The Application of the Functional Molecular Marker in Wheat Breeding

doi:10.13560/j.cnki.biotech.bull.1985.2016.11.003

Abstract

Abstract: Based on the polymorphic sequence of a particular area in a functional gene closely related to phenotype, functional marker is a novel dominant molecular marker developed by correlation analysis, spectrum analysis, RNA interference and QTL mapping method, etc. Using these functional markers, whether or not the target allele from different genetic backgrounds exist can be directly and rapidly determined. In this work, the concept and characteristics of functional markers are briefly introduced, mainly exploring the application and prospect of functional markers as an assistant means in wheat breeding, in order to provide reference for the development of related molecular markers

Key words: wheat, molecular marker, functional gene, assistant breeding

LIU Guo-sheng, ZHANG Da-le. The Application of the Functional Molecular Marker in Wheat Breeding[J]. Biotechnology Bulletin, 2016, 32(11): 18-29.

References

[1] 刘光兴. 遗传标记技术在海洋桡足类生物多样性和系统发生研究中的应用[J]. 中国海洋大学学报, 2007, 37（1）：33-37.
[2] 周延清. DNA分子标记技术在植物研究中的应用[M]. 北京：化学工业出版社, 2005：56-57.
[3] Pang M, Percy RG, Hughs E, et al. Promoter anchored amplified polymorphism based on random amplified polymorphic DNA（PAAP-RAPD）in cotton[J]. Euphytica, 2009, 167（3）：281-291.
[4] Bagge M, Xia X, Lübberstedt T. Functional markers in wheat[J]. Current Opinion in Plant. Biology, 2007, 10（2）：211-216.
[5] Andersen JR, Lübberstedt T. Functional markers in plants[J]. Trends in Plant Science, 2003, 8（11）：554-560.
[6] 杨景华, 王士伟, 刘训言, 等. 高等植物功能性分子标记的开发与利用[J]. 中国农业科学, 2008, 41（11）：3429-3436.
[7] The Arabidopsis genome initiative. analysis of the genome sequence of the flowering plant Arabidopsis thaliana[J]. Nature, 2000, 408（6814）：796-815.
[8] Sherry A, Thuillet Anne-Céline, Yu JM, et al. Maize association population：a high-resolution platform for quantitative trait locus dissection[J]. The Plant Journal, 2005, 44（6）：1054-1064.
[9] Kurowska M, Daszkowska-Golec A, Gruszka D, et al. TILLING-a shortcut in functional genomics[J]. Journal of Applied Genetics, 2011, 52（4）：371-390.
[10] Sunnucks P. Efficient genetic markers for population biology[J]. Trends in Ecology and Evolution, 2000, 15（5）：199-203.
[11] Brenchley R, Spannag M, Pfeifer M, et al. Analysis of the bread wheat genome using whole genome shotgun sequencing[J]. Nature. 2012, 491（7426）：705-710.
[12] Bagge M, Xia XC, Lubberstedt T. Funetional markers in wheat[J]. Current Opinion in Plant Biology, 2007, 10（2）：211-216.
[13] Arnér ESJ, Holmgren A. Physiological functions of thioredoxin and thioredoxin reductase[J]. European Journal of Biochemistry, 2000, 267（20）：6102-6109.
[14] Sun DJ, He ZH, Xia XC, et al. A novel STS marker for polyphenol oxidase activity in bread wheat[J]. Molecular Breeding, 2005, 16（3）：209-218.
[15] 王晓波, 马传喜, 何克勤, 等. 小麦2D染色体上多酚氧化酶（PPO）基因STS标记的开发与应用[J]. 中国农业科学, 2008, 41（6）：1583-1590.
[16] He XY, He ZH, Zhang LP, et al. Allelic variation of polyphenol oxidase（PPO）genes located on chromosomes 2A and 2D and development of functional markers for the PPO genes in common wheat[J]. Theoretical Applied Genetics, 2007, 115（1）：47-58.
[17] He XY, He ZH, Morris CF, et al. Cloning and phylogenetic analysis of polyphenol oxidase genes in common wheat and related species[J]. Genetic Resources and Crop Evolution, 2009, 56（3）：311-321.
[18] Wei JX, Geng HW, Zhang Y, et al. Mapping quantitative trait loci for peroxidase activity and developing gene-specific markers for TaPod-A1 on wheat chromosome 3AL[J]. Theoretical and Applied Genetics, 2015, 128（10）：2067-2076.
[19] Su ZQ, Hao CY, Zhang XY. Identification and development of a functional marker of TaGW2 associated with grain Weight in bread wheat（Triticum aestivum L. ）[J]. Theoretical and Applied Genetics, 2010, 122（1）：211-223.
[20] Yang ZB, Bai ZY, Li XL, et al. SNP identification and allelic-specific PCR markers development for TaGW2, agene finked to wheat kernel weight[J]. Theoretical and Applied Genetics, 2012, 125（5）：1057-1068.
[21] Jiang QY, Hou J, Hao CY, et al. The wheat（T. aestivum）sucrose synthase 2 gene（TaSus2）active in endosperm development is associated with yield traits[J]. Funct Integr Genomics, 2011, 11（1）：49-61.
[22] Zhang YJ, Liu JD, Xia XC, et al. TaGS-D1, an ortholog of rice OsGS3, is associated with grain weight and grain length in common wheat[J]. Mol Breeding, 2014, 34（3）：1097-1107.
[23] Ma DY, Yan J, He ZH, et al. Characterization of a cell wall inverta- se gene TaCwi-A1 on common wheat chromosome 2A and develop-ment of functional markers[J]. Mol Breeding, 2012, 29（1）：43-52.
[24] He XY, He ZH, Ma W, et al. Allelic variants of phytoene synthase 1（Psy1）genes in Chinese and CIMMYT wheat cultivars and development of functional markers for flour colour[J]. Mol Breeding, 2009, 23（4）：553-563.
[25] He XY, Zhang YL, He ZH, et al. Characterization of phytoene synthase 1 gene（Psy1）located on common wheat chromosome 7A and development of a functional marker[J]. Theor Appl Genet, 2008, 116（2）：213-221.
[26] Wang JW, He XY, He Z, et al. Cloning and phylogenetic analysis of phytoene synthase 1（Psy1）genes in common wheat and related species[J]. Hereditas, 2009, 146（5）：208-256.
[27] Zhang CY, Dong CH, He XY, et al. Allelic Variants at the TaZds-D1 locus on wheat chromosome 2DL and their association with yellow pigment content[J]. Crop Sci, 2011, 51（4）：1580-1590.
[28] Dong CH, Ma ZY, Xia XC, et al. Allelic variation at the TaZds-A1 locus on wheat chromossome 2A and development of a functional marker in common wheat[J]. Journal of Integrative Agriculture, 2012, 11（7）：1067-1074.
[29] 董长海. 普通小麦籽粒黄色素含量相关基因的克隆与功能标记开发[D]. 保定：河北农业大学, 2011.
[30] Geng HW, Xia XC, Ghang LP, et al. Development of functional markers for a lipoxygenase gene Talox-B1 on chromosome 4BS in common wheat[J]. Crop Science of America, 2012, 52（2）：568-576.
[31] 吴萍. 小麦籽粒脂肪氧化酶活性功能标记的开发与应用[D]. 合肥：安徽农业大学, 2013.
[32] Guo GA, Song YX, Zhou RH, et al. Discovery, evaluation and distribution of haplotypes of the wheat Ppd-D1 gene[J]. New Phytologist, 2010, 185（3）：841-851.
[33] Slierman JD, Yan L, Talbert L, et al. A PCK marker for growth habit in common wheat based on allelic variation Vrn-A1 gene[J]. Crop Science Society of America, 2004, 44（5）：1832-1838.
[34] Zhao XL, Ma W, Gale KR, et al. Identification of SNPs and development of functional markers for LMW-GS genes at Glu-D3 and Glu-B3 loci in bread wheat（Triticum aestivum L. ）[J]. Molecular Breeding, 2007, 20（3）：223-231.
[35] Liu SX, Chao SM, Anderson JA. New DNA markers for high molecular weight glutenin subunits in wheat[J]. Theor Appl Genet, 2008, 118（1）：177-183.
[36] Ma W, Zhang W, Gale KR. Multiplex-PCR typing of high molecular weight glutenin alleles in wheat[J]. Euphytica, 2003, 134：51-60.
[37] Schwarz G, Felsenstein FG, Wenzel G. Development and validation of a PCR-based marker assayfor negative selection of the HMW glutenin allele Glu-B1-1d（Bx-6）in wheat[J]. Theor Appl Genet, 2004, 109（5）：1064-1069.
[38] Ragupathy R, Naeem HA, Reimer E, et al. Evolutionary origin of the segmentalduplication encompassing the wheat GLU-B1 locus encoding the overexpressed Bx7（Bx7 0E ）high molecular weight glutenin subunit[J]. Theor Appl Genet, 2008, 116（2）：283-296.
[39] Lei ZS, Gale KR, He ZH, et al. Y-type gene specific markers for enhanced discrimination of high-molecular weight glutenin alleles at the Glu-B1 locus in hexaploid wheat[J]. J Cereal Sci, 2006, 43（1）：94-101.
[40] Wang LH, Li GY, Pena RJ, et al. Development of STS markers and establishment of multiplex PCR for Glu-A3 alleles in common wheat（Triticum aestivum L. ）[J]. J Cereal Sci, 2010, 51（3）：305-312.
[41] Wang LH, Zhao XL, He ZH, et al. Characterization of low-molecular-weight glutenin subunit Glu-B3 genes and development of STS markers in commonwheat（Triticum aestivum L. ）[J]. Theor Appl Genet, 2009, 118（3）：525-539.
[42] Mika S, Patricia V, Goro I, et al. A novel codominant marker for selection of the null Wx-B1 allele in wheat breeding programs[J]. Molecular Breeding, 2009, 23（2）：209-217.
[43] 王昊龙, 韩俊杰, 李卫华, 等. 不同抗性淀粉含量的小麦品种（系）SBEⅡa基因启动子序列分析[J]. 石河子大学学报：自然科学版, 2015, 33（1）：60-66.
[44] 鞠丽萍, 张帆, 蒋雷, 等. 小麦TaFer-A1 基因抗旱相关分子标记的开发[J]. 麦类作物学报, 2013, 33（5）：901-906.
[45] 王智兰, 毛新国, 李昂, 等. 小麦蛋白磷酸酶2A结构亚基基因TaPP2Aa的功能标记作图[J], 中国农业科学, 2011, 44（12）：2411-2421.
[46] 张帆, 蒋雷, 鞠丽萍, 等. 一个普通小麦Trx超家族新基因TaNRX的克隆与抗旱相关标记开发[J]. 作物学报, 2014, 40（1）：29-36.
[47] 吕广德. 小麦TaOSCA1.4基因的克隆、标记开发和功能分析[D]. 泰安：山东农业大学. 2015.
[48] Gennaro A, Koebner RMD, Ceoloni C. A candidate for Lr19, an exotic gene conditioning leaf rust resistance in wheat[J]. Funct Integr Genomics, 2009, 9（3）：325-334.
[49] Helguera M, Vanzetti L, Soria M, et al. PCR markers for Triticum speltoides leaf rust resistance gene Lr51 and their use to develop isogenic hard red spring wheat lines[J]. Crop Sci, 2005, 45（2）：728-734.
[50] 刘兴舟. Vrn、Ppd-D1和Lr34/Yr18基因在山东小麦品种中的分子检测和分布的研究[D]. 泰安：山东农业大学, 2009.
[51] Tommasini L, Yahiaoui N, Srichumpa P, et al. Development of functional markers specific for seven Pm3 resistance alleles and their validation in the bread wheat gene pool[J]. Theor Appl Genet, 2006, 114（1）：165-175.
[52] 伍玲, 夏先春, 朱华忠, 等. CIMMYT 273个小麦品种抗病基因Lr34/Yr18/Pm38的分子标记检测[J]. 中国农业科学, 2010, 43（22）：4553-4561.
[53] Lagudah ES, Krattinger SG, Herrera-Foessel S, et al. Gene-specific markers for the wheat gene Lr34/Yr18/Pm38 which confers resistance to multiple fungal pathogens[J]. Theor Appl Genet, 2009, 119（5）：889-898.
[54] Liu D, Xia XC, He ZH, et al. A novel homeobox-like gene associated with reaction to stripe rust and powdery mildew in common wheat[J]. Phytopathology, 2009, 98（12）：1291-1296.
[55] 张照贵. 小麦TaSnRK2_10基因的克隆_标记开发和功能分析[D]. 泰安：山东农业大学, 2014.
[56] 王倩, 毛新国, 昌小平, 等. 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.
[57] Wei B, Jing RL, Wang CS, et al. Dreb1 genes in wheat（Triticum aestivum L. ）development of functional markers and gene mapping based on SNPs[J]. Molecular Breeding, 2009, 23（1）：13-22.
[58] Himi E, Noda K. Red gain colour gene（R）of wheat is a myb-type transcription factor[J]. Euphytica, 2005, 143：239-242.
[59] Himi E, Maekawa M, Miura H, et al. Development of PCR markers for Tamyb10 related to R-1, red grain color gene in wheat[J]. Theor Appl Genet, 2011, 122（8）：1561-1576.
[60] 李婷, 陈杰, 陈锋, 崔党群. 黄淮麦区地方小麦品种子粒颜色相关基因Tamyb10-1等位变异检测[J]. 植物遗传资源学报, 2014, 15（5）：1089-1095.
[61] 陈杰, 陈锋, 詹克慧, 等. 普通小麦籽粒Tamyb10基因等位变异的分子检测[J]. 麦类作物学报, 2013, 33（2）：224-229.
[62] 陈杰. 小麦籽粒和面粉颜色相关性状的基因型鉴定及其功能标记开发[D]. 郑州：河南农业大学, 2013.
[63] Yang Y, Zhao XL, Xia LQ, et al. Development and validation of a Viviparous-1 STS marker for pre-harvest sprouting tolerance in Chinese wheats[J]. Theoretical and Applied Genetics, 2007, 115（7）：971-980.
[64] 刘世鑫. 休眠基因Viviparous-1A在中国小麦3A染色体上等位变异的鉴定及STS分子标记的开发[D]. 呼和浩特：内蒙古农业大学, 2012.
[65] Chen F, Zhang FY, Xia XC, et al. Distribution of puroindoline alleles in bread wheat cultivars of the Yellow and Huai valley of China and discovery of a novel puroindoline a allele without PINA protein[J]. Mol Breeding, 2012, 29（2）：371-378.
[66] Ellis M, Spielmeyer W, Gale R, et al. “Perfect” markers for the Rht-B1b and Rht-Dlb dwarfing genes in wheat[J]. Theoretical and Applied Genetics, 2002, 105（6-7）：1038-1042.
[67] 冉从福, 邵慧, 余静, 等. 小麦CO-like基因TaC09的克隆及结构分析[J]. 麦类作物学报, 2014, 34（10）：1319-1326.
[68] Distelfeld A, Uauy C, Fahima T, et al. Physical map of the wheat high-grain protein content gene Gpc-B1 and development of a high-throughput molecular marker[J]. New Phytologist, 2006, 169（4）：753-763.
[69] Uauy C, Distelfeld A, Fahima T, et al. A NAC gene regulating senescence improves grain protein, zinc, and iron content in wheat[J]. Science, 2006, 314（5803）：1298-1301.
[70] Zhang YJ, Miao XL, Xia XC, et al. Cloning of seed dormancy genes（TaSdr）associated with tolerance to pre-harvest sprouting in common wheat and development of a functional marker[J]. Theor Appl Genet, 2014, 127（4）：855-866.
[71] 李冰, 张照贵, 王佳佳, 等. 小麦GDH1基因克隆及其功能标记开发[J]. 山东农业科学, 2014, 46（10）：6-11.
[72] 刘亚男, 夏先春, 何中虎. 普通小麦TaDep1基因克隆与特异性标记开发[J]. 作物学报, 2013, 39（4）：589-598.
[73] 雷梦林, 李昂, 昌小平, 等. 小麦转录因子基因W16的功能标记作图和关联分析[J]. 中国农业科学, 2012, 45（9）：1667-1675.
[74] Chang JZ, Zhang JN, Mao XG, et al. Polymorphism of TaSAP1-A1 and its association with agronomic traits in wheat[J]. Planta, 2013, 263（6）：1495-1508.
[75] 周渭皓, 孙建喜, 陈杰, 等. 甘肃春小麦八氢番茄红素基因的等位变异[J]. 麦类作物学, 2014, 34（8）：1036-1043.
[76] Slade AJ, Fuerstenberg SI, Loeffler D, et al. A reverse genetic, nontransgenic approach to wheat crop improvement by TILLING[J]. Nature Biotechnology, 2004, 23（1）：75-81.
[77] 张丽, 颜泽洪, 郑有良, 等. 小麦中国春背景下长穗堰麦草E e 染色体组特异AFLP及STS标记的建立[J]. 农业生物技术学报,2008,16（3）：465-473.