Genetic characterization of introgression lines with the genetic background of the Indica-type rice (Oryza sativa L.) cultivar IR 64 under irrigated lowland and upland conditions

We characterized 333 introgression lines (INLs) harboring chromosome segments from new plant type (NTP) and Japonica-type cultivars with the genetic background of the elite Indica-type rice (Oryza sativa L.) cultivar IR 64, by evaluating yield components and dry matter production under irrigated lowland (IL) and upland (UP) culture in 2011 and 2012; and elucidated the relationships between the traits and chromosome segments introduced from the donors. The panicle weight (PW), PW/total plant weight (PW/TW), number of fertile spikelets (FS), and FS/total number of spikelets per panicle (FS/TS) of the INLs increased, while the culm weight (CW) and panicle number (PN) decreased. Most INLs produced more dry matter in the UP than in the IL culture. The INLs were clustered into three groups (A–C) according to their traits in the UP culture, and four groups (I–IV) according to their traits in the IL culture. They were then sorted into six groups (A-I, A-II, B-II, B-III, C-III, and C-IV) according to the relationships between culture conditions. The INLs of group A-II had increased panicle length (PL), PW, PW/TW, FS, and TS, and these traits were stable in both IL and UP culture. In the other groups, the trait values changed with the conditions and season. Association analyses using trait phenotype and genotype data of SSR markers detected 166 quantitative trait loci (QTLs) for 10 traits, distributed on all chromosomes except 3 and 10. Of these, 81 QTLs for DH, CL, PL, CW, PW, PW/TW, PN, FS, TS, and FS/TS were newly detected. The INLs were characterized under different conditions, and dramatic trait modifications in IR64 rice were associated with these QTLs, through introgression from the donor cultivars. Thus, these INLs and QTLs will be useful in genetic studies to identify the gene(s) that modified IR64, and as breeding materials for genetic improvement of Indica-type cultivars.