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Revealing New Candidate Genes for Teat Number Relevant Traits in Duroc Pigs Using Genome-Wide Association Studies

SIMPLE SUMMARY: Number of teats is very important for lactating sows. We conducted genome-wide association studies (GWAS) and estimated the genetic parameters for traits related to teat number. Results showed that there were nine and 22 SNPs exceeding genome-wide significance and suggestive signific...

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Autores principales: Li, Yang, Pu, Lei, Shi, Liangyu, Gao, Hongding, Zhang, Pengfei, Wang, Lixian, Zhao, Fuping
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7998181/
https://www.ncbi.nlm.nih.gov/pubmed/33805666
http://dx.doi.org/10.3390/ani11030806
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author Li, Yang
Pu, Lei
Shi, Liangyu
Gao, Hongding
Zhang, Pengfei
Wang, Lixian
Zhao, Fuping
author_facet Li, Yang
Pu, Lei
Shi, Liangyu
Gao, Hongding
Zhang, Pengfei
Wang, Lixian
Zhao, Fuping
author_sort Li, Yang
collection PubMed
description SIMPLE SUMMARY: Number of teats is very important for lactating sows. We conducted genome-wide association studies (GWAS) and estimated the genetic parameters for traits related to teat number. Results showed that there were nine and 22 SNPs exceeding genome-wide significance and suggestive significance levels, respectively. Eighteen genes annotated near them were concentrated on chromosomes 7 and 10. Among them, three new candidate genes were located on the genomic regions around the significant SNPs. Our findings provide new insight into investigating the complex genetic mechanism of traits related to teat number in pigs. ABSTRACT: The number of teats is related to the nursing ability of sows. In the present study, we conducted genome-wide association studies (GWAS) for traits related to teat number in Duroc pig population. Two mixed models, one for counted and another for binary phenotypic traits, were employed to analyze seven traits: the right (RTN), left (LTN), and total (TTN) teat numbers; maximum teat number on a side (MAX); left minus right side teat number (LR); the absolute value of LR (ALR); and the presence of symmetry between left and right teat numbers (SLR). We identified 11, 1, 4, 13, and 9 significant SNPs associated with traits RTN, LTN, MAX, TTN, and SLR, respectively. One significant SNP (MARC0038565) was found to be simultaneous associated with RTN, LTN, MAX and TTN. Two annotated genes (VRTN and SYNDIG1L) were located in genomic region around this SNP. Three significant SNPs were shown to be associated with TTN, RTN and MAX traits. Seven significant SNPs were simultaneously detected in two traits of TTN and RTN. Other two SNPs were only identified in TTN. These 13 SNPs were clustered in the genomic region between 96.10—98.09 Mb on chromosome 7. Moreover, nine significant SNPs were shown to be significantly associated with SLR. In total, four and 22 SNPs surpassed genome-wide significance and suggestive significance levels, respectively. Among candidate genes annotated, eight genes have documented association with the teat number relevant traits. Out of them, DPF3 genes on Sus scrofa chromosome (SSC) 7 and the NRP1 gene on SSC 10 were new candidate genes identified in this study. Our findings demonstrate the genetic mechanism of teat number relevant traits and provide a reference to further improve reproductive performances in practical pig breeding programs.
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spelling pubmed-79981812021-03-28 Revealing New Candidate Genes for Teat Number Relevant Traits in Duroc Pigs Using Genome-Wide Association Studies Li, Yang Pu, Lei Shi, Liangyu Gao, Hongding Zhang, Pengfei Wang, Lixian Zhao, Fuping Animals (Basel) Communication SIMPLE SUMMARY: Number of teats is very important for lactating sows. We conducted genome-wide association studies (GWAS) and estimated the genetic parameters for traits related to teat number. Results showed that there were nine and 22 SNPs exceeding genome-wide significance and suggestive significance levels, respectively. Eighteen genes annotated near them were concentrated on chromosomes 7 and 10. Among them, three new candidate genes were located on the genomic regions around the significant SNPs. Our findings provide new insight into investigating the complex genetic mechanism of traits related to teat number in pigs. ABSTRACT: The number of teats is related to the nursing ability of sows. In the present study, we conducted genome-wide association studies (GWAS) for traits related to teat number in Duroc pig population. Two mixed models, one for counted and another for binary phenotypic traits, were employed to analyze seven traits: the right (RTN), left (LTN), and total (TTN) teat numbers; maximum teat number on a side (MAX); left minus right side teat number (LR); the absolute value of LR (ALR); and the presence of symmetry between left and right teat numbers (SLR). We identified 11, 1, 4, 13, and 9 significant SNPs associated with traits RTN, LTN, MAX, TTN, and SLR, respectively. One significant SNP (MARC0038565) was found to be simultaneous associated with RTN, LTN, MAX and TTN. Two annotated genes (VRTN and SYNDIG1L) were located in genomic region around this SNP. Three significant SNPs were shown to be associated with TTN, RTN and MAX traits. Seven significant SNPs were simultaneously detected in two traits of TTN and RTN. Other two SNPs were only identified in TTN. These 13 SNPs were clustered in the genomic region between 96.10—98.09 Mb on chromosome 7. Moreover, nine significant SNPs were shown to be significantly associated with SLR. In total, four and 22 SNPs surpassed genome-wide significance and suggestive significance levels, respectively. Among candidate genes annotated, eight genes have documented association with the teat number relevant traits. Out of them, DPF3 genes on Sus scrofa chromosome (SSC) 7 and the NRP1 gene on SSC 10 were new candidate genes identified in this study. Our findings demonstrate the genetic mechanism of teat number relevant traits and provide a reference to further improve reproductive performances in practical pig breeding programs. MDPI 2021-03-13 /pmc/articles/PMC7998181/ /pubmed/33805666 http://dx.doi.org/10.3390/ani11030806 Text en © 2021 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) ).
spellingShingle Communication
Li, Yang
Pu, Lei
Shi, Liangyu
Gao, Hongding
Zhang, Pengfei
Wang, Lixian
Zhao, Fuping
Revealing New Candidate Genes for Teat Number Relevant Traits in Duroc Pigs Using Genome-Wide Association Studies
title Revealing New Candidate Genes for Teat Number Relevant Traits in Duroc Pigs Using Genome-Wide Association Studies
title_full Revealing New Candidate Genes for Teat Number Relevant Traits in Duroc Pigs Using Genome-Wide Association Studies
title_fullStr Revealing New Candidate Genes for Teat Number Relevant Traits in Duroc Pigs Using Genome-Wide Association Studies
title_full_unstemmed Revealing New Candidate Genes for Teat Number Relevant Traits in Duroc Pigs Using Genome-Wide Association Studies
title_short Revealing New Candidate Genes for Teat Number Relevant Traits in Duroc Pigs Using Genome-Wide Association Studies
title_sort revealing new candidate genes for teat number relevant traits in duroc pigs using genome-wide association studies
topic Communication
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7998181/
https://www.ncbi.nlm.nih.gov/pubmed/33805666
http://dx.doi.org/10.3390/ani11030806
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