Transcriptome analysis of grain-filling caryopses reveals involvement of multiple regulatory pathways in chalky grain formation in rice.

Xiaolu Liu,Long Mao,Yingyue Shen,Jianmin Wan,Ning Su,Xiangyuan Wan,Huqu Zhai,Aili Li,Mingzhu Zhu,Bigang Mao,Haiyang Wang,Tao Guo

doi:10.1186/1471-2164-11-730

Xiaolu Liu, Long Mao + Show 10 more

Open Access

https://doi.org/10.1186/1471-2164-11-730

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Abstract

BackgroundGrain endosperm chalkiness of rice is a varietal characteristic that negatively affects not only the appearance and milling properties but also the cooking texture and palatability of cooked rice. However, grain chalkiness is a complex quantitative genetic trait and the molecular mechanisms underlying its formation are poorly understood.ResultsA near-isogenic line CSSL50-1 with high chalkiness was compared with its normal parental line Asominori for grain endosperm chalkiness. Physico-biochemical analyses of ripened grains showed that, compared with Asominori, CSSL50-1 contains higher levels of amylose and 8 DP (degree of polymerization) short-chain amylopectin, but lower medium length 12 DP amylopectin. Transcriptome analysis of 15 DAF (day after flowering) caryopses of the isogenic lines identified 623 differential expressed genes (P < 0.01), among which 324 genes are up-regulated and 299 down-regulated. These genes were classified into 18 major categories, with 65.3% of them belong to six major functional groups: signal transduction, cell rescue/defense, transcription, protein degradation, carbohydrate metabolism and redox homeostasis. Detailed pathway dissection demonstrated that genes involved in sucrose and starch synthesis are up-regulated, whereas those involved in non-starch polysaccharides are down regulated. Several genes involved in oxidoreductive homeostasis were found to have higher expression levels in CSSL50-1 as well, suggesting potential roles of ROS in grain chalkiness formation.ConclusionExtensive gene expression changes were detected during rice grain chalkiness formation. Over half of these differentially expressed genes are implicated in several important categories of genes, including signal transduction, transcription, carbohydrate metabolism and redox homeostasis, suggesting that chalkiness formation involves multiple metabolic and regulatory pathways.

Highlights

Grain endosperm chalkiness of rice is a varietal characteristic that negatively affects the appearance and milling properties and the cooking texture and palatability of cooked rice
Scanning electron microscopy showed that the chalky endosperm is comprised of round and loosely packed starch granules with large air spaces, in contrast to the translucent Asominori grains that are filled with densely packed granules (Figure 1B)
This observation is consistent with the Rapid Visco Analyzer (RVA) profile which provides a comprehensive evaluation of the grain quality (Figure 1D)

Summary

Introduction

Grain endosperm chalkiness of rice is a varietal characteristic that negatively affects the appearance and milling properties and the cooking texture and palatability of cooked rice. Endosperm chalkiness is a varietal characteristic that negatively affects the appearance and milling properties and the cooking texture and palatability of cooked rice [1]. Chalky grains have a lower density of starch granules compared to vitreous ones, and are more prone to breakage during milling [2]. The amylose-extender mutant has reduced activity of branching enzyme II (BEIIb), causing alteration in the fine structure of grain amylopectin [8]. The flo-2 floury endosperm mutant harbors mutations affecting rice branching enzyme I (RBEI) activity [9]. The floury endosperm-4 mutant and the sugary-1 mutant are defective in pyruvate orthophosphate dikinase (PPDK) and debranching enzymes (DBE) activity respectively [4,10]

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