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In recent years, some super hybrid rice varieties were bred with strong culms and large panicles, which are mainly contributed by the  ipa1-2D  locus. A gain-of-function allele of  OsSPL14  is the  ipa1-2D  and it can greatly increase the panicle primary branch number. However, the key downstream genes mediating this trait variation are not fully explored. In this study, we developed high-quality near-isogenic lines (NILs) with a difference of only 30 kb chromosomal segment covering the  ipa1-2D  locus. Using the NILs, we explored the impact of  ipa1-2D  on five sequential stages of early inflorescence development, and found that the locus can greatly enhance the initiation of primary branch meristems. A transcriptomic analysis was performed to unveil the downstream molecular network of  ipa1-2D , and 87 genes were found differentially expressed, many of which are involved in metabolism and catalysis processes. In addition, transgenic lines of overexpression and RNA interference were generated to shape different levels of  OsSPL14 . They were also used to validate the expression variation explored by transcriptome. Based on the gene annotation, twelve potential downstream targets of  ipa1-2D  were selected, and their expression variation was confirmed by qRT-PCR analysis both in NILs and transgenic lines. This research expands the molecular network underlying  ipa1-2D  and provides novel gene information which might be involved in the control of panicle branching. We discussed the potential function of identified genes and highlighted their values for future function exploration and breeding application.

Exploration and Validation of the Potential Downstream Genes Underlying ipa1-2D Locus for Rice Panicle Branching