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. 2009 Jan 21;41(1):14.
doi: 10.1186/1297-9686-41-14.

Large-scale association study for structural soundness and leg locomotion traits in the pig

Bin Fan  1 , Suneel K Onteru, Benny E Mote, Timo Serenius, Kenneth J Stalder, Max F Rothschild
Affiliations

Large-scale association study for structural soundness and leg locomotion traits in the pig

Bin Fan et al. Genet Sel Evol. .

Abstract

Background: Identification and culling of replacement gilts with poor skeletal conformation and feet and leg (FL) unsoundness is an approach used to reduce sow culling and mortality rates in breeding stock. Few candidate genes related to soundness traits have been identified in the pig.

Methods: In this study, 2066 commercial females were scored for 17 traits describing body conformation and FL structure, and were used for association analyses. Genotyping of 121 SNPs derived from 95 genes was implemented using Sequenom's MassARRAY system.

Results: Based on the association results from single trait and principal components using mixed linear model analyses and false discovery rate testing, it was observed that APOE, BMP8, CALCR, COL1A2, COL9A1, DKFZ, FBN1 and VDBP were very highly significantly (P < 0.001) associated with body conformation traits. The genes ALOX5, BMP8, CALCR, OPG, OXTR and WNT16 were very highly significantly (P < 0.001) associated with FL structures, and APOE, CALCR, COL1A2, GNRHR, IHH, MTHFR and WNT16 were highly significantly (P < 0.01) associated with overall leg action. Strong linkage disequilibrium between CALCR and COL1A2 on SSC9 was detected, and haplotype -ACGACC- was highly significantly (P < 0.01) associated with overall leg action and several important FL soundness traits.

Conclusion: The present findings provide a comprehensive list of candidate genes for further use in fine mapping and biological functional analyses.

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Figures

Figure 1
Figure 1
Association analyses results of single marker and haplotype construction of SNPs within CALCR and COL1A2 in SSC9 (The x-axis indicates SNP ID and y-axis indicates -log (P-value). The dbSNP no. for COL1A2_01, COL1A2_02, CALCR_01, CALCR_02, CALCR_03 and CALCR_04 are ss86352086, ss86352087, ss86352109, ss86352112, ss86352113 and ss86352114, respectively. Black boxes indicate r2 values between 0.9 and 1.0, and light boxes indicate r2 values less than 0.80.)
See this image and copyright information in PMC

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