TY - JOUR
T1 - Fine mapping and association analysis of a quantitative trait locus for milk production traits on Bos taurus autosome 4
AU - Rincón, G.
AU - Islas-Trejo, A.
AU - Casellas, J.
AU - Ronin, Y.
AU - Soller, M.
AU - Lipkin, E.
AU - Medrano, J. F.
PY - 2009/2
Y1 - 2009/2
N2 - To fine map a quantitative trait locus (QTL) affecting milk production traits previously associated with microsatellite RM188, we implemented an interval mapping analysis by using microsatellite markers in a large Israeli Holstein half-sib sire family, and linkage disequilibrium (LD) mapping in a large set of US Holstein bulls. Interval mapping located the target QTL to the near vicinity of RM188. For the LD mapping, we identified 42 single nucleotide polymorphisms (SNP) in 15 genes in a 12-Mb region on bovine chromosome 4. A total of 24 tag SNP were genotyped in 882 bulls belonging to the University of California Davis archival collection of Holstein bull DNA samples with predicted transmitted ability phenotypes. Marker-to-marker LD analysis revealed 2 LD blocks, with intrablock r2 values of 0.10 and 0.46, respectively; outside the blocks, r2 values ranged from 0.002 to 0.23. A standard additive/dominance model using the generalized linear model procedure of SAS and the regression module of HelixTree software were used to test marker-trait associations. Single nucleotide polymorphism 9 on ARL4A, SNP10 on XR-027435.1, SNP12 on ETV1, SNP21 on SNX13, and SNP24 were significantly associated with milk production traits. We propose the interval encompassing ARL4A and SNX13 genes as a candidate region in bovine chromosome 4 for a concordant QTL related to milk protein traits in dairy cattle. Functional studies are needed to confirm this result.
AB - To fine map a quantitative trait locus (QTL) affecting milk production traits previously associated with microsatellite RM188, we implemented an interval mapping analysis by using microsatellite markers in a large Israeli Holstein half-sib sire family, and linkage disequilibrium (LD) mapping in a large set of US Holstein bulls. Interval mapping located the target QTL to the near vicinity of RM188. For the LD mapping, we identified 42 single nucleotide polymorphisms (SNP) in 15 genes in a 12-Mb region on bovine chromosome 4. A total of 24 tag SNP were genotyped in 882 bulls belonging to the University of California Davis archival collection of Holstein bull DNA samples with predicted transmitted ability phenotypes. Marker-to-marker LD analysis revealed 2 LD blocks, with intrablock r2 values of 0.10 and 0.46, respectively; outside the blocks, r2 values ranged from 0.002 to 0.23. A standard additive/dominance model using the generalized linear model procedure of SAS and the regression module of HelixTree software were used to test marker-trait associations. Single nucleotide polymorphism 9 on ARL4A, SNP10 on XR-027435.1, SNP12 on ETV1, SNP21 on SNX13, and SNP24 were significantly associated with milk production traits. We propose the interval encompassing ARL4A and SNX13 genes as a candidate region in bovine chromosome 4 for a concordant QTL related to milk protein traits in dairy cattle. Functional studies are needed to confirm this result.
KW - Association analysis
KW - Bos taurus autosome 4
KW - Microsatellite RM188
KW - Milk trait quantitative trait locus
UR - http://www.scopus.com/inward/record.url?scp=59349094954&partnerID=8YFLogxK
U2 - 10.3168/jds.2008-1395
DO - 10.3168/jds.2008-1395
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C2 - 19164688
AN - SCOPUS:59349094954
SN - 0022-0302
VL - 92
SP - 758
EP - 764
JO - Journal of Dairy Science
JF - Journal of Dairy Science
IS - 2
ER -