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

Abstract

GWAS helps to identify QTL and candidate genes of specific traits. Buffalo breeding has primarilyfocused on milk production, but its negative correlation with reproduction traits resulted in unfavorable declineof reproductive performance among buffaloes. 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.The identified 25 significant single nucleotide polymorphisms (SNPs) (P <1×106) are associated with age at first calving (AFC), age at first service (AFS), period from calving to 1st Artifical Insemination (AI), service period (SP) and 6 month body weight (6M). Fifteen genetic variants overlapped with different QTL regions of reported studies. Among the associated loci, outstanding candidate genes for fertility, including AQP1, TRNAE-CUC, NRIP1, CPNE4, and VOPP1, have effect in different fertility traits. AQP1 gene is expressed inovulatory phaseand variousstages of pregnancy. TRNAE-CUC gene is associatedwith AFC and number. of calvings after 4 years of age. Glycogen content-associated geneCPNE4 regulates muscle glycogen and isupregulated during early pregnancy. NRIP1 generegulatesovulation, corpus luteum at pregnancy, and mammary gland development.The objectiveis to identify potential genomic regions and genetic variants associated with economic traits and to selectthe most significant SNP which have positive effect on all the traits.