Indica(
xian)-
japonica(
geng) hybrid rice has many heterosis traits that can improve rice yield. However, the traditional hybrid technology will struggle to meet future needs for the development of higher-yield rice. Available genomics resources can be used to efficiently understand the gene-trait association trait for rice breeding. Based on the previously constructed high-density genetic map of 272 high-generation recombinant inbred lines (RILs) originating from the cross of Luohui 9 (
indica, as female) and RPY geng (
japonica, as male) and high-quality genomes of parents, here, we further explore the genetic basis for an important complex trait: possible causes of grain number per panicle (GNPP). A total of 20 genes related to grains number per panicle (GNPP) with the differences of protein amino acid between LH9 and RPY were used to analyze genotype combinations, and PCA results showed a combination of
PLY1, LAX1, DTH8 and
OSH1 from the RPY geng with
PYL4, SP1, DST and
GNP1 from Luohui 9 increases GNPP. In addition, we also found that the combination of
LAX1-T2 and
GNP1-T3 had the most significant increase in GNPP. Notably, Molecular Breeding Knowledgebase (MBK) showed a few aggregated rice cultivars,
LAX1-T2 and
GNP1-T3, which may be a result of the natural geographic isolation between the two gene haplotypes. Therefore, we speculate that the pyramiding of
japonica-type
LAX-T2 with
indica-type
GNP1-T3 via hybridization can significantly improve rice yield by increasing GNPP.
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