Genomic wide association study (GWAS) related to body conformation traits in different goat breeds

Document Type : Research Paper

Authors

1 MSc student animal breeding and genetics, Faculty of Agriculture and Natural Resources, Arak University, Arak, Iran.

2 Assistant Professor, Department of Animal Sciences, Faculty of Agriculture and Natural Resources, Arak University, Arak, Iran.

3 Associate Professor, Department of Animal Sciences, Faculty of Agriculture and Natural Resources, Arak University, Arak, Iran.

Abstract

The present study aimed to conduct a genome wide association studies based on Gene-set enrichment analysis for identifying the loci associated with conformation traits in some goat genotyped with the Caprine 50K SNP chip. For this purpose, phenotypes records related body length, body height, pubic bone length, heart girth and chest length were obtained. Genome wide association study was performed with conformation traits using GEMMA software. Using the biomaRt2 R package the SNP were assigned to genes if they were within the genomic sequence of the gene or within a flanking region of 15 kb up- and downstream of the gene. Finally, a gene enrichment analysis was performed with the KOBAS platform from online bioinformatics databases for the assignment of the genes to functional categories. In this research, genomic region related to conformation traits on chromosomes 1, 4, 5, 6, 10, 11, 16, 17, 22 and 27 were identified. Also, genes related to body conformations traits in our study included PDE5A, WDR1, ATF3, SIPA1L1, TMTC2, CHCHD3, SHROOM2, TBPL2, ADIPOQ, ASAH1 and LRPPRC. According to pathway analysis, 18 pathways from gene ontology and biological pathways were associated with the conformation traits. The results of our research can be used to understand the genetic mechanism controlling conformation traits and considering, this study supported previous results from GWAS of conformation traits, also revealed additional regions, using these findings could potentially be useful for genetic selection in goat.

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References

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Animal Sciences Journal
Volume 37, Issue 142
June 2024
Pages 59-72

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