单核苷酸多态性(SNP)分子标记在小麦遗传育种中的研究进展
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摘要
为了了解单核苷酸多态性(SNP)标记在小麦遗传育种中的研究进展并为下一步在面粉制品中的应用奠定基础,本研究归纳了SNP分子标记所具有的特点以及应用比较普遍的检测方法,包括DNA构象法、高分辨溶解曲线法及直接测序法等检测方法;总结了近几年SNP标记在小麦遗传图谱的构建、作物育种、全基因组关联分析、遗传多样性和物种进化等方面的研究进展;最后提出可开发不同作物的高通量SNP芯片使SNP的研究向高通量化、全基因组发展,以及培育具有良好面制品感官特性的小麦新品种。
To understand the research progress of single nucleotide polymorphism(SNP)markers in wheat genetic breeding and to lay a foundation for further study of flour products,the characteristics of SNP markers and the commonly used detection methods are summarized,including DNA conformation,high resolution curve and direct sequencing methods.The research progress of SNP markers in construction of genetic map,crop breeding,genome-wide association analysis,genetic diversity and species evolution are reviewed.At last,it is proposed that high-throughput SNP chips of different crops should be developed to make the SNP research in the direction of high-throughput and whole-genome development,and to cultivate wheat varieties with good-flour sensory characteristics.
To understand the research progress of single nucleotide polymorphism(SNP)markers in wheat genetic breeding and to lay a foundation for further study of flour products,the characteristics of SNP markers and the commonly used detection methods are summarized,including DNA conformation,high resolution curve and direct sequencing methods.The research progress of SNP markers in construction of genetic map,crop breeding,genome-wide association analysis,genetic diversity and species evolution are reviewed.At last,it is proposed that high-throughput SNP chips of different crops should be developed to make the SNP research in the direction of high-throughput and whole-genome development,and to cultivate wheat varieties with good-flour sensory characteristics.
引文
[1]袁金红,李俊华,黄小城,等.基于全基因组重测序的SNP分析在作物基因定位中的研究进展[J].植物生理学报,2015,09:1400-1404.
[2]高尚,莫洪君,石浩然,等.利用SNP基因芯片技术进行小麦遗传图谱构建及重要农艺性状QTL分析[J].应用与环境生物学报,2016,01:85-94.
[3]吴秋红,陈永兴,李丹,等.利用SNP芯片和BSA分析规模化定位小麦抗白粉病基因[J].作物学报,2017:1-15.
[4]陈芳,李文静,邓志英,等.小麦5DL上基于SNP序列的新SSR标记的开发[J].山东农业大学学报:自然科学版,2016,47(04):494-500.
[5]韩红超,李文钊,周航,等.发酵时间对馒头品质及面筋蛋白结构的影响[J].食品科学,2017:1-8.
[6] Nasu S, Suzuki J, Ohta R, et al. Search for and analysis of single nucleotide polymorphisms in rice and establishment of SNP markers[J].DNA Res,2002,(9):163-171.
[7]宋伟,王凤格,田红丽,等.利用SNP位点鉴别玉米自交系的研究[J].玉米科学,2013,21(4):28-32.
[8] Somers D J, Irkpatrick R, Moniwa M, et al. Mining singlenucleotide polymorphisms from hexaploid wheat ESTs[J]. Genome,2003,46:431-437.
[9]Lameer D, CaiX, Arterbum M, et al. A single chromosome addition from Thinopyrum elongatum confers a polycarpic,perennial habit to annual wheat[J]. Journal of experimental botany,2004,55(403):1715-1720.
[10] Shabrukov Y. Comparison of SNP and CAPS markers application in genetic research in wheat and barley[J]. BMC Plant Biology,2016,16:11.
[11] Velasco R, Zharkikh A, Ffourtit A J, et al. The genome of the domesticated apple(Malusx domestica Borkh)[J].Nat Genet,2010,42:833-839.
[12] Lamber P, Campoy J A, Pacheco L, et al. Identifying SNP markers tightly associated with six major genes in peach(Prunus persica(L.)Batsch)using a high-density SNP array with an objective of markerassisted selection(MAS)[J]. Tree Genetics&Genomes,2016,12:121.
[13] Hillier L W, Marth G T, Quinlan A R, et al. Whole genome sequencing and variant discovery in C. elegants[J]. Nature methods,2008,5(2):183-188.
[14] Colasuonno P, Incerti O, Lozito M L. DHPLC technology for highthroughput detection of mutations in a durum wheat TILLING population[J]. BMC Genetics,2016,17:43.
[15]刘健,宋倩倩,翁巧琴,等.单核苷酸多态性(SNP)分型的主要方法及研究进展[J].浙江畜牧兽医,2016,03:12-14.
[16] Shen G Q, Abdullah K G, Wang Q K. The TapMan method for SNP genotyping[J]. Methods. Mol. Biol,2009,578:293-306.
[17] Kohnemann S, Pennekamp P, Pfeiffer H. An allelic ladder based upon reference alleles for mtDNA SNP analysis using the SNaPshot technique[J]. Electrophoresis,2011,32(14):1860-1863.
[18]高尚,莫洪君,石浩然,等.利用SNP基因芯片技术进行小麦遗传图谱构建及重要农艺性状QTL分析[J].应用与环境生物学报,2016,01:85-94.
[19] Yang Z G, Chen Z Y, Peng Z X, et al. Development of a highdensity linkage map and mapping of the three-pistil gene(Pis1)in wheat using GBS markers[J]. BMC Genomics,2017,18:567.
[20] Colasuonno P, Gadaeta A, Giancaspro A, et al. Development of a high-density SNP-based linkage map and detection of yellow pigment content QTLs in durum wheat[J]. Molecular Breeding,2014,34(4):1563-1578.
[21]田再民,张立平,王丽辉,等.小麦“BS20×Fu3”DH群体SSR遗传图谱的构建及不育基因的QTL定位[J].植物遗传资源学报,2015,16(04):857-867.
[22] Allen A M, Winfield M O, Burridge A J, et al. Characterisation of a wheat breeder’s array suitable for high throughput SNP genotyping of global accessions of hexaploid bread wheat[J]. Plant biotechnology Journal,2017,15(3):390.
[23] Zanke C, Ling J, Plieske J, et al. Genetic architecture of main effect,QTL for heading date in European winter wheat[J]. Front Plant Science,2014,5:217.
[24] Raz A, Motan N, Tamar E, et al. Ultra-dense genetic map of durum wheat×wild emmer wheat developed using the 90K iSelect SNP genotyping assay[J]. Mol Breeding,2014,34(4):1594-1592.
[25] Stuart J, Luca S, Salantur A, et al. High-throughput SNP genotyping of modern and wild emmer wheat for yield and root morphology using a combined association and linkage analysis[J]. Functional&Integrative Genomics,2017,6(17):667-685.
[26]张颖君.小麦种子休眠基因TaSdr与籽粒大小基因Ta GS的克隆和功能标记发掘[D].北京:中国农业科学院,2013.
[27] Liu J D, He G H, Rasheed A, et al. Genome-wide association mapping of black point reaction in common wheat(Triticum aestivum L.)[J]. BMC Plant Biology,2017,17:220.
[28] TanM K, Ei-bouhssini M, Emebiri L, et al. A SNP marker for the selection of HfrDrd,a Hessian fly-response gene in wheat[J].Molecular Breeding,2015,35:216-225.
[29] Lin M, Cai S, Wang S. et al. Genotyping-by-sequencing(GBS)identified SNP tightly linked to QTL for pre-harvest sprouting resistance[J]. Theoretical and Applied Genetics,2015,128(7):1385-1395.
[30] Gao L, Kielsmeier C J, Bajgain P, et al. Development of genotyping by sequencing(GBS)-and array-derived SNP markers for stem rust resistance gene Sr42[J]. Molecular Breeding,2015,35:207-215.
[31]禹文龙.基于SNP标记的小麦体细胞杂种渐渗系山融3号耐盐相关QTL分析[D].济南:山东大学,2015.
[32] Zhu C, Gore M, Buckler E S, et al. Status and prospects of association mapping in plants[J]. Plant Genome,2008,1:5-20.
[33] Ingvarsson P K, Nathaniel R S. Association genetics of complex traits in plants[J]. New Phytologist,2011,189:909-922.
[34] Palaisa K A, Morgante M, Williams M, et al. Contrasting effects of selection on sequence diversity and linkage disequilibrium at two phytoene synthase loci[J]. Plant Cell,2003,15:1795-1806.
[35] Sivakumar S, Susanne D, Marta L, et al. Genome-wide association study for grain yield and related traits in an elite spring wheat population grown in temperate irrigated environments[J].Theoretical and Applied Genetics,2015,128(2):353-363.
[36] Liu W Z, Maccaferri M, Bulli P, et al. Genome-wide association mapping for seedling and field resistance to Puccinia striiformis f.sp. tritici in elite durum wheat[J]. Theoretical and Applied Genetics,2017,130(4):649-667.
[37]周秀文.基于SNP标记的小麦氮效率性状的关联分析[D].泰安:山东农业大学,2016.
[38] Jighly A, Oyiga B C, Makdis F, et al. Genome-wide DArT and SNP scan for QTL associated with resistance to stripe rust(Puccinia striiformis f. sp. tritici)in elite ICARDA wheat(Triticumaestivum L.)germplasm[J].Theoretical and Applied Genetics,2015,128(7):1277-1295.
[39] Chen G, Zhang H, Deng Z, et al. Genome-wide association study for kernel weight-related traits using SNPs in a Chinese winter wheat population[J]. Euphytica,2016,212(2):173-185.
[40] Lin T, Zhu G, Zhang J, et al. Genomic analyses provide insights into the history of tomato breeding[J]. Nat Genet,2014,46(11):1220-1226.
[41] Zanke C D, Rodemann B, Ling J, et al. Genome-wide association mapping of resistance to eyespot disease(Pseudocercosporella herpotrichoides)in European winter wheat(Triticum aestivum L.)and fine-mapping of Pch1[J]. Theoretical and Applied Genetics,2017,130(3):505-514.
[42] Guttieri M J, Frels K, Regassa T, et al. Variation for nitrogen use efficiency traits in current and historical great plains hard winter wheat[J]. Euphytica. 2017,213:87.
[43] ManginiG,MargiottaB,MarcotuliI,etal.Geneticdiversityandphenetic analysis in wheat(Triticum turgidum subsp. durum and Triticum aestivum subsp. aestivum)landraces based on SNP markers[J].Genetic Resources and Crop Evolution,2017,64(6):1269-1280.
[44] Ren J, Chen L, Sun D, et al. SNP-revealed genetic diversity in wild emmer wheat correlates with ecological factors[J]. BMC Evol Biol,2013,13:169.
[45]曹廷杰,谢菁忠,吴秋红,等.河南省近年审定小麦品种基于系谱和SNP标记的遗传多样性分析[J].作物学报,2015,02:197-206.
[46]刘进英,董雪,冯玉梅,等.不同休眠特性小麦中TaGAMyb-B基因的等位变异及其表达特性[J].麦类作物学报,2016,06:708-713.
[2]高尚,莫洪君,石浩然,等.利用SNP基因芯片技术进行小麦遗传图谱构建及重要农艺性状QTL分析[J].应用与环境生物学报,2016,01:85-94.
[3]吴秋红,陈永兴,李丹,等.利用SNP芯片和BSA分析规模化定位小麦抗白粉病基因[J].作物学报,2017:1-15.
[4]陈芳,李文静,邓志英,等.小麦5DL上基于SNP序列的新SSR标记的开发[J].山东农业大学学报:自然科学版,2016,47(04):494-500.
[5]韩红超,李文钊,周航,等.发酵时间对馒头品质及面筋蛋白结构的影响[J].食品科学,2017:1-8.
[6] Nasu S, Suzuki J, Ohta R, et al. Search for and analysis of single nucleotide polymorphisms in rice and establishment of SNP markers[J].DNA Res,2002,(9):163-171.
[7]宋伟,王凤格,田红丽,等.利用SNP位点鉴别玉米自交系的研究[J].玉米科学,2013,21(4):28-32.
[8] Somers D J, Irkpatrick R, Moniwa M, et al. Mining singlenucleotide polymorphisms from hexaploid wheat ESTs[J]. Genome,2003,46:431-437.
[9]Lameer D, CaiX, Arterbum M, et al. A single chromosome addition from Thinopyrum elongatum confers a polycarpic,perennial habit to annual wheat[J]. Journal of experimental botany,2004,55(403):1715-1720.
[10] Shabrukov Y. Comparison of SNP and CAPS markers application in genetic research in wheat and barley[J]. BMC Plant Biology,2016,16:11.
[11] Velasco R, Zharkikh A, Ffourtit A J, et al. The genome of the domesticated apple(Malusx domestica Borkh)[J].Nat Genet,2010,42:833-839.
[12] Lamber P, Campoy J A, Pacheco L, et al. Identifying SNP markers tightly associated with six major genes in peach(Prunus persica(L.)Batsch)using a high-density SNP array with an objective of markerassisted selection(MAS)[J]. Tree Genetics&Genomes,2016,12:121.
[13] Hillier L W, Marth G T, Quinlan A R, et al. Whole genome sequencing and variant discovery in C. elegants[J]. Nature methods,2008,5(2):183-188.
[14] Colasuonno P, Incerti O, Lozito M L. DHPLC technology for highthroughput detection of mutations in a durum wheat TILLING population[J]. BMC Genetics,2016,17:43.
[15]刘健,宋倩倩,翁巧琴,等.单核苷酸多态性(SNP)分型的主要方法及研究进展[J].浙江畜牧兽医,2016,03:12-14.
[16] Shen G Q, Abdullah K G, Wang Q K. The TapMan method for SNP genotyping[J]. Methods. Mol. Biol,2009,578:293-306.
[17] Kohnemann S, Pennekamp P, Pfeiffer H. An allelic ladder based upon reference alleles for mtDNA SNP analysis using the SNaPshot technique[J]. Electrophoresis,2011,32(14):1860-1863.
[18]高尚,莫洪君,石浩然,等.利用SNP基因芯片技术进行小麦遗传图谱构建及重要农艺性状QTL分析[J].应用与环境生物学报,2016,01:85-94.
[19] Yang Z G, Chen Z Y, Peng Z X, et al. Development of a highdensity linkage map and mapping of the three-pistil gene(Pis1)in wheat using GBS markers[J]. BMC Genomics,2017,18:567.
[20] Colasuonno P, Gadaeta A, Giancaspro A, et al. Development of a high-density SNP-based linkage map and detection of yellow pigment content QTLs in durum wheat[J]. Molecular Breeding,2014,34(4):1563-1578.
[21]田再民,张立平,王丽辉,等.小麦“BS20×Fu3”DH群体SSR遗传图谱的构建及不育基因的QTL定位[J].植物遗传资源学报,2015,16(04):857-867.
[22] Allen A M, Winfield M O, Burridge A J, et al. Characterisation of a wheat breeder’s array suitable for high throughput SNP genotyping of global accessions of hexaploid bread wheat[J]. Plant biotechnology Journal,2017,15(3):390.
[23] Zanke C, Ling J, Plieske J, et al. Genetic architecture of main effect,QTL for heading date in European winter wheat[J]. Front Plant Science,2014,5:217.
[24] Raz A, Motan N, Tamar E, et al. Ultra-dense genetic map of durum wheat×wild emmer wheat developed using the 90K iSelect SNP genotyping assay[J]. Mol Breeding,2014,34(4):1594-1592.
[25] Stuart J, Luca S, Salantur A, et al. High-throughput SNP genotyping of modern and wild emmer wheat for yield and root morphology using a combined association and linkage analysis[J]. Functional&Integrative Genomics,2017,6(17):667-685.
[26]张颖君.小麦种子休眠基因TaSdr与籽粒大小基因Ta GS的克隆和功能标记发掘[D].北京:中国农业科学院,2013.
[27] Liu J D, He G H, Rasheed A, et al. Genome-wide association mapping of black point reaction in common wheat(Triticum aestivum L.)[J]. BMC Plant Biology,2017,17:220.
[28] TanM K, Ei-bouhssini M, Emebiri L, et al. A SNP marker for the selection of HfrDrd,a Hessian fly-response gene in wheat[J].Molecular Breeding,2015,35:216-225.
[29] Lin M, Cai S, Wang S. et al. Genotyping-by-sequencing(GBS)identified SNP tightly linked to QTL for pre-harvest sprouting resistance[J]. Theoretical and Applied Genetics,2015,128(7):1385-1395.
[30] Gao L, Kielsmeier C J, Bajgain P, et al. Development of genotyping by sequencing(GBS)-and array-derived SNP markers for stem rust resistance gene Sr42[J]. Molecular Breeding,2015,35:207-215.
[31]禹文龙.基于SNP标记的小麦体细胞杂种渐渗系山融3号耐盐相关QTL分析[D].济南:山东大学,2015.
[32] Zhu C, Gore M, Buckler E S, et al. Status and prospects of association mapping in plants[J]. Plant Genome,2008,1:5-20.
[33] Ingvarsson P K, Nathaniel R S. Association genetics of complex traits in plants[J]. New Phytologist,2011,189:909-922.
[34] Palaisa K A, Morgante M, Williams M, et al. Contrasting effects of selection on sequence diversity and linkage disequilibrium at two phytoene synthase loci[J]. Plant Cell,2003,15:1795-1806.
[35] Sivakumar S, Susanne D, Marta L, et al. Genome-wide association study for grain yield and related traits in an elite spring wheat population grown in temperate irrigated environments[J].Theoretical and Applied Genetics,2015,128(2):353-363.
[36] Liu W Z, Maccaferri M, Bulli P, et al. Genome-wide association mapping for seedling and field resistance to Puccinia striiformis f.sp. tritici in elite durum wheat[J]. Theoretical and Applied Genetics,2017,130(4):649-667.
[37]周秀文.基于SNP标记的小麦氮效率性状的关联分析[D].泰安:山东农业大学,2016.
[38] Jighly A, Oyiga B C, Makdis F, et al. Genome-wide DArT and SNP scan for QTL associated with resistance to stripe rust(Puccinia striiformis f. sp. tritici)in elite ICARDA wheat(Triticumaestivum L.)germplasm[J].Theoretical and Applied Genetics,2015,128(7):1277-1295.
[39] Chen G, Zhang H, Deng Z, et al. Genome-wide association study for kernel weight-related traits using SNPs in a Chinese winter wheat population[J]. Euphytica,2016,212(2):173-185.
[40] Lin T, Zhu G, Zhang J, et al. Genomic analyses provide insights into the history of tomato breeding[J]. Nat Genet,2014,46(11):1220-1226.
[41] Zanke C D, Rodemann B, Ling J, et al. Genome-wide association mapping of resistance to eyespot disease(Pseudocercosporella herpotrichoides)in European winter wheat(Triticum aestivum L.)and fine-mapping of Pch1[J]. Theoretical and Applied Genetics,2017,130(3):505-514.
[42] Guttieri M J, Frels K, Regassa T, et al. Variation for nitrogen use efficiency traits in current and historical great plains hard winter wheat[J]. Euphytica. 2017,213:87.
[43] ManginiG,MargiottaB,MarcotuliI,etal.Geneticdiversityandphenetic analysis in wheat(Triticum turgidum subsp. durum and Triticum aestivum subsp. aestivum)landraces based on SNP markers[J].Genetic Resources and Crop Evolution,2017,64(6):1269-1280.
[44] Ren J, Chen L, Sun D, et al. SNP-revealed genetic diversity in wild emmer wheat correlates with ecological factors[J]. BMC Evol Biol,2013,13:169.
[45]曹廷杰,谢菁忠,吴秋红,等.河南省近年审定小麦品种基于系谱和SNP标记的遗传多样性分析[J].作物学报,2015,02:197-206.
[46]刘进英,董雪,冯玉梅,等.不同休眠特性小麦中TaGAMyb-B基因的等位变异及其表达特性[J].麦类作物学报,2016,06:708-713.