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Research article - Peer-reviewed, 2016

Identification of QTL on chromosome 18 associated with non-coagulating milk in Swedish Red cows

Duchemin, Sandrine I.; Glantz, Maria; de Koning, Dirk-Jan; Paulsson, Marie; Fikse, Willem F.


Non-coagulating (NC) milk, defined as milk not coagulating within 40 min after rennet-addition, can have a negative influence on cheese production. Its prevalence is estimated at 18% in the Swedish Red (SR)cow population. Our study aimed at identifying genomic regions and causal variants associated with NC milk in SR cows, by doing a GWAS using777k SNP genotypes and using imputed sequences to fine map the most promising genomic region. Phenotypes were available from 382 SR cows belonging to 21herds in the south of Sweden, from which individual morning milk was sampled. NC milk was treated as a binary trait, receiving a score of one in case of non-coagulation within 40 min. For all 382SR cows, 777kSNP genotypes were available as well as the combined genotypes of the genetic variants of a αs1-β-κ-caseins. In addition, whole-genome sequences from the 1000 Bull Genome Consortium (Run 3) were available for 429 animals of 15different breeds. From these sequences, 33sequences belonged to SR and Finish Ayrshire bulls with a large impact in the SR cow population. Single-marker analyses were run in ASReml using an animal model. After fitting the casein loci, 14 associations at -Log10(P-value)>6identified a promising region located on BTA18. We imputed sequences to the 382genotyped SR cows using Beagle 4 for half of BTA18, and ran a region-wide association study with imputed sequences. In a seven mega base-pairs region on BTA18, our strongest association with NC milk explained almost 34% of the genetic variation in NC milk. Since it is possible that multiple QTL are in strong LD in this region,  59 haplotypes were built, genetically differentiated by means of a phylogenetic tree, and tested in phenotype-genotype association studies. Haplotype analyses support thee xistence of one QTL underlying NC milk in SR cows. A candidate gene of interest is the VPS35 gene, for which one of our strongest association is an intron SNP in this gene. The VPS35gene belongs to the mammary gene sets of pre-parturient and of lactating cows.


non-coagulatingmilk; sequences; dairy; cheeseproduction; haplotypes; VPS35

Published in

Frontiers in Genetics
2016, Volume: 7, article number: 57
Publisher: Frontiers Research Foundation / Frontiers Media