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.

The main objectives of IRRI’s variety development should meet the needs of customers/farmers from diverse rice sectors in each target region. The dynamic market change asks rapid variety development with highly valued QTLs/genes. Molecular breeding implemented through the efficient crossing, high throughput genotyping and rapid generation advancement will provide packages to breeders to develop new varieties quickly and more economically. The more efficient and cost-effective marker-assisted backcrossing service will provide the more opportunity for the success in molecular breeding platform. To make MABC system more successful, the development of molecular marker system for the high-throughput SNP genotyping is must. Currently Genotyping Service Lab (GSL) of IRRI provides high-throughput SNP genotyping service using BeadXpress and Fluidigm system. Meanwhile, the linked SNP markers for the specific traits are being developed. For abiotic stress tolerances, the markers for submergence, drought, heat, anaerobic germination, salinity, and phosphorus deficiency for Fluidigm system are being developed and tested in variety diversity panel and segregating populations. In MABC, due to the high number of crossings, the labor- and space-saving crossing system is being developed. As a result of an integrated MABC platform will speed up the development of pre-breeding line which are containing single or multiple QTLs/genes.