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Acta Agron Sin ›› 2017, Vol. 43 ›› Issue (03): 343-353.doi: 10.3724/SP.J.1006.2017.00343

• CROP GENETICS & BREEDING · GERMPLASM RESOURCES · MOLECULAR GENETICS • Previous Articles     Next Articles

Genetic Diversity of ALK Gene and Its Association with Grain Gelatinization Temperature in Currently Cultivated Rice Landraces from Hani’s Terraced Fields in Yunnan Province

LI Chuang1,2,**, LIU Cheng-Chen1,2,**, ZHANG Chang-Quan1, ZHU Ji-Hui1, XU Xiao-Ying2, ZHAO Fu-Wei 3, HUANG Shao-Wen4, JIN Yin-Gen2,*,LIU Qiao-Quan1,*   

  1. 1Jiangsu Key Laboratory of Crop Genetics and Physiology / Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China; 2 College of Biological Science and Technology, Yangzhou University, Yangzhou 225009, China; 3 Nanjing Institute of Environmental Sciences of Ministry of Environmental Protection, Nanjing 210042, China; 4 Yunnan Honghe University, Mengzi 661100, China
  • Received:2016-06-14 Revised:2016-09-18 Online:2017-03-12 Published:2016-09-29
  • Contact: 刘巧泉, E-mail: qqliu@yzu.edu.cn; 金银根, E-mail: ygenjin@hotmail.com
  • Supported by:

    This study was supported by the National Basic Research Program of China (2013CBA01402), the National Natural Science Foundation of China (31561143008, 31300324)and the Natural Sciences Research Project of Higher Learning Institution in Jiangsu Province (13KJB180028).

Abstract:

Yunnan province is one of the centers for genetic diversity of cultivated rice in Asia. A total of 111 rice landraces were collected from Hani’s rice terraces of Yunnan, and their population structure was analyzed by using 51 SSR molecular markers. The 111 rice landraces were divided into japonica group (group I) and indica group (group II); however, each of the two groups was not completely clustered according to its geographical origin. Most of the collected landraces, accounting for 83%, were indica. Gelatinization temperature (GT) is an important parameter affecting rice cooking and eating quality. The GT of rice flour was measured, which was widely different among the collected rice varieties, showing four classed very low (< 66°C), low (66-70°C), high (70-74°C) and very high ( >74°C). Meanwhile, ALK gene, also known as SSSIIa and controlling GT, was sequenced and compared, showing ten haploid types of the ALK gene among tested samples. Association analysis, revealed that GT is mainly controlled by the combination of three SNPs of ALK gene. Among them, the A-GC or G-TT combination type controls the very low and low GT, while the combination of G-GC controls high and very high GT. SNP3402 type T is associated with high and very high GT. It was also noticed that most of the varieties from indica group tended to contain the G-GC mutation and thus showed a relative high GT compared with those from the japonica group. The results have a meaningful value for rice molecular breeding and germplasm resources protection.

Key words: Oryza sativa L., ALK gene, Genetic diversity, Hani’s terrace, Gelatinization temperature

[1]刘承晨, 赵富伟, 吴晓霞, 张昌泉, 朱孔志, 薛达元, 武建勇, 黄绍文, 徐小颖, 金银根, 刘巧泉. 云南哈尼梯田当前栽培水稻遗传多样性及群体结构分析. 中国水稻科学, 2015, 29: 28–34
     Liu C C, Zhao F W, Wu X X, Zhang C Q, Zhu K Z, Xue D Y, Wu J Y, Huang S W, Xu X Y, Jin Y G, Liu Q Q. Genetic diversity and population structure analysis of currently cultivated rice landraces from Hani’s terraced fields in Yunnan Province. Chin J Rice Sci, 2015, 29: 28–34 (in Chinese with English abstract)
[2]Zeng Y W, Shen S Q, Li Z C, Yang Z Y, Wang X K, Zhang H L, Wen G S. Ecogeographic and genetic diversity based on morphological characters of indigenous rice (Oryza sativa L.) in Yunnan, China. Gen Res Crop Evol, 2003, 50: 567–577
[3]王象坤, 孙传清. 中国栽培稻的起源与演化研究专集. 北京: 中国农业大学出版社, 1996. pp 1–233
     Wang X K, Sun C Q. Research Question the Origins and Evolution of Cultivated Rice in China. Beijing: China Agricultural University Press, 1996. pp 1–233 (in Chinese)
[4]Manish K P, Rani N S, Madhav M S, Sundaram R M, Varaprasad G S, Sivaranjani A K P, Abhishek B, Kumar G R, Kumar A. Different isoforms of starch-synthesizing enzymes controlling amylose and amylopectin content in rice (Oryza sativa L.). Biotech Adv, 2012, 30: 1697–1706
[5]董超, 徐福荣, 杨文毅, 汤翠凤, 张恩来, 杨雅云, 阿新祥, 张斐斐, 卢光德, 王艳, 戴陆园. 云南元阳哈尼梯田水稻地方品种月亮谷的遗传变异分析. 中国水稻科学, 2013, 27: 137–144
Dong C, Xu F R, Yang W Y, Tang C F, Zhang E L, Yang Y Y, A X X, Zhang F F, Lu G D, Wang Y, Dai L Y. Genetic variation analysis of paddy rice landrace of Yuelianggu from Yuanyang Hani’s terraced fields in Yunnan Province. Chin J Rice Sci, 2013, 27: 137–144 (in Chinese with English abstract)
[6]董树斌, 卢宝荣, 王云月, 杨慧, 涂敏, 李林. 云南水稻传统品种内的遗传多样性及其维持机制初探. 云南农业大学学报, 2010, 25: 1–9
Dong S B, Lu B R, Wang Y Y, Yang H, Tu M, Li L. Preliminary studies on the within-varietal genetic diversity and its maintenance of traditional rice from Yunnan. J Yunnan Agric Univ, 2010, 25: 1–9 (in Chinese with English abstract)
[7]Gao Z Y, Zeng D L, Cui X ,Zhou Y H, Yan M X, Huang D N, Li J Y, Qian Q. Map-based cloning of the ALK gene, which controls the gelatinization temperature of rice. Sci China C (Life Sci), 2003, 46: 661–668
[8]Bao J S, Corke H, Sun M. Nucleotide diversity in starch synthase IIa and validation of single nucleotide polymorphisms in relation to starch gelatinization temperature and other physicochemical properties in rice (Oryza sativa L.). Theor Appl Genet, 2006, 113: 1113–1171
[9]Nakamura Y, Francisco P B, Hosaka Y, Sato A, Sawada T, Kubo A, Fujita N. Essential amino acid of starch synthase IIa differentiate amylopectin structure and starch quality between japonica and indica rice varieties. Plant Mol Biol Rep, 2005, 58: 213–227
[10]Jeon J S, Ryoo N, Hahn T R, Walia H, Nakamura Y. Starch biosynthesis in cereal endosperm. Plant Physiol Biochem, 2010, 48: 383–392
[11]Umemoto T, Yano M, Satoh H, Shomura A, Nakamura Y. Mapping of a gene responsible for the difference in amylopectin structure between japonica-type and indica-type rice varieties. Theor Appl Genet, 2002, 104: 1–8
[12]Li Z Y, Li D H, Du X H, Wang H, Larroque O, Jenkins C L D, Jobling S A, Morell M K. The barley amo1 locus is tightly linked to the starch synthase IIIa gene and negatively regulates expression of granule-bound starch synthetic genes. J Exp Bot, 2011, 62: 5217–5231
[13]孙川, 陈刚, 饶玉春, 张光恒, 高振宇, 刘坚, 鞠培娜, 胡江, 郭龙彪, 钱前, 曾大力. 水稻基因组DNA简易制备方法. 中国水稻科学, 2010, 24: 677–680
Sun C, Chen G, Rao Y C, Zhang G H,Gao Z Y, Liu J, Ju P N, Hu J, Guo L B, Qian Q, Zeng D L. A simple method for rapid preparation of rice genomic DNA. Chin J Rice Sci, 2010, 24: 677–680 (in Chinese with English abstract)
[14]Zhang C Q, Zhu L J, Shao K, Gu M H, Liu Q Q. Toward underlying reasons for rice starches having low viscosity and high amylose: physiochemical and structural characteristics. J Sci Food Agric, 2013, 93: 1543–1551
[15]Wei X, Wang R S, Cao L R, Yuan N N, Huang J, Qiao W G, Zhang W X, Zeng H L, Yang Q W. Origin of Oryza sativa in China inferred by nucleotide polymorphisms of organelle DNA. PLoS One, 2012, 7: e49546
[16]Yang F, Chen Y L, Tong C, Huang Y, Xu F F, Li K H, Corke H, Sun M, Bao J S. Association mapping of starch physicochemical properties with starch synthesis-related gene markers in nonwaxy rice (Oryza sativa L.). Mol Breed, 2014, 34: 1747–1763
[17]Gao Z Y, Zeng D L, Cheng F M, Tian Z X, Guo L B,Su Y, Yan M X, Jiang H, Dong G J, Huang Y C, Han B, Li J Y, Qian Q. ALK, the key gene for gelatinization temperature, is a modifier gene for gel consistency in rice. J Integr Plant Biol, 2011, 53: 756–765
[18]Zhou Y, Zheng H Y, Wei G C, Zhou H, Han Y N, Bai X F, Xing Y Z, Han Y P. Nucleotide diversity and molecular evolution of the ALK gene in cultivated rice and its wild relatives. Plant Mol Biol Rep, 2016, DOI: 10.1007/s11105-016-0975-1
[19]Kharabian-Masouleh A, Waters D L, Reinke R F, Ward R, Henry R J. SNP in starch biosynthesis genes associated with nutritional and functional properties of rice. Sci Rep, 2012, 2: 557
[20]Zhang Z J, Li M , Fang Y W, Liu F C, Lu Y, Meng Q C, Peng J C, Yi X H, Gu M H, Yan C J. Diversification of the Waxy gene is closely related to variations in rice eating and cooking quality. Plant Mol Biol Rep, 2012, 30: 462–469
[21]Hori Y, Fujimoto R, Sato Y, Nishio T. A novel wx mutation caused by insertion of a retrotransposon-like sequence in a glutinous cultivar of rice (Oryza sativa). Theor Appl Genet, 2007, 115: 217–224
[22]肖鹏, 邵雅芳, 包劲松. 稻米糊化温度的遗传与分子机理研究进展. 中国农业科技导报, 2010, 12: 23–30
Xiao P, Shao Y F, Bao J S. Research progress on genetics and molecular mechanism of starch gelatinization temperature of rice grain. J Agric Sci Tech, 2010, 12: 23–30 (in Chinese with English abstract)
[23]Hoai T T T, Matsusaka H, Toyosawa Y, Suu T D, Satoh H, Kumamaru T. Influence of single-nucleotide polymorphisms in the gene encoding granule-bound starch synthase I on amylose content in Vietnamese rice cultivars. Breed Sci, 2014, 64: 142–148

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