Fine Mapping and Candidate Gene Prediction of the Quantitative Trait Locus qPL8 for Panicle Length in Rice

Rice panicle is the sink organ where assimilation product accumulates,and its morphology determines the rice yield.Panicle length has been suggested as a yield-related trait,but the genetic factor for its control is still limited.In this study,we carried out fine-mapping of qPL8,a QTL identified for panicle length in our previous work.Near isogenic line(NIL)with qPL8 exhibited elongated panicle without obvious effect on other panicle elements.With five key recombinants from NIL population,the locus was finally narrowed down to a 278-kb region,where 44 genes are annotated.By comparing the genomic sequence of two parents,17 genes were identified with SNPs or InDels variations in the coding region.Expression analysis showed that eight genes were up-regulated in the NIL with qPL8.Considering both the coding variation and expression status,several candidate genes for the locus were identified,and OsMADS37 was raised as the most possible candidate.Interestingly,an expression QTL(eQTL)also resides in the locus,leading to a cluster of gene expression variation in the region.This study will facilitate the application of qPL8 locus in rice breeding for yield potential.

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

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.