Bovine chromosomal regions affecting rheological traits in acid-induced skim milk gels

Abstract

The production of fermented milk products has increased worldwide during the last decade and is expected to continue to increase during the coming decade. The quality of these products may be optimized through breeding practices; however, the relations between cow genetics and technological properties of acid milk gels are not fully known. Therefore, the aim of this study was to identify chromosomal regions affecting acid-induced coagulation properties and possible candidate genes. Skim milk samples from 377 Swedish Red cows were rheologically analyzed for acid-induced coagulation properties using low-amplitude oscillation measurements. The resulting traits, including gel strength, coagulation time, and yield stress, were used to conduct a genome-wide association study. Single nucleotide polymorphisms (SNP) were identified using the BovineHD SNPChip (Illumina Inc., San Diego, CA), resulting in almost 621,000 segregating markers. The genome was scanned for putative quantitative trait loci (QTL) regions, haplotypes based on highly associated SNP were inferred, and the additive genetic effects of haplotypes within each QTL region were analyzed using mixed models. A total of 8 genomic regions were identified, with large effects of the significant haplotype explaining between 4.8 and 9.8% of the phenotypic variance of the studied traits. One major QTL was identified to overlap between gel strength and yield stress, the QTL identified with the most significant SNP closest to the gene coding for κ-casein (CSN3). In addition, a chromosome-wide significant region affecting yield stress on BTA 11 was identified to be colocated with PAEP, coding for β-lactoglobulin. Furthermore, the coagulation properties of the genetic variants within the 2 genes were compared with the coagulation properties identified by the patterns of the haplotypes within the regions, and it was discovered that the haplotypes were more diverse and in one case slightly better at explaining the phenotypic variance. Besides these significant QTL comprising the 2 milk proteins, 3 additional genes are proposed as possible candidates, namely RAB22A, CDH13, and STAT1, and all have previously been found to be expressed in the mammary gland. To our knowledge, this is the first attempt to map QTL regions for acid-induced coagulation properties.

Detection of genetic variation affecting milk coagulation properties in Danish Holstein dairy cattle by analyses of pooled whole-genome sequences from phenotypically extreme samples (pool-seq)1

“…Several studies have detected a major QTL on BTA6 associated with milk protein composition located around the casein cluster (Schopen et al, 2009(Schopen et al, , 2011Huang et al, 2012;Gambra et al, 2013) as well as associations to milk coagulation traits (Gregersen et al, 2014;Glantz et al, 2015). In our study, we have detected a major locus comprising SNP in close proximity to CSN3 (Fig.…”

Genome-wide comparative analyses of correlated and uncorrelated phenotypes identify major pleiotropic variants in dairy cattle

“…3 and Supplementary Figure S2 ). These loci included DGAT1 (chromosome, chr14, 1.8 M+) 28 , SDC2 (chr14, 69 M+) 15 , GHR (chr20, 31 M+) 15 , CSN2 (chr6, 87 M+) 15 , MGST1 (chr5, 93 M+) 15 , 25 , PAEP (chr11, 103 M+) 30 and GPAT4 (chr27, 36 M+) 29 . The significance peak on chr18, 57 M+, detected in our study overlapped with reported CTU1 locus associated with calving difficulty 27 .…”

Genome variants associated with RNA splicing variations in bovine are extensively shared between tissues

“…1b ). Variants within CSN3 have long been found to be associated with milk traits [ 34 , 35 ] but only recently have putative causal variants been prioritised [ 25 ]. The milk cell sQTL Chr6:87392580 had perfect linkage disequilibrium ( r = 1) with the variant Chr6:87390576 which has been suggested as a putative causal variant for effects on milk protein yield and percentage [ 25 , 26 ].…”