Genome-Wide Association Studies in Indian Buffalo Revealed Genomic Regions for Lactation and Fertility.

Vikas Vohra,Archana Verma,Gopal Gowane,Sitangsu Mohan Deb,Anupama Mukherjee,Rani Alex,Supriya Chhotaray

doi:10.3389/fgene.2021.696109

Abstract

Murrah breed of buffalo is an excellent dairy germplasm known for its superior milk quality in terms of milk fat and solids-not-fat (SNF); however, it is often reported that Indian buffaloes had lower lactation and fertility potential compared to the non-native cattle of the country. Recent techniques, particularly the genome-wide association studies (GWAS), to identify genomic variations associated with lactation and fertility traits offer prospects for systematic improvement of buffalo. DNA samples were sequenced using the double-digestion restriction-associated DNA (RAD) tag genotyping-by-sequencing. The bioinformatics pipeline was standardized to call the variants, and single-nucleotide polymorphisms (SNPs) qualifying the stringent quality check measures were retained for GWAS. Over 38,000 SNPs were used to perform GWAS on the first two principal components of test-day records of milk yields, fat percentages, and SNF percentages, separately. GWAS was also performed on 305 days’ milk yield; lactation persistency was estimated through the rate of decline after attaining the peak yield method, along with three other standard methods; and breeding efficiency, post-partum breeding interval, and age at sexual maturity were considered fertility traits. Significant association of SNPs was observed for the first principal component, explaining the maximum proportion of variation in milk yield. Furthermore, some potential genomic regions were identified to have a potential role in regulating milk yield and fertility in Murrah. Identification of such genomic regions shall help in carrying out an early selection of high-yielding persistent Murrah buffaloes and, in the long run, would be helpful in shaping their future genetic improvement programs.

Highlights

Buffalo (Bubalus bubalis) is an imperative livestock species and act as a key component for improving agricultural economy and supplying milk, meat, and draft power
genome-wide association studies (GWAS) were performed with 38,560 single-nucleotide polymorphisms (SNPs), and the genome-wide significant threshold was set at the 5% false discovery rate (FDR) level
GWAS were performed on the two foremost variation explaining principal components (PCs) (PC1 and PC2) of TDMY, TDFP, and TDSNF

Summary

Introduction

Buffalo (Bubalus bubalis) is an imperative livestock species and act as a key component for improving agricultural economy and supplying milk, meat, and draft power. Buffalo is well known for its high milk quality, with higher fat (6.4–8.0% vs 4.1– 5.0%) and protein (4.0–4.5% vs 3.4–3.6%) contents than cow milk (Venturini et al, 2014; Khedkar et al, 2016). Buffaloes in the field condition suffer from short lactation of 252–270 days as compared to the standard 300 days (Ganguli, 1981; Griffiths, 2010). This underlines the scope for improving the milk production and fertility potential through implementation of systematic breeding programs for buffaloes in the country. In India, very few works have been done in order to identify the infinitesimally large number of underlying loci regulating the expression of complex traits such as milk production, lactation persistency and fertility

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