Construction of a genetic map of rice RILs based on whole genome sequencing

Objective  The indica cultivar ‘MDS’ and ‘R315’ were used as parents to construct a high-density genetic map, explore the important agronomic traits related genes of rice (Oryza sativa L.) and accelerate the breeding of rice cultivars.

Method  Whole genome sequencing of parents and their 192 recombinant inbred lines (RILs ) were performed to screen high-quality single nucleotide polymorphisms (SNPs) and construct bin markers. The bin markers were sorted using JoinMap4.0 for each linkage group, and perl SVG was used to draw the linkage map. Collinearity analysis was conducted according to the position of the markers on the genome and genetic map.

Result  A total of 221 494 high-quality SNPs were screened between the two parents. The constructed high-density genetic map contained 1 612 bin markers. The total map distance was 1 327.82 cM, and the average genetic map distance between adjacent markers was 0.82 cM. The collinearity analysis showed that the order of most markers on each linkage group was consistent with that on the genome. The collinearity was good and the map was of high quality.

Conclusion  The constructed high-density genetic map is of high quality, providing a preliminary basis for the subsequent identification of functional genes.