IC4R002-RNA-Seq-2015-26355995
Contents
Project Title
Dynamic Analysis of Gene Expression in Rice Superior and Inferior Grains by RNA-Seq
The Background of This Projec
In rice seed development, the grain filling process is the most important factor related to the yield and quality of rice grains. Studies of the reasons of poor grain filling of inferior spikelets are beneficial to improve rice yield for cultivars that have numerous spikelets on the panicle. In this study, researchers performed RNA-seq analysis to explore the transcriptional variations among three rice cultivars, including IR64 [stress-sensitive (SS)], Nagina 22[(N22), drought-tolerant (DT)] and Pokkali [salinity-tolerant (ST)] under control and stress conditions. Genes involved in storage protein accumulation, sucrose and starch biosynthesis, plant hormone metabolism and cell cycle related genes were specifically examined and the potential mechanisms of poor filling of inferior grains were discussed.
Plant Culture & Treatment
- Oryza sativa spp. japonica cv. Xinfeng 2 was planted in field (34°5’ N, 113°35’ E, 94m altitude) which belongs to Henan Agricultural University for field experiments purpose.
- The flower day of spikelet was defined as 0 day after fertilization (DAF). Superior grains were sampled at 10, 15, 21, 27 DAF. After inferior spikelets flowered, which is normally 5~7 days later than superior grains [24], inferior grains were also sampled at 10, 15, 21, 27 days after inferior spikelet flowering.
- Both superior and inferior grains were separated from the panicle and frozen in liquid nitrogen for RNA extraction.
Research Findings
- In the eight sample libraries, 3,181,415 to 6,025,486 raw tags were generated by high throughput sequencing. After removing low quality tags, 3,015,196 to 5,897,726 clean tags were obtained in each library. Of these clean tags, 82.07% to 91.96% could be mapped to rice genes (Rice Genome Annotation Project, Release 7), and 48.36% to 60.56% tags could be unambiguously mapped to known gene locus. Expressions of 10,799 to 16,657 genes were detected in each library, and 19,442 genes were detected in at least one library in total.
- GO slim downloaded from Rice Genome Annotation Project (http://rice.plantbiology.msu.edu/) was used for the functional classification of these genes by cellular component, molecular function, and biological process categories. The inferior grains contained more genes in most GO terms of cellular component, molecular function, and biological process categories. Genes in superior and inferior grains were subjected to singular enrichment analysis by agriGO software [27] using genes in superior grains as input list and genes in inferior grains as background query list.
- In this study, only OsCIN2 (LOC_Os04g33740) and OsCIN7 (LOC_Os09g08072) were detected. Of the two cell wall invertase genes, OsCIN2 was the mainly expressed one, which was also designated as GIF1 gene [1]. In superior grains, the expression of OsCIN2 gene was higher at 10DAF, and dropped afterwards till no signal at 27DAF. While, in inferior grains, OsCIN2 gene was lower at 10DAF, but reached peak expression at 15DAF and dropped afterwards. The expression of OsCIN2 gene in inferior grains was all higher than superior grains at 15, 21, 27DAF.
- Till now, a number of genes controlling rice grain development had been cloned. Of those cloned genes, GIF1, GW5, GW8, GS3, GS5, FLO2, OsTGW6, CYP78A13, GL3.1were found to be involved in grain size development. In our RNA-Seq data, six of those genes were present in the samples.
Labs working on this Project
- Functional and Applied Genomics Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi - 110067, India
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi-110067, India. Correspondence and requests for materials should be addressed to M.J.
