Genetic mapping of the locus, a QTL controlling secondary branch number per panicle in rice.

Secondary branch number (SBN) is an important component affecting spikelet number per panicle (SPP) and yield in rice. During recurrent backcross breeding, four BCF populations derived from the high-yield donor parent IR65598-112-2 and the recurrent parent Tainan 13 (a local cultivar) showed discontinuous variations of SPP and SBN within populations. Genetic analysis of 92 BCF individuals suggested that both SPP and SBN are controlled by a single recessive allele. Two parents and 37 BCF individuals showing high- and low-SBN type phenotypes were analyzed by restriction-site associated DNA sequencing (RAD-seq). Based on 2,522 reliable SNPs, the was mapped to a distal region of the long arm of chromosome 7. Trait-marker association analysis with an additional 166 high-SBN type BCF individuals and 8 newly developed cleaved amplified polymorphic sequence markers further delimited the locus to a 601.4-kb region between the markers SNP2788 and SNP2849. Phenotype evaluation of two BCF backcross inbred lines revealed that increased SPP by 83.2% and SBN by 61.0%. The of IR65598-112-2 could be used for improving reproductive sink capacity in rice.