Genomic analyses provide insights into breed-of-origin effects from purebreds on three-way crossbred pigs

Yu Lin; Qianzi Tang; Yan Li; Mengnan He; Long Jin; Jideng Ma; Xun Wang; Keren Long; Zhiqing Huang; Xuewei Li; Yiren Gu; Mingzhou Li

doi:10.7717/peerj.8009

Genomic analyses provide insights into breed-of-origin effects from purebreds on three-way crossbred pigs

PeerJ. 2019 Nov 11:7:e8009. doi: 10.7717/peerj.8009. eCollection 2019.

Authors

Yu Lin^#¹, Qianzi Tang^#¹, Yan Li¹, Mengnan He¹, Long Jin¹, Jideng Ma¹, Xun Wang¹, Keren Long¹, Zhiqing Huang², Xuewei Li¹, Yiren Gu³, Mingzhou Li¹

Affiliations

¹ Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China.
² Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, Sichuan, China.
³ Sichuan Animal Science Academy, Chengdu, Sichuan, China.

^# Contributed equally.

Abstract

Crossbreeding is widely used aimed at improving crossbred performance for poultry and livestock. Alleles that are specific to different purebreds will yield a large number of heterozygous single-nucleotide polymorphisms (SNPs) in crossbred individuals, which are supposed to have the power to alter gene function or regulate gene expression. For pork production, a classic three-way crossbreeding system of Duroc × (Landrace × Yorkshire) (DLY) is generally used to produce terminal crossbred pigs with stable and prominent performance. Nonetheless, little is known about the breed-of-origin effects from purebreds on DLY pigs. In this study, we first estimated the distribution of heterozygous SNPs in three kinds of three-way crossbred pigs via whole genome sequencing data originated from three purebreds. The result suggested that DLY is a more effective strategy for three-way crossbreeding as it could yield more stably inherited heterozygous SNPs. We then sequenced a DLY pig family and identified 95, 79, 132 and 42 allele-specific expression (ASE) genes in adipose, heart, liver and skeletal muscle, respectively. Principal component analysis and unrestricted clustering analyses revealed the tissue-specific pattern of ASE genes, indicating the potential roles of ASE genes for development of DLY pigs. In summary, our findings provided a lot of candidate SNP markers and ASE genes for DLY three-way crossbreeding system, which may be valuable for pig breeding and production in the future.

Keywords: Allele-specific expression; Breed-of-origin; Crossbreeding; DLY; SNP.

Grants and funding

This work was supported by grants from the National Key R & D Program of China (2018YFD0500403), the National Natural Science Foundation of China (31802044, 31872335 and 31772576), the Sichuan Province & Chinese Academy of Science of Science & Technology Cooperation Project (2017JZ0025), the Science & Technology Support Program of Sichuan (2016NYZ0042 and 2017NZDZX0002), the Earmarked Fund for China Agriculture Research System (CARS-35-01A) and the China Postdoctoral Science Foundation (2018M643514). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.