Use transcriptome analysis to uncover the genetic distinction between superior and inferior rice spikelets of different grain filling efficiency

Hybrid rice can achieve higher yield by producing more spikelets per panicle than conventional cultivars. However, the yield potential of these hybrids is often not fully materialized due to poor grain filling in their late-flowering spikelets. Through our extensive investigations both in the field and in the laboratory, we have identified several factors that could influence grain filling, such as soil drying and N supply, hormones and their interactions, root activities and root-sourced compounds etc. Based on these findings, we have developed and promoted in large scale an alternative wetting and drying (AWD) water management scheme that could increase yield by 8-10% and reduce water usage by 25-30%. However, the key question regarding the molecular and genetic distinction between the early and late flowering spikelets remains largely unanswered. Indeed, few mutants or genes affecting grain filling have been reported so far.

To address this problem from a genome perspective, we have generated preliminary RNA-Seq data for the early flowering (aka superior) spikelets that have higher grain filling rate and the late flowering (aka inferior) spikelets that have low grain filling rate. We have identified 10,110 differentially expressed genes and GO-term analysis has shown that besides the energy metabolism and transport genes, many genes involved in RNA processing are differentially expressed. In addition, we could identify unique alternative splicing events in superior and inferior spikelets, which raised an intriguing question as to whether alternative splicing could have important biological roles in regulating grain filling.

It has been reported that DNA methylation changes are associated with endosperm- specific gene expression in rice and some key carbohydrate metabolism genes such as starch synthase III are targeted by demethylation. We have generated BS-Seq data to analyze DNA methylation in the superior and inferior grains. Together with the transcriptome data, we propose to:
1. Compare gene expression and alternative splicing events in both sink (superior and inferior spikelets) and source (straws) tissues in hybrid and conventional inbred rice cultivars.
2. Compare methylation status of the grain-filling-related differentially expressed genes in sink and source tissues in hybrid and conventional rice cultivars.
3. Select candidate genes for functional tests in order to examine their potential roles in regulating rice grain filling.

This project could provide novel insights into the genetic mechanism regulating rice grain filling and identify crucial regulators for future crop improvement. Information gathered should also help explain why some agronomic practices such as controlled soil drying can enhance grain filling of inferior spikelets.