Sequence polymorphisms in porcine homologs of murine coat colour‐related genes |
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| Authors: | N. Okumura T. Hayashi H. Uenishi N. Fukudome A. Komatsuda A. Suzuki M. Shibata M. Nii T. Yamaguchi C. Kojima‐Shibata N. Hamasima T. Awata |
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| Affiliation: | 1. STAFF‐Institute, Society for Techno‐Innovation of Agriculture, Forestry and Fisheries, Tsukuba, Ibaraki 305‐0854, Japan;2. National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305‐0901, Japan;3. Osumi Regional Promotion Bureau Agriculture, Forestry and Fisheries Department, Soo Branch, Soo, Kagoshima 899‐8102, Japan;4. Ibaraki Branch of National Livestock Breeding Center, Fujigaya, Ibaraki, 308‐0112, Japan;5. Ome Livestock Breeding Center, Tokyo Development Foundation For Agriculture, Forestry and Fisheries, Ome, Tokyo 198‐0024, Japan;6. Shizuoka Swine and Poultry Experiment Station, Kikugawa, Shizuoka 439‐0037, Japan;7. Livestock Research Institute, Tokushima Prefectural Agriculture, Forestry and Fisheries Technology Center, Itano, Tokushima 771‐1310, Japan;8. Chiba Prefectural Livestock Research Center, Yachimata, Chiba 289‐1113, Japan;9. Miyagi Prefecture Animal Industry Experiment Station, Iwadeyama, Miyagi 989‐6445, Japan |
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| Abstract: | Herein, we report the variability among 57 porcine homologs of murine coat colour‐related genes. We identified single nucleotide polymorphisms (SNPs) and insertions/deletions (InDels) within 44 expressed gene sequences by aligning eight pig complementary DNA (cDNA) samples. The sequence alignment revealed a total of 485 SNPs and 15 InDels. The polymorphisms were then validated by performing matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI‐TOF MS) with reference DNA samples obtained from 384 porcine individuals. Of the 384 individuals, three parents of the experimental F2 family were included to detect polymorphisms between them for linkage mapping. We also genotyped previously reported polymorphisms of 12 genes, and one SNP each in three genes that were detected by performing a BLAST search of the Trace database. A total of 211 SNPs and three InDels were successfully genotyped from our porcine DNA panel. We detected SNPs in 33 of the 44 genes among the parents of an experimental F2 family and then constructed a linkage map of the 33 genes for this family. The linkage assignment of each gene to the porcine chromosomes was consistent with the location of the BAC clone in the porcine genome and the corresponding gene sequence. We confirmed complete substitutions of EDNRB and MLPH in the Jinhua and Clawn miniature breeds, respectively. Furthermore, we identified polymorphic alleles exclusive to each pig group: 13 for Jinhua, two for Duroc, three for Meishan, four for the Japanese wild boar, one for the Clawn miniature pig and four for the Potbelly pig. |
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| Keywords: | Coat colour‐related genes InDels Pig SNPs |
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