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Tong X, Zhang Z, Jiao Y, Xu J, Dang H, Chen Y, Jiang Z, Duan J, Zhang H, Li J, Wang C. Association of eight EST-derived SNPs with carcass and meat quality traits in pigs. J Appl Genet 2014; 56:85-95. [PMID: 25081836 DOI: 10.1007/s13353-014-0234-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Revised: 06/29/2014] [Accepted: 07/07/2014] [Indexed: 12/01/2022]
Abstract
The identification of genetic markers associated with important economic traits is fundamental to improving the productivity and quality of livestock. In this investigation, we searched for 177 expressed sequence tags (ESTs) putatively involved in meat quality from the available pig EST database, and detected eight single nucleotide polymorphisms (SNPs) in eight ESTs. We investigated the associations of these SNPs with 18 carcass and meat quality traits in a Landrace × Lantang F2 resource population (n = 257). Association analysis revealed that seven SNPs (except E42) were associated with some of the carcass- and meat quality-related traits. Particularly, significant associations of three SNPs (E53, E82, and E36) with backfat thickness traits were observed. Further, the genetic effects of E53 on four live backfat thickness traits were validated in an independent population (n = 221). More investigations about E53 sequence characteristics were performed, i.e., radiation hybrid (RH) mapping, 3'-RACE, and screening analysis of the positive BAC clones. Our research identified the genetic effects of eight EST-derived SNPs on carcass and meat quality traits, and suggested that E53 may be a useful marker for live backfat thickness traits in pig breeding programs.
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Affiliation(s)
- Xiong Tong
- College of Animal Science, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, South China Agricultural University, Guangzhou, Guangdong, 510642, People's Republic of China
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Huang Y, Bates RO, Ernst CW, Fix JS, Steibel JP. Estimation of U.S. Yorkshire breed composition using genomic data
1. J Anim Sci 2014; 92:1395-404. [DOI: 10.2527/jas.2013-6907] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Y. Huang
- Department of Animal Science, Michigan State University, East Lansing 48824
| | - R. O. Bates
- Department of Animal Science, Michigan State University, East Lansing 48824
| | - C. W. Ernst
- Department of Animal Science, Michigan State University, East Lansing 48824
| | - J. S. Fix
- Smithfield Premium Genetics, Roanoke Rapids, NC 27870
| | - J. P. Steibel
- Department of Animal Science, Michigan State University, East Lansing 48824
- Department of Fisheries and Wildlife, Michigan State University, East Lansing 48824
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Wertz N, Vazquez J, Wells K, Sun J, Butler JE. Antibody repertoire development in fetal and neonatal piglets. XII. Three IGLV genes comprise 70% of the pre-immune repertoire and there is little junctional diversity. Mol Immunol 2013; 55:319-28. [PMID: 23570908 DOI: 10.1016/j.molimm.2013.03.012] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Revised: 03/04/2013] [Accepted: 03/13/2013] [Indexed: 01/17/2023]
Abstract
We characterized 239 lambda rearrangements from fetal and germfree (GF) piglets to: (1) determine if transcripts recovered from the earliest sites of B cell lymphogenesis were unique (2) determine what proportion of the genome is used to form the pre-immune repertoire (3) estimate the degree of somatic hypermutation and junctional diversity during ontogeny and (4) test whether piglets maintained germfree in isolators (GF piglets) have a more diversified repertoire than fetal piglets. We show that all expressed lambda genes belong to the IGLV3 and IGLV8 families and only IGLJ2 and IGLJ3 were expressed and used equally throughout fetal and neonatal life. Only genes of the IGLV8 family were used in yolk sac and fetal liver and in these tissues, IGLV8-10 comprised >50%. However, the IGLV8 genes recovered at these early sites of B cell lymphogenesis were recovered at all stages of development. Thus, no unique lambda rearrangement was recovered at the first sites of B cell development. The frequency of somatic hypermutation (SHM) in fetal piglets was ~5.9 per Kb equivalent, mutation were concentrated in CDR regions and did not increase in GF piglets. The average CDR3 length was 30 nt ± 2.7 and did not change in GF piglets. Similar to the heavy chain pre-immune repertoire in this species, three IGLV genes account for ~70% of the repertoire. Unlike the heavy chain repertoire, junctional diversity was very limited.
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Affiliation(s)
- Nancy Wertz
- Department of Microbiology, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
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Uenishi H, Morozumi T, Toki D, Eguchi-Ogawa T, Rund LA, Schook LB. Large-scale sequencing based on full-length-enriched cDNA libraries in pigs: contribution to annotation of the pig genome draft sequence. BMC Genomics 2012; 13:581. [PMID: 23150988 PMCID: PMC3499286 DOI: 10.1186/1471-2164-13-581] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Accepted: 08/09/2012] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Along with the draft sequencing of the pig genome, which has been completed by an international consortium, collection of the nucleotide sequences of genes expressed in various tissues and determination of entire cDNA sequences are necessary for investigations of gene function. The sequences of expressed genes are also useful for genome annotation, which is important for isolating the genes responsible for particular traits. RESULTS We performed a large-scale expressed sequence tag (EST) analysis in pigs by using 32 full-length-enriched cDNA libraries derived from 28 kinds of tissues and cells, including seven tissues (brain, cerebellum, colon, hypothalamus, inguinal lymph node, ovary, and spleen) derived from pigs that were cloned from a sow subjected to genome sequencing. We obtained more than 330,000 EST reads from the 5'-ends of the cDNA clones. Comparison with human and bovine gene catalogs revealed that the ESTs corresponded to at least 15,000 genes. cDNA clones representing contigs and singlets generated by assembly of the EST reads were subjected to full-length determination of inserts. We have finished sequencing 31,079 cDNA clones corresponding to more than 12,000 genes. Mapping of the sequences of these cDNA clones on the draft sequence of the pig genome has indicated that the clones are derived from about 15,000 independent loci on the pig genome. CONCLUSIONS ESTs and cDNA sequences derived from full-length-enriched libraries are valuable for annotation of the draft sequence of the pig genome. This information will also contribute to the exploration of promoter sequences on the genome and to molecular biology-based analyses in pigs.
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Affiliation(s)
- Hirohide Uenishi
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2 Ikenodai, Tsukuba, Ibaraki, 305-8602, Japan
- Division of Animal Sciences, National Institute of Agrobiological Sciences, 2 Ikenodai, Tsukuba, Ibaraki, 305-8602, Japan
- Animal Genome Research Program, 2 Ikenodai, Tsukuba, Ibaraki, 305-8602, Japan
| | - Takeya Morozumi
- Animal Genome Research Program, 2 Ikenodai, Tsukuba, Ibaraki, 305-8602, Japan
- Animal Research Division, Japan Institute of Association for Techno-innovation in Agriculture, Forestry and Fisheries, 446-1 Ippaizuka, Kamiyokoba, Tsukuba, Ibaraki, 305-0854, Japan
| | - Daisuke Toki
- Animal Genome Research Program, 2 Ikenodai, Tsukuba, Ibaraki, 305-8602, Japan
- Animal Research Division, Japan Institute of Association for Techno-innovation in Agriculture, Forestry and Fisheries, 446-1 Ippaizuka, Kamiyokoba, Tsukuba, Ibaraki, 305-0854, Japan
| | - Tomoko Eguchi-Ogawa
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2 Ikenodai, Tsukuba, Ibaraki, 305-8602, Japan
- Animal Genome Research Program, 2 Ikenodai, Tsukuba, Ibaraki, 305-8602, Japan
| | - Lauretta A Rund
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL, 61801, USA
| | - Lawrence B Schook
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 West Gregory Drive, Urbana, IL, 61801, USA
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Matsumoto T, Okumura N, Uenishi H, Hayashi T, Hamasima N, Awata T. Porcine single nucleotide polymorphism (SNP) development and population structure of pigs assessed by validated SNPs. Biochem Genet 2011; 50:428-39. [PMID: 22170480 DOI: 10.1007/s10528-011-9486-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2011] [Accepted: 06/28/2011] [Indexed: 11/25/2022]
Abstract
In this study, we identified porcine single nucleotide polymorphisms (SNPs) by aligning eight sequences generated with two approaches: amplification of 665 intronic regions using one sample from each of eight breeds, including three East Asian pigs, and amplification of 289 3'-UTR regions using two samples from each of four major commercial breeds. The 1,760 and 599 SNPs were validated using two 384-sample DNA panels by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. The phylogenetic tree and Structure analyses classified the pigs into two large clusters: Euro-American and East Asian populations. The membership proportions, however, differed between inferred clusters for K = 2 generated by the two approaches. With intronic SNPs, Euro-American breeds constituted about 100% of the Euro-American cluster, but with 3'-UTR SNPs, about 17% of the East Asian cluster comprised five Euro-American breeds. The differences in the SNP discovery panels may affect population structure found in study panels of large samples.
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Affiliation(s)
- Toshimi Matsumoto
- Second Research Division, STAFF Institute, Tsukuba, Ibaraki, 305-0854, Japan
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