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

Xiaolu Liu1, Tao Guo2, Xiangyuan Wan1, Haiyang Wang1, Mingzhu Zhu1, Aili Li1, Ning Su1, Yingyue Shen2, Bigang Mao1, Huqu Zhai3, Long Mao1 and Jianmin Wan12*

Author affiliations

1 Institute of Crop Sciences, Chinese Academy of Agriculture Sciences, Beijing, 100081, China

2 State Key Laboratory of Crop Genetics and Germplasm Enhancement/Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China

3 Chinese Academy of Agriculture Sciences, Beijing, 100081, China

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Citation and License

BMC Genomics 2010, 11:730  doi:10.1186/1471-2164-11-730

Published: 30 December 2010



Grain 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.


A 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.


Extensive 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.