QTL mapping of agronomic traits using an RIL population derived from a cross between temperate japonica cultivars in rice (Oryza sativa L.)

Abstract

To employ molecular marker-aided selection for developing japonica rice (Oryza sativa L.) cultivars with high yielding potential and good eating quality, we carried out QTL analysis for agronomic and grain traits using 231 recombinant inbred lines (RIL) from a cross between two temperate japonica cultivars, Suweon365 and Chucheongbyeo. A linkage map with 221 loci, including 134 simple sequence repeats (SSRs), 66 amplified fragment length polymorphisms (AFLPs), and 21 miniature inverted repeat transposable elements (MITEs)-anchored markers, was constructed covering 2,227 cM of the twelve rice chromosomes, with an average distance of 11.0 cM between markers. The proportion of polymorphic bands between parents averaged 19.5%, 12.9% and 42.3% for SSRs, AFLPs and MITEs, respectively. Construction of maps without AFLP or MITE markers indicated that expansion of this map is due to the incorporation of AFLP markers, and this result is consistent with previous reports. Twenty-seven QTLs for ten traits were identified over two years, and fourteen were consistently detected in two consecutive years. When the locations of each QTL detected in this study were compared with those in previous QTLs studies, eight QTLs for culm length, spikelets per panicle and, thickness, length and shape of grain, had not been reported in previous mapping studies, indicating potentially novel alleles of japonica rice. Interestingly, a cluster of seven QTLs, including heading date and grain morphology traits, was detected on the long arm of chromosome 7. The markers linked to these QTLs would be valuable in a marker-assisted breeding program for japonica cultivars.

Alleles Affecting 30 Traits for Productivity in Two Japonica Rice Varieties, Koshihikari and Nipponbare (Oryza sativaL.)

“…Similar results have been reported for a number of traits on various genetic materials (Mei et al, 2003;Kwon et al, 2008;Takeuchi et al, 2008). The main cause of these results was that heading date strongly affected other traits.…”

Validation and Characterization of Ghd7.1, a Major Quantitative Trait Locus with Pleiotropic Effects on Spikelets per Panicle, Plant Height, and Heading Date in Rice (Oryza sativa L.)

“…Previous studies of primary QTL mapping populations identified several QTLs for HD, PH, and SPP in the vicinity of Ghd7.1 (Yan et al ; Kwon et al ; Xing et al ). Analysis of NIL populations enabled fine mapping of Hd2 (Yano et al ; Shibaya et al ) and qDTH‐7‐2 (Fujino and Sekiguchi ) to a small region near Ghd7.1 .…”

Major QTLs for eating quality of an elite Japanese rice cultivar, Koshihikari, on the short arm of chromosome 3

“…In general, very small variations have been observed in these traits in populations developed from temperate japonica × japonica crosses. A few genetic analyses have demonstrated QTLs for such traits using japonica × japonica crosses (Kobayashi et al 2007, Kwon et al 2008. In these studies, two QTLs for grain weight, tw3 (Kobayashi et al 2007) and gy3 (Kwon et al 2008), were detected on the short arm of chr.…”