Genetic improvement of economic traits in Murrah buffalo using significant SNPs from genome wide association study

Abstract

Abstract GWAS helps to identify QTL and candidate genes of specific traits. Buffalo breeding mainly focused on milk production but its negative correlation with reproduction traits resulted in unfavourable decline in reproductive performance of buffalo. A genome wide scan was performed on a total of 120 Murrah buffaloes genotyped by ddRAD sequencing for 13 traits related to female fertility, production and growth. Identified 25 significant SNPs (P < 1x106) associated with Age at first calving (AFC), Age at first service (AFS), period from calving to 1st AI, Service period (SP) and 6 month body weight (6M). 15 genetic variants overlapped with different QTL regions of reported studies. Among the associated loci, outstanding candidate genes for fertility include, AQP1, TRNAE-CUC, NRIP1, CPNE4 and VOPP1 have role in different fertility traits. AQP1 gene expressed on different stages of pregnancy and in ovulatory phase. TRNAE-CUC gene related with AFC and no. of calving after 4 yrs of age. CPNE4 is glycogen content associated gene regulate muscle glycogen and upregulated in early pregnancy. NRIP1 gene have regulation over corpus luteum at pregnancy and control over ovulation and in mammary gland development. Objective to identify potential genomic regions and genetic variants associated with fertility related traits, milk production and growth traits and select most significant SNP which have positive effect on all the traits.