Candidate genes and signature of selection associated with different biological aspects and general characteristics of goat

Saleh, Ahmed A.; Rashad, Amr M.A.; Hassanine, Nada N A M; Sharaby, Mahmoud A.

doi:10.1016/j.eas.2022.100013

Cited by 7 publications

(8 citation statements)

References 70 publications

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“…Goats, as subjects of genetic research, are increasingly attracting the attention of scientists. With the development of the GoatSNP50 BeadChip by Illumina Inc. [27], GWASs (genome-wide association studies) became available for goats of different productivity directions [9,21]. Through these studies, it has been possible to identify certain genes associated with various economically important traits in goats, such as fiber productivity, including fiber color [28][29][30], meat productivity traits [31][32][33], reproduction [34][35][36], and adaptation ability [37][38][39].…”

Section: Discussionmentioning

confidence: 99%

“…Although genome-wide association studies (GWASs) on goats have been conducted in many countries and on different breeds, the loci associated with quantitative and qualitative traits of milk production remain largely unknown (Saleh, A.A., 2022 [21]). This applies to the study of milk production in Karachai goats as well, which justifies the relevance of this research.…”

Section: Introductionmentioning

confidence: 99%

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Genome-Wide Association Study of Milk Composition in Karachai Goats

Selionova,

Trukhachev,

Aibazov

et al. 2024

Animals

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This study is first to perform a genome-wide association study (GWAS) to investigate the milk quality traits in Karachai goats. The objective of the study was to identify candidate genes associated with milk composition traits based on the identification and subsequent analysis of all possible SNPs, both genome-wide (high-confidence) and suggestive (subthreshold significance). To estimate the milk components, 22 traits were determined, including several types of fatty acids. DNA was extracted from ear tissue or blood samples. A total of 167 Karachai goats were genotyped using an Illumina GoatSNP53K BeadChip panel (Illumina Inc., San Diego, CA, USA). Overall, we identified 167 highly significant and subthreshold SNPs associated with the milk components of Karachai goats. A total of 10 SNPs were located within protein-coding genes and 33 SNPs in close proximity to them (±0.2 Mb). The largest number of genome-wide significant SNPs was found on chromosomes 2 and 8 and some of them were associated with several traits. The greatest number of genome-wide significant SNPs was identified for crude protein and lactose (6), and the smallest number—only 1 SNP—for freezing point depression. No SNPs were identified for monounsaturated and polyunsaturated fatty acids. Functional annotation of all 43 SNPs allowed us to identify 66 significant candidate genes on chromosomes 1, 2, 3, 4, 5, 8, 10, 13, 16, 18, 21, 23, 25, 26, and 27. We considered these genes potential DNA markers of the fatty acid composition of Karachai goat milk. Also, we found 12 genes that had a polygenic effect: most of them were simultaneously associated with the dry matter content and fatty acids (METTL, SLC1A 8, PHACTR1, FMO2, ECI1, PGP, ABCA3, AMDHD2). Our results suggest that the genes identified in our study affecting the milk components in Karachai goats differed from those identified in other breeds of dairy goats.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Genome-Wide Association Study of Milk Composition in Karachai Goats

Selionova,

Trukhachev,

Aibazov

et al. 2024

Animals

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“…Recently, numerous studies have been conducted to analyze the genetic architecture of goats, as one of the most common domestic species, well adapted to extreme environmental conditions and possessing phenotypic diversity [51]. In the course of these studies, it was possible to identify some genes associated with a variety of economically important traits of goats, such as down and milk productivity and reproduction [16,[52][53][54].…”

Section: Discussionmentioning

confidence: 99%

“…Further research is likely to be related to the identification of new genes, as well as their selection signatures (SS) and the study of multiple effects on economic and even non-economic traits that are important in the selection of desirable or elimination of undesirable goat genotypes, in the development of breeding programs in goat farming [51]. However, the study of goat genomes is still in its infancy compared to other livestock species.…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Association and Pathway Analysis of Carcass and Meat Quality Traits in Karachai Young Goats

Selionova,

Aibazov,

Sermyagin

et al. 2023

Animals

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Goats with diverse economic phenotypic traits play an important role in animal husbandry. However, the genetic mechanisms underlying complex phenotypic traits are unclear in goats. Genomic studies of variations provided a lens to identify functional genes. The work aimed to search for candidate genes related to body measurements and body weight of Karachai goats and develop an experimental PCR-RV test system for genotyping significant SNPs. Comparison of GWAS results for ages 4 and 8 months revealed 58 common SNPs for significant genotypes. 11 common SNPs were identified for body weight, 4 SNPs—for group of traits withers height, rump height, body length, 2 SNPs—for withers height and rump height, 1 SNP—for body length and chest depth. Structural annotation of genomic regions covering a window of ±0.20 Mb showed the presence of 288 genes; 52 of them had the described functions in accordance with gene ontology. The main molecular functions of proteins encoded by these genes are the regulation of transcription, cell proliferation, angiogenesis, body growth, fatty acid and lipid metabolism, nervous system development, and spermatogenesis. SNPs common to body weight and localized within a window of ±200 kb from the structural genes CRADD, HMGA2, MSRB3, FUT8, MAX, and RAB15 were selected to create a test system. The study of meat productivity after slaughter and chemical analysis of muscle tissue in Karachai goats at the age of 8 months of different genotypes according to the identified SNPs revealed that rs268269710 is the most promising for further research and use in breeding. The GG genotype is associated with a larger live weight of animals, a larger carcass yield, the content of the boneless part in it, and the ratio of protein and adipose tissue in meat preferred for dietary nutrition. These results will contribute to the genetic improvement of Karachai goats.

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“…revealed a favourable connection between the molecular marker among MSTN, HEG1, FGF10, FGF14, GHRH, and SLAIN genes linked to live body mass at age four months old. It was also demonstrated by SNP genotyping and their use for discovering selection signatures and applying them as part of GWAS for identifying polymorphic loci associated with various biological aspects and body size in sheep and goats(Gu et al 2022;Saleh et al 2022). As a result, this research led to the nding that the polymorphisms in the GH gene in goat populations might be responsible for the superior growth traits.…”

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confidence: 99%

Genetic polymorphism of the growth hormone gene and their effects on growth metrics in the Assam Hill and Sirohi goats under subtropical climatic condition

Kumar

Kadirvel

Khargharia

et al. 2023

Preprint

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Growth hormone (GH) is a gene that regulates milk production, reproduction, and growth in animals. Therefore, the purpose of this study was to identify GH gene variations and their associations with growth metrics in Sirohi and Assam hill goats. We identified two polymorphic loci (GH1-HaeIII & GH2-HaeIII) which were connected to growth attributes in 161 animals of Assam hill (n = 114) and Sirohi (n = 47) goats using the methods of PCR-RFLP. According to PCR-RFLP results, the GH gene's GH1-HaeIII locus contains two alleles (A and B) and two genotypes (AA and AB), whereas the GH2-HaeIII locus contains two alleles (C and D) and two genotypes (CC and CD). In the two goat breeds, the allele frequencies of A and B were 0.36 − 0.28 and 0.64–0.72, respectively, while the frequencies of alleles C and D were 0.71 − 0.70 and 0.29–0.30. The polymorphic loci were demonstrated to be in a state of Hardy-Weinberg disequilibrium in both breeds of goats (P < 0.05). The growth characteristics of the Assam hill goat breed were shown to be correlated with GH gene variations. In both breeds, AB and CD genotypes displayed slightly higher values in most of the morphometric traits compared to AA and CC genotypes; however, only in Assam hill goats body length and chest girth were positively significant (P < 0.05). Hence, the AB and CD genotypes have been proposed as potential markers for improved growth parameters in the breeds that were tested. Therefore, we came to the view that the two variant loci of the GH gene will utilize as marker assisted selection for enhancing growth attributes in goats; however, more research with a bigger sample size is necessary to verify the validity of this conclusion.

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Candidate genes and signature of selection associated with different biological aspects and general characteristics of goat

Cited by 7 publications

References 70 publications

Genome-Wide Association Study of Milk Composition in Karachai Goats

Genome-Wide Association Study of Milk Composition in Karachai Goats

Genome-Wide Association and Pathway Analysis of Carcass and Meat Quality Traits in Karachai Young Goats

Genetic polymorphism of the growth hormone gene and their effects on growth metrics in the Assam Hill and Sirohi goats under subtropical climatic condition

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