IC4R006-miRNA-2014-25052585

Project Title

Differentially expressed microRNA cohorts in seed development may contribute to poor grain filling of inferior spikelets in rice

The Background of This Project

Figure 1. GWA Analysis of Al Tolerance within and across Rice Subpopulations.

• The inferior spikelets are defined to be those at portions where the grains receive less photosynthetic products during the seed development. The typical inferior spikelets are physically located on the proximal secondary branches in a rice panicle and traditionally characterized by a later flowering time and a slower grain-filling rate, compared to those so-called superior spikelets. Grains produced on the inferior spikelets are consequently under-developed and lighter in weight than those formed on the superior spikelets. MicroRNAs (miRNAs) are recognized as key players in regulating plant development through post-transcriptional gene regulations. We previously presented the evidence that miRNAs may influence grain-filling rate and played a role in determining the grain weight and yield in rice.
• Rice (Oryza sativa L.) is one of the most important food crops in the world, providing calories for over 21% of global population and 76% of South East Asian. The yield of rice is determined primarily by two vital factors, the grain filling rate and subsequently the grain weight. It has been demonstrated by many researches that grain weight and the grain plumpness (a parameter describing the grain quality) are mostly positional-dependent in a rice panicle. A rice panicle is composed of numerous branches termed spikelets with some having high quality seeds termed superior spikelets and some with poor quality seeds termed inferior spikelets. In general, the superior spikelets flower earlier and subse- quently have a faster grain-filling rate in seed development, producing high-quality seeds. The flowers or seeds on superior spikelets are typically located on apical primary branches in a panicle. In contrast, the inferior spikelets flower later with a lower grain-filling rate and are located on the proximal secondary branches, resulting in low-quality seeds.
• MicroRNAs (miRNAs), a type of endogenous non-coding small RNAs produced from stem-loop structured precursors, have been proved to play curial roles in many aspects of plant development, such as organ morphogenesis, stress response, flowering control, phytohormone homeostasis, and grain/fruit development. The expressions of various miRNAs are extremely dynamic during rice grain development, revealed by a series of studies utilizing small RNA high-throughput sequencing technology. For example, in one study, most miRNAs were shown to be equally expressed or expressed much higher in grains of 6–10 days than those of 1–5 days after fertilization. A similar study showed that a high proportion of the detected miRNAs were up-regulated in seeds of 5 to 7 days after fertilization. The analysis of 445 known miRNAs and 45 novel miRNAs in our previous studies suggests the expressions of these miRNAs in rice grain were in a developmental stage dependent manner. The expressions of most known miRNAs increased gradually as rice grain filling went on [16]. These observations were also in contrast to another study showing that about half of the known miRNAs were up-regulated, while the remaining miRNAs were down-regulated during indica rice grain development.

Research Findings

• In this study, further analyses of the expressed small RNAs in superior and inferior spikelets were conducted at five distinct developmental stages of grain development. Totally, 457 known miRNAs and 13 novel miRNAs were analyzed, showing a differential expression of 141 known miRNAs between superior and inferior spikelets with higher expression levels of most miRNAs associated with the superior than the inferior spikelets during the early stage of grain filling. Genes targeted by those differentially expressed miRNAs (i.e. miR156, miR164, miR167, miR397, miR1861, and miR1867) were recognized to play roles in multiple developmental and signaling pathways related to plant hormone homeostasis and starch accumulation.

[[File:|700px|thumb|right|Figure 2. Haplotype analysis of the Nrat1 gene region.]]

• In general, the rice grain filling processes were dynamic in spikelets according to their locations on the rachis/panicle branches. Superior spikelets are on the top of the panicle, always flower earlier, have grains filling faster, and the higher final grain weight and plumpness than the inferior spikelets which are located on the base of the panicle [3,6,7]. Specifically, grain filling rates of superior spikelets (1.3-1.4 mg per grain per day) at the initial 5 to 10 DAF are 4 times faster than those of the inferior spikelets (0.2-0.3 mg per grain per day). Within 20 DAF, the majority of the grains in superior spikelets were filled up at the highest rate and then the filling rate dropped to a level that is comparable to the highest filling rate of the inferior grains (Figure 1A). In comparison, the grain filling rate in inferior spikelets (~0.6 mg per grain per day) was only less than 50% of the highest filling rate of the superior spikelets (~1.5 mg per grain per day) at this time point. The overall process of grain filling of superior spikelets took about 30 days with a much higher filling rate showing an asymmetrical curve, whereas that of the inferior spikelets took 45 days with a significantly lower filling rate showing a symmetrical normal curve (Figure 1A). Consequently, grains from superior spikelets were phenotypically larger and fully plump, while those from inferior spikelets appeared smaller with partial filling (Figure 1B and C).

Labs working on this Project

• Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University, Zhengzhou 450002, China
• Research Center for Rice Engineering in Henan Province, Henan Agricultural University, Zhengzhou 450002, China

Corresponding Author

• Quanzhi Zhao (qzzhaoh@126.com)