Genome-wide association studies to identify quantitative trait loci affecting milk production traits in water buffalo

Abstract

Water buffalo is the second largest resource of milk supply around the world, and it is well known for its distinctive milk quality in terms of fat, protein, lactose, vitamin, and mineral contents. Understanding the genetic architecture of milk production traits is important for future improvement by the buffalo breeding industry. The advance of genome-wide association studies (GWAS) provides an opportunity to identify potential genetic variants affecting important economical traits. In the present study, GWAS was performed for 489 buffaloes with 1,424 lactation records using the 90K Affymetrix Buffalo SNP Array (Affymetrix/Thermo Fisher Scientific, Santa Clara, CA). Collectively, 4 candidate single nucleotide polymorphisms (SNP) in 2 genomic regions were found to associate with buffalo milk production traits. One region affecting milk fat and protein percentage was located on the equivalent of Bos taurus autosome (BTA)3, spanning 43.3 to 43.8 Mb, which harbored the most likely candidate genes MFSD14A, SLC35A3, and PALMD. The other region on the equivalent of BTA14 at 66.5 to 67.0 Mb contained candidate genes RGS22 and VPS13B and influenced buffalo total milk yield, fat yield, and protein yield. Interestingly, both of the regions were reported to have quantitative trait loci affecting milk performance in dairy cattle. Furthermore, we suggest that buffaloes with the C allele at AX-85148558 and AX-85073877 loci and the G allele at AX-85106096 locus can be selected to improve milk fat yield in this buffalo-breeding program. Meanwhile, the G allele at AX-85063131 locus can be used as the favorable allele for improving milk protein percentage. Genomic prediction showed that the reliability of genomic estimated breeding values (GEBV) of 6 milk production traits ranged from 0.06 to 0.22, and the correlation between estimated breeding values and GEBV ranged from 0.23 to 0.35. These findings provide useful information to understand the genetic basis of buffalo milk properties and may play a role in accelerating buffalo breeding programs using genomic approaches.

Asian water buffalo: domestication, history and genetics

“…These investigations also suggested that sex chromosome data should be included in GWASs to avoid missing important information and that animals carrying specific alleles could be used in selection plans to improve production traits, particularly milk fat yield or milk protein percentage . Liu et al (2018), in particular, identified one region containing the candidate genes MFSD14A, SLC35A3 and PALMD affecting fat and protein content, whereas a second region harbouring RGS22 and VPS13B candidate genes affected milk, fat and protein yields. Interestingly, the corresponding regions located on chromosomes BTA3 and BTA14 in the cattle genome were reported to harbour QTL influencing milk performance in dairy cattle (Harder et al 2006;Wibowo et al 2008), but the comparative analysis of the allelic variants involved in cattle and in buffalo suggested that, despite the similarities in genome arrangement, the variants associated with production traits could be different between the two species, particularly those affecting fat production (de Camargo et al 2015;Liu et al 2018).…”

“…Based on the SNPs involved in significant associations, candidate genes that were either trait‐specific or with pleiotropic effects could be identified. These investigations also suggested that sex chromosome data should be included in GWASs to avoid missing important information and that animals carrying specific alleles could be used in selection plans to improve production traits, particularly milk fat yield or milk protein percentage (Liu et al ).…”

“…Liu et al (), in particular, identified one region containing the candidate genes MFSD14A , SLC35A3 and PALMD affecting fat and protein content, whereas a second region harbouring RGS22 and VPS13B candidate genes affected milk, fat and protein yields. Interestingly, the corresponding regions located on chromosomes BTA3 and BTA14 in the cattle genome were reported to harbour QTL influencing milk performance in dairy cattle (Harder et al ; Wibowo et al .…”

“…Interestingly, the corresponding regions located on chromosomes BTA3 and BTA14 in the cattle genome were reported to harbour QTL influencing milk performance in dairy cattle (Harder et al ; Wibowo et al . ), but the comparative analysis of the allelic variants involved in cattle and in buffalo suggested that, despite the similarities in genome arrangement, the variants associated with production traits could be different between the two species, particularly those affecting fat production (de Camargo et al ; Liu et al ).…”

“…Until now genetic studies have mainly addressed genetic diversity (Barker et al ; Lei et al ; Kumar et al ; Zhang et al ; Colli et al ) and identification of genes and molecular markers that are associated with desirable traits (de Camargo et al ; Yusnizar et al ; Iannaccone et al ; Liu et al ), but to date only a few epigenetic studies have been carried out on water buffalo (Verma et al ; Agrawal et al ; Sharma et al ).…”