Candidate gene screening for lipid deposition using combined transcriptomic and proteomic data from Nanyang black pigs

Liyuan Wang,Hao Zhang,Yawen Zhang,Bo Zhang,Haian Zhong,Yunfeng Lu

doi:10.1186/s12864-021-07764-2

Abstract

BackgroundLower selection intensities in indigenous breeds of Chinese pig have resulted in obvious genetic and phenotypic divergence. One such breed, the Nanyang black pig, is renowned for its high lipid deposition and high genetic divergence, making it an ideal model in which to investigate lipid position trait mechanisms in pigs. An understanding of lipid deposition in pigs might improve pig meat traits in future breeding and promote the selection progress of pigs through modern molecular breeding techniques. Here, transcriptome and tandem mass tag-based quantitative proteome (TMT)-based proteome analyses were carried out using longissimus dorsi (LD) tissues from individual Nanyang black pigs that showed high levels of genetic variation.ResultsA large population of Nanyang black pigs was phenotyped using multi-production trait indexes, and six pigs were selected and divided into relatively high and low lipid deposition groups. The combined transcriptomic and proteomic data identified 15 candidate genes that determine lipid deposition genetic divergence. Among them, FASN, CAT, and SLC25A20 were the main causal candidate genes. The other genes could be divided into lipid deposition-related genes (BDH2, FASN, CAT, DHCR24, ACACA, GK, SQLE, ACSL4, and SCD), PPARA-centered fat metabolism regulatory factors (PPARA, UCP3), transcription or translation regulators (SLC25A20, PDK4, CEBPA), as well as integrin, structural proteins, and signal transduction-related genes (EGFR).ConclusionsThis multi-omics data set has provided a valuable resource for future analysis of lipid deposition traits, which might improve pig meat traits in future breeding and promote the selection progress in pigs, especially in Nanyang black pigs.

Highlights

Lower selection intensities in indigenous breeds of Chinese pig have resulted in obvious genetic and phenotypic divergence
By combining the backfat thickness, IMF, fat content in the issue slices, and total fatty acids (TFA)/total dry matter analyses 6 Nanyang black pigs were selected for further analysis and identified as high-fat deposition (HF) and low-fat deposition (LF) groups
Transcriptomic analysis between the high and low lipid deposition groups The cufflinks program identified a total of 342.8 million clean reads and approximately 94.94% of the clean reads were mapped to the Sus scrofa genome sequence

Summary

Introduction

Lower selection intensities in indigenous breeds of Chinese pig have resulted in obvious genetic and phenotypic divergence. Subcutaneous, visceral, and intramuscular adipose tissues deposited within muscle fibers, well known as intramuscular fat (IMF or marbling), are the major components of the lipid deposition trait in pigs These lipid tissues have unique metabolic mechanisms [4], they maintain a positive genetic correlation with the subcutaneous, visceral, and intramuscular adipose tissues [5,6,7]. Current commercial breeds such as Landrace and Yorkshire have undergone long-term and high-intensity selection processes for growth rate and muscle deposition characteristics, and this has resulted in a low lipid deposition trait. Several studies have previously attempted to identify genes and pathways involved in lipid deposition traits, to the best of our knowledge, sufficient phenotyping samples are currently lacking or do not consider the noise from the different genetic backgrounds, especially between western commercial and Chinese indigenous breeds

Methods

Results

Discussion

Conclusion