AUTHOR=Liu Huatao , Song Hailiang , Jiang Yifan , Jiang Yao , Zhang Fengxia , Liu Yibing , Shi Yong , Ding Xiangdong , Wang Chuduan 

TITLE=A Single-Step Genome Wide Association Study on Body Size Traits Using Imputation-Based Whole-Genome Sequence Data in Yorkshire Pigs

JOURNAL=Frontiers in Genetics

VOLUME=12

YEAR=2021

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2021.629049

DOI=10.3389/fgene.2021.629049

ISSN=1664-8021

ABSTRACT=<p>The body shape of a pig is the most direct production index, which can fully reflect the pig’s growth status and is closely related to important economic traits. In this study, a genome-wide association study on seven body size traits, the body length (BL), height (BH), chest circumference (CC), abdominal circumference (AC), cannon bone circumference (CBC), rump width (RW), and chest width (CW), were conducted in Yorkshire pigs. Illumina Porcine 80K SNP chips were used to genotype 589 of 5,572 Yorkshire pigs with body size records, and then the chip data was imputed to sequencing data. After quality control of imputed sequencing data, 784,267 SNPs were obtained, and the averaged linkage disequilibrium (<italic>r</italic><sup>2</sup>) was 0.191. We used the single-trait model and the two-trait model to conduct single-step genome wide association study (ssGWAS) on seven body size traits; a total of 198 significant SNPS were finally identified according to the <italic>P</italic>-value and the contribution to the genetic variance of individual SNP. 11 candidate genes (<italic>CDH13</italic>, <italic>SIL1</italic>, <italic>CDC14A</italic>, <italic>TMRPSS15</italic>, <italic>TRAPPC9</italic>, <italic>CTNND2</italic>, <italic>KDM6B</italic>, <italic>CHD3</italic>, <italic>MUC13</italic>, <italic>MAPK4</italic>, and <italic>HMGA1</italic>) were found to be associated with body size traits in pigs; <italic>KDM6B</italic> and <italic>CHD3</italic> jointly affect AC and CC, and <italic>MUC13</italic> jointly affect RW and CW. These genes are involved in the regulation of bone growth and development as well as the absorption of nutrients and are associated with obesity. <italic>HMGA1</italic> is proposed as a strong candidate gene for body size traits because of its important function and high consistency with other studies regarding the regulation of body size traits. Our results could provide valuable information for pig breeding based on molecular breeding.</p>