Dataset Information

Association study of candidate genes for primary cataracts and fine-mapping of a candidate region on dog chromosome 1 in Entlebucher mountain dogs.

ABSTRACT: PURPOSE: The Entlebucher mountain dog (EMD) shows a high incidence of primary non-congenital cataracts (CAT). Because of the late-onset of CAT, it is difficult to exclude affected animals from breeding. A screen of candidate genes should help to identify the genes associated with CAT in EMD. METHODS: We genotyped 39 flanking microsatellite markers for 31 cataract candidate genes in 10 EMD families and tested them for linkage and association. For delimitation of a linked chromosome region on canine chromosome 1 (CFA1), we interrogated CFA1 by genotyping 30 additional microsatellites. We also sequenced the whole coding sequence with flanking intronic and untranslated regions of two candidate genes on CFA1. RESULTS: We found a genome-wide significant genomic region on CFA1, which showed a significantly associated haplotype with the CAT phenotype in the EMDs. Sequencing two candidate genes located on CFA1 revealed three single nucleotide polymorphisms (SNPs), which were not associated with CAT. CONCLUSIONS: We identified a putative CAT region that peaked at 96.07 Mb with genome-wide significant test statistics and extended over 1.3 Mb on CFA1 in the EMD. A significant marker-trait association based on haplotypes corroborated this CAT region. Further research is necessary to determine the gene responsible for CAT that is harbored by this linked and associated genomic region.

SUBMITTER: Muller C

PROVIDER: S-EPMC2386508 | biostudies-literature | 2008

REPOSITORIES: biostudies-literature

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Association study of candidate genes for primary cataracts and fine-mapping of a candidate region on dog chromosome 1 in Entlebucher mountain dogs.

Müller Christina C Distl Ottmar O

Molecular vision 20080516

<h4>Purpose</h4>The Entlebucher mountain dog (EMD) shows a high incidence of primary non-congenital cataracts (CAT). Because of the late-onset of CAT, it is difficult to exclude affected animals from breeding. A screen of candidate genes should help to identify the genes associated with CAT in EMD.<h4>Methods</h4>We genotyped 39 flanking microsatellite markers for 31 cataract candidate genes in 10 EMD families and tested them for linkage and association. For delimitation of a linked chromosome r ...[more]

PMID: 18490961

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Project description:BACKGROUND: Porcine chromosome X harbors four QTL strongly affecting backfat thickness (BFT), ham weight (HW), intramuscular fat content (IMF) and loin eye area (LEA). The confidence intervals (CI) of these QTL overlap and span more than 30 cM, or approximately 80 Mb. This study therefore attempts to fine map these QTL by joint analysis of two large-scale F? populations (Large White × Meishan and White Duroc × Erhualian constructed by INRA and JXAU respectively) and furthermore, to determine whether these QTL are caused by mutations in three positional candidate genes (ACSL4, SERPINA7 and IRS4) involved in lipid biosynthesis. RESULTS: A female-specific linkage map with an average distance of 2 cM between markers in the initial QTL interval (SW2456-SW1943) was created and used here. The CI of QTL for BFT, HW and LEA were narrowed down to 6-7 cM, resulting from the joint analysis. For IMF, two linked QTL were revealed in the INRA population but not in the JXAU population, causing a wider CI (13 cM) for IMF QTL. Linkage analyses using two subsets of INRA F? dam families demonstrate that the BFT and HW QTL were segregating in the Meishan pigs. Moreover, haplotype comparisons between these dams suggest that within the refined QTL region, the recombination coldspot (~34 Mb) flanked by markers MCSE3F14 and UMNP1218 is unlikely to contain QTL genes. Two SNPs in the ACSL4 gene were identified and showed significant association with BFT and HW, but they and the known polymorphisms in the other two genes are unlikely to be causal mutations. CONCLUSION: The candidate QTL regions have been greatly reduced and the QTL are most likely located downstream of the recombination coldspot. The segregation of SSCX QTL for BFT and HW within Meishan breed provides an opportunity for us to make effective use of Meishan chromosome X in crossbreeding. Further studies should attempt to identify the impact of additional DNA sequence (e.g. CNV) and expression variation in the three genes or their surrounding genes on these traits.

Dataset Information

Association study of candidate genes for primary cataracts and fine-mapping of a candidate region on dog chromosome 1 in Entlebucher mountain dogs.

Publications

Association study of candidate genes for primary cataracts and fine-mapping of a candidate region on dog chromosome 1 in Entlebucher mountain dogs.

Similar Datasets

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