Identification of QTLs for Salt Tolerance at the Germination and Early Seedling Stage Using Linkage and Association Analysis in japonica  Rice

doi:10.3969/j.issn.1001-7216.2014.04. 004

Abstract

Abstract: QTL for salt tolerance at the germination and early seedling stage in rice were detected via linkage and association analyses. A BC2F2:3 population was constructed including 190 BC2F3 lines, derived from a cross between Dongnong 425 (highyielding rice variety with good grain quality, as the recurrent parent) and Changbai 10 (salt tolerant rice variety, as the donor parent). QTLs were detected for salt tolerance at the germination and early seedling stage including relative germination rate (RGR), relative seedling height (RSH), relative root number (RRN), relative root length (RRL) were detected by using ICIM with a genetic linkage map constructed with 137 SSR markers. A total of 11 QTLs were identified. A panel of 341 japonica rice accessions from different geographical origins were used for both wholegenome association and targeted regional association mapping. The accessions were genotyped with 160 selected SSR markers, and then association analysis between SSR markers and traits were performed using TASSEL 21 GLM and MLM programs. A total of 22 significant markertrait associations were identified within 18 markers, and 5 QTLs reported by linkage mapping were validated, and 9 novel alleles at these loci were mined from the set of japonica rice. By comparing the chromosomal positions of the 5 QTLs with those previously identified, four of them located in the same or near genome regions, qRRL7 was reported for the first time.

Key words: japonica rice, germination stage, early seedling stage, salt tolerance, QTL, linkage mapping, association mapping

摘要： 通过连锁分析和关联分析两种方法寻找与水稻芽期和幼苗前期耐盐性QTL，并进一步挖掘优异等位变异及载体材料。连锁分析以高产优质水稻品种东农425为轮回亲本，耐盐性水稻品种长白10号为供体亲本构建BC2F2:3群体，利用137个SSR标记构建遗传连锁图谱，采用ICIM法对相对发芽率(RGR)、相对苗高(RSH)、相对根数(RRN)和相对根长(RRL)等4个与水稻芽期和幼苗前期耐盐性相关的性状进行QTL定位分析，共检测到11个QTL。关联分析以341份粳稻种质组成的自然群体为研究材料，利用160个SSR标记进行群体基因型检测，采用Tassel 2.1的GLM和MLM模型进行标记与性状的关联分析，共检测到22个关联位点，并验证了连锁分析中的5个QTL，进一步鉴定得到9个优异等位基因。通过比较图谱发现，经验证的5个QTL中有4个与前人定位在同一或相邻的染色体区域，而qRRL7在前人研究中未见报道。

关键词: 粳稻, 芽期, 幼苗前期, 耐盐, QTL, 连锁分析, 关联分析

CLC Number:

ZHENG Hongliang, LIU Bowen, ZHAO Hongwei, WANG Jingguo, LIU Hualong, SUN Jian, XING Jun, ZOU Detang*. Identification of QTLs for Salt Tolerance at the Germination and Early Seedling Stage Using Linkage and Association Analysis in japonica Rice[J]. Chinese Journal of Rice Science, 2014, 28(4): 358-366.

郑洪亮,刘博文,赵宏伟,王敬国,刘化龙,孙健,邢军,邹德堂*. 利用连锁和关联分析定位粳稻芽期及幼苗前期耐盐性QTL[J]. 中国水稻科学, 2014, 28(4): 358-366.

References

\[1\]薛亚光, 杨建昌. 水稻超高产生理特性与栽培技术. 作物杂志, 2009, 06: 812.

\[2\]孙勇, 藏金萍, 王韵, 等. 利用回交导入系群体发掘水稻种质资源中的有利耐盐QTL. 作物学报, 2007, 10: 16111617.

\[3\]Lin H X, Zhu M Z, Yano M, et al. QTLs for Na+ and K+ uptake of the shoots and roots controlling rice salt tolerance. Theor Appl Genet, 2004, 108: 253260.

\[4\]Takehisa H, Shimodate T, Fukuta Y, et al. Identification of quantitative trait loci for plant growth of rice in paddy field flooded with salt water. Field Crops Res, 2004, 89: 8595.

\[5\]Lee S Y, Ahn J H, Cha Y S, et al. Mapping of quantitative trait loci for salt tolerance at the seedling stage in rice. Mol Cell, 2006, 21(2): 192196.

\[6\]汪斌, 兰涛, 吴为人. 盐胁迫下水稻苗期Na+含量的QTL定位. 中国水稻科学, 2007, 21(6): 585590.

\[7\]藏金萍, 孙勇, 王韵, 等. 利用回交导入系剖析水稻苗期和分蘖期耐盐性的遗传重叠. 中国科学C辑: 生命科学, 2008, 38(9): 841850.

\[8\]顾兴友, 梅曼彤, 严小龙, 等. 水稻耐盐性数量性状位点的初步检测. 中国水稻科学, 2000, 14(2): 27.

\[9\]Shannon M C. Principles and strategies in breeding for higher salt tolerance. Plant Soil, 1985, 89: 227241.

\[10\]Johnson D W, Smith S E, Dobrenz A K. Genetic and phenotypic relationships in response to NaCl at different developmental stages in alfalfa. Theor Appl Genet, 1992, 83: 833838.

\[11\]Foolad M R, Lin G Y. Absence of a relationship between salt tolerance during germination and vegetative growth in tomato. Plant Breeding, 1997, 116: 363367.

\[12\]李慧慧, 张鲁燕, 王建康. 数量性状基因定位研究中若干常见问题的分析与解答. 作物学报, 2010, 36(6): 918931.

\[13\]FlintGarcia S A, Thomsberry J M, Iv B. Structure of linkage disequilibrium in plants. Annu Rev Plant Biol, 2003, 54: 357374.

\[14\]Weng J, Xie C, Hao Z, et al. 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.

\[15\] Li Y, Huang Y, Bergelson J, Nordborg M, et al. Association mapping of local climatesensitive quantitative traitloci in Arabidopsis thaliana. Proc Natl Acad Sci USA, 2010, 107(49): 2119921204.

\[16\]Huang X, Wei X, Sang T, et al. Genomewide association studies of 14 agronomic traits in rice landraces. Nat Genet, 2010, 42(11): 961967.

\[17\]于海霞, 田纪春. 小麦淀粉糊化特性与DArT标记的关联分析. 作物学报, 2012, 38(11): 19972006.

\[18\]Niu Y, Xu Y, Liu X F, et al. Association mapping for seed size and shape traits in soybean cultivars. Mol Breeding, 2013, 31: 785794.

\[19\] Korte A, Farlow A. The advantages and limitations of trait analysis with GWAS. Plant Methods, 2013, 9(1): 29.

\[20\]韩龙植, 张媛媛, 乔永利, 等. 水稻低温发芽势的遗传及数量性状基因座分析. 遗传学报, 2006, 33(11): 9981006.

\[21\] Doyle J J, Doyle J I. Isolation of plant DNA from fresh tissue. Focus, 1990, 12: 149151.

\[22\] van Ooijen J W, Voorrips R E. JoinMap 3.0, software for the calculation of genetic linkage maps. Wageningen, The Netherlands:Plant Research International. 2001.

\[23\]Li H H, Ye G Y, Wang J K. A modified algorithm for the improvement of composite interval mapping. Genetics, 2007, 175(1): 361374.

\[24\] McCouch S R. Gene nomenclature system for rice. Rice, 2008, 1: 7284.

\[25\]Stuber C W, Lincoln S E, Wolff D W, et al. Identification of genetic factors contributing to heterosis in a hybrid from two elite maize inbred lines using molecular markers. Genetics, 1992, 132: 823839.

\[26\]Temnykh S, DeClerck G, Lukashova A, el at. Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): Frequency, length variation, transposon associations, and genetic marker potential. Genom Res, 2001, 11(8): 14411452.

\[27\]McCouch S R, Teytelman L, Xu Y, et al. Development and mapping of 2240 new SSR markers for rice(Oryza sativa L.). DNA Res, 2002, 9: 199207.

\[28\]Pritchard J K, Stephens M, Rosenberg N A, et al. Association mapping in structured populations. Am J Hum Genet, 2000, 67: 170181.

\[29\]Evanno G, Regnaut S, Goudet J. Detecting the number of clusters of individuals using the software STRUCTURE: A simulation study. Mol Ecol, 2005, 14: 26112620.

\[30\] Bradbury P J, Zhang Z, Kroon D E, et al. TASSEL: Software for association mapping of complex traits in diverse samples. Bioinformatics, 2007, 23: 26332635.

\[31\]Zheng T, Yang J, Zhong W, et al. Novel loci for field resistance to blackstreaked dwarf and stripe viruses identified in a set of reciprocal introgression lines of rice (Oryza sativa L.). Mol Breeding, 2012, 29(4): 925938.

\[32\] Koyama M L, Levesley A, Koebner R M, et al. Quantitative trait loci for component physiological traits determining salt tolerance in rice. Plant Physiol, 2001, 125(1): 406422.

\[33\] Flowers T J, Koyama M L, Flowers S A, et al. QTL: Their place in engineering tolerance of rice to salinity. J Exp Bot, 2000, 51(342): 99106.

\[34\] Pandit A, Rai V, Bal S, et al. Combining QTL mapping and transcriptome profiling of bulked RILs for identification of functional polymorphism for salt tolerance genes in rice (Oryza sativa L.). Mol Genet Genom, 2010, 284(2): 121136.

\[35\] Mohammadi R, Mendioro M S, Diaz G Q, et al. Mapping quantitative trait loci associated with yield and yield components under reproductive stage salinity stress in rice (Oryza sativa L.). J Genet, 2013: 92.

\[36\] Thomson M J, de Ocampo M, Egdane J, et al. Characterizing the saltol quantitative trait locus for salinity tolerance in rice. Rice, 2010, 3(2/3): 148160.

\[37\] Wang Z, Cheng J, Chen Z, et al. Identification of QTLs with main, epistatic and QTL× environment interaction effects for salt tolerance in rice seedlings under different salinity conditions. Theor Appl Genet, 2012, 125(4): 807815.

\[38\] Wang Z, Wang J, Bao Y, et al. Quantitative trait loci controlling rice seed germination under salt stress. Euphytica, 2011, 178(3): 297307.

\[39\] Tian L, Tan L B, Liu F X, et al. Identification of quantitative trait loci associated with salt tolerance at seedling stage from Oryza rufipogon. J Genet Genom, 2011, 38(12): 593601.

\[40\] Sabouri H, Rezai A M, Moumeni A, et al. QTLs mapping of physiological traits related to salt tolerance in young rice seedlings. Biol Plant, 2009, 53(4): 657662.

\[41\] Ammar M H M, Pandit A, Singh R K, et al. Mapping of QTLs controlling Na+, K+ and Cl- ion concentrations in salt tolerant indica rice variety CSR27. J Plant Biochem Biotechnol, 2009, 18(2): 139150.

\[42\] Breseghello F, Sorrells M E. Association mapping of kernel size and milling quality in wheat (Triticumae stivum L.) cultivars. Genetics, 2006, 172: 11651177.

[1]	ZHU Yujing, GUI Jinxin, GONG Chengyun, LUO Xinyang, SHI Jubin, ZHANG Haiqing, HE Jiwai. QTL Mapping for Tiller Angle in Rice by Genome-wide Association Analysis [J]. Chinese Journal OF Rice Science, 2024, 38(3): 266-276.
[2]	LIU Zhongqi, ZHANG Haiqing, HE Jiwai, GUI Jinxin. Genome-wide Association Analysis of Rice Seed Dehydration Rate at Maturity Stage [J]. Chinese Journal OF Rice Science, 2024, 38(2): 150-159.
[3]	HOU Benfu, YANG Chuanming, ZHANG Xijuan, YANG Xianli, WANG Lizhi, WANG Jiayu, LI Hongyu, JIANG Shukun. Mapping of Grain Shape QTLs Using RIL Population from Longdao 5/Zhongyouzao 8 [J]. Chinese Journal OF Rice Science, 2024, 38(1): 13-24.
[4]	HU Jiaxiao, LIU Jin, CUI Di, LE Si, ZHOU Huiying, HAN Bing, MENG Bingxin, YU Liqin, HAN Longzhi, MA Xiaoding, LI Maomao. Mapping Major QTLs for Panicle Traits Using CSSLs of Dongxiang Wild Rice (Oryza rufipogon Griff.) [J]. Chinese Journal OF Rice Science, 2023, 37(6): 597-608.
[5]	XIE Kaizhen, ZHANG Jianming, CHENG Can, ZHOU Jihua, NIU Fuan, SUN Bin, ZHANG Anpeng, WEN Weijun, DAI Yuting, HU Qiyan, QIU Yue, CAO Liming, CHU Huangwei. Identification and QTL Mapping of Rice Germplasm Resources with Low Amylose Content [J]. Chinese Journal OF Rice Science, 2023, 37(6): 609-616.
[6]	YAO Xiaoyun, CHEN Chunlian, XIONG Yunhua, HUANG Yongping, PENG Zhiqing, LIU Jin, YIN Jianhua. Identification of QTL for Milling and Appearance Quality Traits in Rice (Oryza sativa L.) [J]. Chinese Journal OF Rice Science, 2023, 37(5): 507-517.
[7]	WEI Minyi, MA Zengfeng, HUANG Dahui, QIN Yuanyuan, LIU Chi, LU Yingping, LUO Tongping, LI Zhenjing, ZHANG Yuexiong, QIN Gang. QTL-Seq Analysis for Identification of Resistance Locus to Bacterial Leaf Streak in Rice [J]. Chinese Journal OF Rice Science, 2023, 37(2): 133-141.
[8]	LIU Jin, CUI Di, YU Liqin, ZHANG Lina, ZHOU Huiying, MA Xiaoding, HU Jiaxiao, HAN Bing, HAN Longzhi, LI Maomao. Screening and QTL Mapping of Heat-tolerant Rice (Oryza sativa L.) Germplasm Resources at Seedling Stage [J]. Chinese Journal OF Rice Science, 2022, 36(3): 259-268.
[9]	HUANG Tao, WANG Yanning, ZHONG Qi, CHENG Qin, YANG Mengmeng, WANG Peng, WU Guangliang, HUANG Shiying, LI Caijing, YU Jianfeng, HE Haohua, BIAN Jianmin. Mapping and Analysis of QTLs for Rice Grain Weight and Grain Shape Using Chromosome Segment Substitution Line Population [J]. Chinese Journal OF Rice Science, 2022, 36(2): 159-170.
[10]	DONG Zheng, WANG Yamei, LI Yongchao, XIONG Haibo, XUE Canhui, PAN Xiaowu, LIU Wenqiang, WEI Xiucai, LI Xiaoxiang. Genome-wide Association Analysis of Cadmium Content in Rice Based on MAGIC Population [J]. Chinese Journal OF Rice Science, 2022, 36(1): 35-42.
[11]	Jie LI, Rongrong TIAN, Tianliang BAI, Chunyan ZHU, Jiawei SONG, Lei TIAN, Shuaiguo MA, Jiandong LÜ, Hui HU, Zhenyu WANG, Chengke LUO, Yinxia ZHANG, Peifu LI. Comprehensive Evaluation and QTL Analysis for Flag Leaf Traits Using a Backcross Population in Rice [J]. Chinese Journal OF Rice Science, 2021, 35(6): 573-585.
[12]	Qing ZHANG, Baowei GUO, Yajie HU, Hongcheng ZHANG, Yufeng XU, Xiaojie XU, Banghui ZHU, Jiefen XU, Zhongyi NIU, Rongwen TU. Differences in Yield and Rice Quality of Soft <i>japonica </i>Rice with High Quality and High Yield Under Different Nitrogen Levels [J]. Chinese Journal OF Rice Science, 2021, 35(6): 606-616.
[13]	Xina CHEN, Zeke YUAN, Zhenzhen HU, Quanzhi ZHAO, Hongzheng SUN. QTL-Seq Mapping of Head Rice Rate QTLs in japonica Rice [J]. Chinese Journal OF Rice Science, 2021, 35(5): 449-454.
[14]	Chengxing DU, Huali ZHANG, Dongqing DAI, Mingyue WU, Minmin LIANG, Junyu CHEN, Liangyong MA. QTL Analysis for Grain Weight and Shape and Validation of qTGW1.2/qGL1.2 [J]. Chinese Journal OF Rice Science, 2021, 35(4): 359-372.
[15]	Yujun ZHU, Ziwei ZUO, Zhenhua ZHANG, Yeyang FAN. A New Approach for Fine-mapping and Map-based Cloning of Minor-Effect QTL in Rice [J]. Chinese Journal OF Rice Science, 2021, 35(4): 407-414.

Identification of QTLs for Salt Tolerance at the Germination and Early Seedling Stage Using Linkage and Association Analysis in japonica Rice

利用连锁和关联分析定位粳稻芽期及幼苗前期耐盐性QTL

PDF

Knowledge

Abstract

Cite this article

share this article

References

Related Articles 15

Recommended Articles

Metrics