栽培稻芽期耐低温全基因组关联分析

doi:10.3864/j.issn.0578-1752.2022.21.001

中国农业科学 ›› 2022, Vol. 55 ›› Issue (21): 4091-4103.doi: 10.3864/j.issn.0578-1752.2022.21.001

• 作物遗传育种·种质资源·分子遗传学 • 上一篇下一篇

栽培稻芽期耐低温全基因组关联分析

逄洪波¹(),程露¹,于茗兰¹,陈强²,李玥莹¹,吴隆坤³,王泽¹,潘孝武⁴,郑晓明^5,⁶()

¹沈阳师范大学生命科学学院，沈阳 110034
²沈阳师范大学实验教学中心，沈阳 110034
³沈阳师范大学粮食学院，沈阳 110034
⁴湖南省农业科学院水稻研究所，长沙 410125
⁵中国农业科学院作物科学研究所，北京 100081
⁶海南三亚中国农业科学院国家南繁研究院，海南三亚 571700

收稿日期:2022-07-15 接受日期:2022-08-17 出版日期:2022-11-01 发布日期:2022-11-09
通讯作者: 逄洪波,郑晓明
基金资助:
国家自然科学基金(31970237);辽宁省自然科学基金面上项目(2022-MS-309);沈阳市中青年科技创新人才计划(RC190223);沈阳师范大学“百人计划”拔尖人才项目(SSDBRJH2002012);沈阳师范大学重大项目孵化工程(ZD202104)

Genome-Wide Association Study of Cold Tolerance at the Germination Stage of Rice

PANG HongBo¹(),CHENG Lu¹,YU MingLan¹,CHEN Qiang²,LI YueYing¹,WU LongKun³,WANG Ze¹,PAN XiaoWu⁴,ZHENG XiaoMing^5,⁶()

¹College of Life Science, Shenyang Normal University, Shenyang 110034
²Experiment Teaching Center, Shenyang Normal University, Shenyang 110034
³College of Grain Science and Technology, Shenyang Normal University, Shenyang 110034
⁴Rice Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125
⁵Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081
⁶Sanya National Research Institute of Breeding in Hainan, Chinese Academy of Agricultural Sciences, Sanya 571700, Hainan

Received:2022-07-15 Accepted:2022-08-17 Online:2022-11-01 Published:2022-11-09
Contact: HongBo PANG,XiaoMing ZHENG

摘要/Abstract

摘要：

【目的】水稻是重要的粮食作物，芽期是水稻生长发育过程中最脆弱的时期，直播稻遭遇冷害时发芽率大幅降低，减产严重。深入了解耐冷性的遗传机制，为培育芽期强耐受性水稻品种奠定基础。【方法】以世界范围内14个国家代表性的238份水稻种质资源为试验材料，于2021和2022年在沈阳开展表型鉴定试验，统计不同水稻品种在人工气候培养箱15℃低温条件下第1—10天的发芽率和相对发芽率，利用R语言绘制5—10 d的频率直方图，通过表型丰富度Hill值选择宜作关联分析的天数，将发芽率和相对发芽率表型数据与重测序数据相结合，进行基于混合线性模型MLM（QK）的全基因组关联分析，并对所获得的SNP位点进行耐冷候选基因的预测。【结果】发芽率频数分布直方图和表型丰富度计算结果显示第8天发芽率多态性最好，其Hill值为0.84，高于其他几天发芽率（0.48—0.83），可用于全基因组关联分析;主成分分析结果显示，这些水稻品种可以分为indica、aus、temperate japonica、tropical japonica和aromatic 5个亚群;2个指标进行的GWAS分析检测到3个相同的显著性SNP位点，均位于第4染色体，解释表型的11.9%—25.4%;在上下游各50 kb进行基因搜索，共发现24个相关候选基因，进一步开展LD和单倍型分析，发现LOC_Os04g24840和LOC_Os04g25140的不同单倍型耐冷性之间存在极显著差异。LOC_Os04g24840被编码区SNP分为5个单倍型，且Hap_3的耐冷性显著强于Hap_1;LOC_Os04g25140被编码区SNP分为18个单倍型，且77 bp处的氨基酸变异（S>L）存在籼粳差异。结果表明，编码糖基转移酶的基因LOC_Os04g24840和编码F-box蛋白基因LOC_Os04g25140可能与水稻芽期耐冷性密切相关。【结论】在238份水稻种质资源中共检测到3个与芽期耐冷性显著关联的SNP位点，筛选出2个与水稻芽期耐冷性相关的候选基因。

关键词: 水稻, 芽期, 耐冷性, 发芽率, 全基因组关联分析

Abstract:

【Objective】Rice is an important food crop, and its growth and development are most vulnerable at the germination stage. Under cold stress, direct-seeded rice exhibited significantly reduced germination rates (GRs) and yield compared with normally grown plants. Thus, a better understanding of genetic mechanisms regulating cold tolerance will enable to develop rice varieties with improved tolerance during germination. 【Method】238 representative rice germplasm resources from 14 countries worldwide were tested in phenotypic identification in Shenyang in 2021 and 2022; the low-temperature germination rate and relative low-temperature germination rate (LTGR and relative LTGR; 1-10 days under 15℃) were evaluated in an artificial climate incubator, and a 5-10 day LTGR histogram was constructed using R. The day suitable for GWAS was determined by phenotypic variation (Hill) and a mixed linear model combining LTGR and relative LTGR phenotype data with resequencing data. 【Result】LTGR histogram and phenotypic variation showed optimal GR on day 8 (Hill=0.84), i.e., it was higher than on other days (Hill=0.48-0.83), which could be used for GWAS. The principal component analysis results divided all germplasms into five groups—indica, aus, temperate japonica, tropical japonica, and aromatic. GWAS analysis of two indicators detected three identical significant single nucleotide polymorphisms (SNPs) related to cold tolerance in rice at the germination stage. These were located on chromosome 4, which could explain 11.9%-25.4% of the phenotype. In addition, 24 candidate genes were screened in the 50-kb region upstream and downstream of these three SNPs. Further linkage disequilibrium analysis and haplotype analysis were carried out and highly significant differences were found between different haplotypes of the LOC_Os04g24840 and LOC_Os04g25140 genes for cold tolerance. LOC_Os04g24840 was divided into five haplotypes by the coding region SNP, and Hap_3 was significantly more cold tolerant than Hap_1; LOC_Os04g25140 was divided into 18 haplotypes by the coding region SNP and the amino acid variation (S>L) at 77 bp was different in japonica and indica rice. These results showed that the genes encoding glycosyltransferases (LOC_Os04g24840) and F-box protein (LOC_Os04g25140) might be closely related to cold tolerance in rice.【Conclusion】 A total of three SNP loci were detected in 238 rice germplasm resources, and two candidate genes were screened for their association with cold tolerance during germination in rice.

Key words: Oryza sativa L., seed germinability, cold tolerance, germination rate, GWAS

逄洪波, 程露, 于茗兰, 陈强, 李玥莹, 吴隆坤, 王泽, 潘孝武, 郑晓明. 栽培稻芽期耐低温全基因组关联分析[J]. 中国农业科学, 2022, 55(21): 4091-4103.

PANG HongBo, CHENG Lu, YU MingLan, CHEN Qiang, LI YueYing, WU LongKun, WANG Ze, PAN XiaoWu, ZHENG XiaoMing. Genome-Wide Association Study of Cold Tolerance at the Germination Stage of Rice[J]. Scientia Agricultura Sinica, 2022, 55(21): 4091-4103.

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链接本文: https://www.chinaagrisci.com/CN/10.3864/j.issn.0578-1752.2022.21.001

https://www.chinaagrisci.com/CN/Y2022/V55/I21/4091

图/表 7

图1

图2

图3

图4

表1

24个候选基因其基因注释"

染色体 Chr.	基因号 Gene ID	基因注释 Annotation
Chr.4	LOC_Os04g24830	含锌指、CCHC型结构域的蛋白质 Zinc finger, CCHC-type domain containing protein
Chr.4	LOC_Os04g24840	糖基转移酶，推测，表达Glycosyltransferase, putative, expressed
Chr.4	LOC_Os04g24850	细胞分裂素-O-葡糖基转移酶2，假定的，表达Cytokinin-O-glucosyltransferase 2, putative, expressed
Chr.4	LOC_Os04g24860	逆转录酶子蛋白，推定，未分类，表达Retrotransposon protein, putative, unclassified, expressed
Chr.4	LOC_Os04g24870	逆转录酶子蛋白，推定，未分类Retrotransposon protein, putative, unclassified
Chr.4	LOC_Os04g24880	逆转录酶子蛋白，推定，未分类，表达Retrotransposon protein, putative, unclassified, expressed
Chr.4	LOC_Os04g24900	表达蛋白Expressed protein
Chr.4	LOC_Os04g24910	表达蛋白Expressed protein
Chr.4	LOC_Os04g24920	转座子蛋白，推定，CACTA，En/Spm亚类，表达 Transposon protein, putative, CACTA, En/Spm sub-class, expressed
Chr.4	LOC_Os04g24930	表达蛋白Expressed protein
Chr.4	LOC_Os04g24940	表达蛋白Expressed protein
Chr.4	LOC_Os04g24950	假定的蛋白质Hypothetical protein
Chr.4	LOC_Os04g24960	转座子蛋白，推定，CACTA，En/Spm亚类，表达 Transposon protein, putative, CACTA, En/Spm sub-class, expressed
Chr.4	LOC_Os04g25100	转座子蛋白，推定，未分类，表达Transposon protein, putative, unclassified, expressed
Chr.4	LOC_Os04g25110	Ulp1蛋白酶家族，含有C端催化域的蛋白，表达式ulp1; Ulp1 protease family, C-terminal catalytic domain containing protein, expressedulp1
Chr.4	LOC_Os04g25120	表达蛋白Expressed protein
Chr.4	LOC_Os04g25130	逆转录子蛋白，推定，LINE亚类，表达Retrotransposon protein, putative, LINE subclass, expressed
Chr.4	LOC_Os04g25140	OsFBDUF20-含有F-box和DUF结构域的蛋白，已表达; OsFBDUF20- F-box and DUF domain containing protein, expressed
Chr.4	LOC_Os04g25150	花粉过敏原，推定，表达Pollen allergen, putative, expressed
Chr.4	LOC_Os04g25160	花粉过敏原，推定，表达Pollen allergen, putative, expressed
Chr.4	LOC_Os04g25170	逆转录酶原蛋白，推定，未分类，表达Retrotransposon protein, putative, unclassified, expressed
Chr.4	LOC_Os04g25180	假定的蛋白质Hypothetical protein
Chr.4	LOC_Os04g25190	花粉过敏原，推定，表达Pollen allergen, putative, expressed
Chr.4	LOC_Os04g25210	转座子蛋白，推定，未分类，表达Transposon protein, putative, unclassified, expressed

表1

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图6

参考文献 63

[1]	ZHENG S, LIU S, FENG J, WANG W, WANG Y, YU Q, LIAO Y, MO Y, XU Z, LI L, GAO X, JIA X, ZHU J, CHEN R. Overexpression of a stress response membrane protein gene OsSMP1 enhances rice tolerance to salt, cold and heavy metal stress. Environmental and Experimental Botany, 2021, 182: 104327.
[2]	WANG H, LEE A R, PARK S Y, JIN S H, LEE J, HAM T H, PARK Y, ZHAO W G, KWON S W. Genome-wide association study reveals candidate genes related to low temperature tolerance in rice (Oryza sativa) during germination. 3 Biotech, 2018, 8(5): 1-13.
[3]	CHENG S H, CAO L Y, ZHUANG J Y, CHEN S G, ZHAN X D, FAN Y Y, ZHU D F, MIN S K. Super hybrid rice breeding in China: Achievements and prospects. Journal of Integrative Plant Biology, 2007, 49(6): 805-810.
[4]	VILAS J M, CORIGLIANO M G, CLEMENTE M, MAIALE S J, RODRIGUEZ A A. Close relationship between the state of the oxygen evolving complex and rice cold stress tolerance. Plant Science, 2020, 296: 110488.
[5]	SIPASEUTH, BASNAYAKE J, FUKAI S, FARRELL T C, SENTHONGHAE M, SENGKEO, PHAMIXAY S, LINQUIST B, CHANPHENGSAY M. Opportunities to increasing dry season rice productivity in low temperature affected areas. Field Crops Research, 2007, 102(2): 87-97.
[6]	ZHANG M, YE J, XU Q, FENG Y, YUAN X, YU H, WANG Y, WEI X, YANG Y. Genome-wide association study of cold tolerance of Chinese indica rice varieties at the bud burst stage. Plant Cell Reports, 2018, 37(3): 529-539.
[7]	SUH J P, JEUNG J U, LEE J I, CHOI Y H, YEA J D, VIRK P S, MACKILL D J, JENA K K. Identification and analysis of QTLs controlling cold tolerance at the reproductive stage and validation of effective QTLs in cold-tolerant genotypes of rice (Oryza sativa L.). Theoretical and Applied Genetics, 2010, 120(5): 985-995.
[8]	FUJINO K, MATSUDA Y. Genome-wide analysis of genes targeted by qLTG3-1 controlling low-temperature germinability in rice. Plant Molecular Biology, 2010, 72(1): 137-152.
[9]	FUJINO K, SEKIGUCHI H, MATSUDA Y, SUGIMOTO K, ONO K, YANO M. Molecular identification of a major quantitative trait locus, qLTG3-1, controlling low-temperature germinability in rice. Proceedings of the National Academy of Sciences of the United States of America, 2008, 105(34): 12623-12628.
[10]	SAITO K, HAYANO-SAITO Y, MARUYAMA-FUNATSUKI W, SATO Y, KATO A. Physical mapping and putative candidate gene identification of a quantitative trait locus Ctb1 for cold tolerance at the booting stage of rice. Theoretical and Applied Genetics, 2004, 109(3): 515-522.
[11]	FUJINO K, SEKIGUCHI H, SATO T, KIUCHI H, NONOUE Y, TAKEUCHI Y, ANDO T, LIN S Y, YANO M. Mapping of quantitative trait loci controlling low-temperature germinability in rice (Oryza sativa L.). Theoretical and Applied Genetics, 2004, 108(5): 794-799.
[12]	ANDAYA V C, TAI T H. Fine mapping of the qCTS12 locus, a major QTL for seedling cold tolerance in rice. Theoretical and Applied Genetics, 2006, 113(3): 467-475.
[13]	LOU Q, CHEN L, SUN Z, XING Y, LI J, XU X, MEI H, LUO L. A major QTL associated with cold tolerance at seedling stage in rice (Oryza sativa L.). Euphytica, 2007, 158(1): 87-94.
[14]	KUMAR V, LADHA J K. Direct seeding of rice. recent developments and future research needs. Advances in Agronomy, 2011, 111: 297-413.
[15]	IWATA N, SHINADA H, KIUCHI H, SATO T, FUJINO K. Mapping of QTLs controlling seedling establishment using a direct seeding method in rice. Breeding Science, 2010, 60(4): 353-360.
[16]	ZHANG Z H, QU X S, WAN S, CHEN L H, ZHU Y G. Comparison of QTL controlling seedling vigour under different temperature conditions using recombinant inbred lines in rice (Oryza sativa). Annals of Botany, 2005, 95(3): 423-429.
[17]	CHEN L, LOU Q J, SUN Z X, XING Y Z, XIN-QIAO Y U, LUO L J. QTL mapping of low temperature on germination rate of rice. Rice Science, 2006, 13(2): 93-98.
[18]	JI S L, JIANG L, WANG Y H, ZHANG W W, LIU X, LIU S J, CHEN L M, ZHAI H Q, WAN J M. Quantitative trait loci mapping and stability for low temperature germination ability of rice. Plant Breeding, 2009, 128(4): 387-392.
[19]	WAN J M, JIANG L, TANG J Y, WANG C M, HOU M Y, JING W, ZHANG L X. Genetic dissection of the seed dormancy trait in cultivated rice (Oryza sativa L.). Plant Science, 2006, 170(4): 786-792.
[20]	SUGIMOTO K, TAKEUCHI Y, EBANA K, MIYAO A, HIROCHIKA H, HARA N, ISHIYAMA K, KOBAYASHI M, BAN Y, HATTORI T, YANO M. Molecular cloning of Sdr4, a regulator involved in seed dormancy and domestication of rice. Proceedings of the National Academy of Sciences of the United States of America, 2010, 107(13): 5792-5797.
[21]	SHARIFI P. Evaluation on sixty-eight rice germplasms in cold tolerance at germination stage. Rice Science, 2010, 17(1): 77-81.
[22]	LI L, LIU X, XIE K, WANG Y, LIU F, LIN Q, WANG W, YANG C, LU B, LIU S, CHEN L, JIANG L, WAN J. qLTG-9, a stable quantitative trait locus for low-temperature germination in rice (Oryza sativa L.). Theoretical and Applied Genetics, 2013, 126(9): 2313-2322.
[23]	ALBINANA C, GROVE J, MCGRATH J J, AGERBO E, WRAY N R, BULIK C M, NORDENTOFT M, HOUGAARD D M, WERGE T, BORGLUM A D, MORTENSEN P B, PRIVE F, VILHJALMSSON B J. Leveraging both individual-level genetic data and GWAS summary statistics increases polygenic prediction. American Journal of Human Genetics, 2021, 108(6): 1001-1011.
[24]	HUANG X, WEI X, SANG T, ZHAO Q, FENG Q, ZHAO Y, LI C, ZHU C, LU T, ZHANG Z, LI M, FAN D, GUO Y, WANG A, WANG L, DENG L, LI W, LU Y, WENG Q, LIU K, HUANG T, ZHOU T, JING Y, LI W, LIN Z, BUCKLER E S, QIAN Q, ZHANG Q F, LI J, HAN B. Genome-wide association studies of 14 agronomic traits in rice landraces. Nature Genetics, 2010, 42(11): 961-967.
[25]	HUANG X, ZHAO Y, WEI X, LI C, WANG A, ZHAO Q, LI W, GUO Y, DENG L, ZHU C, FAN D, LU Y, WENG Q, LIU K, ZHOU T, JING Y, SI L, DONG G, HUANG T, LU T, FENG Q, QIAN Q, LI J, HAN B. Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm. Nature Genetics, 2011, 44(1): 32-39.
[26]	ZHAO K, TUNG C W, EIZENGA G C, WRIGHT M H, ALI M L, PRICE A H, NORTON G J, ISLAM M R, REYNOLDS A, MEZEY J, MCCLUNG A M, BUSTAMANTE C D, MCCOUCH S R. Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa. Nature Communications, 2011, 2(1): 1-10.
[27]	HSIAO C F, CHIU Y F, CHIANG F T, HO L T, LEE W J, HUNG Y J, CHEN Y D, DONLON T A, JORGENSON E, CURB D, RISCH N, HSIUNG C A, GROUP S A S. Genome-wide linkage analysis of lipids in nondiabetic Chinese and Japanese from the SAPPHIRe family study. American Journal of Hypertension, 2006, 19(12): 1270-1277.
[28]	NICOLAE D L, GAMAZON E, ZHANG W, DUAN S, DOLAN M E, COX N J. Trait-associated SNPs are more likely to be eQTLs: Annotation to enhance discovery from GWAS. PLoS Genetics, 2010, 6(4): e1000888.
[29]	YANG J, FERREIRA T, MORRIS A P, MEDLAND S E, GENETIC INVESTIGATION OF A T C, REPLICATION D I G, META ANALYSIS C, MADDEN P A, HEATH A C, MARTIN N G, MONTGOMERY G W, WEEDON M N, LOOS R J, FRAYLING T M, MCCARTHY M I, HIRSCHHORN J N, GODDARD M E, VISSCHER P M. Conditional and joint multiple-SNP analysis of GWAS summary statistics identifies additional variants influencing complex traits. Nature Genetics, 2012, 44(4): 369-375.
[30]	LI Y H, LI D, JIAO Y Q, SCHNABLE J C, LI Y F, LI H H, CHEN H Z, HONG H L, ZHANG T, LIU B, LIU Z X, YOU Q B, TIAN Y, GUO Y, GUAN R X, ZHANG L J, CHANG R Z, ZHANG Z, REIF J, ZHOU X A, SCHNABLE P S, QIU L J. Identification of loci controlling adaptation in Chinese soya bean landraces via a combination of conventional and bioclimatic GWAS. Plant Biotechnology Journal, 2020, 18(2): 389-401.
[31]	HWANG E Y, SONG Q, JIA G, SPECHT J E, HYTEN D L, COSTA J, CREGAN P B. A genome-wide association study of seed protein and oil content in soybean. BMC Genomics, 2014, 15(1): 1-12.
[32]	WU S, ALSEEKH S, CUADROS-INOSTROZA A, FUSARI C M, MUTWIL M, KOOKE R, KEURENTJES J B, FERNIE A R, WILLMITZER L, BROTMAN Y. Combined use of genome-wide association data and correlation networks unravels key regulators of primary metabolism in Arabidopsis thaliana. PLoS Genetics, 2016, 12(10): e1006363.
[33]	WENG J, XIE C, HAO Z, WANG J, LIU C, LI M, ZHANG D, BAI L, ZHANG S, LI X. Genome-wide association study identifies candidate genes that affect plant height in Chinese elite maize (Zea mays L.) inbred lines. PLoS ONE, 2011, 6(12): e29229.
[34]	WU J, FENG F, LIAN X, TENG X, WEI H, YU H, XIE W, YAN M, FAN P, LI Y, MA X, LIU H, YU S, WANG G, ZHOU F, LUO L, MEI H. Genome-wide association study (GWAS) of mesocotyl elongation based on re-sequencing approach in rice. BMC Plant Biology, 2015, 15: 218.
[35]	LI Z, WANG X, CUI Y, QIAO K, ZHU L, FAN S, MA Q. Comprehensive genome-wide analysis of thaumatin-like gene family in four cotton species and functional identification of GhTLP19 involved in regulating tolerance to Verticillium dahlia and drought. Frontiers in Plant Science, 2020, 11: 575015.
[36]	FUJINO K, OBARA M, SHIMIZU T, KOYANAGI K O, IKEGAYA T. Genome-wide association mapping focusing on a rice population derived from rice breeding programs in a region. Breeding Science, 2015, 65(5): 403-410.
[37]	PAN Y, ZHANG H, ZHANG D, LI J, XIONG H, YU J, LI J, RASHID M A, LI G, MA X, CAO G, HAN L, LI Z. Genetic analysis of cold tolerance at the germination and booting stages in rice by association mapping. PLoS ONE, 2015, 10(3): e0120590.
[38]	HAN L Z, ZHANG Y Y, QIAO Y L, CAO G L, ZHANG S Y, KIM J H, KOH H J. Genetic and QTL analysis for low-temperature vigor of germination in rice. Acta Genetica Sinica, 2006, 33(11): 998-1006.
[39]	ZHOU X, STEPHENS M. Genome-wide efficient mixed-model analysis for association studies. Nature Genetics, 2012, 44(7): 821-824.
[40]	PEET R K. The measurement of species diversity. Annual Review of Ecology and Systematics, 1974, 5(1): 285-307.
[41]	YANG J, YANG M, SU L, ZHOU D, HUANG C, WANG H, GUO T, CHEN Z. Genome-wide association study reveals novel genetic loci contributing to cold tolerance at the germination stage in indica rice. Plant Science, 2020, 301: 110669.
[42]	LIN J, ZHU W Y, ZHANG Y D, ZHU Z, ZHAO L, CHEN T, ZHAO Q Y, ZHOU L H, FANG X W, WANG Y P, WANG C L. Detection of QTL for cold tolerance at bud bursting stage using chromosome segment substitution lines in rice (Oryza sativa). Rice Science, 2011, 18(1): 71-74.
[43]	XIAO H, CHEN J F, ZHANG Z X. Influence of deposition temperature on the structure of Si3N4 thin film prepared by MWECR-PECVD. Plasma Science & Technology, 2004, 6(5): 2485-2488.
[44]	纪素兰, 江玲, 王益华, 刘世家, 刘喜, 翟虎渠, 吉村醇, 万建民. 水稻种子耐低温发芽力的QTL定位及上位性分析. 作物学报, 2008, 34(4): 551-556.
	JI S L, JIANG L, WANG Y H, LIU S J, LIU X, ZHAI H Q, YOSHIMURA A, WAN J M. QTL and epistasis for low temperature germinability in rice. Acta Agronomica Sinica, 2008, 34(4): 551-556. (in Chinese)
[45]	MIURA K, LIN S Y, YANO M, NAGAMINE T. Mapping quantitative trait loci controlling low temperature germinability in rice (Oryza sativa L.). Breeding Science, 2001, 51(4): 293-299.
[46]	HYUN D Y, OH M, CHOI Y M, LEE S, LEE M C, OH S. Morphological and molecular evaluation for germinability in rice varieties under low-temperature and anaerobic conditions. Journal of Crop Science and Biotechnology, 2017, 20(1): 21-27.
[47]	ANGAJI S A, SEPTININGSIH E M, MACKILL D J, ISMAIL A M. QTLs associated with tolerance of flooding during germination in rice (Oryza sativa L.). Euphytica, 2009, 172(2): 159-168.
[48]	CRUZ R P, MILACH S C K. Cold tolerance at the germination stage of rice: Methods of evaluation and characterization of genotypes. Scientia Agricola, 2004, 61(1): 1-8.
[49]	YE C, FUKAI S, GODWIN I, REINKE R, SNELL P, SCHILLER J, BASNAYAKE J. Cold tolerance in rice varieties at different growth stages. Crop and Pasture Science, 2009, 60(4): 328-338.
[50]	WANG X, WANG H, LIU S, FERJANI A, LI J, YAN J, YANG X, QIN F. Genetic variation in ZmVPP1 contributes to drought tolerance in maize seedlings. Nature Genetics, 2016, 48(10): 1233-1241.
[51]	WAN H, CHEN L, GUO J, LI Q, WEN J, YI B, MA C, TU J, FU T, SHEN J. Genome-wide association study reveals the genetic architecture underlying salt tolerance-related traits in rapeseed (Brassica napus L.). Frontiers in Plant Science, 2017, 8: 593.
[52]	JIA L, YAN W, ZHU C, AGRAMA H A, JACKSON A, YEATER K, LI X, HUANG B, HU B, MCCLUNG A, WU D. Allelic analysis of sheath blight resistance with association mapping in rice. PLoS ONE, 2012, 7(3): e32703.
[53]	KANG H, WANG Y, PENG S, ZHANG Y, XIAO Y, WANG D, QU S, LI Z, YAN S, WANG Z, LIU W, NING Y, KORNILIEV P, LEUNG H, MEZEY J, MCCOUCH S R, WANG G L. Dissection of the genetic architecture of rice resistance to the blast fungus Magnaporthe oryzae. Molecular Plant Pathology, 2016, 17(6): 959-972.
[54]	YANG W, GUO Z, HUANG C, DUAN L, CHEN G, JIANG N, FANG W, FENG H, XIE W, LIAN X, WANG G, LUO Q, ZHANG Q, LIU Q, XIONG L. Combining high-throughput phenotyping and genome- wide association studies to reveal natural genetic variation in rice. Nature Communications, 2014, 5(1): 1-9.
[55]	WANG D, LIU J, LI C, KANG H, WANG Y, TAN X, LIU M, DENG Y, WANG Z, LIU Y, ZHANG D, XIAO Y, WANG G L. Genome-wide association mapping of cold tolerance genes at the seedling stage in rice. Rice, 2016, 9(1): 61.
[56]	JIANG L, LIU S, HOU M, TANG J, CHEN L, ZHAI H, WAN J. Analysis of QTLs for seed low temperature germinability and anoxia germinability in rice (Oryza sativa L.). Field Crops Research, 2006, 98(1): 68-75.
[57]	LI J, ZENG Y, PAN Y, ZHOU L, ZHANG Z, GUO H, LOU Q, SHUI G, HUANG H, TIAN H, GUO Y, YUAN P, YANG H, PAN G, WANG R, ZHANG H, YANG S, GUO Y, GE S, LI J, LI Z. Stepwise selection of natural variations at CTB2 and CTB4a improves cold adaptation during domestication of japonica rice. New Phytologist, 2021, 231(3): 1056-1072.
[58]	LI P, LI Y J, ZHANG F J, ZHANG G Z, JIANG X Y, YU H M, HOU B K. Arabidopsis UDP‐glycosyltransferases UGT79B2 and UGT79B3, contribute to cold, salt and drought stress tolerance via modulating anthocyanin accumulation. The Plant Journal, 2017, 89(1): 85-103.
[59]	SHI Y, HUY P, LIU Y, CAO S, ZHANG Z, CHU C, SCHLPPI M R. Glycosyltransferase OsUGT90A1 helps protect the plasma membrane during chilling stress in rice. Journal of Experimental Botany, 2020, 71(9): 2723-2739.
[60]	SAITO K, HAYANO-SAITO Y, KUROKI M, SATO Y. Map-based cloning of the rice cold tolerance gene Ctb1. Plant Science, 2010, 179(1/2): 97-102.
[61]	CALLIS D J. Ubiquitin,hormones and biotic stress in plants. Annals of Botany, 2007, 99(5): 787-822.
[62]	YAN Y S, CHEN X Y, YANG K., SUN Z X, FU Y P, ZHANG Y M, FANG R X. Overexpression of an F-box protein gene reduces abiotic stress tolerance and promotes root growth in rice. Molecular Plant, 2011, 4(1): 190-197.
[63]	KOCH K. Sucrose metabolism: Regulatory mechanisms and pivotal roles in sugar sensing and plant development. Current Opinion in Plant Biology, 2004, 7(3): 235-246.

栽培稻芽期耐低温全基因组关联分析

Genome-Wide Association Study of Cold Tolerance at the Germination Stage of Rice

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