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

Duchemin, Sandrine I.; Glantz, Maria LU ; De Koning, Dirk Jan; Paulsson, Marie LU and Fikse, Willem F. (2016) In Frontiers in Genetics 7.
Abstract

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 using 777k SNP genotypes and using imputed sequences to fine map the most promising genomic region. Phenotypes were available from 382 SR cows belonging to 21 herds 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 382 SR cows, 777k SNP genotypes were available as... (More)

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 using 777k SNP genotypes and using imputed sequences to fine map the most promising genomic region. Phenotypes were available from 382 SR cows belonging to 21 herds 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 382 SR cows, 777k SNP genotypes were available as well as the combined genotypes of the genetic variants of as1-β-κ-caseins. In addition, whole-genome sequences from the 1000 Bull Genome Consortium (Run 3) were available for 429 animals of 15 different breeds. From these sequences, 33 sequences 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) > 6 identified a promising region located on BTA18. We imputed sequences to the 382 genotyped 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 the existence 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 VPS35 gene belongs to the mammary gene sets of pre-parturient and of lactating cows.

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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
Cheese production, Dairy, Haplotypes, Non-coagulating milk, Sequences, VPS35
in
Frontiers in Genetics
volume
7
publisher
Frontiers
external identifiers
  • scopus:84964807480
ISSN
1664-8021
DOI
10.3389/fgene.2016.00057
language
English
LU publication?
yes
id
191beb10-5945-435f-a209-158aea4dc950
date added to LUP
2016-07-07 07:25:08
date last changed
2017-05-21 04:52:13
@article{191beb10-5945-435f-a209-158aea4dc950,
  abstract     = {<p>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 using 777k SNP genotypes and using imputed sequences to fine map the most promising genomic region. Phenotypes were available from 382 SR cows belonging to 21 herds 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 382 SR cows, 777k SNP genotypes were available as well as the combined genotypes of the genetic variants of as1-β-κ-caseins. In addition, whole-genome sequences from the 1000 Bull Genome Consortium (Run 3) were available for 429 animals of 15 different breeds. From these sequences, 33 sequences 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 -Log<sub>10</sub>(P-value) &gt; 6 identified a promising region located on BTA18. We imputed sequences to the 382 genotyped 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 the existence 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 VPS35 gene belongs to the mammary gene sets of pre-parturient and of lactating cows.</p>},
  articleno    = {57},
  author       = {Duchemin, Sandrine I. and Glantz, Maria and De Koning, Dirk Jan and Paulsson, Marie and Fikse, Willem F.},
  issn         = {1664-8021},
  keyword      = {Cheese production,Dairy,Haplotypes,Non-coagulating milk,Sequences,VPS35},
  language     = {eng},
  month        = {04},
  publisher    = {Frontiers},
  series       = {Frontiers in Genetics},
  title        = {Identification of QTL on chromosome 18 associated with non-coagulating milk in Swedish Red cows},
  url          = {http://dx.doi.org/10.3389/fgene.2016.00057},
  volume       = {7},
  year         = {2016},
}