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Analyses of porcine public SNPs in coding-gene regions by re-sequencing and phenotypic association studies

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Abstract

The Porcine SNP database has a huge number of SNPs, but these SNPs are mostly found by computer data-mining procedures and have not been well characterized. We re-sequenced 1,439 porcine public SNPs from four commercial pig breeds and one Korean domestic breed (Korean Native pig, KNP) by using two DNA pools from eight unrelated animals in each breed. These SNPs were from 419 protein-coding genes covering the 18 autosomes, and the re-sequencing in breeds confirmed 690 public SNPs (47.9%) and 226 novel mutations (173 SNPs and 53 insertions/deletions). Thus, totally, 916 variations were found from our study. Of the 916 variations, 148 SNPs (16.2%) were found across all the five breeds, and 199 SNPs (21.7%) were breed specific polymorphisms. According to the SNP locations in the gene sequences, these 916 variations were categorized into 802 non-coding SNPs (785 in intron, 17 in 3′-UTR) and 114 coding SNPs (86 synonymous SNPs, 28 non-synonymous SNPs). The nucleotide substitution analyses for these SNPs revealed that 70.2% were from transitions, 20.0% from transversions, and the remaining 5.79% were deletions or insertions. Subsequently, we genotyped 261 SNPs from 180 genes in an experimental KNP × Landrace F2 cross by the Sequenom MassARRAY system. A total of 33 traits including growth, carcass composition and meat quality were analyzed for the phenotypic association tests using the 132 SNPs in 108 genes with minor allele frequency (MAF) >0.2. The association results showed that five marker-trait combinations were significant at the 5% experiment-wise level (ADCK4 for rear leg, MYH3 for rear leg, Hunter B, Loin weight and Shearforce) and four at the 10% experiment-wise level (DHX38 for average daily gain at live weight, LGALS9 for crude lipid, NGEF for front leg and LIFR for pH at 24 h). In addition, 49 SNPs in 44 genes showing significant association with the traits were detected at the 1% comparison-wise level. A large number of genes that function as enzymes, transcription factors or signalling molecules were considered as genetic markers for pig growth (RNF103, TSPAN31, DHX38, ABCF1, ABCC10, SCD5, KIAA0999 and FKBP10), muscling (HSPA5, PTPRM, NUP88, ADCK4, PLOD1, DLX1 and GRM8), fatness (PTGIS, IDH3B, RYR2 and NOL4) and meat quality traits (DUSP4, LIFR, NGEF, EWSR1, ACTN2, PLXND1, DLX3, LGALS9, ENO3, EPRS, TRIM29, EHMT2, RBM42, SESN2 and RAB4B). The SNPs or genes reported here may be beneficial to future marker assisted selection breeding in pigs.

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Acknowledgments

This work was supported by grants titled “High-throughput sequencing and validation for genetic markers development in Korean Native animals” (National Institute of Animal Science) and “Genetic improvement maximization of Korean native pigs using marker-assisted selection, and construction of commercial line production system” from the BioGreen 21 Program of the Korea Rural Development Administration, ROK.

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Authors and Affiliations

  1. Department of Animal Science, Chungbuk National University, Cheongju, Chungbuk, 361-763, South Korea

    Xiaoping Li, Sang-Wook Kim, Kyoung-Tag Do, You-Kyoung Ha & Kwan-Suk Kim

  2. Department of Animal Technology, Huazhong Agricultural University, Wuhan, 430070, China

    Xiaoping Li

  3. School of Biotechnology, Yeungnam University, Gyeongsan, South Korea

    Yun-Mi Lee & Jong-Joo Kim

  4. Department of Food and Animal Biotechnology, Seoul National University, Seoul, South Korea

    Suk-Hee Yoon & Hee-Bal Kim

  5. National Institute of Animal Science, Suwon, South Korea

    Bong-Hwan Choi

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  1. Xiaoping Li
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Correspondence to Jong-Joo Kim, Bong-Hwan Choi or Kwan-Suk Kim.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Additional file 1 – summary of putative public SNPs in STS sequences

This Excel file contains the putative SNPs in STS sequences with gene name. The SNPs were categorized into noncoding SNPs (intronic SNP, iSNP; 3’-UTR SNP) and coding SNPs (non synonymous SNP, ns SNP; synonymous SNP, sSNP). (XLS 180 kb)

Additional file 2 – Primer sequences in this study

This Excel spreadsheet lists all the PCR primers: 449 sets of primers for PCR pooling sequencing and 261 sets of sequenom primers for SNP genotyping. (XLS 211 kb)

Additional file 3 – validated or new detected SNPs and other mutations

This Excel file contains all the validated or detected SNPs, deletions/insertions from the PCR sequencing. The 261 SNPs further genotyped in resource population were noted with a bold red number at the SNP site in STS sequences. (XLS 267 kb)

Additional file 4 – SNPs segregating in five breeds

This Excel file lists the detected SNPs segregating in Berkshire, Duroc, Landrace, Yorkshire and Korean Native Pig (KNP). (XLS 45 kb)

Additional file 5 – SNPs in one certain breed

This Excel spreadsheet lists the detected SNPs which were polymorphic in only one breed. (XLS 90 kb)

Additional file 6 – summary of phenotype traits tested for association study

This Excel file summarizes the growth, carcass composition and meat quality traits used for association analyses. (XLS 29 kb)

Additional file 7 – Allele frequency of 261 genotyped SNPs

This Excel file lists the allele frequency of SNPs genotyped for association analyses. (XLS 139 kb)

11033_2010_496_MOESM8_ESM.xls

Additional file 8 – SNPs displayed significant association with phenotypes at least at the 1% comparison-wise level in the F2 animals (XLS 149 kb)

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Li, X., Kim, SW., Do, KT. et al. Analyses of porcine public SNPs in coding-gene regions by re-sequencing and phenotypic association studies. Mol Biol Rep 38, 3805–3820 (2011). https://doi.org/10.1007/s11033-010-0496-1

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  • DOI: https://doi.org/10.1007/s11033-010-0496-1

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