Construction of an SNP-based high-density genetic map for Japanese plum in a Chinese population using specific length fragment sequencing

Abstract

The Japanese plum (Prunus salicina Lindl.) is one of the most important stone fruit crops in China. High-density linkage map is valuable resources which enhance functional genomics and genetic breeding studies. So far several Japanese plum linkage maps have been reported using different kinds of molecular markers; however, the marker numbers and chromosome coverage are limited. Recently, a newly developed strategy which genome sequencing towards specific-locus amplified fragments (SLAF) markers, has been proven to be powerful for rapid genotyping of genome-wide markers and for high-density genetic map construction. In this study, SLAF was used to genotype markers with 114 F1 seedlings from the ‘09–16’ × ‘Fortune’ cross. Suitable SLAF markers (160,344 out of 343,436,902 pair-end reads) were chosen to conduct genetic map construction, 16.31% of which were polymorphic. The overall integrated map contained 3,341 high quality SLAFs and 720 loci that were grouped in eight genetic linkage groups with a total length of 869.9 cM and an average distance of 1.21 cM, and only five gaps with a genetic distance > 5 cM between adjacent markers occurred in linkage group (LG) 3 and LG6. The number of markers with each LG ranged from 82.3 cM (LG3) to 138.3 cM (LG1). Aligning the map against the peach reference genome sequence (Prunus persica L.) indicated a strictly co-linear relationship between the LGs and peach genome, demonstrating the markers on ours LGs were well ordered. Overall, our studies identified large-scale of genetic markers and constructed high-density linkage maps for Japanese plum, which will obviously provide a solid foundation for marker-assisted selection and sequence assembly of the Japanese plum reference genome.