Mapping quantitative trait loci and meta-analysis for cold tolerance in rice at booting stage

Abstract

Low temperature at the booting stage is a major abiotic stress-limiting rice production. In this study, Cold stress tolerance index of panicle traits of a recombinant inbred line was used to identify cold tolerance at booting stage for three consecutive years. The purpose was to locate the stable QTL linked to cold tolerance at booting stage. Combined with meta-analysis model, candidate genes for cold tolerance were mined. The results showed that a total of 17 cold resistant QTLs were detected, of which 5 were pleiotropic interval (CTB2-1, CTB6-2, CTB7-1, CTB7-2 and CTB7-4). However, only three traits obtained the same QTLs in different years, which indicated that cold tolerant QTL at the booting stage was greatly affected by environment. The six selected progenys with cold tolerance alleles can be used in cross combinations. A total of 47 cold tolerance meta-QTLs (MCqtl) were obtained from the meta-analysis, of which 8 reported cold response genes were found in 7 MCqtl regions, and 18 candidate genes conferring cold tolerance were identified, of which 10 candidate genes showed hits to ESTs expressed in the reproductive tissue. These results would lay a foundation for fine mapping of QTLs/genes related to cold tolerance in booting stage and marker-assisted selection for breeding in rice.