Identification and Characterization of Differentially Expressed Genes in Inferior and Superior Spikelets of Rice Cultivars with Contrasting Panicle-Compactness and Grain-Filling Properties.

Sudhanshu Sekhar,Kaushik Das,Trupti Mohaptra,Binay Bhushan Panda,Sachin Ashruba Gharat,Pravat Kumar Mohapatra,Ekamber Kariali,Birendra Prasad Shaw

doi:10.1371/journal.pone.0145749

Sudhanshu Sekhar, Kaushik Das + Show 6 more

Open Access

https://doi.org/10.1371/journal.pone.0145749

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Journal: PloS one	Publication Date: Dec 28, 2015
Citations: 18	License type: CC BY 4.0

Affiliation: Institute of Life Sciences, Sambalpur University

Abstract

Breeding programs for increasing spikelet number in rice have resulted in compactness of the panicle, accompanied by poor grain filling in inferior spikelets. Although the inefficient utilization of assimilate has been indicated as responsible for this poor grain filling, the underlying cause remains elusive. The current study utilized the suppression subtractive hybridization technique to identify 57 and 79 genes that overexpressed in the superior and inferior spikelets (with respect to each other), respectively, of the compact-panicle rice cultivar Mahalaxmi. Functional categorization of these differentially expressed genes revealed a marked metabolic difference between the spikelets according to their spatial location on the panicle. The expression of genes encoding seed storage proteins was dominant in inferior spikelets, whereas genes encoding regulatory proteins, such as serine-threonine kinase, zinc finger protein and E3 ligase, were highly expressed in superior spikelets. The expression patterns of these genes in the inferior and superior spikelets of Mahalaxmi were similar to those observed in another compact-panicle cultivar, OR-1918, but differed from those obtained in two lax-panicle cultivars, Upahar and Lalat. The results first suggest that the regulatory proteins abundantly expressed in the superior spikelets of compact-panicle cultivars and in both the superior and inferior spikelets of lax-panicle cultivars but poorly expressed in the inferior spikelets of compact-panicle cultivars promote grain filling. Second, the high expression of seed-storage proteins observed in the inferior spikelets of compact-panicle cultivars appears to inhibit the grain filling process. Third, the low expression of enzymes of the Krebs cycle in inferior spikelets compared with superior spikelets of compact-panicle cultivars is bound to lead to poor ATP generation in the former and consequently limit starch biosynthesis, an ATP-consuming process, resulting in poor grain filling.

Highlights

Rice is a staple food for the majority of the worldwide population, accounting for nearly 23% of the human consumption of carbohydrates in the form of cereals [1]
All of the selected genes that showed high EST abundance in apical-forward SSH cDNA library (AFL) were expressed at higher levels in superior compared with inferior spikelets at all of the tested time points (Fig 1I); those showing high EST abundance in basal-reverse SSH cDNA library (BRL) showed higher expression levels in inferior compared with superior spikelets (Fig 1II)
Differences in the expression of genes encoding seed storage proteins, such as glutelin, prolamin and globulin, were found compared with other genes. Their expression began on 3 days after anthesis (DAA) in inferior spikelets and on 6 DAA in superior spikelets, after which similar expression levels were observed in both spikelets

Summary

Introduction

Rice is a staple food for the majority of the worldwide population, accounting for nearly 23% of the human consumption of carbohydrates in the form of cereals [1]. It has been observed that the synthesis of starch in the endosperm cells of spikelets on secondary branches is poor [13] and that the assimilates partitioned to these cells remain unused [8], suggesting that the sink rather than the source may be responsible for the observed effect in the transport and storage of assimilates [8,9] This possibility is reflected in the findings that the grainfilling rate of several rice cultivars, including NPT lines, is not associated with light-saturated photosynthesis [2] and that low activity and/or gene expression levels of starch-biosynthesisrelated enzymes is associated with poor grain filling in basal spikelets [6,9]. The basic mechanism regulating this process remains elusive because the removal of some of the primary branches from the axis improves the grain-filling percentage compared with that obtained in uncut panicles [14]

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