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

Abstract

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.

Whole‐genome resequencing uncovers diversity and selective sweep in Kazakh cattle

“…The protein that results from the MAX gene is a bHLHZ transcription factor family member. The SNP in the MAX gene is known to be strongly correlated with goat development (Easa et al., 2022).…”

Genome-Wide Association Study of Body Conformation Traits in Tashi Goats (Capra hircus)

“…Given the above discussion on several aspects of the effects of body size on livestock production, it is difficult to discover the genes related to body conformation traits at the genome level, especially using GWAS. As described before, the GWAS method has been used to mine the genetic architecture underlying goat body conformation traits [18,19]. In Russian Karachai goats, 241 SNPs and 238 candidate genes related to body conformation traits were identified, highlighting genes such as CRADD, HMGA2, and MSRB3 for breeding improvements [19].…”

“…As described before, the GWAS method has been used to mine the genetic architecture underlying goat body conformation traits [18,19]. In Russian Karachai goats, 241 SNPs and 238 candidate genes related to body conformation traits were identified, highlighting genes such as CRADD, HMGA2, and MSRB3 for breeding improvements [19].…”

“…Although genome resequencing is more expensive than other methodologies, it obtains more numerous and more effective SNPs. The GWAS technique has enabled the identification of genes linked to various traits in goats, such as milk quality [14,15], meat quality (fat and protein content) [16], growth traits (weaning mass) [17,18], and body conformation traits (body height and length) [19,20]. The genetic insights gleaned from these studies not only present promising avenues for selective breeding but also pave the way for sustainable enhancements in productive performance.…”

Genome-Wide Association Study Revealed Putative SNPs and Candidate Genes Associated with Growth and Meat Traits in Japanese Quail

“…Recently domesticated Japanese quail are valuable as a model avian species for genetic studies and as a remarkable agricultural commodity [ 10 , 47 ]. One of the important prerequisites of genomic selection aimed at improving livestock farming efficiency is the identification and mapping of SNPs and candidate genes (e.g., [ 74 ]) that are associated with, and control, the manifestation of phenotypes of interest and selection of relevant quantitative traits using GWAS technology (e.g., [ 75 , 76 , 77 ]). We reported here a GWAS for meat performance characteristics in male quails of an F 2 reference population.…”