Genome-wide screening of genetic structureand differentially selected regions amongLandrace, Erhualianand Meishanpig using SLAF-seq technology

Pig is a most important domestic animals in China. Two typical Chinese indigenous pig breeds, Meishan and Erhualian have been widely used to produce new strain or breed in the world. However, the genetic basis of characteristics from these pig breeds, such as high reproductive performance and excellent meat quality, are still largely unknown.To shed light to this issue, a genome-wide screening was performed to Landrace, Erhualian and Meishan pigs using specific locus amplified fragment sequencing (SLAF-seq) technology.Over 300,000 SNPs (single nucleotide polymorphisms) equivalent 5 fold SNP numbers of Illumina PorcineSNP60 BeadChip were developedby SLAF-seq. After quality-control, 165,699 SNPs, including 161,406 autosomal SNPs, 4,293 SNPs on chromosome X, were used in the further analysis. The results showed that Landrace had distinct genetic relationship compared to Erhualian(FST=0.5480) and Meishan (FST=0.5800) respectively, while Erhualian and Meishanhad the closest relationship (FST=0.2335). Moreover, a genome-wide scanning of differentially selected regions (DSRs) found that 268 DSRs with 732 genes and 256 DSRs with 272 genes were discovered between Landrace and two Chinese indigenous breeds and between Erhualian and Meishan, respectively. Some important candidatesrelated to different economically important traits, such as ESR1, RBBP4 and GNRHRfor reproductive performance, EXOC2 and KIT for pigmentation, and ACSL6, RAPGEF1 and KDR for meat quality, were also identified in DSRs between Landrace and two Chinese indigenous breeds. Taken together, our studydevelop a novel cost-effective method for genome-wide related study in pig and establish a genetic foundation of these pig breeds, thus improving our understanding of character and formation mechanism of genetic difference between China and European origin pig breeds.