Genome‐wide association study of fleece traits in Inner Mongolia Cashmere goats

Wang, F. H.; Zhang, L.; Gong, Guoyi; Yan, Xiaomin; Zhang, F. T.; Liu, H. F.; Lv, Qi; Wang, Z. Y.; Wang, R. J.; Zhang, Y. J.; Liu, Z. H.; He, Libing; Su, Rui; Zhao, Yanyan; Li, Jin Quan

doi:10.1111/age.13053

Cited by 21 publications

(20 citation statements)

References 23 publications

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“…Lv et al [ 108 ] reported a regulating role of FGF12 gene in the sheep hair follicle development process. In addition, our finding supported by Wang et al [ 109 ] study that reported the role of FGF12 gene in hair follicle development in cashmere goats. The SLC7A11 gene (CNVR_Chr7:73.54–73.57 Mb) is an amino acid transporter which mediates the extracellular cysteine in exchange for glutamate [ 110 ].…”

Section: Discussionsupporting

confidence: 91%

Genome-wide detection of copy number variation in American mink using whole-genome sequencing

et al. 2022

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Background Copy number variations (CNVs) represent a major source of genetic diversity and contribute to the phenotypic variation of economically important traits in livestock species. In this study, we report the first genome-wide CNV analysis of American mink using whole-genome sequence data from 100 individuals. The analyses were performed by three complementary software programs including CNVpytor, DELLY and Manta. Results A total of 164,733 CNVs (144,517 deletions and 20,216 duplications) were identified representing 5378 CNV regions (CNVR) after merging overlapping CNVs, covering 47.3 Mb (1.9%) of the mink autosomal genome. Gene Ontology and KEGG pathway enrichment analyses of 1391 genes that overlapped CNVR revealed potential role of CNVs in a wide range of biological, molecular and cellular functions, e.g., pathways related to growth (regulation of actin cytoskeleton, and cAMP signaling pathways), behavior (axon guidance, circadian entrainment, and glutamatergic synapse), lipid metabolism (phospholipid binding, sphingolipid metabolism and regulation of lipolysis in adipocytes), and immune response (Wnt signaling, Fc receptor signaling, and GTPase regulator activity pathways). Furthermore, several CNVR-harbored genes associated with fur characteristics and development (MYO5A, RAB27B, FGF12, SLC7A11, EXOC2), and immune system processes (SWAP70, FYN, ORAI1, TRPM2, and FOXO3). Conclusions This study presents the first genome-wide CNV map of American mink. We identified 5378 CNVR in the mink genome and investigated genes that overlapped with CNVR. The results suggest potential links with mink behaviour as well as their possible impact on fur quality and immune response. Overall, the results provide new resources for mink genome analysis, serving as a guideline for future investigations in which genomic structural variations are present.

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Section: Discussionsupporting

confidence: 91%

Genome-wide detection of copy number variation in American mink using whole-genome sequencing

et al. 2022

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“…For example, significant associations with body weight, growth-related and body conformation traits were identified by GWAS in 150 Dazu Black goats [ 18 ], in 95 Sudanese goats [ 28 ], in 69 Egyptian Barki sheep [ 33 ], and in 96 Baluchi sheep [ 34 ]. Genome-wide associations with other economic important traits were found in sample sizes of 192 animals [ 35 , 36 ]. In this regard, we believe that it possible to use a sample of 269 animals for our research.…”

Section: Discussionmentioning

confidence: 99%

Identification of Genomic Regions and Candidate Genes Associated with Body Weight and Body Conformation Traits in Karachai Goats

Easa

Selionova

Aibazov

et al. 2022

Genes

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The objective of this study was to identify the SNPs and candidate genes related to body weight and seven body conformation traits at the age of 8 months in the Russian aboriginal Karachai goats (n = 269) by conducting genome-wide association studies (GWAS), using genotypes generated by Goat SNP BeadChip (Illumina Inc., San Diego, CA, USA). We identified 241 SNPs, which were significantly associated with the studied traits, including 47 genome-wide SNPs (p < 10−5) and 194 suggestive SNPs (p < 10−4), distributed among all goat autosomes except for autosome 23. Fifty-six SNPs were common for two and more traits (1 SNP for six traits, 2 SNPs for five traits, 12 SNPs for four traits, 20 SNPs for three traits, and 21 SNPs for two traits), while 185 SNPs were associated with single traits. Structural annotation within a window of 0.4 Mb (±0.2 Mb from causal SNPs) revealed 238 candidate genes. The largest number of candidate genes was identified at Chr13 (33 candidate genes for the five traits). The genes identified in our study were previously reported to be associated with growth-related traits in different livestock species. The most significant genes for body weight were CRADD, HMGA2, MSRB3, MAX, HACL1 and RAB15, which regulate growth processes, body sizes, fat deposition, and average daily gains. Among them, the HMGA2 gene is a well-known candidate for prenatal and early postnatal development, and the MSRB3 gene is proposed as a candidate gene affecting the growth performance. APOB, PTPRK, BCAR1, AOAH and ASAH1 genes associated with withers height, rump height and body length, are involved in various metabolic processes, including fatty acid metabolism and lipopolysaccharide catabolism. In addition, WDR70, ZBTB24, ADIPOQ, and SORCS3 genes were linked to chest width. KCNG4 was associated with rump height, body length and chest perimeter. The identified candidate genes can be proposed as molecular markers for growth trait selection for genetic improvement in Karachai goats.

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“…The quantile-quantile plots (Q-Q plots) and Manhattan plots from GWAS analyses were produced using the ggplot2 in the R package. The suggestive genome-wide association significance threshold was p<1.20×10 −6 (0.05/41784), and the chromosome-wide significance level threshold was p<3.58×10 −5 (0.05/41784/30), as referred to Wang et al [ 11 ]. The most significant SNPs per trait were selected as the lead SNPs, and the candidate genes were further searched.…”

Section: Methodsmentioning

confidence: 98%

“…litter size [ 3 , 4 ] and nipple number [ 5 – 7 ], morphological traits, e.g. coat color [ 8 ], skin color [ 9 , 10 ], wool [ 11 , 12 ], and wattle [ 13 ] in different sheep and goat breeds by GWAS, which has led to the identification of different candidate genes or SNPs. However, the lack of consistency among these findings has suggested the complexity of the genetic basis of these traits.…”

Section: Introductionmentioning

confidence: 99%

Genome-wide association analysis of nine reproduction and morphological traits in three goat breeds from Southern China

et al. 2023

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Genome‐wide association study of fleece traits in Inner Mongolia Cashmere goats

Cited by 21 publications

References 23 publications

Genome-wide detection of copy number variation in American mink using whole-genome sequencing

Genome-wide detection of copy number variation in American mink using whole-genome sequencing

Identification of Genomic Regions and Candidate Genes Associated with Body Weight and Body Conformation Traits in Karachai Goats

Genome-wide association analysis of nine reproduction and morphological traits in three goat breeds from Southern China

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