Regulatory gene network from a genome-wide association study for sow lifetime productivity traits

J. H. Kang; E. A. Lee; K. C. Hong; J. M. Kim

doi:10.1111/age.12640

Regulatory gene network from a genome-wide association study for sow lifetime productivity traits

J. H. Kang, E. A. Lee, K. C. Hong, J. M. Kim

Research output: Contribution to journal › Article › peer-review

8 Citations (Scopus)

Abstract

Among swine reproductive traits, sow lifetime productivity (SLP) is considered a profitable trait in commercial pig farming. Notably, longevity and efficiency in SLP can be adopted as the key phenotype representing SLP. In this study, we conducted a co-association network analysis using results from a genome-wide association study for SLP-related traits. A total of 656 purebred Landrace female pigs were genotyped using a 60K SNP array. Significantly associated SNPs identified from the GWAS were annotated for the specific genes. Then, we constructed an association weight matrix to build a network based on the co-associations between the genes and 10 SLP traits. The entire network consisted of 495 nodes and 37 755 significant edges. We identified three key regulatory transcription factors: STAT2 (signal transducer and activator of transcription 2), MYF6 (myogenic factor 6) and TFCP2L1 (transcription factor CP2 like 1). The network revealed that the STAT2 and MYF6 regulatory modules cooperate with each other and specifically influence the longevity and efficiency of sows, whereas the TFCP2L1 family specifically affects the improvement of litter size.

Original language	English
Pages (from-to)	254-258
Number of pages	5
Journal	Animal Genetics
Volume	49
Issue number	3
DOIs	https://doi.org/10.1111/age.12640
Publication status	Published - 2018 Jun

Bibliographical note

Funding Information:
This research was supported by the Bio-industry Technology Development Program (grant number 114065) and the Ministry of Agriculture, Food and Rural Affairs and carried out with the support of the 2017 the RDA Fellowship Program of the NIAS and the Cooperative Research Program for Agriculture Science and Technology Development (Project No. PJ01187601), Rural Development Administration, Republic of Korea. We especially thank Dr. K. Srikanth for proofreading this manuscript.

Publisher Copyright:
© 2018 Stichting International Foundation for Animal Genetics

Keywords

GWAS
Landrace
association weight matrix
network analysis
reproductive traits

ASJC Scopus subject areas

Animal Science and Zoology
Genetics

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10.1111/age.12640

Cite this

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title = "Regulatory gene network from a genome-wide association study for sow lifetime productivity traits",

abstract = "Among swine reproductive traits, sow lifetime productivity (SLP) is considered a profitable trait in commercial pig farming. Notably, longevity and efficiency in SLP can be adopted as the key phenotype representing SLP. In this study, we conducted a co-association network analysis using results from a genome-wide association study for SLP-related traits. A total of 656 purebred Landrace female pigs were genotyped using a 60K SNP array. Significantly associated SNPs identified from the GWAS were annotated for the specific genes. Then, we constructed an association weight matrix to build a network based on the co-associations between the genes and 10 SLP traits. The entire network consisted of 495 nodes and 37 755 significant edges. We identified three key regulatory transcription factors: STAT2 (signal transducer and activator of transcription 2), MYF6 (myogenic factor 6) and TFCP2L1 (transcription factor CP2 like 1). The network revealed that the STAT2 and MYF6 regulatory modules cooperate with each other and specifically influence the longevity and efficiency of sows, whereas the TFCP2L1 family specifically affects the improvement of litter size.",

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author = "Kang, {J. H.} and Lee, {E. A.} and Hong, {K. C.} and Kim, {J. M.}",

note = "Funding Information: This research was supported by the Bio-industry Technology Development Program (grant number 114065) and the Ministry of Agriculture, Food and Rural Affairs and carried out with the support of the 2017 the RDA Fellowship Program of the NIAS and the Cooperative Research Program for Agriculture Science and Technology Development (Project No. PJ01187601), Rural Development Administration, Republic of Korea. We especially thank Dr. K. Srikanth for proofreading this manuscript. Publisher Copyright: {\textcopyright} 2018 Stichting International Foundation for Animal Genetics",

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N2 - Among swine reproductive traits, sow lifetime productivity (SLP) is considered a profitable trait in commercial pig farming. Notably, longevity and efficiency in SLP can be adopted as the key phenotype representing SLP. In this study, we conducted a co-association network analysis using results from a genome-wide association study for SLP-related traits. A total of 656 purebred Landrace female pigs were genotyped using a 60K SNP array. Significantly associated SNPs identified from the GWAS were annotated for the specific genes. Then, we constructed an association weight matrix to build a network based on the co-associations between the genes and 10 SLP traits. The entire network consisted of 495 nodes and 37 755 significant edges. We identified three key regulatory transcription factors: STAT2 (signal transducer and activator of transcription 2), MYF6 (myogenic factor 6) and TFCP2L1 (transcription factor CP2 like 1). The network revealed that the STAT2 and MYF6 regulatory modules cooperate with each other and specifically influence the longevity and efficiency of sows, whereas the TFCP2L1 family specifically affects the improvement of litter size.

AB - Among swine reproductive traits, sow lifetime productivity (SLP) is considered a profitable trait in commercial pig farming. Notably, longevity and efficiency in SLP can be adopted as the key phenotype representing SLP. In this study, we conducted a co-association network analysis using results from a genome-wide association study for SLP-related traits. A total of 656 purebred Landrace female pigs were genotyped using a 60K SNP array. Significantly associated SNPs identified from the GWAS were annotated for the specific genes. Then, we constructed an association weight matrix to build a network based on the co-associations between the genes and 10 SLP traits. The entire network consisted of 495 nodes and 37 755 significant edges. We identified three key regulatory transcription factors: STAT2 (signal transducer and activator of transcription 2), MYF6 (myogenic factor 6) and TFCP2L1 (transcription factor CP2 like 1). The network revealed that the STAT2 and MYF6 regulatory modules cooperate with each other and specifically influence the longevity and efficiency of sows, whereas the TFCP2L1 family specifically affects the improvement of litter size.

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Regulatory gene network from a genome-wide association study for sow lifetime productivity traits

Abstract

Bibliographical note

Keywords

ASJC Scopus subject areas

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