Integrating Genomic Selection and a Genome-Wide Association Study to Improve Days Open in Thai Dairy Holstein Cattle: A Comprehensive Genetic Analysis

Potential SNPs and candidate genes influencing growth characteristics in Pakistani Beetal goat identified by GWAS analysis

Background

A higher body weight at a younger age is an economically important trait for profitable goat farming. This study focussed on the identification of regions of the genome that harbour genetic variants associated with body weight using the Illumina GoatSNP50K Bead Chip. A total of 631 purebred Beetal goats (151 males and 480 females) were recorded for body weight, age and body measurement and then genotyped. Genome-wide association analysis was carried out with GEMMA.

Results

After application of quality control filters with Plink 1.9 i.e. call rate less than or equal to 0.9, minor allele frequency < 0.05 and HWE P value < 0.001, 594 animals and 45,744 SNPs were used to carry out the analyses for association. The association analysis for body weight with covariates of age, sex, morphometric measurements and contemporary group returned 10 significant SNPs (P =  − log10e-4 to − log10e-6). Three associated SNPs were present within genes i.e. BTAF1 (snp1131-scaffold1029-1983670 on chromosome 26), NTM (snp53070-scaffold799-1,702,189 on chromosome 29) and GRID1 (snp3363-scaffold1102-797993 on chromosome 28) when blasted against ARS1(accession GCA_001704415.1). Moreover, some associated SNPs were localized close to genes i.e. CEP78 (snp44634-scaffold606-4621460 on chromosome 8), ROBO1 (snp11793-scaffold1437-557,127 on chromosome 1), ZFP36L2 (snp9758-scaffold135-2,388,277 on chromosome 11), SPTLC3 (snp25720-scaffold265-581,526 on chromosome 13), CTR9 (snp31951-scaffold358-554,703 on chromosome 15) and ZFHX3 (snp9581-scaffold1344-19,492 on chromosome 18) genes.

Conclusions

The study identified SNPs and genes with potential role in growth of goat which may be useful for generation of customized chip in the future.