Abstract
In China, sparerib is one of the most valuable parts of the pork carcass. As a result, candidate gene mining for number of ribs has become an interesting study focus. To examine the genetic basis for this major trait, we genotyped 596 individuals from an F2 Large White × Minzhu intercross pig population using the PorcineSNP60 Genotyping BeadChip. The genome-wide association study identified a locus for number of ribs in a 2.38-Mb region on Sus scrofa chromosome 7 (SSC7 of Sus scrofa genome assembly, Sscrofa10.2). We identified the top significant SNP ASGA0035536, which explained 16.51 % of the phenotypic variance. A previously reported candidate causal mutation (g.19034 A>C) in vertebrae development-associated gene VRTN explained 8.79 % of the phenotypic variation on number of ribs and had a much lower effect than ASGA0035536. Haplotype sharing analysis in F1 boars localized the rib number QTL to a 951-kb interval on SSC7. This interval encompassed 17 annotated genes in Sscrofa10.2, including the previously reported VRTN candidate gene. Of the 17 candidate genes, LTBP2, which encodes a latent transforming growth factor beta binding protein, was previously reported to indirectly regulate the activity of growth differentiation factor Gdf11, which has been shown to increase the number of ribs in knock-out mice. Thus, we propose LTBP2 as a good new candidate gene for number of ribs in the pig population. This finding advances our understanding of the genetic architecture of rib number in pigs.
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Long-Chao Zhang declares that he has no conflict of interest. Jing-Wei Yue declares that she has no conflict of interest. Lei Pu declares that she has no conflict of interest. Li-Gang Wang declares that he has no conflict of interest. Xin Liu declares that she has no conflict of interest. Jing Liang declares that he has no conflict of interest. Hua Yan declares that she has no conflict of interest. Ke-Bin Zhao declares that he has no conflict of interest. Na Li declares that she has no conflict of interest. Hui-Bi Shi declares that he has no conflict of interest. Yue-Bo Zhang declares that he has no conflict of interest. Li-Xian Wang declares that he has no conflict of interest.
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Communicated by M. Fredholm.
L.-C. Zhang, J.-W. Yue and L. Pu contributed equally to this work.
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Zhang, LC., Yue, JW., Pu, L. et al. Genome-wide study refines the quantitative trait locus for number of ribs in a Large White × Minzhu intercross pig population and reveals a new candidate gene. Mol Genet Genomics 291, 1885–1890 (2016). https://doi.org/10.1007/s00438-016-1220-1
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DOI: https://doi.org/10.1007/s00438-016-1220-1