Genome-wide Association Studies for Production, Respiratory Disease, and Immune-related Traits in Landrace Pigs

Overview

Journal Sci Rep

Specialty Science

Date 2021 Aug 5

PMID 34349215

Citations 9

Authors

Yoshinobu Uemoto

Kasumi Ichinoseki

Toshimi Matsumoto

Nozomi Oka

Hironori Takamori

Hiroshi Kadowaki

Chihiro Kojima-Shibata

Eisaku Suzuki

Toshihiro Okamura

Hisashi Aso

Haruki Kitazawa

Masahiro Satoh

Hirohide Uenishi

Keiichi Suzuki

Affiliations

Soon will be listed here.

Abstract

Identification of a quantitative trait locus (QTL) related to a chronic respiratory disease such as Mycoplasmal pneumonia of swine (MPS) and immune-related traits is important for the genetic improvement of disease resistance in pigs. The objective of this study was to detect a novel QTL for a total of 22 production, respiratory disease, and immune-related traits in Landrace pigs. A total of 874 Landrace purebred pigs, which were selected based on MPS resistance, were genotyped using the Illumina PorcineSNP60 BeadChip. We performed single nucleotide polymorphism (SNP)-based and haplotype-based genome-wide association studies (GWAS) to detect a novel QTL and to evaluate the possibility of a pleiotropic QTL for these traits. SNP-based GWAS detected a total of six significant regions in backfat thickness, ratio of granular leucocytes to lymphatic cells, plasma concentration of cortisol at different ages, and complement alternative pathway activity in serum. The significant region detected by haplotype-based GWAS was overlapped across the region detected by SNP-based GWAS. Most of these detected QTL regions were novel regions with some candidate genes located in them. With regard to a pleiotropic QTL among traits, only three of these detected QTL regions overlapped among traits, and many detected regions independently affected the traits.

Citing Articles

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References

Sun Y, Zhao G, Liu R, Zheng M, Hu Y, Wu D . The identification of 14 new genes for meat quality traits in chicken using a genome-wide association study. BMC Genomics. 2013; 14:458. PMC: 3707761. DOI: 10.1186/1471-2164-14-458. View

Takada Y, Kamimura D, Jiang J, Higuchi H, Iwami D, Hotta K . Increased urinary exosomal SYT17 levels in chronic active antibody-mediated rejection after kidney transplantation via the IL-6 amplifier. Int Immunol. 2020; 32(10):653-662. DOI: 10.1093/intimm/dxaa032. View

Uemoto Y, Sato S, Kikuchi T, Egawa S, Kohira K, Sakuma H . Genomic evaluation using SNP- and haplotype-based genomic relationship matrices in a closed line of Duroc pigs. Anim Sci J. 2017; 88(10):1465-1474. DOI: 10.1111/asj.12805. View

Lu X, Fu W, Luo Y, Ding X, Zhou J, Liu Y . Genome-wide association study for T lymphocyte subpopulations in swine. BMC Genomics. 2012; 13:488. PMC: 3481476. DOI: 10.1186/1471-2164-13-488. View

Ousova O, Guyonnet-Duperat V, Iannuccelli N, Bidanel J, Milan D, Genet C . Corticosteroid binding globulin: a new target for cortisol-driven obesity. Mol Endocrinol. 2004; 18(7):1687-96. DOI: 10.1210/me.2004-0005. View

Yagi R, Zhu J, Paul W . An updated view on transcription factor GATA3-mediated regulation of Th1 and Th2 cell differentiation. Int Immunol. 2011; 23(7):415-20. PMC: 3123974. DOI: 10.1093/intimm/dxr029. View

Zhou X, Stephens M . Genome-wide efficient mixed-model analysis for association studies. Nat Genet. 2012; 44(7):821-4. PMC: 3386377. DOI: 10.1038/ng.2310. View

Nicolazzi E, Caprera A, Nazzicari N, Cozzi P, Strozzi F, Lawley C . SNPchiMp v.3: integrating and standardizing single nucleotide polymorphism data for livestock species. BMC Genomics. 2015; 16:283. PMC: 4399246. DOI: 10.1186/s12864-015-1497-1. View

Debnath M, Berk M . Functional Implications of the IL-23/IL-17 Immune Axis in Schizophrenia. Mol Neurobiol. 2016; 54(10):8170-8178. DOI: 10.1007/s12035-016-0309-1. View

10.

Druet T, Farnir F . Use of ancestral haplotypes in genome-wide association studies. Methods Mol Biol. 2013; 1019:347-80. DOI: 10.1007/978-1-62703-447-0_15. View

11.

Guan F, Zhang T, Liu X, Han W, Lin H, Li L . Evaluation of voltage-dependent calcium channel γ gene families identified several novel potential susceptible genes to schizophrenia. Sci Rep. 2016; 6:24914. PMC: 4840350. DOI: 10.1038/srep24914. View

12.

Clapperton M, Glass E, Bishop S . Pig peripheral blood mononuclear leucocyte subsets are heritable and genetically correlated with performance. Animal. 2012; 2(11):1575-84. DOI: 10.1017/S1751731108002929. View

13.

Gorres A, Ponsuksili S, Wimmers K, Murani E . Analysis of non-synonymous SNPs of the porcine SERPINA6 gene as potential causal variants for a QTL affecting plasma cortisol levels on SSC7. Anim Genet. 2015; 46(3):239-46. DOI: 10.1111/age.12276. View

14.

Bolormaa S, Pryce J, Reverter A, Zhang Y, Barendse W, Kemper K . A multi-trait, meta-analysis for detecting pleiotropic polymorphisms for stature, fatness and reproduction in beef cattle. PLoS Genet. 2014; 10(3):e1004198. PMC: 3967938. DOI: 10.1371/journal.pgen.1004198. View

15.

Lu X, Liu J, Fu W, Zhou J, Luo Y, Ding X . Genome-wide association study for cytokines and immunoglobulin G in swine. PLoS One. 2013; 8(10):e74846. PMC: 3788770. DOI: 10.1371/journal.pone.0074846. View

16.

Sato T, Okamura T, Kojima-Shibata C, Kadowaki H, Suzuki E, Uenishi H . Correlated response of peripheral blood cytokines with selection for reduced mycoplasma pneumonia of swine lesions in Landrace pigs. Anim Sci J. 2015; 87(4):477-83. DOI: 10.1111/asj.12462. View

17.

Okamura T, Maeda K, Onodera W, Kadowaki H, Kojima-Shibata C, Suzuki E . Correlated responses of respiratory disease and immune capacity traits of Landrace pigs selected for Mycoplasmal pneumonia of swine (MPS) lesion. Anim Sci J. 2015; 87(9):1099-105. DOI: 10.1111/asj.12560. View

18.

Huang X, Huang T, Deng W, Yan G, Qiu H, Huang Y . Genome-wide association studies identify susceptibility loci affecting respiratory disease in Chinese Erhualian pigs under natural conditions. Anim Genet. 2016; 48(1):30-37. DOI: 10.1111/age.12504. View

19.

Maes D, Segales J, Meyns T, Sibila M, Pieters M, Haesebrouck F . Control of Mycoplasma hyopneumoniae infections in pigs. Vet Microbiol. 2007; 126(4):297-309. PMC: 7130725. DOI: 10.1016/j.vetmic.2007.09.008. View

20.

Soma Y, Uemoto Y, Sato S, Shibata T, Kadowaki H, Kobayashi E . Genome-wide mapping and identification of new quantitative trait loci affecting meat production, meat quality, and carcass traits within a Duroc purebred population. J Anim Sci. 2010; 89(3):601-8. DOI: 10.2527/jas.2010-3119. View