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Secondary branch number (SBN) is an important component affecting spikelet number per panicle (SPP) and yield in rice. During recurrent backcross breeding, four BC 2 F 4 populations derived from the high-yield donor parent IR65598-112-2 and the recurrent parent Tainan 13 (a local japonica cultivar) showed discontinuous variations of SPP and SBN within populations. Genetic analysis of 92 BC 2 F 4 individuals suggested that both SPP and SBN are controlled by a single recessive allele. Two parents and 37 BC 2 F 4 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 qSBN7 was mapped to a distal region of the long arm of chromosome 7. Trait-marker association analysis with an additional 166 high-SBN type BC 2 F 4 individuals and 8 newly developed cleaved amplified polymorphic sequence markers further delimited the qSBN7 locus to a 601.4-kb region between the markers SNP2788 and SNP2849. Phenotype evaluation of two BC 2 F 5 backcross inbred lines revealed that qSBN7 increased SPP by 83.2% and SBN by 61.0%. The qSBN7 of IR65598-112-2 could be used for improving reproductive sink capacity in rice.

Genetic mapping of the <i>qSBN7</i> locus, a QTL controlling secondary branch number per panicle in rice