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Genome-wide association analysis reveals genomic regions on Chromosome 13 affecting litter size and candidate genes for uterine horn length in Erhualian pigs

Published online by Cambridge University Press:  14 March 2018

X. Ma ,
P. H. Li ,
M. X. Zhu ,
L. C. He ,
S. P. Sui ,
S. Gao ,
G. S. Su ,
N. S. Ding ,
Y. Huang  and
Z. Q. Lu
...Show all authors
X. Ma
Affiliation:
Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China
P. H. Li*
Affiliation:
Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China
M. X. Zhu
Affiliation:
Jiangsu Animal Husbandry Station, Nanjing 210036, China
L. C. He
Affiliation:
Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China
S. P. Sui
Affiliation:
Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China
S. Gao
Affiliation:
Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China
G. S. Su
Affiliation:
Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, Tjele 8830, Denmark
N. S. Ding
Affiliation:
College of Animal Science and Veterinary Medicine, Jiangxi Agricultural University, Nanchang 330045, China
Y. Huang
Affiliation:
Changzhou Jiaoxi Cooperatives of Erhualian Pigs, Changzhou 213116, China
Z. Q. Lu
Affiliation:
Changshu Animal Husbandry and Veterinary Station, Suzhou 215500, China
X. G. Huang
Affiliation:
Sutai Enterprise Co., Ltd, Suzhou 215000, China
R. H. Huang*
Affiliation:
Institute of Swine Science, Nanjing Agricultural University, Nanjing 210095, China
*
†E-mail: lipinghua718@njau.edu.cn; rhhuang@njau.edu.cn
†E-mail: lipinghua718@njau.edu.cn; rhhuang@njau.edu.cn
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Abstract

Litter size has a great impact on the profit of swine producers. Uterine development is an important determinant of reproduction efficiency and could hence affect litter size. Chinese Erhualian pig is one of the most prolific breeds in the world, even though large phenotypic variation in litter size was observed within Erhualian sows. To dissect the genetic basis of the phenotypic variation, we herein conducted genome-wide association studies for total number born and number born alive (NBA) of Erhualian sows. In total, one significant single nucleotide polymorphism (SNP) (P<1.78e−06) and 11 suggestive SNPs (P<3.57e−05) were identified on 10 chromosomes, confirming seven previously reported quantitative trait loci (QTL) and uncovering six QTL for litter size or uterus length. One locus on Sus scrofa chromosome (SSC) 13 (79.28 to 90.43 Mb) harbored a cluster of suggestive SNPs associated with multiparous NBA. The SNP (rs81447100) within this region was confirmed to be significantly (P<0.05) associated with litter size in Erhualian (n=313), Sutai (n=173) and Yorkshire (n=488) populations. Retinol binding protein 2 and retinol binding protein 1 functionally related to the development of uterus were located in a region of 2 Mb around rs81447100. Moreover, four genes related to embryo implantation and development were also detected around other significant SNPs. Taken together, our findings provide a potential marker (rs81447100) for the genetic improvement of litter size not only in Chinese Erhualian pigs but also in European commercial pig breeds like Yorkshire, and would facilitate the final identification of causative variant(s) underlying the effect of SSC13 QTL on litter size.

Keywords

pigfertility phenotypic variationrs81447100potential marker
Type
Research Article
Information
animal , Volume 12 , Issue 12 , December 2018 , pp. 2453 - 2461
Copyright
© The Animal Consortium 2018 

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