Fine-mapping milk production quantitative trait loci on BTA6: analysis of the bovine osteopontin gene

Abstract

Bovine chromosome six (BTA6) harbors up to six quantitative trait loci (QTL) influencing the milk production of dairy cattle. In stark contrast to human, there is long-range linkage disequilibrium in dairy cattle, which has previously made it difficult to identify the mutations underlying these QTL. Using 38 microsatellite markers in a pedigree of 3,147 Holstein bulls, we fine mapped regions of BTA6 that had previously been shown to harbor QTL. Next, we sequenced a 12.3-kb region harboring Osteopontin, a positional candidate for the statistically most significant of the identified QTL. Nine mutations were identified, and only genotypes for the OPN3907 indel were concordant with the QTL genotypes of eight bulls that were established by segregation analysis. Four of these mutations were genotyped, and a joint linkage/linkage disequilibrium mapping analysis was used to demonstrate the existence of only two functionally distinct clusters of haplotypes within the QTL region, which were uniquely defined by OPN3907 alleles. We estimate a probability of 0.40 that no other mutation within this region is concordant with the QTL genotypes of these eight bulls. Finally, we demonstrate that the motif harboring OPN3907, which is upstream of the promoter and within a region known to harbor tissue-specific osteopontin regulatory elements, is moderately conserved among mammals. The motif was not retrieved from database queries and may be a novel regulatory element.

Fig. 1.

BF profiles. PP (a), FP (b), and MY (c) using loki. The x axis is the chromosomal position (cM). Red (black) lines include (exclude) OPN SNPs in the map. Green lines fit OPN3907 as a fixed effect. Gray dotted lines align peak locations between loki and ldvcm analyses.

Fig. 2.

lod profiles. PP (a), FP (b), and MY (c) using LDVCM. The x axis is the chromosomal position (cM). The blue line indicates LK, and remaining lines are combined LK/LD analyses. Red (black) lines include (exclude) OPN SNPs in the map. The green line fits OPN3907 as a fixed effect. Yellow diamonds are individual marker analyses. Gray dotted lines align peak locations between loki and ldvcm analyses.

Fig. 3.

Unweighted pair group method with arithmatic mean (UPGMA) haplotype dendrogram constructed at the OPN3492–OPN3907 interval midpoint reveals two haplotype clusters at the first node (green arrow) uniquely defined by OPN3907 alleles. Red (blue) bars indicate haplotypes containing T₁₀ (T₉). Black bars indicate clusters containing core BMS2508-OPN3379-OPN3490-OPN3492-OPN3907-MNB175 haplotypes. The undefined BMS2508 allele is identified as NA.

Fig. 4.

Multiple sequence alignment of the OPN3907 region.