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Animals
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Genetics and Breeding in Ruminants
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Genetics and Breeding in Ruminants

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

Deadline for manuscript submissions: closed (10 February 2025) | Viewed by 7376

Special Issue Editor

Prof. Dr. Huaiping Shi

E-Mail Website
Guest Editor
College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
Interests: biotechnology; animal breeding

Special Issue Information

Dear Colleagues,

Ruminants provide meat, milk, wool, and skins, indicating strong economic and ecological value worldwide. When preparing to meet the demand for high-quality livestock products, it is essential to breed animals with desired production characteristics, such as enhanced milk yield, and to develop more potential and productive livestock. Genetics and breeding in ruminants are crucial areas in animal husbandry, involving how to utilize animal genetic resources to improve variety and increase yield and quality, as well as how to effectively manage the breeding process to achieve expected goals. Genetics and modern technological means can improve key functional traits, which opens up new possibilities for genetics studies and breeding programs. The scientific practice of genetics and breeding can improve the production efficiency of ruminant husbandry and protect and inherit precious genetic resources.

We invite original research papers and review articles on genetic improvement, breeding management, reproductive physiology, conservation of genetic diversity, and genetic variability of traits related to the milking ability of dairy ruminants such as cows and dairy goats.

Prof. Dr. Huaiping Shi
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Animals is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2400 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

  • ruminants
  • genetics
  • variety improvement
  • reproductive physiology
  • genetic diversity
  • genetic variability
  • product quality

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Published Papers (7 papers)

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Research

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11 pages, 1679 KiB  
Article
Missense Mutations in FDNC5 Associated with Morphometric Traits and Meat Quality in Hainan Black Goats
by Jing Huang, Mengning Xu, Yuelang Zhang, Jiancheng Han, Hanlin Zhou and Ke Wang
Animals 2025, 15(4), 565; https://doi.org/10.3390/ani15040565 - 15 Feb 2025
Viewed by 451
Abstract
Goats are widely recognized for their adaptability and resource efficiency, making them an excellent choice for sustainable farming. However, the Hainan Black goat (HNBG), a vital breed in southern China’s tropical regions, faces significant challenges that threaten its productivity and economic viability. Specifically, [...] Read more.
Goats are widely recognized for their adaptability and resource efficiency, making them an excellent choice for sustainable farming. However, the Hainan Black goat (HNBG), a vital breed in southern China’s tropical regions, faces significant challenges that threaten its productivity and economic viability. Specifically, young HNBGs exhibit stunted growth and poor muscle development, indicating the breed may have more genetic defects that cause the poor phenotypes. The FNDC5 gene, which encodes the protein irisin, plays a key role in promoting mitochondrial biogenesis and oxidative metabolism by activating critical signaling molecules such as PGC-1α, thereby enhancing muscle endurance and metabolic efficiency. This study aimed to investigate the impact of missense mutations in the FNDC5 gene on growth and meat quality traits in HNBGs. We sequenced a population of HNBGs and identified three SNPs that could lead to amino acid substitutions. Notably, SNP1 (p.119A/V) and SNP2 (p.135R/H) showed strong linkage. Predictions on the structural effects of these mutations indicated that SNP1 (p.119A/V) and SNP3 (p.170W/G) could alter the secondary structure of the FNDC5 protein. Association analyses revealed that SNP1 (p.119A/V) and SNP2 (p.135R/H) were significantly associated with morphometric traits and meat quality. The phenotypic values of SNP1 and SNP2 co-mutants were significantly lower than those of other combined genotypes. Furthermore, gene expression levels of FNDC5 varied notably across individuals with different SNP1 genotypes. These findings suggest that FNDC5-SNP1 (p.119A/V) could serve as a promising genetic marker for selecting HNBGs with improved growth and muscle development, offering a potential pathway for enhancing key economic traits in this breed. Full article
(This article belongs to the Special Issue Genetics and Breeding in Ruminants)
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12 pages, 2994 KiB  
Article
Molecular Genetic Assessment Aids in Clarifying Phylogenetic Status of Iranian Kerman Wild Sheep
by Arsen V. Dotsev, Mohammad Hossein Moradi, Tatiana E. Deniskova, Ali Esmailizadeh, Neckruz F. Bakoev, Olga A. Koshkina, Darren K. Griffin, Michael N. Romanov and Natalia A. Zinovieva
Animals 2025, 15(2), 238; https://doi.org/10.3390/ani15020238 - 16 Jan 2025
Viewed by 665
Abstract
Two species of wild sheep inhabit Iran: Asiatic mouflon (Ovis gmelini) and urial (O. vignei). Phylogenetic relationships between populations distributed in this country are complex and still remain unclear. This study aimed to clarify, by genetic assessment, the phylogenetic [...] Read more.
Two species of wild sheep inhabit Iran: Asiatic mouflon (Ovis gmelini) and urial (O. vignei). Phylogenetic relationships between populations distributed in this country are complex and still remain unclear. This study aimed to clarify, by genetic assessment, the phylogenetic status of Kerman wild sheep, considered to be a hybrid of the two species. For this purpose, we created a dataset that included specimens of O. gmelini, O. vignei, and Kerman sheep. We applied genome-wide SNP genotyping technology to analyze population structure and genetic diversity of these groups. Using Neighbor-Net and PCA plots, it was demonstrated that Kerman sheep were differentiated from other groups and occupy an intermediate position between O. gmelini and O. vignei. Using Admixture analysis, two ancestral components were identified in this population; however, admixed ancestry was not confirmed by f3 statistics. Genetic diversity in Kerman wild sheep was significantly higher than in any group of O. vignei, but lower than in O. gmelini. Additionally, we examined complete mitochondrial genomes and it was demonstrated that the matrilineal ancestor of Kerman sheep belonged to O. vignei. Our results lead to the conclusion that Kerman wild sheep can be recognized as a separate subspecies of O. vignei. Full article
(This article belongs to the Special Issue Genetics and Breeding in Ruminants)
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15 pages, 9694 KiB  
Article
Comparative Whole-Genome Analysis of Production Traits and Genetic Structure in Baiyu and Chuanzhong Black Goats
by Jing Luo, Qi Min, Xueliang Sun, Xinyu Guo, Meijun Song, Xuehui Zeng, Jiazhong Guo, Hongping Zhang, Yanguo Han and Li Li
Animals 2024, 14(24), 3616; https://doi.org/10.3390/ani14243616 - 15 Dec 2024
Cited by 1 | Viewed by 916
Abstract
Natural selection and artificial breeding are crucial methods for developing new animal groups. The Baiyu black goats and Chuanzhong black goats are indigenous goat breeds from distinct ecological regions in Sichuan Province, with dramatically different growth and reproductivity. This study aimed to systematically [...] Read more.
Natural selection and artificial breeding are crucial methods for developing new animal groups. The Baiyu black goats and Chuanzhong black goats are indigenous goat breeds from distinct ecological regions in Sichuan Province, with dramatically different growth and reproductivity. This study aimed to systematically elucidate the differences in production performance and genetic traits between Baiyu black goats and Chuanzhong black goats. We quantified growth and reproductive attributes for both breeds. Furthermore, we conducted a comprehensive analysis of genetic diversity, population structure, and selection signatures using whole-genome resequencing data. This dataset included 30 individuals from the Baiyu black goat breed, 41 from the Chuanzhong black goat breed, and an additional 59 individuals representing Chengdu grey goats, Tibetan cashmere goats, and Jianchang black goats, totaling 130 individuals across five goat breeds. The comparative analysis of production performance revealed that the weight and body size of Chuanzhong black goats were significantly higher than those of Baiyu black goats (p < 0.01). At the same time, the average kidding rate and kid-weaning survival rate of Chuanzhong black goats were also notably superior to those of Baiyu black goats (p < 0.01). The Baiyu black goats exhibited a more abundant genetic diversity and distinct genetic differences compared to the Chuanzhong black goat, according to an analysis grounded on genomic variation. The Baiyu black goats are more closely related to Tibetan cashmere goats, whereas Chuanzhong black goats share a closer genetic relationship with Chengdu grey goats. Additionally, we employed the π, Fst, and XP-EHH methodologies to identify genes related to immunity (TRIM10, TRIM15, TRIM26, and TRIM5), neurodevelopment (FOXD4L1, PCDHB14, PCDHB4, PCDHB5, PCDHB6, and PCDHB7), reproduction (BTNL2 and GABBR1), body size (NCAPG, IBSP, and MKNK1), and meat quality traits (SUCLG2 and PGM5). These results provide a theoretical basis for further resource conservation and breeding improvement of the Baiyu black goat and Chuanzhong black goat. Full article
(This article belongs to the Special Issue Genetics and Breeding in Ruminants)
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11 pages, 1122 KiB  
Article
Polymorphisms of TXK and PLCE1 Genes and Their Correlation Analysis with Growth Traits in Ashidan Yaks
by Juanxiang Zhang, Xita Zha, Guowu Yang, Xiaoming Ma, Yongfu La, Xiaoyun Wu, Xian Guo, Min Chu, Pengjia Bao, Ping Yan and Chunnian Liang
Animals 2024, 14(23), 3506; https://doi.org/10.3390/ani14233506 - 4 Dec 2024
Viewed by 713
Abstract
The tyrosine protein kinase (TXK) gene, as a member of the non-receptor tyrosine kinase Tec family, plays a vital role in signal transduction mediation. Phospholipase C epsilon 1 (PLCE1), a membrane-associated enzyme, is of paramount importance for the differentiation [...] Read more.
The tyrosine protein kinase (TXK) gene, as a member of the non-receptor tyrosine kinase Tec family, plays a vital role in signal transduction mediation. Phospholipase C epsilon 1 (PLCE1), a membrane-associated enzyme, is of paramount importance for the differentiation of myoblasts and the normal functioning of muscle tissue. In recent years, both of these genes have been reported to be associated with the economic traits of animals. This study aimed to investigate the relationship between single nucleotide polymorphisms (SNPs) in the TXK and PLCE1 genes and growth traits in Ashidan yaks and to search for potential molecular marker loci that can influence Ashidan yak breeding. A cGPS liquid microarray was utilized to genotype 232 Ashidan yaks and to analyze correlations between two SNP loci in the TXK and PLCE1 genes and yak body weight, body height, body length, and chest circumference at different periods. The results indicated that the g.55,999,531C>T locus of the TXK gene and the g.342,350T>G locus of the PLCE1 gene were significantly correlated with the growth traits of Ashidan yaks. Among these, individuals with the CC genotype at the g.55,999,531C>T locus showed a significantly higher body length at 6 months old compared to TT individuals, and those with the CT genotype at 12 months old had a significantly higher chest circumference than TT individuals. At the g.342,350T>G locus, the body height of GG genotype individuals at 18 months of age was significantly higher than that of TT genotype individuals and TG genotype individuals. The above findings can be used as theoretical support for the subsequent improvement of Ashidan yak breeding. Full article
(This article belongs to the Special Issue Genetics and Breeding in Ruminants)
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10 pages, 1525 KiB  
Article
Characterisation of Ovine KRTAP19-3 and Its Impact on Wool Traits in Chinese Tan Sheep
by Lingrong Bai, Huitong Zhou, Jinzhong Tao and Jon G. H. Hickford
Animals 2024, 14(19), 2772; https://doi.org/10.3390/ani14192772 - 25 Sep 2024
Viewed by 959
Abstract
Wool, a natural fibre derived from sheep, can present a challenge to wool processing and manufacturing industries because of the variation in fibre traits. Genetic improvement offers one solution to this challenge, and having a better understanding of the genes that affect wool [...] Read more.
Wool, a natural fibre derived from sheep, can present a challenge to wool processing and manufacturing industries because of the variation in fibre traits. Genetic improvement offers one solution to this challenge, and having a better understanding of the genes that affect wool fibre traits is therefore important. Here, we describe ovine KRTAP19-3, a new member of the KAP19 gene family. Phylogenetic analysis revealed its relationship to other known KRTAP19 gene sequences, and an analysis of the nucleotide sequence variation in KRTAP19-3 from 288 sheep of a variety of breeds revealed six unique variant sequences. Among these variants, eleven single nucleotide polymorphisms (SNPs) were detected, with six located in the coding region. Three of these coding region SNPs were non-synonymous and would result in amino acid changes. Associations were observed between the presence of specific sequence variants in Chinese Tan sheep and wool trait variation, particularly an increase in fibre diameter variability in the heterotypic hair fibres. These findings enhance our understanding of the genes that encode sheep wool proteins. Full article
(This article belongs to the Special Issue Genetics and Breeding in Ruminants)
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18 pages, 3790 KiB  
Article
Genome-Wide Association Analyses and Population Verification Highlight the Potential Genetic Basis of Horned Morphology during Polled Selection in Tibetan Sheep
by Dehong Tian, Zian Zhang, Bin Huang, Buying Han, Xue Li and Kai Zhao
Animals 2024, 14(15), 2152; https://doi.org/10.3390/ani14152152 - 24 Jul 2024
Cited by 1 | Viewed by 1089
Abstract
The types and morphology of sheep horns have been extensively researched, yet the genetic foundation underlying the emergence of diverse horn characteristics during the breeding of polled Tibetan sheep has remained elusive. Genome-wide association analysis (GWAS) was performed on 103 subtypes (normal large [...] Read more.
The types and morphology of sheep horns have been extensively researched, yet the genetic foundation underlying the emergence of diverse horn characteristics during the breeding of polled Tibetan sheep has remained elusive. Genome-wide association analysis (GWAS) was performed on 103 subtypes (normal large horn, scurs, and polled) differentiated from G2 (offspring (G2) of parent (G1) of polled) of the polled core herd. Six single nucleotide polymorphisms (SNPs) located on chromosome 10 of the relaxin family peptide receptor 2 (RXFP2) gene exhibited positive correlations with horn length, horn base circumference, and horn base interval. Furthermore, in genotyping 382 G2 individuals, significant variations were observed for each specific horn type. Three additional mutations were identified near the target SNP upstream of the amplification product. Finally, the RXFP2-specific haplotype associated with the horned trait effectively maintained horn length, horn base circumference, and horn base interval in Tibetan sheep, as confirmed by population validation of nine loci in a sample size of 1125 individuals. The present study offers novel insights into the genetic differentiation of the horned type during improvement breeding and evolution, thereby establishing a robust theoretical foundation for polled Tibetan sheep breeding and providing valuable guidance for practical production. Full article
(This article belongs to the Special Issue Genetics and Breeding in Ruminants)
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26 pages, 1079 KiB  
Perspective
Genetics of Wool and Cashmere Fibre: Progress, Challenges, and Future Research
by Huitong Zhou, Lingrong Bai, Shaobin Li, Wenhao Li, Jiqing Wang, Jinzhong Tao and Jon G. H. Hickford
Animals 2024, 14(22), 3228; https://doi.org/10.3390/ani14223228 - 11 Nov 2024
Cited by 2 | Viewed by 1886
Abstract
Wool (sheep) and cashmere (goat) fibres have unique biological, physical, and chemical properties and these fibres are becoming more important as the demand for natural products increases. However, these complex protein fibres are at times compromised by natural variability in their properties, and [...] Read more.
Wool (sheep) and cashmere (goat) fibres have unique biological, physical, and chemical properties and these fibres are becoming more important as the demand for natural products increases. However, these complex protein fibres are at times compromised by natural variability in their properties, and this can impact their use and value. Genetic improvement via selection and breeding can partly overcome this problem, enabling the farming of sheep and goats that produce more desirable fibre. This review explores the challenges in improving wool and cashmere fibre characteristics using genetics, with a focus on improving our understanding of the key protein components of fibres, wool keratins and keratin-associated proteins (KAPs). Despite progress in our knowledge of these proteins, gaining a better understanding of them and how they affect these fibres remains an ongoing challenge. This is not straight-forward, given the large number of similar yet unique genes that produce the proteins and the gaps that remain in their identification and characterisation. More research is required to clarify gene and protein sequence variability and the location and patterns of gene expression, which in turn limits our understanding of fibre growth and variation. Several aspects that currently hinder our progress in this quest include the incomplete identification of all the genes and weaknesses in the approaches used to characterise them, including newer omics technologies. We describe future research directions and challenges, including the need for ongoing gene identification, variation characterisation, and gene expression analysis and association studies to enable further improvement to these valuable natural fibres. Full article
(This article belongs to the Special Issue Genetics and Breeding in Ruminants)
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