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Genetics and Breeding in Sheep and Goats
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Genetics and Breeding in Sheep and Goats

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

Deadline for manuscript submissions: closed (20 December 2024) | Viewed by 12012

Special Issue Editor

Dr. Shaobin Li

E-Mail Website
Guest Editor
College of Animal Science and Technology/Gansu Key Laboratory of Herbivorous Animal Biotechnology, Gansu Agricultural University, Lanzhou 730070, China
Interests: small ruminant; functional gene; animal genetics; animal breeding; gene regulation

Special Issue Information

Dear Colleagues,

Domestic sheep and goats are valuable farm animals that provide us with meat, milk, and textile fiber. Most of these traits are quantitative and controlled by multiple genes and environments. Elucidating the genetic and epigenetic mechanisms of these economic traits is critical to understanding how a trait comes into being. The existence of gene polymorphism contributes to the difference of phenotypic characteristics and susceptibility to environmental factors among different individuals. As for epigenetics, DNA methylation, histone modification, chromatin remodeling, and non-coding RNA are key factors involved in gene expression regulation. The objective of this issue is to explore genetic and epigenetic factors affecting sheep and goat phenotypes. We focus on not only the economic traits of sheep and goats, but also their resistance and adaptability. We welcome original research articles, brief research reports, and reviews covering (but not limited to) the following topics:

  • Functional gene variation affecting phenotypes;
  • Identification of gene function;
  • Gene regulatory network;
  • Gene expression regulation;
  • Epigenetic regulation (DNA methylation, histone modification, chromatin remodeling and non-coding RNA);
  • Genetic factors affecting the resistance and adaptation of sheep and goats.

Dr. Shaobin Li
Guest Editor

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Keywords

  • sheep
  • goat
  • phenotype
  • gene polymorphism
  • gene expression regulation
  • gene function
  • DNA methylation
  • chromatin remodeling
  • non-coding RNA

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Published Papers (7 papers)

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Research

14 pages, 2661 KiB  
Article
Identification of Key Proteins Related to Cashmere Fiber Diameter by Integrated Proteomics and Bioinformatic Analyses in the Alpas and Alxa Goat Breeds
by Chongyan Zhang, Qing Qin, Yichuan Wang, Zhixin Wang and Zhihong Liu
Genes 2024, 15(9), 1154; https://doi.org/10.3390/genes15091154 - 1 Sep 2024
Viewed by 1245
Abstract
Background: Goats (Capra hircus) have always been a source of fiber for human use and hold an important place in international high-end textiles. Fiber diameter is the most concerning economic indicator for producers. Understanding the formation mechanism of fiber diameter and [...] Read more.
Background: Goats (Capra hircus) have always been a source of fiber for human use and hold an important place in international high-end textiles. Fiber diameter is the most concerning economic indicator for producers. Understanding the formation mechanism of fiber diameter and its related key proteins can help optimize and control the production of cashmere. Methods: Cashmere goats (n = 36) of the Alpas (n = 18) and Alxa (n = 18) breeds, with a similar age (2 years old) and live weight (25–26 kg), were selected from the Yiwei White Cashmere Goat Breeding Farm, Erdos, Inner Mongolia. Using phenotypic indicators, we evaluated the diameter of the cashmere fibers in Alxa and Alpas goats. We also used electron microscopy to examine the cashmere fiber’s structure and label-free liquid chromatography–tandem mass spectrometry to determine the protein content of the two cashmere fibers. The proteins affecting fiber diameter were identified and analyzed by Western blot, Co-Immunoprecipitation, and bioinformatics analysis. Results: The average diameter of the Alxa breed was smaller (p < 0.05) than that of the Alpas breed (Alxa’s cashmere vs. Alpas’ cashmere). Proteomics technology enabled the highly confident detection of 171 proteins. A total of 68 differentially expressed proteins were identified in the two types of cashmere; 131 proteins were specifically expressed in Alpas goats, and 40 proteins were specifically expressed in Alxa goats. A key protein group that could cause variations in fiber diameter was found using the protein–protein interaction network. To ascertain the reason for the variation in fiber diameter, a structural study of the major protein groups was carried out. Conclusions: KRT10, KRT14, KRT17, and KRT82 are the main proteins impacting the diameter difference, and they have a substantial effect on the average fiber diameter. Full article
(This article belongs to the Special Issue Genetics and Breeding in Sheep and Goats)
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8 pages, 215 KiB  
Article
Effects of KRTAP20-1 Gene Variation on Wool Traits in Chinese Tan Sheep
by Lingrong Bai, Huitong Zhou, Jinzhong Tao and Jon G. H. Hickford
Genes 2024, 15(8), 1060; https://doi.org/10.3390/genes15081060 - 12 Aug 2024
Cited by 2 | Viewed by 1110
Abstract
Chinese Tan sheep lambs are recognised for having tight ‘spring-like’ curly wool when young, but this phenotype disappears with age. This wool consists of shorter, fine wool fibres (which are usually unmedullated) and heterotypic hair fibres (which are frequently medullated), which are referred [...] Read more.
Chinese Tan sheep lambs are recognised for having tight ‘spring-like’ curly wool when young, but this phenotype disappears with age. This wool consists of shorter, fine wool fibres (which are usually unmedullated) and heterotypic hair fibres (which are frequently medullated), which are referred to as ‘halo hair’. Both the wool and hair fibres consist of α-keratin proteins embedded in a keratin-associated protein (KAP) matrix. Of these KAPs, the KAP20-1 gene (designated KRTAP20-1) and its effect on four fibre traits (mean fibre curvature, mean fibre diameter, fibre diameter standard deviation, and coefficient of variation of fibre diameter) of Tan lambs was studied. Seven previously identified KRTAP20-1 variants (A, B, D, E, F, G, and H) of KRTAP20-1 were revealed, but the previously identified variant C was not present. Of the seven variants detected, only two (A and G) were common and present at frequencies greater than 5%, and the effect of these on the fibre traits of the finer wool fibres was assessed. It was found that variant G was associated with an increased mean fibre curvature in these wool fibres. This suggests that KRTAP20-1 might possibly be expressed differentially in the two fibre types, which may be of future value in breeding. Full article
(This article belongs to the Special Issue Genetics and Breeding in Sheep and Goats)
10 pages, 2029 KiB  
Article
Genetic Variations of MSTN and Callipyge in Tibetan Sheep: Implications for Early Growth Traits
by Kai Zhao, Xue Li, Dehui Liu, Lei Wang, Quanbang Pei, Buying Han, Zian Zhang, Dehong Tian, Song Wang, Jincai Zhao, Bin Huang and Fuqiang Zhang
Genes 2024, 15(7), 921; https://doi.org/10.3390/genes15070921 - 15 Jul 2024
Cited by 1 | Viewed by 1215
Abstract
Tibetan sheep are vital to the ecosystem and livelihood of the Tibetan Plateau; however, traditional breeding methods limit their production and growth. Modern molecular breeding techniques are required to improve these traits. This study identified a single nucleotide polymorphism (SNP) in myostatin ( [...] Read more.
Tibetan sheep are vital to the ecosystem and livelihood of the Tibetan Plateau; however, traditional breeding methods limit their production and growth. Modern molecular breeding techniques are required to improve these traits. This study identified a single nucleotide polymorphism (SNP) in myostatin (MSTN) and Callipyge in Tibetan sheep. The findings indicated notable associations between MSTN genotypes and growth traits including birth weight (BW), body length (BL), chest width (ChW), and chest circumference (ChC), as well as a particularly strong association with cannon circumference (CaC) at 2 months of age. Conversely, Callipyge polymorphisms did not have a significant impact on Tibetan sheep. Moreover, the analyses revealed a significant association between sex and BW or hip width (HW) at 2 months of age and ChW, ChC, and CaC at 4 months of age. Furthermore, the study’s results suggested that the genotype of MSTN as a GA was associated with a notable sex effect on BW, while the genotype of Callipyge (CC) showed a significant impact of sex on CaC at 2 months of age. These results indicated that the SNP of MSTN could potentially serve as a molecular marker for early growth traits in Tibetan sheep. Full article
(This article belongs to the Special Issue Genetics and Breeding in Sheep and Goats)
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8 pages, 1581 KiB  
Article
Ovine KRT81 Variants and Their Influence on Selected Wool Traits of Commercial Value
by Wenhao Li, Lingrong Bai, Huitong Zhou, Zhihe Zhang, Zhijie Ma, Guofang Wu, Yuzhu Luo, Jasmine Tanner and Jon G. H. Hickford
Genes 2024, 15(6), 681; https://doi.org/10.3390/genes15060681 - 24 May 2024
Cited by 3 | Viewed by 1145
Abstract
Keratins are the main structural protein components of wool fibres, and variation in them and their genes (KRTs) is thought to influence wool structure and characteristics. The PCR–single strand conformation polymorphism technique has been used previously to investigate genetic variation in [...] Read more.
Keratins are the main structural protein components of wool fibres, and variation in them and their genes (KRTs) is thought to influence wool structure and characteristics. The PCR–single strand conformation polymorphism technique has been used previously to investigate genetic variation in selected coding and intron regions of the type II sheep keratin gene KRT81, but no variation was identified. In this study, we used the same technique to explore the 5′ untranslated region of KRT81 and detected three sequence variants (A, B and C) that contain four single nucleotide polymorphisms. Among the 389 Merino × Southdown cross sheep investigated, variant B was linked to a reduction in clean fleece weight, while C was associated with an increase in both greasy fleece weight and clean fleece weight. No discernible effects on staple length or mean-fibre-diameter-related traits were observed. These findings suggest that variation in ovine KRT81 might influence wool growth by changing the density of wool follicles in the skin, the density of individual fibres, or the area of the skin producing fibre, as opposed to changing the rate of extrusion of fibres or their diameter. Full article
(This article belongs to the Special Issue Genetics and Breeding in Sheep and Goats)
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10 pages, 1756 KiB  
Article
Identification of FASN Gene Polymorphisms, Expression and Their Relationship with Body Size Traits in Guizhou White Goat (Capra hircus) with Different Genders
by Qingming An, Lingli Zeng, Wenying Wang, Jiangyu Yang, Jinzhu Meng, Yuanyuan Zhao and Xingchao Song
Genes 2024, 15(6), 656; https://doi.org/10.3390/genes15060656 - 22 May 2024
Cited by 1 | Viewed by 1205
Abstract
To investigate the nucleotide variation sites (SNPs) and expression differences of the fatty acid synthase gene (FASN) in Guizhou white goats, the relationship between the variation and body size traits was investigated. In this study, DNA was extracted from the blood [...] Read more.
To investigate the nucleotide variation sites (SNPs) and expression differences of the fatty acid synthase gene (FASN) in Guizhou white goats, the relationship between the variation and body size traits was investigated. In this study, DNA was extracted from the blood of 100 samples of white goats from different regions in Guizhou province, China, and the variation sites were screened using pooled sequencing by mixing DNA samples, and 242 blood samples with body size traits were used for association analysis. The allele frequency, genotype frequency, homozygosity, heterozygosity and effective gene number were calculated by using PopGene 32.0 software, the population polymorphism information content was calculated by using PIC software (Version 0.6), and the state of genetic balance of the genes was analyzed by using the chi-square test. The mRNA of FASN gene expression levels in male and female goats were investigated by using real-time fluorescence quantitative PCR (RT-qPCR). The general linear mixed model of MINTAB software (Version 16.0) was used to analyze the association between FASN gene nucleotide mutation sites and body size traits. The results showed that there was one nucleotide mutation site g.141 C/T in the target fragment of FASN gene amplification, and revealed two alleles, C and T, and three genotypes CC, CT and TT. The genotype frequencies for CC, CT and TT were 0.4308, 0.4205 and 0.1487, respectively. The allele frequencies for C and T were 0.6410 and 0.3590, respectively. The genetic homozygosity (Ho) was higher than the heterozygosity (He). The χ2 test showed that the mutation site was in the Hardy–Weinberg equilibrium state (p > 0.05). The RT-qPCR results showed that the FASN gene had different expression levels in the longissimus dorsi muscle of male and female goats, and its expression was significantly higher in male goats than in female goats. The association analysis results showed that the mutation of the FASN gene had different effects on body size traits of male and female goats, and the presence of the populations of the T allele and the TT genotype recorded higher body size traits (body weight, heart girth and wither height) in female populations. Therefore, the site of the FASN gene can be used as a candidate marker for the early selection of growth traits in Guizhou white goats. Full article
(This article belongs to the Special Issue Genetics and Breeding in Sheep and Goats)
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11 pages, 2079 KiB  
Article
Spatiotemporal Expression Characterization of KRTAP6 Family Genes and Its Effect on Wool Traits
by Hongxian Sun, Zhaohua He, Fangfang Zhao, Jiang Hu, Jiqing Wang, Xiu Liu, Zhidong Zhao, Mingna Li, Yuzhu Luo and Shaobin Li
Genes 2024, 15(1), 95; https://doi.org/10.3390/genes15010095 - 14 Jan 2024
Cited by 1 | Viewed by 1725
Abstract
Keratin-related proteins (KAPs) are structural components of wool fibers and are thought to play a key role in regulating the physical and mechanical properties of fibers. Among all KAP genes (KRTAPs), KRTAP6 gene family (KRTAP6-1, KRTAP6-2, KRTAP6-3, [...] Read more.
Keratin-related proteins (KAPs) are structural components of wool fibers and are thought to play a key role in regulating the physical and mechanical properties of fibers. Among all KAP genes (KRTAPs), KRTAP6 gene family (KRTAP6-1, KRTAP6-2, KRTAP6-3, KRTAP6-4, and KRTAP6-5) is a very important member with high polymorphism and notable association with some wool traits. In this study, we used real-time fluorescence quantitative PCR (RT-qPCR) and in situ hybridization to investigate spatiotemporal expression of KRTAP6s. The results revealed that KRTAP6 family genes were significantly expressed during anagen compared to other stages (p < 0.05). And it was found the five genes were expressed predominantly in the dermal papillae, inner and outer root sheaths, and showed a distinct spatiotemporal expression pattern. Also, it was found that KRTAP6-1 and KRTAP6-5 mRNA expression was negatively correlated with wool mean fiber diameter (MFD) and mean staple strength (MSS) (p < 0.05). In summary, the KRTAP6 family genes share a similar spatiotemporal expression pattern. And KRTAP6-1 and KRTAP6-5 may regulate the MFD and MSS of Gansu Alpine fine-wool sheep wool by changing the expression. Full article
(This article belongs to the Special Issue Genetics and Breeding in Sheep and Goats)
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15 pages, 3169 KiB  
Article
Genomic Landscape of Copy Number Variations and Their Associations with Climatic Variables in the World’s Sheep
by Hosein Salehian-Dehkordi, Jia-Hui Huang, Nasrollah Pirany, Hossein Mehrban, Xiao-Yang Lv, Wei Sun, Ali Esmailizadeh and Feng-Hua Lv
Genes 2023, 14(6), 1256; https://doi.org/10.3390/genes14061256 - 13 Jun 2023
Cited by 8 | Viewed by 2890
Abstract
Sheep show characteristics of phenotypic diversity and adaptation to diverse climatic regions. Previous studies indicated associations between copy number variations (CNVs) and climate-driven adaptive evolution in humans and other domestic animals. Here, we constructed a genomic landscape of CNVs (n = 39,145) [...] Read more.
Sheep show characteristics of phenotypic diversity and adaptation to diverse climatic regions. Previous studies indicated associations between copy number variations (CNVs) and climate-driven adaptive evolution in humans and other domestic animals. Here, we constructed a genomic landscape of CNVs (n = 39,145) in 47 old autochthonous populations genotyped at a set of high-density (600 K) SNPs to detect environment-driven signatures of CNVs using a multivariate regression model. We found 136 deletions and 52 duplications that were significantly (Padj. < 0.05) associated with climatic variables. These climate-mediated selective CNVs are involved in functional candidate genes for heat stress and cold climate adaptation (e.g., B3GNTL1, UBE2L3, and TRAF2), coat and wool-related traits (e.g., TMEM9, STRA6, RASGRP2, and PLA2G3), repairing damaged DNA (e.g., HTT), GTPase activity (e.g., COPG), fast metabolism (e.g., LMF2 and LPIN3), fertility and reproduction (e.g., SLC19A1 and CCDC155), growth-related traits (e.g., ADRM1 and IGFALS), and immune response (e.g., BEGAIN and RNF121) in sheep. In particular, we identified significant (Padj. < 0.05) associations between probes in deleted/duplicated CNVs and solar radiation. Enrichment analysis of the gene sets among all the CNVs revealed significant (Padj. < 0.05) enriched gene ontology terms and pathways related to functions such as nucleotide, protein complex, and GTPase activity. Additionally, we observed overlapping between the CNVs and 140 known sheep QTLs. Our findings imply that CNVs can serve as genomic markers for the selection of sheep adapted to specific climatic conditions. Full article
(This article belongs to the Special Issue Genetics and Breeding in Sheep and Goats)
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