Genomic signatures reveal selection of characteristics within and between Meishan pig populations

The Chinese Meishan pig breed is well known for its high prolificacy. Moreover, this breed can be divided into three types based on their body size: big Meishan, middle Meishan (MMS) and small Meishan (SMS) pigs. Few studies have reported on the genetic signatures of Meishan pigs, particularly on a genome-wide scale. Exploring for genetic signatures could be quite valuable for revealing the genetic architecture of phenotypic variation. Thus, we performed research in two parts based on the genome reducing and sequencing data of 143 Meishan pigs (74 MMS pigs, 69 SMS pigs). First, we detected the selection signatures among all Meishan pigs studied using the relative extended haplotype homozygosity test. Second, we detected the selection signatures between MMS and SMS pigs using the cross-population extended haplotype homozygosity and F_ST methods. A total of 111 398 SNPs were identified from the sequenced genomes. In the population analysis, the most significant genes were associated with the mental development (RGMA), reproduction (HDAC4, FOXL2) and lipid metabolism (ACACB). From the cross-population analysis, we detected genes related to body weight (SPDEF, PACSIN1) in both methods. We suggest that rs341373351, located within the PACSIN1 gene, might be the causal variant. This study may have achieved consistency between selection signatures and characteristics within and between Meishan pig populations. These findings can provide insight into investigating the molecular background of high prolificacy and body size in pig.