New QTLs were identified for high grain yield with long panicle in rice. A total of 137 F15 recombinant inbred lines (RILs) derived from a cross between Dasanbyeo (Tongil) and TR22183 (japonica), together with the parents were evaluated for 16 agronomic traits at IRRI in dry and wet seasons under different phosphorus (P) and irrigation conditions. A linkage map was constructed using 236 polymorphic markers in 384-plex Bead Xpress indica-japonica single nucleotide polymorphism (SNP) platform. P and water effects were significant in both wet and dry seasons. Both parents and RILs showed varying degree of sensitivities to scarcities in water and phosphorus in terms of panicle length. Collocating with 20 yield-related QTLs, the panicle QTLs on chromosomes 1 (pl01) ,2 (pl02), 9 (pl09), and 11 (pl11) under low P and rainfed conditions were identified. RILs with TR22183 allele at pl11 showed longer panicle length under low P input rainfed condition in dry and wet seasons. The whole-genome sequences of the two varieties are being compared to design the molecular markers for fine-mapping and candidate gene identification. Based on Nipponbare MSU 7.0 annotation, a total of 1464 genes with predicted function were identified within the four QTL regions. Candidate genes identified in other studies for QTLs under low P and water conditions, such as calmodulin and dehydrin genes, were targeted for designing molecular markers for fine-mapping and expression analysis. Pyramiding the panicle length QTLs correlating with yield QTLs will provide an opportunity of improving yield traits.

This study aims to identify major quantitative trait loci (QTL) for yield components under low-input systems in tropical regions in rice. A total of 156 highly advanced recombinant inbred lines (RILs) have been developed from a cross between two temperate rice varieties, Dasanbyeo (Tongil-type indica) and TR22183 (japonica). Both parental lines and RILs were tested under two different regimes of irrigation and phosphorus (P) application levels. During the wet season of 2012, under mild drought conditions, TR22183 showed more vigorous root growth at 15 days after sowing than Dasanbyeo. The early root establishment of TR22183 may have contributed to the enhanced P uptake from the top soil in the early growth stage. The linkage map for DT-RILs was constructed with 312 single nucleotide polymorphism markers aided by 384-plex platform of BeadXpress high-throughput genotyping system. For the vegetative growth, major QTLs on chromsome 6 for plant height and tiller numbers were identified. For the grain yield related traits, major QTLs on chromsome 2 were closely linked to each other. On the other hand, panicle length QTLs were identified on chromsomes 2 and 9. We are currently analyzing phenotypic data and the experiment is being repeated in dry season and temperate region.