小麦TaSnRK2.10的多态性及与农艺性状的关联

doi:10.3864/j.issn.0578-1752.2014.10.001

摘要/Abstract

摘要： 【目的】蔗糖非发酵蛋白激酶（SnRK）是一类丝氨酸/苏氨酸蛋白激酶，在植物信号传递途径中发挥着重要作用。研究小麦TaSnRK2.10的多态性，开发其功能标记，并进行标记-表型性状关联分析，为利用分子标记进行遗传改良和种质创新提供依据。【方法】以30份多态性较高的六倍体普通小麦及其野生近缘种的二倍体和四倍体为材料，通过测序分析TaSnRK2.10-A的序列多态性；利用中国春缺-四体材料对该基因进行染色体定位；利用RIL群体（偃展1号×内乡188）对基因进行遗传定位；根据TaSnRK2.10-A序列多态性，开发分子标记，以262份普通小麦构成的自然群体为材料分析基因单倍型与表型性状的关联特性。【结果】克隆了小麦TaSnRK2.10的A、D基因组序列，在由30份多态性较高的小麦材料组成的自然群体中，没有检测到来自D基因组的TaSnRK2.10-D序列多态性；TaSnRK2.10-A全长4 688 bp，包括启动子1 934 bp、5′-UTR 343 bp、编码区2 319 bp及3′-UTR 92 bp。在基因全长序列中共检测到15个SNP、2个InDel。其中，启动子区有8个SNP，5′-UTR有2个，编码区有5个。位于编码区的5个SNP中，2个存在于外显子，其中一个是非同义突变。2个InDel均位于编码区。根据序列多态性分别设计了启动子区的分子标记PM1和PM2，以及基因编码区的分子标记GM1和GM2。利用中国春缺-四体材料将TaSnRK2.10-A定位于小麦染色体4A，利用RIL群体将TaSnRK2.10-A定位在染色体4A的标记Xwpt7001和WMC48之间，与2个侧翼标记的遗传距离分别为5.1 cM和25.7 cM。利用开发的4个分子标记，将自然群体的262份材料分为4种单倍型，分别与千粒重、单株穗数和每穗小穗数显著相关或极显著相关，HapⅡ和HapⅢ是提高千粒重的优异单倍型。4 184 bp位点为C时，为高千粒重的优异等位变异。【结论】小麦TaSnRK2.10-A位于染色体4A。HapⅡ和HapⅢ是提高千粒重的优异单倍型，HapⅣ是提高单株穗数的优异单倍型，4 184 bp位点的胞嘧啶（C）是优异等位变异。

关键词: 小麦 , TaSnRK2.10 , 多态性 , 功能标记 , 单倍型 , 关联分析

Abstract: 【Objective】 The sucrose non-fermenting protein kinase (SnRK) is a kind of Ser/Thr protein kinase found widely in plants and participates a variety of transductions in signaling pathway in plants. TaSnRK2.10 is an important SnRK2 member involved in response to various abiotic stresses in wheat (Triticum aestivum L.). The objective of this study is to detect the single nucleotide polymorphism (SNP) of TaSnRK2.10, develop and map its functional markers, analyze the relationship between its haplotypes and phenotypic traits, and provide a basis for the genetic improvement and germplasm enhancement by molecular marker assisted selection in wheat. 【Method】 Thirty hexaploid wheat accessions with high polymorphism and their diploid and tetraploid wild relative species were selected to detect the nucleotide polymorphism in TaSnRK2.10-A gene by sequencing. A set of Chinese Spring nulli-tetrasomic lines and the recombinant inbred lines (RIL) derived from a cross of “Yanzhan 1 × Neixiang 188” were used to map TaSnRK2.10-A on chromosome. Based on the polymorphism in the sequence of TaSnRK2.10-A molecular markers were developed. The relevance between TaSnRK2.10-A haplotypes and phenotypic traits was analyzed using a natural population consisted of 262 historical wheat accessions. 【Result】 The sequences of TaSnRK2.10 on genomes A and D were cloned, named as TaSnRK2.10-A and TaSnRK2.10-D. There was no SNP detected in the sequence of TaSnRK2.10-D, but the full length of TaSnRK2.10-A was 4 688 bp with 15 SNPs and 2 InDels. Among them, 8 SNPs were identified in the promoter region, 2 SNPs in 5′-UTR region, and 5 SNPs in the coding region with 2 SNPs in exon. One of SNPs in exon was non-synonymous mutation. Four markers were developed. They were PM1 and PM2 for the promoter region, GM1 and GM2 for the coding region. TaSnRK2.10-A was mapped in the intervals between markers Xwpt7001 and WMC48 on chromosome 4A, with 5.1 cM and 25.7 cM from the flanking markers. In the natural populations consisted of 262 accessions, four haplotypes of TaSnRK2.10-A were detected by four markers that were associated with 1000-grain weight, spike per plant and spikelet per spike. The HapⅡand HapⅢ of TaSnRK2.10-A are considered as potential superior haplotypes for the improvement of 1000-grain weight. The base C at the site of 4 184 bp is a superior allele for high 1000-grain weight. 【Conclusion】 The present research mapped TaSnRK2.10-A on the chromosome 4A. The HapⅡand HapⅢ of TaSnRK2.10-A are considered as potential superior haplotypes for the improvement of 1000-grain weight, while HapⅣ is a potential superior haplotype for spike per plant. The cytosine (C) at the position of 4 184 bp is the superior allele.

Key words: wheat , TaSnRK2.10 , SNP , functional marker , haplotype , association analysis

王倩1, 2, 毛新国2, 昌小平2, 贾继增2, 刘惠民1, 景蕊莲2. 小麦TaSnRK2.10的多态性及与农艺性状的关联[J]. 中国农业科学, 2014, 47(10): 1865-1877.

WANG Qian-1, 2 , MAO Xin-Guo-2, CHANG Xiao-Ping-2, JIA Ji-Zeng-2, LIU Hui-Min-1, JING Rui-Lian-2. Polymorphism of TaSnRK2.10 and Its Association with Yield-Related Traits in Wheat[J]. Scientia Agricultura Sinica, 2014, 47(10): 1865-1877.

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参考文献

[1]Zheng Z, Xu X, Crosley R A, Greenwalt S A, Sun Y, Blakeslee B, Wang L, Ni W, Sopko M S, Yao C, Yau K, Burton S, Zhuang M, McCaskill D G, Gachotte D, Thompson M, Greene T W. The protein kinase SnRK2.6 mediates the regulation of sucrose metabolism and plant growth in Arabidopsis. Plant Physiology, 2010, 153: 99-113.

[2]Zhang H Y, Mao X G, Wang C S, Jing R L. Overexpression of a common wheat gene TaSnRK2.8 enhances tolerance to drought, salt and low temperature in Arabidopsis. PLoS One, 2010, 5: e16041.

[3]Mao X G, Zhang H Y, Tian S J, Chang X P, Jing R L. TaSnRK2.4, an SNF1-type serine/threonine protein kinase of wheat (Triticum aestivum L.), confers enhanced multistress tolerance in Arabidopsis. Journal of Experimental Botany, 2010, 61: 683-696.

[4]Kobayashi Y, Yamamoto S, Minami H, Kagaya Y, Hattori T. Differential activation of the rice sucrose nonfermenting1-related protein kinase2 family by hyperosmotic stress and abscisic acid. The Plant Cell, 2004, 16: 1163-1177.

[5]Boudsocq M, Barbier-Brygoo H, Lauriere C. Identification of nine sucrose nonfermenting 1-related protein kinases 2 activated by hyperosmotic and saline stresses in Arabidopsis thaliana. The Journal of Biological Chemistry, 2004, 279: 41758-41766.

[6]McLoughlin F, Galvan-Ampudia C S, Julkowska M M, Caarls L, van der Does D, Lauriere C, Munnik T, Haring M A, Testerink C. The Snf1-related protein kinases SnRK2.4 and SnRK2.10 are involved in maintenance of root system architecture during salt stress. The Plant Journal, 2012, 72: 436-449.

[7]Coello P, Hey S J, Halford N G. The sucrose non-fermenting-1-related (SnRK) family of protein kinases: Potential for manipulation to improve stress tolerance and increase yield. Journal of Experimental Botany, 2011, 62: 883-893.

[8]Zhang H Y, Mao X G, Jing R L. SnRK2 acts within an intricate network that links sucrose metabolic and stress signaling in wheat. Plant Signaling & Behavior, 2011, 6: 652-654.

[9]Fujii H, Verslues P E, Zhu J K. Arabidopsis decuple mutant reveals the importance of SnRK2 kinases in osmotic stress responses in vivo. Proceedings of the National Academy of Sciences of the USA, 2011, 108: 1717-1722.

[10]Huai J, Wang M, He J, Zheng J, Dong Z, Lv H, Zhao J, Wang G. Cloning and characterization of the SnRK2 gene family from Zea mays. Plant Cell Report, 2008, 27: 1861-1868.

[11]Zhang H Y, Mao X G, Jing R L, Chang X P, Xie H M. Characterization of a common wheat (Triticum aestivum L.) TaSnRK2.7 gene involved in abiotic stress responses. Journal of Experimental Botany, 2011, 62: 975-988.

[12]Tian S J, Mao X G, Zhang H Y, Yang S M, Jing R L. Cloning and characterization of TaSnRK2.3, a novel SnRK2 gene in common wheat. Journal of Experimental Botany, 2013, 64: 2063-2080.

[13]张洪映, 毛新国, 景蕊莲, 谢惠民, 昌小平. 小麦TaPK7基因的克隆及其在多种胁迫条件下的表达分析. 麦类作物学报, 2008, 28(2): 177-182.

Zhang H Y, Mao X G, Jing R L, Xie H M, Chang X P. Cloning and expression analysis of TaPK7 under different abiotic stresses in wheat. Journal of Triticeae Crops, 2008, 28(2): 177-182. (in Chinese)

[14]连魏卫, 唐益苗, 高世庆, 张朝, 赵昌平. 小麦TaSnRK2.9蛋白激酶基因克隆与生物信息学分析. 中国农学通报, 2011, 27(33): 6-12.

Lian W W, Tang Y M, Gao S Q, Zhang C, Zhao C P. Identification and bioinformatics analysis of TaSnRK2.9 in wheat. Chinese Agriculture Science Bulletin, 2011, 27(33): 6-12. (in Chinese)

[15]张洪映, 毛新国, 景蕊莲, 谢惠民, 昌小平. 小麦TaPK7基因单核苷酸多态性与抗旱性的关系. 作物学报, 2008, 34(9): 1537-1543.

Zhang H Y, Mao X G, Jing R L, Xie H M, Chang X P. Relationship between single nucleotide polymorphism of TaPK7 gene and drought tolerance in wheat. Acta Agronomica Sinica, 2008, 34(9): 1537-1543. (in Chinese)

[16]Zhang H Y, Mao X G, Zhang J N, Chang X P, Wang C S, Jing R L. Genetic diversity analysis of abiotic stress response gene TaSnRK2.7-A in common wheat. Genetica, 2011, 139: 743-753.

[17]Zhang H Y, Mao X G, Zhang J N, Chang X P, Jing R L. Single-nucleotide polymorphisms and association analysis of drought- resistance gene TaSnRK2.8 in common wheat. Plant Physiology and Biochemistry, 2013, 70: 174-181.

[18]Garces-Claver A, Fellman S M, Gil-Ortega R, Jahn M, Arnedo-Andres M S. Identification, validation and survey of a single nucleotide polymorphism (SNP) associated with pungency in Capsicum spp. Theoretical and Applied Genetic, 2007, 115: 907-916.

[19]Sachidanandam R, Weissman D, Schmidt S C, Kakol J M, Stein L D, Marth G, Sherry S, Mullikin J C, Mortimore B J, Willey D L, Hunt S E, Cole C G, Coggill P C, Rice C M, Ning Z, Rogers J, Bentley D R, Kwok P-Y, Mardis E R, Yeh R T, Schultz B, Cook L, Davenport R, Dante M, Fulton L, Hillier L, Waterston R H, McPherson J D, Gilman B, Schaffner S, Etten W J V, Reich D, Higgins J, Daly M J, Blumenstiel B, Baldwin J, Stange-Thomann N, Zody M C, Linton L, Lander E S, Altshuler D. A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature, 2001, 409: 928-933.

[20]Nasu S, Suzuki J, Ohta R, Hasegawa K, Yui R, Kitazawa N, Monna L, Minobe Y. Search for and analysis of single nucleotide polymorphisms (SNPs) in rice (Oryza sativa, Oryza rufipogon) and establishment of SNP markers. DNA Research, 2002, 9: 163-171.

[21]Ching A, Caldwell K S, Jung M, Dolan M, Smith O S, Tingey S, Morgante M, Rafalski A J. SNP frequency,haplotype structure and linkage disequilibrium in elite maize inbred lines. BMC Genetic, 2002, 3: 19.

[22]郝岗平, 杨清, 吴忠义, 曹鸣庆, 黄丛林. 植物的单核苷酸多态性及其在作物遗传育种中的应用. 植物学通报, 2004, 21(5): 618-624.

Hao G P, Yang Q, Wu Z Y, Cao M Q, Huang C L. Single nuleotide polymorphism (SNP) and its applications in crop genetics and breeding. Chinese Bulletin of Botany, 2004, 21(5): 618-624. (in Chinese)

[23]Liu Y N, He Z H, Appels R, Xia X C. Functional markers in wheat: current status and future prospects. Theoretical and Applied Genetic, 2012, 125: 1-10.

[24]李玮瑜, 张斌, 张嘉楠, 昌小平, 李润植, 景蕊莲. 利用关联分析发掘小麦自然群体旗叶叶绿素含量的优异等位变异. 作物学报, 2012, 38(6): 962-970.

Li W Y, Zhang B, Zhang J N, Chang X P, Li R Z, Jing R L. Exploring elite elleles for chlorophyll content of flag leaf in natural population of wheat by association analysis. Acta Agronomica Sinica, 2012, 38(6): 962-970. (in Chinese)

[25]宋彦霞. 小麦抽穗期及其农艺性状的QTL分析[D]. 雅安：四川农业大学, 2005.

Song Y X. QTL analysis of the wheat earing period and other agronomic characters[D]. Yaan: Sichuan Agricultural University, 2005. (in Chinese)

[26]Librado P, Rozas J. DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics, 2009, 25: 1451-1452.

[27]Bradbury P J, Zhang Z, Kroon D E, Casstevens T M, Ramdoss Y, Buckler E S. TASSEL: Software for association mapping of complex traits in diverse samples. Bioinformatics, 2007, 23: 2633-2635.

[28]Gupta P K, Rustgi S, Kulwal P L. Linkage disequilibrium and association studies in higher plants: Present status and future prospects. Plant Molecular Biology, 2005, 57: 461-485.

[29]Zondervan K T, Cardon L R. The complex interplay among factors that influence allelic association. Genetics, 2004, 5: 89-100.

[30]赵曦, 王荣焕, 于永涛, 王天宇, 黎裕. 关联分析在玉米遗传学研究中的应用. 玉米科学, 2008, 16(1): 52-55.

Zhao X, Wang R H, Yu Y T, Wang T Y, Li Y. Application of association analysis in maize genetics. Journal of Maize Sciences, 2008, 16(1): 52-55. (in Chinese)

[31]Agrama H A, Eizenga G C, Yan W. Association mapping of yield and its components in rice cultivars. Molecular Breeding, 2007, 19: 341-356.

[32]Eizenga G C, Agrama H A, Lee F N, Yan W, Jia Y. Identifying novel resistance genes in newly introduced blast resistant rice germplasm. Crop Science, 2006, 46: 1870-1878.

[33]Roy J K, Bandopadhyay R, Rustgi S, Balyan H S, Gupta P K. Association analysis of agronomically important traits using SSR, SAMPL and AFLP markers in bread wheat. Current Science, 2006, 90: 683-689.

[34]雷梦林, 李昂, 昌小平, 徐兆师, 马有志, 刘惠民, 景蕊莲. 小麦转录因子基因W16的功能标记作图和关联分析. 中国农业科学, 2012, 45(9): 1667-1675.

Lei M L, Li A, Chang X P, Xu Z S, Ma Y Z, Liu H M, Jing R L. Functional marker mapping and association analysis of gene W16 in common wheat. Scientia Agricultura Sinica, 2012, 45(9): 1667-1675. (in Chinese)

[35]刘丽华. 小麦4A染色体六个农艺性状的关联分析[D]. 武汉: 华中农业大学, 2009.

Liu L H. Association mapping of six agronomic traits on chromosome 4A of wheat[D]. Wuhan: Huazhong Agricultural University, 2009. (in Chinese)

[36]崔法. 高密度小麦遗传连锁图谱构建及产量相关性状QTL定位[D]. 泰安: 山东农业大学, 2011.

Cui F. Construction of high-density wheat molecular genetic map and QTL analysis for yield-related traits[D]. Taian: Shandong Agricultural University, 2011. (in Chinese)

[37]Yang D L, Jing R L, Chang X P, Li W. Identification of quantitative trait loci and environmental interactions for accumulation and remobilization of water-soluble carbohydrates in wheat (Triticum aestivum L.) stems. Genetics, 2007, 176: 571-584.

[38]Su J Y, Zheng Q, Li H W, Li B, Lian R L, Tong Y P, Li Z S. Detection of QTLs for phosphorus use efficiency in relation to agronomic performance of wheat grown under phosphorus sufficient and limited conditions. Plant Science, 2009, 176: 824-836.