A meta-analysis of genome-wide association studies for average daily gain and lean meat percentage in two Duroc pig populations.

Animals Canada Genome-Wide Association Study Meat Phenotype Polymorphism, Single Nucleotide Quantitative Trait Loci Sus scrofa / genetics Swine / genetics
Average daily gain GWAS Lean meat percentage Meta-analysis Pigs

Journal

BMC genomics
ISSN: 1471-2164
Titre abrégé: BMC Genomics
Pays: England
ID NLM: 100965258

Informations de publication

Date de publication:
06 Jan 2021
Historique:
received: 02 06 2020
accepted: 28 11 2020
entrez: 7 1 2021
pubmed: 8 1 2021
medline: 15 5 2021
Statut: epublish

Résumé

Average daily gain (ADG) and lean meat percentage (LMP) are the main production performance indicators of pigs. Nevertheless, the genetic architecture of ADG and LMP is still elusive. Here, we conducted genome-wide association studies (GWAS) and meta-analysis for ADG and LMP in 3770 American and 2090 Canadian Duroc pigs. In the American Duroc pigs, one novel pleiotropic quantitative trait locus (QTL) on Sus scrofa chromosome 1 (SSC1) was identified to be associated with ADG and LMP, which spans 2.53 Mb (from 159.66 to 162.19 Mb). In the Canadian Duroc pigs, two novel QTLs on SSC1 were detected for LMP, which were situated in 3.86 Mb (from 157.99 to 161.85 Mb) and 555 kb (from 37.63 to 38.19 Mb) regions. The meta-analysis identified ten and 20 additional SNPs for ADG and LMP, respectively. Finally, four genes (PHLPP1, STC1, DYRK1B, and PIK3C2A) were detected to be associated with ADG and/or LMP. Further bioinformatics analysis showed that the candidate genes for ADG are mainly involved in bone growth and development, whereas the candidate genes for LMP mainly participated in adipose tissue and muscle tissue growth and development. We performed GWAS and meta-analysis for ADG and LMP based on a large sample size consisting of two Duroc pig populations. One pleiotropic QTL that shared a 2.19 Mb haplotype block from 159.66 to 161.85 Mb on SSC1 was found to affect ADG and LMP in the two Duroc pig populations. Furthermore, the combination of single-population and meta-analysis of GWAS improved the efficiency of detecting additional SNPs for the analyzed traits. Our results provide new insights into the genetic architecture of ADG and LMP traits in pigs. Moreover, some significant SNPs associated with ADG and/or LMP in this study may be useful for marker-assisted selection in pig breeding.

Sections du résumé

BACKGROUND BACKGROUND
Average daily gain (ADG) and lean meat percentage (LMP) are the main production performance indicators of pigs. Nevertheless, the genetic architecture of ADG and LMP is still elusive. Here, we conducted genome-wide association studies (GWAS) and meta-analysis for ADG and LMP in 3770 American and 2090 Canadian Duroc pigs.
RESULTS RESULTS
In the American Duroc pigs, one novel pleiotropic quantitative trait locus (QTL) on Sus scrofa chromosome 1 (SSC1) was identified to be associated with ADG and LMP, which spans 2.53 Mb (from 159.66 to 162.19 Mb). In the Canadian Duroc pigs, two novel QTLs on SSC1 were detected for LMP, which were situated in 3.86 Mb (from 157.99 to 161.85 Mb) and 555 kb (from 37.63 to 38.19 Mb) regions. The meta-analysis identified ten and 20 additional SNPs for ADG and LMP, respectively. Finally, four genes (PHLPP1, STC1, DYRK1B, and PIK3C2A) were detected to be associated with ADG and/or LMP. Further bioinformatics analysis showed that the candidate genes for ADG are mainly involved in bone growth and development, whereas the candidate genes for LMP mainly participated in adipose tissue and muscle tissue growth and development.
CONCLUSIONS CONCLUSIONS
We performed GWAS and meta-analysis for ADG and LMP based on a large sample size consisting of two Duroc pig populations. One pleiotropic QTL that shared a 2.19 Mb haplotype block from 159.66 to 161.85 Mb on SSC1 was found to affect ADG and LMP in the two Duroc pig populations. Furthermore, the combination of single-population and meta-analysis of GWAS improved the efficiency of detecting additional SNPs for the analyzed traits. Our results provide new insights into the genetic architecture of ADG and LMP traits in pigs. Moreover, some significant SNPs associated with ADG and/or LMP in this study may be useful for marker-assisted selection in pig breeding.

Identifiants

DOI: 10.1186/s12864-020-07288-1 PMID: 33407097 PMC: PMC7788875
pubmed: 33407097
doi: 10.1186/s12864-020-07288-1
pii: 10.1186/s12864-020-07288-1
pmc: PMC7788875
doi:

Types de publication

Journal Article Meta-Analysis

Langues

eng

Sous-ensembles de citation

IM

Pagination

12

Subventions

Organisme : Natural Science Foundation of Guangdong Province
ID : 2018B030315007
Organisme : Peral River Nova Program of Guangzhou (CN)
ID : 201906010011

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Auteurs

Shenping Zhou (S)

College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China.

Rongrong Ding (R)

College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China.

Fanming Meng (F)

State Key Laboratory of Livestock and Poultry Breeding / Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, Guangdong, People's Republic of China.

Xingwang Wang (X)

College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China.

Zhanwei Zhuang (Z)

College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China.

Jianping Quan (J)

College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China.

Qian Geng (Q)

College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China.

Jie Wu (J)

College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China.

Enqin Zheng (E)

College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China.

Zhenfang Wu (Z)

College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China.

Jianhui Yang (J)

YueYang Vocational Technical College, Yueyang, 414000, Hunan, People's Republic of China. 178479769@qq.com.

Jie Yang (J)

College of Animal Science and National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China. jieyang2012@hotmail.com.
ORCID: 0000-0002-7031-2160

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