Identification and characterization of the chalkiness endosperm gene CHALK-H in rice (Oryza sativa L.)

doi:10.1016/j.jia.2023.04.020

Journal of Integrative Agriculture

2023, Vol. 22

Issue (10): 2921-2933 DOI: 10.1016/j.jia.2023.04.020

Crop Science

Advanced Online Publication | Current Issue | Archive | Adv Search

Identification and characterization of the chalkiness endosperm gene CHALK-H in rice (Oryza sativa L.)

PIAO Ri-hua¹, CHEN Mo-jun¹, MENG Fan-mei¹, QI Chun-yan¹, KOH Hee-jong³, GAO Meng-meng⁴, SONG An-qi⁴, JIN Yong-mei^2#, YAN Yong-feng^1#

¹Rice Research Institute, Jilin Academy of Agricultural Sciences, Gongzhuling 136100, P.R.China
² Research Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun 130033, P.R.China
³ Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Republic of Korea
⁴College of Agricultural Sciences, Yanbian University, Yanji 133000, P.R.China

Abstract
References

Download: PDF in ScienceDirect
Export: BibTeX | EndNote (RIS)

摘要

垩白是水稻育种中最重要的农艺性状之一，直接影响稻米的品质。本研究利用化学诱变剂MNU处理韩国粳稻品种Hwacheong（HC），获得一个稳定遗传的垩白突变体chalk-h。与野生型HC相比，chalk-h突变体籽粒表现出垩白特性，叶片呈黄绿色，株高降低。扫描电镜(SEM)分析表明，chalk-h突变体淀粉粒大小不规则、排列松散、颗粒间间隙大、呈椭圆形或圆形。MutMap分析显示，chalk-h突变体的垩白表型由编码seryl-tRNA合成酶的单隐性基因LOC_Os11g39670控制，该基因被重新命名为CHALK-H。在chalk-h突变体中CHALK-H基因的第6外显子(第791核苷酸)发生点突变，其腺嘌呤(A)被胸腺嘧啶(T)取代，导致氨基酸密码子由谷氨酰胺(Glu)变为缬氨酸(Val)。chalk-h突变体从三叶期开始表现为黄绿色叶片、色素含量降低等热敏表型。与野生型HC相比，chalk-h突变体在不同灌浆期淀粉合成相关基因的转录表达下调，随着温度的升高，chalk-h突变体中光合相关基因的表达下调。将CHALK-H基因过量表达于chalk-h突变体，其垩白胚乳和黄绿叶片颜色恢复为野生型。研究结果表明，CHALK-H控制稻米垩白和叶片颜色。CHALK-H是已报道参与高温下叶绿体发育相关基因TSCD11的等位基因。我们认为，CHALK-H/TSCD11在水稻生长发育过程中不仅参与叶绿体发育，而且参与光合作用和淀粉合成，在水稻优质高产育种中具有广阔的应用前景。

Abstract

Chalkiness is one of the most important agronomic traits in rice breeding, which directly affects the quality of rice seed. In this study, we identified a chalkiness endosperm mutant, chalk-h, from N-methyl-N-nitrosourea (MNU)-induced japonica rice cultivar Hwacheong (HC). Compared with wild type (WT)-HC, chalk-h showed severe chalkiness in the endosperm, yellowish green leaves, as well as reduced plant height. Scanning electron microscopy (SEM) analysis showed that starch grains in the chalk-h mutant were irregular in size and loosely arranged, with large gaps between granules, forming ovoid or orbicular shapes. MutMap analysis revealed that the phenotype of chalk-h is controlled by a single recessive gene LOC_Os11g39670 encoding seryl-tRNA synthetase, which is renamed as CHALK-H. A point mutation occurs in chalk-h on the sixth exon (at nucleotide 791) of CHALK-H, in which adenine (A) is replaced by thymidine (T), resulting in an amino acid codon change from glutamine (Glu) to valine (Val). The chalk-h mutant exhibited a heat-sensitive phenotype from the 3-leaf stage, including yellow-green leaves and reduced pigment content. The transcriptional expression of starch synthesis-related genes was down-regulated in the chalk-h mutants compared to WT-HC at different grain-filling stages. With an increase in temperature, the expression of photosynthesis-related genes was down-regulated in the chalk-h mutant compared to WT-HC. Overexpression of CHALK-H rescued the phenotype of chalk-h, with endosperm and leaf color similar to those of WT-HC. Our findings reveal that CHALK-H is a causative gene controlling chalkiness and leaf color of the chalk-h mutant. CHALK-H is the same gene locus as TSCD11, which was reported to be involved in chloroplast development under high temperature. We suggest that CHALK-H/TSCD11 plays important roles not only in chloroplast development, but also in photosynthesis and starch synthesis during rice growth and development, so it has great application potential in rice breeding for high quality and yield.

Keywords: CHALK-H Seryl-tRNA synthetase chalkiness rice

Received: 22 December 2022 Accepted: 17 March 2023

Fund: This research was supported by the Administration of Central Funds Guiding the Local Science and Technology Development, China (202002069JC) and the earmarked fund for the China Agriculture Research System (CARS-01-10).

About author: #Correspondence YAN Yong-feng, E-mail: yanyongfeng@126.com; JIN Yong-mei, E-mail: ymjin0303@163.com

	Service
	E-mail this article
	Add to citation manager
	E-mail Alert
	RSS
	Articles by authors
	PIAO Ri-hua
	CHEN Mo-jun
	MENG Fan-mei
	QI Chun-yan
	KOH Hee-Jong
	GAO Meng-meng
	SONG An-qi
	JIN Yong-mei
	YAN Yong-feng

Cite this article:

PIAO Ri-hua, CHEN Mo-jun, MENG Fan-mei, QI Chun-yan, KOH Hee-Jong, GAO Meng-meng, SONG An-qi, JIN Yong-mei, YAN Yong-feng. 2023. Identification and characterization of the chalkiness endosperm gene CHALK-H in rice (Oryza sativa L.). Journal of Integrative Agriculture, 22(10): 2921-2933.

Abe A, Kosugi S, Yoshida K, Natsume S, Takagi H, Kanzaki H, Matsumura H, Yoshida K, Mitsuoka C, Tamiru M, Innan H, Cano L, Kamoun S, Terauchi R. 2012. Genome sequencing reveals agronomically important loci in rice using MutMap. Nature Biotechnology, 30, 174–178.

Bian J M, Shi H, Li C J, Zhu C L, Yu Q Y, Peng X S, Fu J R, He X P, Chen X R, Hu L F, Ouyang L J, He H H. 2013. QTL mapping and correlation analysis for 1 000-grain weight and percentage of grains with chalkiness in rice. Journal of Genetics, 92, 281–287.

Cai Y, Li S, Jiao G, Sheng Z, Wu Y, Shao G, Xie L, Peng C, Xu J, Tang S, Wei X, Hu P. 2018. OsPK2 encodes a plastidic pyruvate kinase involved in rice endosperm starch synthesis, compound granule formation and grain filling. Plant Biotechnology Journal, 16, 1878–1891.

Cakir B, Shiraishi S, Tuncel A, Matsusaka H, Satoh R, Singh S, Crofts N, Hosaka Y, Fujita N, Hwang S K, Satoh H, Okita T W. 2016. Analysis of the rice ADP-glucose transporter (OsBT1) indicates the presence of regulatory processes in the amyloplast stroma that control ADP-glucose flux into starch. Plant Physiology, 170, 1271–1283.

Chen C, He B, Liu X, Ma X, Liu Y, Yao H Y, Zhang P, Yin J, Wei X, Koh H J, Yang C, Xue H W, Fang Z, Qiao Y. 2020. Pyrophosphate-fructose 6-phosphate 1-phosphotransferase (PFP1) regulates starch biosynthesis and seed development via heterotetramer formation in rice (Oryza sativa L.). Plant Biotechnology Journal, 18, 83–95.

Chen C, Wang Y L, He M, Li Z, Shen L, Li Q, Re D, Hu J, Zhu L, Zhang G, Gao Z, Zeng D, Guo L, Qian Q, Zhang Q. 2023. OsPPR9 encodes a DYW-type PPR protein that affects editing efficiency of multiple RNA editing sites and is essential for chloroplast development. Journal of Integrative Agriculture, 22, 972–980.

Fang G, Yang S, Ruan B, Liu C, Zhang A, Jiang H, Ding S, Tian B, Zhang Y, Jahan N, Zhu L, Zhang G, Dong G, Zhang Q, Zeng D, Guo L, Gao Z, Qian Q. 2020. Isolation of TSCD11 gene for early chloroplast development under high temperature in rice. Rice, 13, 49.

Fang P F, Li S F, Jiao G A, Xie L H, Hu P S, Wei X J, Tang S Q. 2014. Physicochemical property analysis and gene mapping of a floury endosperm mutant flo7 in rice. Chinese Journal of Rice Science, 106, 11. (in Chinese)

Guo T, Liu X, Wan X, Weng J, Liu S, Liu X, Chen M, Li J, Su N, Wu F, Cheng Z, Guo X, Lei C, Wang J, Jiang L, Wan J. 2011. Identification of a stable quantitative trait locus for percentage grains with white chalkiness in rice (Oryza sativa). Journal of Integrative Plant Biology, 53, 598–607.

Hirose T, Terao T. 2004. A comprehensive expression analysis of the starch synthase gene family in rice (Oryza sativa L.). Planta, 220, 9–16.

Kang H G, Park S, Matsuoka M, An G. 2005. White-core endosperm floury endosperm-4 in rice is generated by knockout mutations in the C-type pyruvate orthophosphate dikinase gene (OsPPDKB). Plant Journal, 42, 901–911.

Kawagoe Y, Kubo A, Satoh H, Takaiwa F, Nakamura Y. 2005. Roles of isoamylase and ADP-glucose pyrophosphorylase in starch granule synthesis in rice endosperm. Plant Journal, 42, 164–174.

Kim Y K, Lee, J Y, Cho H S, Lee S S, Ha H J, Kim S, Choi D, Pai H S. 2005. Inactivation of organellar glutamyl- and seryl-tRNA synthetases leads to developmental arrest of chloroplasts and mitochondria in higher plants. Journal of Biological Chemistry, 280, 37098–37106.

Kubo A, Fujita N, Harada K, Matsuda T, Satoh H, Nakamura Y. 1999. The starch-debranching enzymes isoamylase and pullulanase are both involved in amylopectin biosynthesis in rice endosperm. Plant Physioloy, 121, 399–410.

Li Y, Fan C, Xing Y, Yun P, Luo L, Yan B, Peng B, Xie W, Wang G, Li X, Xiao J, Xu C, He Y. 2014. Chalk5 encodes a vacuolar H+-translocating pyrophosphatase influencing grain chalkiness in rice. Natrure Genetics, 46, 398–404.

Liu X, Fu Y, Zhu Y, Li Y, Wang Y. 2007. Physiological and genecis mechanism of rhce chalkiness formation. Plant Physiology Communications, 43, 569–575.

Liu X, Wan X, Ma X, Wan J. 2011. Dissecting the genetic basis for the effect of rice chalkiness, amylose content, protein content, and rapid viscosity analyzer profile characteristics on the eating quality of cooked rice using the chromosome segment substitution line population across eight environments. Genome, 54, 64–80.

Nakamura Y. 2002. Towards a better understanding of the metabolic system for amylopectin biosynthesis in plants: rice endosperm as a model tissue. Plant Cell and Physiology, 43, 718–725.

Nishimura A, Aichi I, Matsuoka M. 2006. A protocol for Agrobacterium-mediated transformation in rice. Nature Protocol, 1, 2796–2802.

NY/T 11-1985. 1985. Determination of Crude Starch in Cereals Seeds. National Standard of the People’s Republic of China. (in Chinese)

NY/T 55-1987. 1987. Determination of Amylose in Grains of Rice, Maize and Millet. National Standard of the People’s Republic of China. (in Chinese)

Ohdan T, Francisco P B J, Sawada T, Hirose T, Terao T, Satoh H, Nakamura Y. 2005. Expression profiling of genes involved in starch synthesis in sink and source organs of rice. Journal of Exprimental Botany, 56, 3229–3244.

Pak D, Kim Y, Burton Z F. 2018. Aminoacyl-tRNA synthetase evolution and sectoring of the genetic code. Transcription, 9, 205–224.

Peng B, Wang L, Fan C, Jiang G, Luo L, Li Y, He Y. 2014. Comparative mapping of chalkiness components in rice using five populations across two environments. BMC Genetics, 15, 49.

Peng C, Wang Y, Liu F, Ren Y, Zhou K, Lv J, Zheng M, Zhao S, Zhang L, Wang C, Jiang L, Zhang X, Guo X, Bao Y, Wan J. 2014. FLOURY ENDOSPERM6 encodes a CBM48 domain-containing protein involved in compound granule formation and starch synthesis in rice endosperm. Plant Journal, 77, 917–930.

Piao R, Jiang W, Ham T H, Choi M S, Qiao Y, Chu S H, Park J H, Woo M O, Jin Z, An G, Lee J, Koh H J. 2009. Map-based cloning of the ERECT PANICLE 3 gene in rice. Theoretical and Applied Genetics, 119, 1497–1506.

Qiao Y, Lee SI, Piao R, Jiang W, Ham T H, Chin J H, Piao Z, Han L, Kang S Y, Koh H J. 2010. Fine mapping and candidate gene analysis of the floury endosperm gene, FLO(a), in rice. Molecules and Cells, 29, 167–174.

Ryoo, N, Yu C, Park C S, Baik M Y, Park I M, Cho M H, Bhoo S H, An G, Hahn T R, Jeon J S. 2007. Knockout of a starch synthase gene OsSSIIIa/Flo5 causes white-core floury endosperm in rice (Oryza sativa L.). Plant Cell Reports, 26, 1083–1095.

Wang Y, Ren Y, Liu X, Jiang L, Chen L, Han X, Jin M, Liu S, Liu F, Lv J, Zhou K, Su N, Bao Y, Wan J. 2010. OsRab5a regulates endomembrane organization and storage protein trafficking in rice endosperm cells. Plant Journal, 64, 812–824.

Woo M O, Ham T H, Ji H S, Choi M S, Jiang W, Chu S H, Piao R, Chin J H, Kim J A, Park B S, Seo H S, Jwa N S, McCouch S, Koh H J. 2008. Inactivation of the UGPase1 gene causes genic male sterility and endosperm chalkiness in rice (Oryza sativa L.). Plant Journal, 54, 190–204.

Wu B, Yun P, Zhou H, Xia D, Gu Y, Li P, Yao J, Zhou Z, Chen J, Liu R, Cheng S, Zhang H, Zheng Y, Lou G, Chen P, Wan S, Zhou M, Li Y, Gao G, Zhang Q, et al. 2022. Natural variation in WHITE-CORE RATE 1 regulates redox homeostasis in rice endosperm to affect grain quality. Plant Cell, 34, 1912–1932.

Wu Y P, Pu C H, Lin H Y, Huang H Y, Huang Y C, Hong C Y, Chang M C, Lin Y R. 2015. Three novel alleles of FLOURY ENDOSPERM2 (FLO2) confer dull grains with low amylose content in rice. Plant Science, 233, 44–52.

Zhang L, Ren Y, Lu B, Yang C, Feng Z, Liu Z, Chen J, Ma W, Wang Y, Yu X, Wang Y, Zhang W, Wang Y, Liu S, Wu F, Zhang X, Guo X, Bao Y, Jiang L, Wan J. 2016. FLOURY ENDOSPERM7 encodes a regulator of starch synthesis and amyloplast development essential for peripheral endosperm development in rice. Journal of Exprimental of Botany, 67, 633–647.

Zheng L, L W, Zhang W, Liu S, Chen L, Liu X, Chen X, Ma J, Chen W, Zhao Z, Jiang L, Wan J. 2012. Genetic relationship between grain chalkiness, protein content, and paste viscosity properties in a backcross inbred population of rice. Journal of Cereal Science, 56, 153–160.

Zhou L J, Jiang L, Zhai H Q, Wan J M. 2009. Current status and strategies for improvement of rice grain chalkiness. Heredita, 31, 563–572.

[1]	Gaozhao Wu, Xingyu Chen, Yuguang Zang, Ying Ye, Xiaoqing Qian, Weiyang Zhang, Hao Zhang, Lijun Liu, Zujian Zhang, Zhiqin Wang, Junfei Gu, Jianchang Yang. An optimized strategy of nitrogen-split application based on the leaf positional differences in chlorophyll meter readings[J]. >Journal of Integrative Agriculture, 2024, 23(8): 2605-2617.
[2]	Shuang Cheng, Zhipeng Xing, Chao Tian, Mengzhu Liu, Yuan Feng, Hongcheng Zhang. Optimized tillage methods increase mechanically transplanted rice yield and reduce the greenhouse gas emissions [J]. >Journal of Integrative Agriculture, 2024, 23(4): 1150-1163.
[3]	Jingnan Zou, Ziqin Pang, Zhou Li, Chunlin Guo, Hongmei Lin, Zheng Li, Hongfei Chen, Jinwen Huang, Ting Chen, Hailong Xu, Bin Qin, Puleng Letuma, Weiwei Lin, Wenxiong Lin. The underlying mechanism of variety–water–nitrogen–stubble damage interactions on yield formation in ratoon rice with low stubble height under mechanized harvesting [J]. >Journal of Integrative Agriculture, 2024, 23(3): 806-823.
[4]	Min Jiang, Zhang Chen, Yuan Li , Xiaomin Huang, Lifen Huang, Zhongyang Huo. Rice canopy temperature is affected by nitrogen fertilizer [J]. >Journal of Integrative Agriculture, 2024, 23(3): 824-835.
[5]	Fubing Liao, Xiangqian Feng, Ziqiu Li, Danying Wang, Chunmei Xu, Guang Chu, Hengyu Ma, Qing Yao, Song Chen. A hybrid CNN-LSTM model for diagnosing rice nutrient levels at the rice panicle initiation stage [J]. >Journal of Integrative Agriculture, 2024, 23(2): 711-723.
[6]	Tingting Zhou, Qian Zhao, Chengzhou Li, Lu Ye, Yanfang Li, Nemat O. Keyhani, Zhen Huang. Synergistic effects of the entomopathogenic fungus Isaria javanica and low doses of dinotefuran on the efficient control of the rice pest Sogatella furcifera[J]. >Journal of Integrative Agriculture, 2024, 23(2): 621-638.
[7]	GAO Peng, ZHANG Tuo, LEI Xing-yu, CUI Xin-wei, LU Yao-xiong, FAN Peng-fei, LONG Shi-ping, HUANG Jing, GAO Ju-sheng, ZHANG Zhen-hua, ZHANG Hui-min. Improvement of soil fertility and rice yield after long-term application of cow manure combined with inorganic fertilizers[J]. >Journal of Integrative Agriculture, 2023, 22(7): 2221-2232.
[8]	TIAN Chang, SUN Ming-xue, ZHOU Xuan, LI Juan, XIE Gui-xian, YANG Xiang-dong, PENG Jian-wei. Increase in yield and nitrogen use efficiency of double rice with long-term application of controlled-release urea[J]. >Journal of Integrative Agriculture, 2022, 21(7): 2106-2118.
[9]	GAO Zhi-ping, XU Min-li, ZHANG Hai-zi, LÜ Chuan-gen, CHEN Guo-xiang. Photosynthetic properties of the mid-vein and leaf lamina of field-grown, high-yield hybrid rice during senescence[J]. >Journal of Integrative Agriculture, 2022, 21(7): 1913-1926.
[10]	ZHOU Tian-yang, LI Zhi-kang, LI En-peng, WANG Wei-lu, YUAN Li-min, ZHANG Hao, LIU Li-jun, WANG Zhi-qin, GU Jun-fei, YANG Jian-chang. Optimization of nitrogen fertilization improves rice quality by affecting the structure and physicochemical properties of starch at high yield levels[J]. >Journal of Integrative Agriculture, 2022, 21(6): 1576-1592.
[11]	Christian Adler PHARES, Selorm AKABA. Co-application of compost or inorganic NPK fertilizer with biochar influenced soil quality, grain yield and net income of rice[J]. >Journal of Integrative Agriculture, 2022, 21(12): 3600-3610.
[12]	Muhammad Amjad BASHIR, ZHAI Li-mei, WANG Hong-yuan, LIU Jian, Qurat-Ul-Ain RAZA, GENG Yu-cong, Abdur REHIM, LIU Hong-bin. Apparent variations in nitrogen runoff and its uptake in paddy rice under straw incorporation[J]. >Journal of Integrative Agriculture, 2022, 21(11): 3356-3367.
[13]	HUANG Li-ying, Li Xiao-xiao, ZHANG Yun-bo, Shah FAHAD, WANG Fei. dep1 improves rice grain yield and nitrogen use efficiency simultaneously by enhancing nitrogen and dry matter translocation[J]. >Journal of Integrative Agriculture, 2022, 21(11): 3185-3198.
[14]	CHEN Zhong-du, LI Feng-bo, XU Chun-chun, JI Long, FENG Jin-fei, FANG Fu-ping. Spatial and temporal changes of paddy rice ecosystem services in China during the period 1980–2014[J]. >Journal of Integrative Agriculture, 2022, 21(10): 3082-3093.
[15]	CHEN Yun-feng, XIA Xian-ge, HU Cheng, LIU Dong-hai, QIAO Yan, LI Shuang-lai, FAN Xian-peng. Effects of long-term straw incorporation on nematode community composition and metabolic footprint in a rice–wheat cropping system[J]. >Journal of Integrative Agriculture, 2021, 20(8): 2265-2276.

No Suggested Reading articles found!

Viewed

Full text

Abstract

Cited

Shared

Discussed

Cite this article:

About JIA

Editorial board

For authors