the cows were evaluated from 2011 to 2015. The main dataset was reduced based on imposed restrictions (e.g., on age of calving, stage of lactation and day of first trial milking). The dataset prepared in this manner comprised 391,615 cows. It was then reduced to daughters of 10% randomly selected sires for computational reasons. Finally, for genetic parameter estimation, 13,280 records of cows were used. The linear observation model included additive random effects of animal, fixed effects of herd-year-season of calving subclass (HYS) and lactation phase, fixed regressions on cow age at calving and the percent of HF breed genes in the cow genotype. Heritabilities estimated based on pedigree data were 0.12 (±0.0067) for MS and 0.08 (±0.0063) for MT, the genetic correlation between MS and MT was estimated at 0.05 (±0.0002) and the phenotypic correlation coefficient was estimated at 0.14 (±0.0004). The inclusion of genomic information of sire bulls had no clear effect on the size of the estimated WT genetic parameters. The heritabilities of MS and MT were 0.11 (±0.0065) and 0.09 (±0.0012), respectively. The genetic and phenotypic correlation coefficients were 0.07 (±0.0003) and 0.12 (±0.0005), respectively. The sizes of the obtained heritabilities of WT and of the genetic and phenotypic correlation between these traits indicate the possibility of effective population improvement for both WT traits. Full article

(This article belongs to the Special Issue Animal Genetics and Livestock Production: The Biodiversity Challenge)

14 pages, 276 KiB

Open AccessArticle

Dietary Supplementation with Camelina sativa (L. Crantz) Forage in Autochthonous Ionica Goats: Effects on Milk and Caciotta Cheese Chemical, Fatty Acid Composition and Sensory Properties

by Maria Antonietta Colonna, Francesco Giannico, Vincenzo Tufarelli, Vito Laudadio, Maria Selvaggi, Giuseppe De Mastro and Luigi Tedone

Animals 2021, 11(6), 1589; https://doi.org/10.3390/ani11061589 - 28 May 2021

Cited by 10 | Viewed by 4182

Abstract

The research studied the effects of dietary supplementation with Camelina sativa fresh forage on the chemical and fatty acid composition of milk and Caciotta cheese, and its sensory properties. Twenty Ionica goats were randomly assigned to the following two groups (n = 10): the control received a traditional forage mixture (Avena sativa, 70%; Vicia sativa, 20%; Trifolium spp., 10%), while the experimental group was given Camelina sativa fresh forage (CAM). All of the dams grazed on pasture and received a commercial feed (500 g/head/day) at housing. The milk from the CAM group showed a higher (p < 0.05) content of dry matter, fat, lactose and concentrations of C6:0, C11:0, C14:0, C18:2 n-6, CLA and PUFA, while lower (p < 0.05) amounts of C12:0, C18:0 and saturated long chain FA (SLCFA). The Caciotta cheese from the CAM group showed a greater (p < 0.05) content of n-6 FA and n-6/n-3 ratio, although close to four, thus resulting adequate under the nutritional point of view. The overall liking, odour, taste, hardness, solubility and “goaty” flavour were better (p < 0.05) in the CAM cheeses. Further investigation would be advisable in order to evaluate the effect of feeding Camelina forage obtained from different phenological stages, and the application of ensiling techniques. Full article

(This article belongs to the Special Issue Animal Genetics and Livestock Production: The Biodiversity Challenge)

15 pages, 1803 KiB

Open AccessArticle

Comparison of Growth Performance and Meat Quality Traits of Commercial Cross-Bred Pigs versus the Large Black Pig Breed

by Yongjie Wang, Keshari Thakali, Palika Morse, Sarah Shelby, Jinglong Chen, Jason Apple and Yan Huang

Animals 2021, 11(1), 200; https://doi.org/10.3390/ani11010200 - 15 Jan 2021

Cited by 24 | Viewed by 4229

Abstract

The meat quality of different pig breeds is associated with their different muscle tissue physiological processes, which involves a large variety of genes related with muscle fat and energy metabolism. Understanding the differences of biological processes of muscle after slaughter is helpful to reveal the meat quality development of different breeds. Therefore, eight native Large Black pigs (BP), with high fat content in meat, and seven cross-bred commercial pigs (CP), which had a high feed efficiency with high lean meat, were used to investigate the differences in their meat quality and RNA transcriptomes. The average daily gain (ADG) and hot carcass weight (HCW) of CP were higher than BP, but the back-fat thickness of BP was higher than CP (p < 0.05). The CP had higher a* (redness) but lower h (hue angle) than BP (p < 0.05). The metmyoglobin (MMb) percentage of CP was higher (p < 0.05) than BP. The fat content and oxygen consumption of longissimus dorsi (LD) muscles in BP were higher (p < 0.05) than CP. BP had higher monounsaturated fatty acids (MUFA) content, but CP had higher polyunsaturated fatty acids (PUFA) content (p < 0.05). The RNA-seq data highlighted 201 genes differentially expressed between the two groups (corrected false discovery rate (FDR) p < 0.05), with 75 up-regulated and 126 down-regulated genes in BP compared with CP using the fold change (FC). The real-time PCR was used to validate the results of RNA-seq for eight genes, and the genes related to lipid and energy metabolism were highly expressed in BP (p < 0.05). Based on the results, BP had superior intramuscular fat content to CP, while the growth performance of CP was better, and the transcriptomic differences between these two groups of pigs may cause the meat quality and growth performance variance. Full article

(This article belongs to the Special Issue Animal Genetics and Livestock Production: The Biodiversity Challenge)

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11 pages, 2083 KiB

Open AccessArticle

cAMP Response Element Binding Protein 1 (CREB1) Promotes Monounsaturated Fatty Acid Synthesis and Triacylglycerol Accumulation in Goat Mammary Epithelial Cells

by Dawei Yao, Chunlei Yang, Jing Ma, Lili Chen, Jun Luo, Yi Ma and Juan. J. Loor

Animals 2020, 10(10), 1871; https://doi.org/10.3390/ani10101871 - 14 Oct 2020

Cited by 10 | Viewed by 2457

Abstract

cAMP response element binding protein 1 (CREB1) is a member of the leucine zipper transcription factor family of DNA binding proteins. Although studies in non-ruminants have demonstrated a crucial role of CREB1 in lipid synthesis in liver and adipose tissue, it is unknown if this transcription regulator exerts control of fatty acid synthesis in ruminant mammary cells. To address this question, we first defined the expression dynamics of CREB1 in mammary tissue during lactation. Analysis of CREB1 in mammary tissue revealed higher mRNA abundance in mammary tissue harvested at peak lactation. Overexpression of CREB1 markedly upregulated sterol regulatory element binding transcription factor 1 (SREBP1), fatty acid synthase (FASN), acetyl-coenzyme A carboxylase α (ACACA), elongase of very long chain fatty acids 6 (ELOVL6), lipoprotein lipase (LPL), fatty acid binding protein 3 (FABP3), lipin 1 (LPIN1) and diacylglycerol acyltransferase 1 (DGAT1), but had no effect on glycerol-3-phosphate acyltransferase, mitochondrial (GPAM) or 1-acylglycerol-3-phosphate O-acyltransferase 6 (AGPAT6). In addition, overexpressing CREB1 led to a significant increase in the concentration and desaturation index of C16:1 (palmitoleic acid) and C18:1 (oleic acid), along with increased concentration of triacylglycerol. Taken together, these results highlight an important role of CREB1 in regulating lipid synthesis in goat mammary epithelial cells. Thus, manipulation of CREB1 in vivo might be one approach to improve the quality of goat milk. Full article

(This article belongs to the Special Issue Animal Genetics and Livestock Production: The Biodiversity Challenge)

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13 pages, 1936 KiB

Open AccessArticle

Genetic Characterization of the Local Pirenaica Cattle for Parentage and Traceability Purposes

by David Gamarra, Masaaki Taniguchi, Noelia Aldai, Aisaku Arakawa, Andres Lopez-Oceja and Marian M. de Pancorbo

Animals 2020, 10(9), 1584; https://doi.org/10.3390/ani10091584 - 05 Sep 2020

Cited by 5 | Viewed by 2757

Abstract

Pirenaica is the most important autochthonous cattle breed within the Protected Geographic Indication (PGI) beef quality label in the Basque region, in northern Spain. The short tandem repeats (STRs) are powerful markers to elucidate forensic cases and traceability across the agri-food sector. The main objective of the present work was to study the phylogenetic relationships of Pirenaica cattle and other breeds typically raised in the region and provide the minimum number of STR markers for parentage and traceability purposes. The 30-STR panel recommended by the International Society of Animal Genetics-Food and Agriculture Organization of the United Nations (ISAG-FAO) was compared against other commercial STR panels. The 30-STR panel showed a combined matching probability of 1.89 × 10⁻²⁵ and a power of exclusion for duos of 0.99998. However, commercial STR panels showed a limited efficiency for a reliable parentage analysis in Pirenaica, and at least a 21-STR panel is needed to reach a power of exclusion of 0.9999. Machine-learning analysis also demonstrated a 95% accuracy in assignments selecting the markers with the highest F_ST in Pirenaica individuals. Overall, the present study shows the genetic characterization of Pirenaica and its phylogeny compared with other breeds typically raised in the Basque region. Finally, a 21-STR panel with the highest F_ST markers is proposed for a confident parentage analysis and high traceability. Full article

(This article belongs to the Special Issue Animal Genetics and Livestock Production: The Biodiversity Challenge)

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7 pages, 1242 KiB

Open AccessCommunication

Investigating the Polymorphism of Bone Morphogenetic Protein Receptor-1B (BMPR1B) Gene in Markhoz Goat Breed

by Sheila Pourali Dogaheh, Seyed Ziaeddin Mirhoseini, Vincenzo Tufarelli, Navid Ghavi Hossein-Zadeh, Sajad Badbarin, Maria Antonietta Colonna, Alireza Seidavi and Maria Selvaggi

Animals 2020, 10(9), 1582; https://doi.org/10.3390/ani10091582 - 04 Sep 2020

Cited by 7 | Viewed by 2649

Abstract

Reproductive traits in livestock species are genetically controlled by the action of single genes with a major effect, commonly known as fecundity genes. One of the genes involved in controlling prolificacy is BMPR1B (FecB), a dominant autosomal gene located in chromosome 6 responsible for the fecundity and twinning rate in sheep and goat species. Markhoz goat is a valuable Iranian genetic resource endangered by extinction. Increasing the genetic variability and reproductive performances of Markhoz goat could preserve and enhance its economic value. This study was carried out to detect possible polymorphisms in BMPR1B gene in a sample of 100 Markhoz goats from Iran. DNA samples were screened by PCR–RFLP to assess the presence of the previously reported FecB mutation. Finally, the amplicons from seven goats out of the 100 samples were sequenced. The results showed that all the analyzed individuals did not carry the previously reported FecB mutant allele. However, our findings revealed two novel possible mutations in exon 8 of BMPR1B gene (775A > G and 777G > A) that need further investigations. Full article

(This article belongs to the Special Issue Animal Genetics and Livestock Production: The Biodiversity Challenge)

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16 pages, 1481 KiB

Open AccessArticle

Mitochondrial DNA Diversity in Large White Pigs in Russia

by Lyubov Getmantseva, Siroj Bakoev, Nekruz Bakoev, Tatyana Karpushkina and Olga Kostyunina

Animals 2020, 10(8), 1365; https://doi.org/10.3390/ani10081365 - 06 Aug 2020

Cited by 8 | Viewed by 3019

Abstract

The Large White pig is the most commonly raised commercial pig breed in the world. The aim of this work was to investigate D-loop mtDNA in Large White pigs (n = 402) of various selections bred in the Russian Federation from 2000 to 2019. The general sample consisted of three groups: Old (n = 78) (Russian selection, 2000–2010); Imp (n = 123) (imported to Russia in 2008–2014); New (n = 201) (2015–2019). The synthesized score (Fz) was calculated by analyzing the main PCA (principal component analysis components). An affiliation to Asian or European haplogroups was determined according to the NCBI (National Center for Biotechnology Information). In the study, we defined 46 polymorphic sites and 42 haplotypes. Significant distinctions between groups Old, Imp and New in frequencies of haplotypes and haplogroups were established. The distribution of Asian and European haplotypes in the groups was Old: 50%/50%, Imp: 43%/57%, New: 75%/25%, respectively. The variety of haplotypes and haplogroups in the pigs of the group New is related to the farms in which they breed. Haplotype frequencies significantly differ between the clusters Old_Center, Old_Siberia and Old_South. This study will provide information on the genetic diversity of Large White breed pigs. The results will be useful for the conservation and sustainable use of these resources. Full article

(This article belongs to the Special Issue Animal Genetics and Livestock Production: The Biodiversity Challenge)

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