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

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.

Within- and between-Breed Selection Signatures in the Original and Improved Valachian Sheep

“…The other genes in the region were also related to body size ( LYN , MOS ) but also fertility and dystocia ( RPS20 ) [ 72 ]. The second signal indicated just by a single SNP on chromosome 9 was around 67.7Mb around the SYBU gene, which was related to milk fat synthesis, transport, and metabolism [ 73 , 74 ].…”

Selection and Drift: A Comparison between Historic and Recent Dutch Friesian Cattle and Recent Holstein Friesian Using WGS Data

“…EIF5A2 has been reported as a candidate gene for age at sexual maturity in Indian Buffalo [39] and for infertility in human [40]. RPL22L1 is also described as a candidate gene for age at sexual maturity in Indian Buffalo [39]. Furthermore, RPL22L1 is reported as associated gene in low-fertility buffalo bull spermatozoa [41].…”

“…EIF5A2 is associated with fertility traits. EIF5A2 has been reported as a candidate gene for age at sexual maturity in Indian Buffalo [39] and for infertility in human [40]. RPL22L1 is also described as a candidate gene for age at sexual maturity in Indian Buffalo [39].…”

Genomic Identification, Evolution, and Expression Analysis of Bromodomain Genes Family in Buffalo

“…Bioinformatics, combined with next-generation sequencing, can provide high-throughput genomic data. These data can be used to identify the genes for the favorable traits in buffalo, for instance, the systematic analysis of candidate genes for buffalo milk production and fertility traits [ 23 , 24 ], whole-genome sequencing and characterization for selective breeding in buffalo [ 25 ], and characterization of the diacylglycerol acyltransferases gene family, collagen gene family, and heat-shock protein gene family [ 26 , 27 , 28 ]. The above studies, together with a nearly complete genome map of the buffalo [ 29 , 30 , 31 , 32 ], make it possible to study gene families at the genome-wide level in buffalo.…”