|本期目录/Table of Contents|

[1]薛晓杰,杜晓云,盖艺,等.基于GBS测序开发SNP在植物上的应用进展[J].江苏农业科学,2020,48(13):62-68.
　Xue Xiaojie,et al.Application progress of SNPs in plants based on GBS sequencing[J].Jiangsu Agricultural Sciences,2020,48(13):62-68.
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基于GBS测序开发SNP在植物上的应用进展(PDF)
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《江苏农业科学》[ISSN:1002-1302/CN:32-1214/S]

卷:
第48卷
期数:
2020年第13期
页码:
62-68
栏目:
专论与综述
出版日期:
2020-07-05

文章信息/Info

Title:
Application progress of SNPs in plants based on GBS sequencing
作者:
薛晓杰1;  杜晓云2;  盖艺1;  唐岩2;  孙燕霞2;  宋来庆2;  姜中武1; 2
1.烟台大学生命科学学院，山东烟台 264005； 2.山东省烟台市农业科学研究院，山东烟台265500
Author(s):
Xue Xiaojie; et al
关键词:
SNP分子标记; GBS技术; 简化基因组测序; 遗传图谱构建; QTL定位; 基因定位
Keywords:
-
分类号:
S184
DOI:
-
文献标志码:
A
摘要:
基因分型测序(genotyping by sequencing，GBS)因具有实现相对简单、成本较低、可产生高通量SNP的优点而受到青睐。单核苷酸多态性(single nucleotide polymorphism，SNP)因简单、快速、特异性强、稳定遗传、便于检测等特点已成为目前最广泛使用的分子标记之一。本文就利用GBS技术开发SNP分子标记近年来在亲缘关系评价、重要农艺性状鉴定、遗传多样性研究、遗传图谱构建以及基因定位等方面在国内外的研究进展进行综述，并对其今后的研究提出展望，以期为其在植物上的更广泛应用提供参考。
Abstract:
-

参考文献/References:

［1］Kim C，Guo H，Kong W Q，et al. Application of genotyping by sequencing technology to a variety of crop breeding programs［J］. Plant Science，2016，242：14-22.
［2］Lander E S.The new genomics： global views of biology［J］. Science，1996，274(5287)：536-539.
［3］Brookes A J.The essence of SNPs［J］. Gene，1999，234(2)：177-186.
［4］Wang D G，Fan J B，Siao C J，et al.Large-scale identification，mapping and genotyping of single-nucleotide polymorphisms in the human genome［J］. Science，1998，280(5366)：1077-1082.
［5］He J F，Zhao X，Laroche A，et al.Genotyping-by-sequencing(GBS)，an ultimate marker-assisted selection (MAS) tool to accelerate plant breeding［J］. Frontiers in Plant Science，2014，5：484.
［6］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.
［7］Baird Nathan A，Etter Paul D，Atwood Tressa S，et al.Rapid SNP discovery and genetic mapping using sequenced RAD markers［J］. PLoS One，2008，3(10)：e3376.
［8］Hwang K，Oh S，Kim K，et al.Genotyping-by-sequencing approaches using optimized two-enzyme combinations in Asian pears (Pyrus spp.)［J］. Molecular Breeding，2019，39(12)：1-9.
［9］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.
［10］Glaubitz J C，Casstevens T M，Lu F，et al.TASSEL-GBS： a high capacity genotyping by sequencing analysis pipeline［J］. PLoS One，2014，9(2)：e90346.
［11］Melo A T O，Bartaula R，Hale I. GBS-SNP-CROP：a reference-optional pipeline for SNP discovery and plant germplasm characterization using variable length，paired-end genotyping-by-sequencing data［J］. BMC Bioinformatics，2016，17(1)：29.
［12］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，2016，16(8)：e0161333.
［13］Taranto F，DAgostino N，Greco B，et al.Genome-wide SNP discovery and population structure analysis in pepper (Capsicum annuum) using genotyping by sequencing［J］. BMC Genomics，2016，17(1)：943.
［14］王小柯，江东，孙珍珠. 利用GBS技术研究240份宽皮柑橘的系统演化［J］. 中国农业科学，2017，50(9)：1666-1673.
［15］Zhao P，Zhou H J，Potter D，et al.Population genetics，phylogenomics and hybrid speciation of Juglans in China determined from whole chloroplast genomes transcriptomes and genotyping-by-sequencing (GBS)［J］. Molecular Phylogenetics and Evolution，2018，126：250-265.
［16］Wu X B，Alexander L W. Genetic diversity and population structure analysis of big leaf hydrangea using genotyping-by-sequencing［J］. Journal of the American Society for Horticultural Science，2019，144(4)：257-263.
［17］Niu S Z，Song Q F，Koiwa H，et al.Genetic diversity，linkage disequilibrium，and population structure analysis of the tea plant (Camellia sinensis) from an origin center，Guizhou plateau，using genome-wide SNPs developed by genotyping-by-sequencing［J］. BMC Plant Biology，2019，19(1)：328.
［18］Pavan S，Marcotrigiano A R，Ciani E，et al.Genotyping-by-sequencing of a melon (Cucumis melo L.) germplasm collection from a secondary center of diversity highlights patterns of genetic variation and genomic features of different gene pools［J］. BMC Genomics，2017，18(1)：53.
［19］Solomon A M，Han K，Lee J H，et al.Genetic diversity and population structure of Ethiopian Capsicum germplasms［J］. PLoS One，2019，14(5)：e0216886.
［20］周萍萍，颜红海，彭远英，等. 基于高通量GBS-SNP标记的栽培燕麦六倍体起源研究［J］. 作物学报，2019，45(10)：1604-1612.
［21］Pootakham W，Jomchai N，Ruang-Areerate P，et al. Genome-wide SNP discovery and identification of QTL associated with agronomic traits in oil palm using genotyping-by-sequencing (GBS)［J］. Genomics，2015，105(5-6)：288-295.
［22］Lee J，Izzah N K，Choi B S，et al.Genotyping-by-sequencing map permits identification of clubroot resistance QTLs and revision of the reference genome assembly in cabbage (Brassica oleracea L.)［J］. DNA Research，2016，23(1)：29-41.
［23］Ipek A，Ipek M，Ercisli S，et al.Transcriptome-based SNP discovery by GBS and the construction of a genetic map for olive［J］. Functional & Integrative Genomics，2017，17(5)：493-501.
［24］Jo J，Purushotham P M，Han K，et al. Development of a genetic map for onion (Allium cepa L.) using reference-free genotyping-by-sequencing and SNP assays［J］. Frontiers in Plant Science，2017，8：1606.
［25］Li X，Kong C C，Yu H L，et al. Identification of a major QTL for seed number per silique in cabbage (Brassica oleracea L. var. capitata) using genotyping by sequencing［J］. Euphytica，2019，215(7)：UNSP 133.
［26］Carrasco B，Gonzalez M，Gebauer M，et al. Construction of a highly saturated linkage map in Japanese plum (Prunus salicina L.) using GBS for SNP marker calling［J］. PLoS One，2018，13(12)：e0208032.
［27］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.
［28］Diouf L，Pan Z E，He S P，et al. High-density linkage map construction and mapping of salt-tolerant QTLs at seedling stage in upland cotton using genotyping by sequencing (GBS)［J］. International Journal of Molecular Sciences，2017，18(12)：2622.
［29］Bhattarai U，Subudhi P K.Identification of drought responsive QTLs during vegetative growth stage of rice using a saturated GBS-based SNP linkage map［J］. Euphytica，2018，214(2)：38.
［30］Zhang L，Guo D L，Guo L L，et al.Construction of a high-density genetic map and QTLs mapping with GBS from the interspecific F1 population of P. ostii ‘Fengdan Bai’ and P. suffruticosa ‘Xin Riyuejin’［J］. Scientia Horticulturae，2019，246：190-200.
［31］Gabay G，Dahan Y，Izhaki Y，et al. High-resolution genetic linkage map of European pear (Pyrus communis) and QTL fine-mapping of vegetative budbreak time［J］. BMC Plant Biology，2018，18(1)：175.
［32］Passianotto A L D，Sonah H，Dias W P，et al.Genome-wide association study for resistance to the southern root-knot nematode (Meloidogyne incognita) in soybean［J］. Molecular Breeding，2017，37(12)：1-11.
［33］郭 燕，乔大河，杨 春，等.基于全基因组SNP的贵州久安古茶树遗传关系分析［J］. 植物遗传资源学报，2019，20(1)：26-36.
［34］Gerardo N L，Cristóbal B，Catalina P，et al.High-density genetic map and QTL analysis of soluble solid content，maturity date，and mealiness in peach using genotyping by sequencing［J］. Scientia Horticulturae，2019，2579(17 )：108734.
［35］高美玲，梁晓雪，刘秀杰，等.基于极端个体GBS测序初步定位西瓜果形基因［J］. 分子植物育种，2020，18 (10)：3164- 3171.
［36］杨 柳，周鹤莹，薄文浩，等.基于选择清除分析鉴定影响枣果实大小的基因［J］. 北京林业大学学报，2019，41(10)：30-36.
［37］Guajardo V，Solis S，Sagredo B，et al.Construction of high density sweet cherry(Prunus avium L.) linkage maps using microsatellite markers and snps detected by genotyping-by-sequencing (GBS)［J］. PLoS One，2015，10(5)：e0127750.
［38］Zhou Z，Zhang C，Zhou Y，et al. Genetic dissection of maize plant architecture with an ultra-high density bin map based on recombinant inbred lines［J］. BMC Genomics，2016，17：178.
［39］Celik I，Bodur S，Frary A，et al.Genome-wide SNP discovery and genetic linkage map construction in sunflower (Helianthus annuus L.) using a genotyping by sequencing (GBS) approach［J］. Molecular Breeding，2015，36(9)：133，
［40］Lee J，Izzah N K，Choi B S，et al.Genotyping-by-sequencing map permits identification of clubroot resistance QTLs and revision of the reference genome assembly in cabbage (Brassica oleracea L.)［J］. DNA Research，2016，23(1)：29-41.
［41］Bielenberg D G，Rauh B，Fan S H，et al.Genotyping by sequencing for SNP-based linkage map construction and QTL analysis of chilling requirement and bloom date in peach ［Prunus persica (L.) Batsch［J］. PLoS One，2015，10(10)：e0139406.
［42］Gardner K M，Brown P，Cooke T F，et al. Fast and cost-effective genetic mapping in apple using next-generation sequencing［J］. G3 (Bethesda)，2014，4(9)：1681-1687.
［43］Manickavelu A，Jighly A，Ban T.Molecular evaluation of orphan Afghan common wheat (Triticum aestivum L.) landraces collected by Dr. Kihara using single nucleotide polymorphic markers［J］. BMC Plant Biology，2014，14(1)：320.
［44］Nimmakayala P，Tomason Y R，Abburi V L，et al.Genome-wide differentiation of various melon horticultural groups for use in GWAS for fruit firmness and construction of a high resolution genetic map［J］. Frontiers in Plant Science，2016，7：1437.
［45］Tanhuanpaa P，Erkkila M，Tenhola-Roininen T，et al.SNP diversity within and among Brassica rapa accessions reveals no geographic differentiation［J］. Genome，2016，59(1)：11-21.
［46］Ashraf B H，Byrne S，Fe D，et al. Estimating genomic heritabilities at the level of family-pool samples of perennial ryegrass using genotyping-by-sequencing［J］. Theoretical and applied Genetics，2016，129(1)：45-52.
［47］Pavan S，Lotti C，Marcotrigiano A，et al. A distinct genetic cluster in cultivated chickpea as revealed by genome-wide marker discovery and genotyping［J］. Plant Genome，2017，10(2)：1-9.
［48］Otto L G，Mondal P，Brassac J，et al. Use of genotyping-by-sequencing to determine the genetic structure in the medicinal plant chamomile，and to identify flowering time and alpha-bisabolol associated SNP-loci by genome-wide association mapping［J］. BMC Genomics，2017，18(1)：1-18.
［49］Kumar S，Kirk C，Deng C，et al.Genotyping-by-sequencing of pear (Pyrus spp.) accessions unravels novel patterns of genetic diversity and selection footprints［J］. Horticulture Research，2017，4(1)：17015.
［50］蔡 露，杨 欢，王 勇，等.利用GBS技术开发烟草SNP标记及遗传多样性分析［J］. 中国烟草科学，2018，39(5)：17-24.
［51］Wang X，Bao K，Reddy U K，et al.The USDA cucumber (Cucumis sativus L.) collection：genetic diversity，population structure，genome-wide association studies，and core collection development［J］. Horticulture Research，2018，5(1)：64.
［52］Lee S R，Gaskin J F，Kim Y D. Molecular diagnosis for a Tamarix species from two reclaimed lands along the Yellow Sea in Korea inferred from genome wide SNP markers［J］. Journal of Systematics and Evolution，2018，57(3)：247-255.
［53］Ryu J，Kim W J，Im J，et al.Single nucleotide polymorphism (SNP) discovery through genotyping-by-sequencing (GBS) and genetic characterization of Dendrobium mutants and cultivars［J］. Scientia Horticulturae，2019，244：225-233.
［54］Upadhyaya H D，Vetriventhan M，Deshpande S P，et al.Population genetics and structure of a global foxtail millet germplasm collection［J］. Plant Genome，2015，8(3)：1-13.
［55］Ertiro B T，Ogugo V，Worku M，et al. Comparison of kompetitive allele specific PCR (KASP) and genotyping by sequencing (GBS) for quality control analysis in maize［J］. BMC Genomics，2015，16(1)：908.
［56］Chitwood J，Shie A N，Mou B Q，et al.Population structure and association analysis of bolting，plant height，and leaf erectness in spinach［J］. Hortscience，2016，51(5)：481-486.
［57］Wiersma A T，Pulman J A，Brown L K，et al. Identification of Pm58 from Aegilops tauschii［J］. Theoretical and Applied Genetics，2017，130(6)：1123-1133.
［58］董艳辉，宇凤，温鑫，等.基于高通量测序的藜麦连作根际土壤微生物多样性研究［J］. 华北农学报，2019，34(2)：205-211.
［59］Liu X P，Yu L X.Genome-wide association mapping of loci associated with plant growth and Forage production under salt stress in alfalfa (Medicago sativa L.)［J］. Frontiers in Plant Science，2017，8：853.
［60］Zaid I U，Tang W J，Liu E B，et al. Genome-wide single-nucleotide polymorphisms in CMS and restorer lines discovered by genotyping using sequencing and association with marker-combining ability for 12 yield-related traits in Oryza sativa L. subsp japonica［J］. Frontiers in Plant Science，2017，8：143.
［61］Kang Y J，Lee B M，Nam M，et al.Identification of quantitative trait loci associated with flowering time in perilla using genotyping-by-sequencing［J］. Molecular Biology Reports，2018，46(4)：4397-4407.
［62］Hussain W，Baenziger P S，Belamkar V，et al.Genotyping-by-sequencing derived high-density linkage map and its application to QTL mapping of flag leaf traits in bread wheat［J］. Scientific Reports，2017，7(1)：1-15.
［63］Bajgain P，Rouse M N，Tsilo T J，et al. Nested association mapping of stem rust resistance in wheat using genotyping by sequencing［J］. PLoS One，2016，11(5)：e0155760.
［64］de Leon T B，Linscombe S，Subudhi P K. Molecular dissection of seedling salinity tolerance in rice (Oryza sativa L.) using a high-density GBS-based SNP linkage map［J］. Rice，2016，9(1)：52.
［65］Moncada M D，Tovar E，Montoya J C，et al.A genetic linkage map of coffee (Coffea arabica L.) and QTL for yield，plant height，and bean size［J］. Tree Genetics & Genomes，2016，12(1)：5.
［66］McClure K A，Gardner K M，Toivonen P M A，et al.QTL analysis of soft scald in two apple populations［J］. Horticulture Research，2016，3：16043.
［67］Qi H K，Wang N，Qiao W Q，et al.Construction of a high-density genetic map using genotyping by sequencing (GBS) for quantitative trait loci (QTL) analysis of three plant morphological traits in upland cotton (Gossypium hirsutum L.)［J］. Euphytica，2017，213(4)：83.
［68］Ravelombola W，Qin J，Shi A N，et al.Association mapping revealed SNP markers for adaptation to low phosphorus conditions and rock phosphate response in USDA cowpea ［Vigna unguiculata (L.) Walp.］ germplasm［J］. Euphytica，2017，213(8)：14.
［69］Shimray P W，Bajaj D，Srivastava R，et al.Identifying transcription factor genes associated with yield traits in chickpea［J］. Plant Molecular Biology Reporter，2017，35(5)：562-574.
［70］Zhang J P，Long Y，Wang L M，et al.Consensus genetic linkage map construction and QTL mapping for plant height-related traits in linseed flax (Linum usitatissimum L.)［J］. BMC Plant Biology，2018，18(1)：1-12.
［71］Gali K K，Liu Y，Sindhu A，et al.Construction of high-density linkage maps for mapping quantitative trait loci for multiple traits in field pea (Pisum sativum L.)［J］. BMC Plant Biology，2018，18：172.
［72］Talukder Z I，Long Y M，Seiler G J，et al.Introgression and monitoring of wild Helianthus praecox alien segments associated with Sclerotinia basal stalk rot resistance in sunflower using genotyping-by-sequencing［J］. PLoS One，2019，14(3)：e0213065.
［73］Perez-de-Castro A，Esteras C，Alfaro-Fernandez，et al.Fine mapping of wmv1551，a resistance gene to Watermelon mosaic virus in melon［J］. Molecular Breeding，2019，39(7)：93.

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[1]陈坤,刘亚利,覃宏宇,等.基于SNP标记的玉米散粉吐丝间隔期QTL定位[J].江苏农业科学,2024,52(16):79.
　Chen Kun,et al.QTL mapping of maize anthesis silking interval based on SNP markers[J].Jiangsu Agricultural Sciences,2024,52(13):79.

备注/Memo

备注/Memo:
收稿日期：2020-040-02
基金项目：山东省外专双百计划(编号：WST2018013)；山东省重点研发项目(编号：2018GHZ005)。
作者简介：薛晓杰(1994—)，女，山东烟台人，硕士研究生，主要从事果树分子与生理技术研究，E-mail：xuexiaojieYT@163.com；共同第一作者：杜晓云(1979—)，女，山西吕梁人，博士，高级农艺师，主要从事果树生物技术育种研究，E-mail：duxiaoyunduzi@163.com。
通信作者：姜中武，博士，研
更新日期/Last Update: 2020-07-05