Whole-genome selective sweep analysis of Danish Large White and Chinese indigenous pig populations

The pig industry is an important component of Chinese agriculture. Chinese indigenous and Western commercial pig breeds provide valuable genetic resources for sustainable development of the pig industry, and selective signal analysis can advance our understanding of artificial and natural selective processes. In this study, we used whole genome re-sequencing data to analyze selection signatures in 43 Danish Large White [LW] pigs and 60 Chinese indigenous pigs (24 Anqing six-end white [AQ], 6 Asian wild [SS] pigs, 15 Diqing Tibetan [DQZ], and 15 Diannan small-ear [DN] pigs). We employed two calculation methods (F_ST and π ratio) to identify the selection signals of LW and Chinese indigenous pigs (top 1%). Among the selective sweep regions, 15 and 117 candidate genes were identified in Chinese indigenous pigs and LW pigs, respectively. The <i>PIK3IP1</i>, <i>TUG1</i>, and <i>SELENOM</i> genes were related to environmental adaptation in Chinese indigenous pigs; <i>ALDH1A2, APC2</i>, <i>PTBP1</i>, <i>APQ9</i>, and <i>FGF7</i> were related to reproductive performance in LW pigs. Our findings provide insights into the genetic basis of economic traits of LW and Chinese indigenous pigs and offer a useful reference for future pig breeding and production.