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Identification of SNPs and Candidate Genes for Milk Production Ability in Yorkshire Pigs

Sow milk production ability is an important limiting factor impacting suboptimal growth and the survival of piglets. Through pig genetic improvement, litter sizes have been increased. Larger litters need more suckling mammary glands, which results in increased milk from the lactating sow. Hence, the...

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Autores principales: Shi, Lijun, Li, Yang, Liu, Qian, Zhang, Longchao, Wang, Ligang, Liu, Xin, Gao, Hongmei, Hou, Xinhua, Zhao, Fuping, Yan, Hua, Wang, Lixian
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8523896/
https://www.ncbi.nlm.nih.gov/pubmed/34675963
http://dx.doi.org/10.3389/fgene.2021.724533
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author Shi, Lijun
Li, Yang
Liu, Qian
Zhang, Longchao
Wang, Ligang
Liu, Xin
Gao, Hongmei
Hou, Xinhua
Zhao, Fuping
Yan, Hua
Wang, Lixian
author_facet Shi, Lijun
Li, Yang
Liu, Qian
Zhang, Longchao
Wang, Ligang
Liu, Xin
Gao, Hongmei
Hou, Xinhua
Zhao, Fuping
Yan, Hua
Wang, Lixian
author_sort Shi, Lijun
collection PubMed
description Sow milk production ability is an important limiting factor impacting suboptimal growth and the survival of piglets. Through pig genetic improvement, litter sizes have been increased. Larger litters need more suckling mammary glands, which results in increased milk from the lactating sow. Hence, there is much significance to exploring sow lactation performance. For milk production ability, it is not practical to directly measure the milk yield, we used litter weight gain (LWG) throughout sow lactation as an indicator. In this study, we estimated the heritability of LWG, namely, 0.18 ± 0.07. We then performed a GWAS, and detected seven significant SNPs, namely, Sus scrofa Chromosome (SSC) 2: ASGA0010040 (p = 7.73E-11); SSC2:MARC0029355 (p = 1.30E-08), SSC6: WU_10.2_6_65751151 (p = 1.32E-10), SSC7: MARC0058875 (p = 4.99E-09), SSC10: WU_10.2_10_49571394 (p = 6.79E-08), SSC11: M1GA0014659 (p = 1.19E-07), and SSC15: MARC0042106 (p = 1.16E-07). We performed the distribution of phenotypes corresponding to the genotypes of seven significant SNPs and showed that ASGA0010040, MARC0029355, MARC0058875, WU_10.2_10_49571394, M1GA0014659, and MARC0042106 had extreme phenotypic values that corresponded to the homozygous genotypes, while the intermediate values corresponded to the heterozygous genotypes. We screened for flanking regions ± 200 kb nearby the seven significant SNPs, and identified 38 genes in total. Among them, 28 of the candidates were involved in lactose metabolism, colostrum immunity, milk protein, and milk fat by functional enrichment analysis. Through the combined analysis between 28 candidate genes and transcriptome data of the sow mammary gland, we found nine commons (ANO3, MUC15, DISP3, FBXO6, CLCN6, HLA-DRA, SLA-DRB1, SLA-DQB1, and SLA-DQA1). Furthermore, by comparing the chromosome positions of the candidate genes with the quantitative trait locus (QTLs) as previously reported, a total of 17 genes were found to be within 0.86–94.02 Mb of the reported QTLs for sow milk production ability, in which, NAV2 was found to be located with 0.86 Mb of the QTL region ssc2: 40936355. In conclusion, we identified seven significant SNPs located on SSC2, 6, 7, 10, 11, and 15, and propose 28 candidate genes for the ability to produce milk in Yorkshire pigs, 10 of which were key candidates.
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spelling pubmed-85238962021-10-20 Identification of SNPs and Candidate Genes for Milk Production Ability in Yorkshire Pigs Shi, Lijun Li, Yang Liu, Qian Zhang, Longchao Wang, Ligang Liu, Xin Gao, Hongmei Hou, Xinhua Zhao, Fuping Yan, Hua Wang, Lixian Front Genet Genetics Sow milk production ability is an important limiting factor impacting suboptimal growth and the survival of piglets. Through pig genetic improvement, litter sizes have been increased. Larger litters need more suckling mammary glands, which results in increased milk from the lactating sow. Hence, there is much significance to exploring sow lactation performance. For milk production ability, it is not practical to directly measure the milk yield, we used litter weight gain (LWG) throughout sow lactation as an indicator. In this study, we estimated the heritability of LWG, namely, 0.18 ± 0.07. We then performed a GWAS, and detected seven significant SNPs, namely, Sus scrofa Chromosome (SSC) 2: ASGA0010040 (p = 7.73E-11); SSC2:MARC0029355 (p = 1.30E-08), SSC6: WU_10.2_6_65751151 (p = 1.32E-10), SSC7: MARC0058875 (p = 4.99E-09), SSC10: WU_10.2_10_49571394 (p = 6.79E-08), SSC11: M1GA0014659 (p = 1.19E-07), and SSC15: MARC0042106 (p = 1.16E-07). We performed the distribution of phenotypes corresponding to the genotypes of seven significant SNPs and showed that ASGA0010040, MARC0029355, MARC0058875, WU_10.2_10_49571394, M1GA0014659, and MARC0042106 had extreme phenotypic values that corresponded to the homozygous genotypes, while the intermediate values corresponded to the heterozygous genotypes. We screened for flanking regions ± 200 kb nearby the seven significant SNPs, and identified 38 genes in total. Among them, 28 of the candidates were involved in lactose metabolism, colostrum immunity, milk protein, and milk fat by functional enrichment analysis. Through the combined analysis between 28 candidate genes and transcriptome data of the sow mammary gland, we found nine commons (ANO3, MUC15, DISP3, FBXO6, CLCN6, HLA-DRA, SLA-DRB1, SLA-DQB1, and SLA-DQA1). Furthermore, by comparing the chromosome positions of the candidate genes with the quantitative trait locus (QTLs) as previously reported, a total of 17 genes were found to be within 0.86–94.02 Mb of the reported QTLs for sow milk production ability, in which, NAV2 was found to be located with 0.86 Mb of the QTL region ssc2: 40936355. In conclusion, we identified seven significant SNPs located on SSC2, 6, 7, 10, 11, and 15, and propose 28 candidate genes for the ability to produce milk in Yorkshire pigs, 10 of which were key candidates. Frontiers Media S.A. 2021-10-05 /pmc/articles/PMC8523896/ /pubmed/34675963 http://dx.doi.org/10.3389/fgene.2021.724533 Text en Copyright © 2021 Shi, Li, Liu, Zhang, Wang, Liu, Gao, Hou, Zhao, Yan and Wang. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Genetics
Shi, Lijun
Li, Yang
Liu, Qian
Zhang, Longchao
Wang, Ligang
Liu, Xin
Gao, Hongmei
Hou, Xinhua
Zhao, Fuping
Yan, Hua
Wang, Lixian
Identification of SNPs and Candidate Genes for Milk Production Ability in Yorkshire Pigs
title Identification of SNPs and Candidate Genes for Milk Production Ability in Yorkshire Pigs
title_full Identification of SNPs and Candidate Genes for Milk Production Ability in Yorkshire Pigs
title_fullStr Identification of SNPs and Candidate Genes for Milk Production Ability in Yorkshire Pigs
title_full_unstemmed Identification of SNPs and Candidate Genes for Milk Production Ability in Yorkshire Pigs
title_short Identification of SNPs and Candidate Genes for Milk Production Ability in Yorkshire Pigs
title_sort identification of snps and candidate genes for milk production ability in yorkshire pigs
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8523896/
https://www.ncbi.nlm.nih.gov/pubmed/34675963
http://dx.doi.org/10.3389/fgene.2021.724533
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