A composite strategy of genome-wide association study and copy number variation analysis for carcass traits in a Duroc pig population

• DOI: 10.1186/s12864-022-08804-1
• Publication Date: 2022-08-13T10:02:42Z
• Authors: Rongrong Ding; Zhanwei Zhuang; Yibin Qiu; Xingwang Wang; Jie Wu; Shenping Zhou; Donglin Ruan; Cineng Xu; Linjun Hong; Ting Gu; Enqin Zheng; Gengyuan Cai; Wen Huang; Zhenfang Wu; Jie Yang
• Keywords: Genome-wide Association Study; Variation (astronomy)

Abstract Background Carcass traits are important in pig breeding programs for improving pork production. Understanding the genetic variants underlies complex phenotypes can help explain trait variation pigs. In this study, we integrated a weighted single-step genome-wide association study (wssGWAS) and copy number (CNV) analyses to map variations genes associated with loin muscle area (LMA), depth (LMD) lean meat percentage (LMP) Duroc Results Firstly, performed analysis CNV detection using GeneSeek Porcine SNP50 Bead chip data of 3770 A total 11,100 CNVs were detected, which aggregated by overlapping 695 regions (CNVRs). Next, investigated pigs from same population whole-genome resequencing. 21 revealed 23,856 CNVRs that further divided into three categories (851 gain, 22,279 loss, 726 mixed), covered 190.8 Mb (~ 8.42%) autosomal genome. Further, identified used determine an overall validation rate 68.5% accuracy data. CNVR one LMA, LMD eight LMP after applying stringent Bonferroni correction. The wssGWAS eight, six five explaining more than 1% additive variance LMP, respectively. common regions, LMA two LMP. Four ( DOK7 , ARAP1 ELMO2 SLC13A3 ) highlighted as promising candidates according their function. Conclusions We determined low-density constructed genomic resequencing, thereby proving value resource genome research. Furthermore, our utilized composite strategy pigs, will contribute elucidating architecture may be influenced regulated multiple forms variations.