Genetic mapping of the qSBN7 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 BC₂F₄ 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 BC₂F₄ individuals suggested that both SPP and SBN are controlled by a single recessive allele. Two parents and 37 BC₂F₄ 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 BC₂F₄ 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 BC₂F₅ 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.