Combining QTL mapping and transcriptome profiling for an insight into genes for grain number in rice (Oryza sativa L.)

The number of grains per panicle is an important yield contributing trait in rice, but so far only two genes, cytokinin oxidase 2 (CKX2) and aberrant panicle organization 1 (APO1) have been identified as regulator of grain number. Since grain number Is a polygenic or quantitative trait, attempt was made to find additional genes for this important trait. A combination of QTL mapping and transcriptome profiling was used to identify candidate genes in a major QTL for grain number (qGN4-1) on rice chromosome 4. The QTL was identified based on three year phenotyping data on a set of recombinant Inbred lines derived from a cross between Pusa 1266 (325 grains) and Pusa Basmati 1 (190 grains). The qGN4-1 Is co-located with major QTLs for number of primary and secondary branches per panicle and number of panicles per plant. The qGN4-1 interval between marker nksssr 04-02 and nksssr 04-19 has 148 predicted genes of which 117 have evidence of expression In the EST database. This list Is too large to pinpoint the candidate gene(s) for grain number. Hence, to complement OTL mapping, a genome-wide transcriptome profiling was done using Affymetrix gene chip array. Microarray-based transcriptome profiling revealed eighteen genes In the qGN4-1 region between the two parents, and three differentially expressed genes between the high and low grain number bulks of ten lines each. A gene belonging to glycosyl hydrolase family was highly down regulated in the RILs with high grain number. Its role in controlling grain number in rice needs further validation by genetic transformation studies.