Genetic basis analysis for indica germinability under low temperature using a new RILs population genotyping by whole-genome resequencing

Abstract Background : Improving the cold tolerance of rice at germination stage is an important objective to maintain rice yields. However, less analyses were carried out to detect the quantitative trait loci (QTLs) associated with cold tolerance using indica/indica population. Therefore, the genetic basis of cold tolerance of the indica varieties should be provided considerable attentionResults: In this study, a recombinant inbred lines (RILs) population comprising 126 lines derived from two widely used double-cropped indica rice varieties Wufeng B (WFB) and Changhui T025 (CHT025) was used to construct a high-density linkage map based on whole-genome resequencing. The high-density genetic map included 2,578 bins on 12 linkage groups and was 1762.80 cM in length, with an average interlocus distance of 0.68 cM. On the basis of newly constructed high-density genetic map, a total of 18 additive QTLs ranging from 34.55 to 315.21 kb on Nipponbare genome and two pairs of epistatic QTLs associated with cold stress at germination stage were detected, which indicated that the genetic basis of cold tolerance of WFB and CHT025 at germination stage is manly due to additive effects of several QTLs. Otherwise, the phylogenetic analysis showed that WFB is a typical indica variety while CHT025 is an interphyletic rice variety. Most of the favorable QTLs harbouring in indica WFB showed different chromosomal region from the QTLs associating with cold stress from japonica rice in previous studies, which indicated that indica might have different cold stress genetic mechanism comparing to japonica subspecies. Furthermore, we can incorporate these favorable QTLs existing in WFB into rice varieties to breed new cold tolerance indica male sterile maintenance line via marker-assisted selection; CHT025 is a better source of these cold tolerance favorable QTLs only only for the improvement of indcia but also for japonica restorer line germinability under low temperature via marker-assisted selection.Conclusion : This population with high density genetic map will serve as better choice for identifying important quantitative traits of these two good indica germplasms, and these favorable QTLs exist in WFB and CHT025 can be used to breed new cold tolerance indica varieties via marker-assisted selection. These authors have contributed equally to this work