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

Lin Zhang1,2,*, Dong Xie1, Zhong Bian1, Yiting Zou1, Han Zhou1, Wenlu Cai1, Hadi Yeilaghi1, Xiaolei Fan1,2, Changquan Zhang1,2, Qiaoquan Liu1,2,*

1 Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, 225009, China
2 Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, 225009, China

* Corresponding Authors: Lin Zhang. Email: email; Qiaoquan Liu. Email: email

(This article belongs to this Special Issue: High-Yield Rice Physiology & Genetics)

Phyton-International Journal of Experimental Botany 2021, 90(3), 773-787.


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.


Cite This Article

Zhang, L., Xie, D., Bian, Z., Zou, Y., Zhou, H. et al. (2021). Exploration and Validation of the Potential Downstream Genes Underlying ipa1-2D Locus for Rice Panicle Branching. Phyton-International Journal of Experimental Botany, 90(3), 773–787.

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