Mapping of QTLs for vascular bundle system and spike morphology in rice, Oryza sativa L.

We carried out quantitative trait loci (QTL) analysis for three years to identify genes controlling the number of vascular bundles (Vb) in the peduncle and primary rachis branch (Rb) in rice (Oryza sativa L.). Sixty-five recombinant inbred lines derived from the cross between a japonica variety Asominori and an indica variety IR24 were used for QTL mapping and 289 markers were employed to identify QTLs. Nine QTLs for Vb were detected on chromosomes 1 (two regions), 4, 5(two regions), 6 (two regions), II and 12. One of the QTLs on chromosome 6 was detected in all 3 tested years. Three QTLs on chromosomes 1, 4 and 12 were identified in 2 years. Most effective QTLs were found on chromosomes 4 and 6, explaining 20-23% of the total variance. The alleles of IR24 increased Vb except for QTL on chromosome 4. One of the 9 QTLs for Vh was located close to the region established as QTLs for the number of spikelet and grain. For the number of Rb, three QTLs on chromosomes 2 and 8 (2 of 4 regions) were commonly detected in all 3 tested years and five others on chromosomes 4, 6 and 8 were found in at least one year. The QTL on chromosome 8 was the most effective and explained 18- 25% of the total variance. Except for QTL on chromosome 6, the alleles of Asominori increased Rb. The expression of QTLs was more stable in Rb than in Vb. The QTLs for Vb and Rb and gene loci of diagnostic traits for the differentiation between indica and japonica types are discussed.