Whole-genome resequencing reveals candidate mutations for pig prolificacy

Author:

Li Wen-Ting12ORCID,Zhang Meng-Meng1,Li Qi-Gang3,Tang Hui4,Zhang Li-Fan5,Wang Ke-Jun12,Zhu Mu-Zhen1,Lu Yun-Feng6,Bao Hai-Gang1,Zhang Yuan-Ming7,Li Qiu-Yan8,Wu Ke-Liang1,Wu Chang-Xin1

Affiliation:

1. College of Animal Science and Technology, China Agricultural University, Beijing 100193, People's Republic of China

2. College of Animal Sciences and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, People's Republic of China

3. State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, People's Republic of China

4. College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Taian 271018, People's Republic of China

5. College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, People's Republic of China

6. School of Life Science and Technology, Nanyang Normal University, No. 1638 Wolong Road, Nanyang Henan 473061, People's Republic of China

7. College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, People's Republic of China

8. State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100193, People's Republic of China

Abstract

Changes in pig fertility have occurred as a result of domestication, but are not understood at the level of genetic variation. To identify variations potentially responsible for prolificacy, we sequenced the genomes of the highly prolific Taihu pig breed and four control breeds. Genes involved in embryogenesis and morphogenesis were targeted in the Taihu pig, consistent with the morphological differences observed between the Taihu pig and others during pregnancy. Additionally, excessive functional non-coding mutations have been specifically fixed or nearly fixed in the Taihu pig. We focused attention on an oestrogen response element (ERE) within the first intron of the bone morphogenetic protein receptor type-1B gene ( BMPR1B ) that overlaps with a known quantitative trait locus (QTL) for pig fecundity. Using 242 pigs from 30 different breeds, we confirmed that the genotype of the ERE was nearly fixed in the Taihu pig. ERE function was assessed by luciferase assays, examination of histological sections, chromatin immunoprecipitation, quantitative polymerase chain reactions, and western blots. The results suggest that the ERE may control pig prolificacy via the cis-regulation of BMPR1B expression. This study provides new insight into changes in reproductive performance and highlights the role of non-coding mutations in generating phenotypic diversity between breeds.

Funder

Huazhong Agricultural University Scientific and Technological Self-Innovation Foundation

program for Changjiang Scholars and Innovation Research Teams in the University

National Transgenic Animal Breeding Grand Project

National Basic Research Program of China

Beijing Innovation Consortium of Swine Research System

Publisher

The Royal Society

Subject

General Agricultural and Biological Sciences,General Environmental Science,General Immunology and Microbiology,General Biochemistry, Genetics and Molecular Biology,General Medicine

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