AUTHOR=Liang Mang , An Bingxing , Deng Tianyu , Du Lili , Li Keanning , Cao Sheng , Du Yueying , Xu Lingyang , Zhang Lupei , Gao Xue , Cao Yang , Zhao Yuming , Li Junya , Gao Huijiang 

TITLE=Incorporating genome-wide and transcriptome-wide association studies to identify genetic elements of longissimus dorsi muscle in Huaxi cattle

JOURNAL=Frontiers in Genetics

VOLUME=13

YEAR=2023

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2022.982433

DOI=10.3389/fgene.2022.982433

ISSN=1664-8021

ABSTRACT=<p>Locating the genetic variation of important livestock and poultry economic traits is essential for genetic improvement in breeding programs. Identifying the candidate genes for the productive ability of Huaxi cattle was one crucial element for practical breeding. Based on the genotype and phenotype data of 1,478 individuals and the RNA-seq data of 120 individuals contained in 1,478 individuals, we implemented genome-wide association studies (GWAS), transcriptome-wide association studies (TWAS), and Fisher’s combined test (FCT) to identify the candidate genes for the carcass trait, the weight of longissimus dorsi muscle (LDM). The results indicated that GWAS, TWAS, and FCT identified seven candidate genes for LDM altogether: <italic>PENK</italic> was located by GWAS and FCT, <italic>PPAT</italic> was located by TWAS and FCT, and <italic>XKR4</italic>, <italic>MTMR3</italic>, <italic>FGFRL1</italic>, <italic>DHRS4</italic>, and <italic>LAP3</italic> were only located by one of the methods. After functional analysis of these candidate genes and referring to the reported studies, we found that they were mainly functional in the progress of the development of the body and the growth of muscle cells. Combining advanced breeding techniques such as gene editing with our study will significantly accelerate the genetic improvement for the future breeding of Huaxi cattle.</p>