Genome-wide association study for udder health traits of Thai dairy cattle using weighted single-step approach with random regression test-day model
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Abstract
Genome-wide association studies (GWAS) are a powerful tool to identify genomic regions and variants associated with phenotypes. However, only limited mutual confirmation from different studies is available. The objectives of this study were to identify genomic regions associated with udder health trait in Thai dairy cattle, and to identify genes and pathways that may influence this trait. The studied data set contained 82,378 monthly test-day somatic cell score (TD-SCS). A density of single nucleotide polymorphisms (SNP) panel (BovineSNP50 BeadChip, Illumina Inc., San Diego, CA, USA) was used for genotyping. After genomic data quality control, 41,930 SNPs were retained from 632 animals that had both genotypes and phenotypes. Effects of SNPs were estimated by a weighted single-step GWAS (WssGWAS), which back-solved the genomic BLUP from single-step genomic best linear unbiased prediction (ssGBLUP) using single-trait random regression test-day models. Genomic regions that explained at least 0.5 % of the total genetic variance were selected for further analyses of candidate genes. The main genomic regions associated with SCS were located on chromosomes BTA 11, 16 and 21. Many genomic regions explained a small fraction of the genetic variance, indicating polygenic inheritance of the studied trait. We compared the results with databases (NCBI, Genecards and UniProt) and found 20 reported QTLs related to SCS. A large member of Interleukin superfamily (IL1A, IL1B, IL1F10, IL36A, IL36B, IL36G and IL37) as well as other genes (MIA3, PPP1R13B and TRAF3) related to immunity significantly influencing SCS were identified. The biological networks including the immunological pathway such as lymphocyte activation are closely related to SCS. The candidate genes identified in this study can be used as target genes in studies of gene expression. Further research including more animals, records, and genotypes is required to validate our findings.
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References
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