GBS技术在植物中的研究进展
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摘要
随着高通量测序技术的发展,一种高效而经济的SNP(single nucleotide polymorphism)发掘和基因分型技术GBS(genotyping by sequencing)被开发出来,避免了传统基因型鉴别方法的不足,现已被广泛应用于植物遗传图谱构建、全基因组关联分析、基因多样性研究以及种质鉴定和品种识别等多个领域。从GBS技术的原理、流程、特点以及应用等方面对近年来植物应用GBS技术所进行的研究进展进行综述,并提出了今后GBS技术的研究重点,以期为GBS技术在植物的应用研究提供参考。
With the development of high throughput sequencing technology,GBS(genotyping by sequencing)technique,an economic technique to discover SNP and genotype myriad of crop germpasms in an effective way,has been developed,which avoids the deficiency of traditional genotypic identification methods. It has been widely used in many fields including construction of genetic map,genome-wide association study,genetic diversity and germplasm dentification and variety identification. In this paper,the research progress of GBS technology in plants was reviewed from the principle,process,characteristics and application. And the research emphasis on GBS technology was putting forward in the future,which was expected to provide reference for the future research of GBS technology on plants.
With the development of high throughput sequencing technology,GBS(genotyping by sequencing)technique,an economic technique to discover SNP and genotype myriad of crop germpasms in an effective way,has been developed,which avoids the deficiency of traditional genotypic identification methods. It has been widely used in many fields including construction of genetic map,genome-wide association study,genetic diversity and germplasm dentification and variety identification. In this paper,the research progress of GBS technology in plants was reviewed from the principle,process,characteristics and application. And the research emphasis on GBS technology was putting forward in the future,which was expected to provide reference for the future research of GBS technology on plants.
引文
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[2] Harismendy O,Ng P C,Strausberg R L,et al.. Evaluation of next generation sequencing platforms for population targeted sequencing studies[J]. Genome Biol.,2009,10(3):1-13.
[3] Elshire R J,Glaubitz J C,Sun Q,et al.. A robust,simple genotyping-by-sequencing(GBS)approach for high diversity species[J]. PLoS ONE,2011,6(5):e19379.
[4] Poland J A,Brown P J,Sorrells M E,et al.. Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach[J]. PLoS ONE,2012,7(2):e32253.
[5] Sonah H,Bastien M,Iquira E,et al.. An improved genotyping by sequencing(GBS)approach offering increased versatility and efficiency of SNP discovery and genotyping[J]. PLoS ONE,2013,8(1):e54603.
[6] Narum S R,Buerkle C A,Davey J W,et al.. Genotyping-bysequencing in ecological and conservation genomics[J]. Mol.Ecol.,2013,22(11):2841-2847.
[7] Beissinger T M,Hirsch C N,Sekhon R S,et al.. Marker density and read depth for genotyping populations using genotyping-by-sequencing[J]. Genetics,2013,193(4):1073-1081.
[8] Spindel J,Wright M,Chen C,et al.. Bridging the genotyping gap:Using genotyping by sequencing(GBS)to add highdensity SNP markers and new value to traditional bi-parental mapping and breeding populations[J]. Theor. Appl. Genetics,2013,126(11):2699-2716.
[9] De M D,Peters S O,Mitchell S E,et al.. Genotyping-bysequencing(GBS):A novel, efficient and cost-effective genotyping method for cattle using next-generation sequencing[J]. PLoS ONE,2013,8(5):e62137.
[10] Crossa J,Beyene Y,Kassa S,et al.. Genomic prediction in maize breeding populations with genotyping-by-sequencing[J].G3,2013,3(11):1903-1926.
[11]李翔,范成明,卢龙斗,等.甘蓝型油菜遗传图谱构建及重要性状遗传解析的研究进展[J].分子植物育种,2016,14(1):98-116.Li X,Fan C M,Lu L D,et al.. Research on construction of genetic maps and dissection of important traits in Brassica napus[J]. Mol. Plant Breed.,2016,14(1):98-116.
[12]秦伟伟,李永祥,李春辉,等.基于高密度遗传图谱的玉米籽粒性状QTL定位[J].作物学报,2015,41(10):1510-1518.Qin W W,Lin Y X,Lin C H,et al.. QTL mapping for kernel related traits based on a high-density genetic map[J]. Acta Agron. Sin.,2015,41(10):1510-1518.
[13]罗昕.基于下一代测序的玉米高通量SNP开发及关联分析[D].武汉:华中农业大学,硕士学位论文,2015.Luo X. Development and correlation analysis of maize high throughput SNP based on next-generation sequencing[D].Wuhan:Huazhong Agricultural University, Master Dissertation,2015.
[14] Sonah H,Bastien M,Iquira E,et al.. An improved genotyping by sequencing(GBS)approach offering increased versatility and efficiency of SNP discovery and genotyping[J]. PLoS ONE,2013,8(1):e54603.
[15] Gardner K M,Brown P,Cooke T F,et al.. Fast and costeffective genetic mapping in apple using next-generation sequencing.[J]. G3-Genes Genomes Genetics,2014,4(9):1681-1687.
[16]李春辉.玉米高密度重组图谱构建及耐旱相关性状的遗传解析[D].北京中国农业科学院,博士学位论文,2015.Lin C H. Construction of high density recombination map and genetic analysis of drought tolerance traits in maize[D].Beijing:Chinese Academy of Agricultural Sciences, Doctor Dissertation,2015.
[17] Li H,Vikram P,Singh R P,et al.. A high density GBS map of bread wheat and its application for dissecting complex disease resistance traits[J]. BMC Genomics,16,1(2015-03-19),2015,16(1):216.
[18] Liu C,Zhu S,Tang S,et al.. QTL analysis of four main stem bark traits using a GBS-SNP-based high-density genetic map in ramie[J]. Sci. Rep.,2017,7:13458.
[19] Edae E A,Olivera P D,Jin Y,et al.. Genotype-by-sequencing facilitates genetic mapping of a stem rust resistance locus in Aegilops umbellulata,a wild relative of cultivated wheat[J].BMC Genomics,2016,17(1):1039.
[20] Heffelfinger C,Fragoso C A,Moreno M A,et al.. Flexible and scalable genotyping-by-sequencing strategies for population studies[J]. BMC Genomics,2014,15(1):979.
[21] Huang Y F,Poland J A,Wight C P,et al.. Using genotypingby-sequencing(GBS)for genomic discovery in cultivated oat[J]. PLoS ONE,2014,9(7):e102448.
[22] Wong M M L, Gujariaverma N, Ramsay L, et al..Classification and characterization of species within the genus Lens using genotyping-by-sequencing(GBS)[J]. PLoS ONE,2015,10(3):e0122025.
[23]沈登锋.不同海拔藏川杨遗传多样性评估及苗期表型关联分析[D].北京:北京林业大学,博士学位论文,2014.Shen D F. Genetic diversity analysis of Tibetan poplar(Populus szechunanica var. Tibetica)population collected from different altitudes and phenotype of seedlings association analysis[D].Beijing:Beijing Forestry University, Doctor Dissertation,2014.
[24]黄之涛.基于Bin map高密度连锁图谱定位玉米容重及相关性状的QTL[D].四川雅安:四川农业大学,硕士学位论文,2014.Huang Z T. QTL analysis for maize test weight related traits using the high density linkage map Bin map[D]. Sichuan Yaan:Sichuan Agricultural University,Master Dissertation,2014.
[25]赖国荣,张静,刘函,等.基于GBS构建玉米高密度遗传图谱及营养品质性状QTL定位[J].农业生物技术学报,2017,25(9):1400-1410.Lai G R,Zhang J,Liu H,et al.. Construction of high density genetic map via GBS technology and QTL mapping for nutritional auality traits in maize(Zea mays)[J]. J. Agric.Biotechnol.,2017,25(9):1400-1410.
[26]牛璐瑶.一个人工合成玉米群体的基因组变异分析[D].武汉:华中农业大学,硕士学位论文,2016.Niu L Y. Genomic variation of a diverse synthetic population in maize[D]. Wuhan:Huazhong Agricultural University,Master Dissertation,2016.
[27]王明.玉米抗丝黑穗病的全基因组关联分析[D].武汉:华中农业大学,博士学位论文,2012.Wang M. Genome-wide association study(GWAS)of resistance to head smut in maize(Zea mays L.)[D]. Wuhan:Huazhong Agricultural University,Doctor Dissertation,2012.
[28] Torkamaneh D,Laroche J,Belzile F. Genome-wide SNP calling from genotyping by sequencing(GBS)data:A comparison of seven pipelines and two sequencing technologies[J]. PLoS ONE,2016,11(8):e0161333.
[29] Faville M J,Ganesh S,Cao M,et al.. Predictive ability of genomic selection models in a multi-population perennial ryegrass training set using genotyping-by-sequencing[J].Theor. Appl. Genetics,2018,131(3):703-720.
[30] Ward J A,Jasbir B,Felicidad F F,et al.. Saturated linkage map construction inRubus idaeususing genotyping by sequencing and genome-independent imputation[J]. BMC Genomics,2013,14(1):2.
[31] Rocher S, Jean M, Castonguay Y, et al.. Validation of genotyping-by-sequencing analysis in populations of tetraploid alfalfa by 454 sequencing[J]. PLoS ONE, 2015, 10(6):e0131918.
[32] Liu H,Bayer M,Druka A,et al.. An evaluation of genotyping by sequencing(GBS)to map the Breviaristatum-e(ari-e)locus in cultivated barley[J]. BMC Genomics,2014,15(1):104-104.
[33] Yu L X,Zheng P,Zhang T,et al.. Genotyping-by-sequencing based genome-wide association studies on Verticillium wilt resistance in autotetraploid alfalfa(Medicago sativa L.)[J].Mol.Plant Pathol.,2016,18(2):187-194.
[34] Reasor E H,Brosnan J T,Staton M E,et al.. Genotypic and phenotypic evaluation of off-type grasses in hybrid Bermudagrass[Cynodon dactylon(L.)Pers.×C.transvaalensis Burtt-Davy] putting greens using genotyping-bysequencing and morphological characterization:[J]. Hereditas,2018,155(1):8.
[35] Arbizu C I,Ellison S L,Senalik D,et al.. Genotyping-bysequencing provides the discriminating power to investigate the subspecies of Daucus carota(Apiaceae)[J]. BMC Evol.Biol.,2016,16(1):234.
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