LI Jing,LI Xinyun,MIAO Yu,et al.Genetic Diversity Analysis of Common Eggplant Germplasm Resources in Yunnan Based on SLAF-seq[J].Northern Horticulture,2023,(15):24-32.[doi:10.11937/bfyy.20224138]
基于SLAF-seq对云南常见茄子种质资源遗传多样性分析
- Title:
- Genetic Diversity Analysis of Common Eggplant Germplasm Resources in Yunnan Based on SLAF-seq
- Keywords:
- Yunnan Province; eggplant resources; simplify genome sequencing; genetic diversity; SNP tag
- 文献标志码:
- A
- 摘要:
- 以从云南各州市收集的35份茄子种质资源为试材，运用简化基因组测序技术(specificlocus amplified fragment sequencing，SLAF-seq)对其进行遗传多样性分析，研究云南常见茄子种质资源的遗传多样性及开发特异性SNP标记，以期为云南茄子资源种质创新、杂交育种及砧木筛选提供参考依据。结果表明：从35份茄子种质资源中共获得147.42 Mb读长数据，不同资源的reads数目范围在1 474 699～8 628 640。测序获得的GC含量在38.29％～46.40％，平均GC含量为39.72％，对照为41.96％。测序质量值Q30在88.11％～93.56％，平均Q30值为91.00％，对照Q30为88.11％。根据测序结果共获得SLAF标签159 847个，其中多态性标签共84 119个，共筛选出3 006 351个高效性SNP标记。运用获得的SNP标记对35份茄子资源进行遗传多样性分析、聚类分析及群体PCA分析，结果表明35份茄子种质资源可分为5组。
- Abstract:
- Thirty five eggplant germplasm resources collected by the research team from Yunnan Provinces and cities were used to analyze their genetic diversity by using specific location amplified fragment sequencing (SLAF-seq).The genetic diversity of common eggplant germplasm resources in Yunnan and develop specific SNP markers were studied，in order to provide reference for germplasm innovation，cross breeding and rootstock selection of eggplant resources in Yunnan.The results showed that 147.42 Mb read length data were obtained from 35 eggplant germplasm resources，and the number of reads from different resources ranged from 1 474 699 to 8 628 640.The GC content obtained by sequencing was 38.29%-46.40%，the average GC content was 39.72%，and the control was 41.96%.The sequencing quality value Q30 was in the range of 88.11%-93.56%，the average Q30 value was 91.00%，and the control Q30 was 88.11%.According to the sequencing results，159 847 SLAF tags were obtained，included 84 119 polymorphic tags，and 3 006 351 highly efficient SNP tags were screened.The genetic diversity，cluster analysis and population PCA analysis of 35 eggplant germplasm resources were conducted by using the obtained SNP markers.The results showed that 35 eggplant germplasm resources could be divided into 5 groups.
参考文献/References:
[1]TAHER D,SOLBERG S ,PROHENS J,et al.World vegetable center eggplant collection：Origin，composition,seed dissemination and utilization in breeding[J].Frontiers in Plant Science,2017（8）:1484.[2]王锦秀.《植物名实图考》中一些百合科植物考证兼论茄子在中国的栽培起源和传播[D].北京:中国科学院研究生院(植物研究所),2005.[3]连勇,刘富中,田时炳,等.“十二五”我国茄子遗传育种研究进展[J].中国蔬菜,2017,1(2):14-22.[4]高寿梅,沈力,孟金贵.云南茄属野生植物资源及其分布特点[J].南方园艺,2014,25(4):21-22.[5]吴丽艳,龚亚菊,黎志彬,等.云南野茄资源形态学性状的多元统计与分析[J].云南大学学报(自然科学版),2014,36(S1):135-142.[6]廖秋石.茄属种质资源表型性状评价及遗传多样性SSR分析[D].南昌:江西农业大学,2020.[7]LI H Z，CHEN H Y，ZHUANG T M，et al.Analysis of genetic variation in eggplant and related Solanum species using sequencErelated amplified polymorphism markers[J].Scientia Horticulturae，2010，125(1)：19-24.[8]廖毅,孙保娟,黎振兴,等.茄子及其近缘野生种遗传多样性及亲缘关系的AFLP分析[J].热带作物学报,2009,30(6):781-787.[9]齐东霞,张映,刘富中,等.中俄茄子种质资源遗传多样性研究[J].植物遗传资源学报,2017,18(3):404-412.[10]SUN X W，LIU D Y，ZHANG X F，et al SLAFseq：An efficient method of largEscale de novo SNP discovery and genotyping using highthroughput sequencing[J].PLoS One,2013,8(3):e58700.[11]张一中,范昕琦,杨慧勇,等.基于简化基因组测序高粱育种材料亲缘关系的分析[J].生物技术通报，2020,36(12)：51-63.[12]李慧峰,黄咏梅,李彦青,等.基于SLAFseq技术的甘薯种质资源群体遗传进化分析[J].热带作物学报,2019,40(12):2390-2396.[13]WEN Y Z.A Highdensity genetic map for cucumber (Cucumis sativus L.) based on specific length amplified fragment (SLAF) sequencing and QTL analysis of fruit traits in cucumber[J].Frontiers in Plant Science，2016（7）：437.[14]蔡羽.基于简化基因组测序的中国大麦地方品种遗传多样性分析[D].雅安:四川农业大学,2019.[15]蒋舒蕊,王怀正,李静，等.云南野生茄科砧木资源农艺性状调查与4种土传病害抗病鉴定[J].南方农业学报,2021,52(10):2786-2796.[16]李信云,蒋舒蕊,李静，等.云南省部分野生茄子农艺性状调查与分析[J].北方园艺,2022(14):1-8.[17]KOZICH J J，WESTCOTT S L，BAXTER N T，et al.Development of a dualindex sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform[J].Applied and environmental microbiology，2013，79(17)：5112-5120.[18]LI H，DURBIN R.Fast and accurate short read alignment with Burrows Wheeler transform[J].Bioinformatics，2009，25(14)：1754-1760.[19]MCKENNA A，HANNA M，BANKS E，et al.The genome analysis toolkit：A map reduce framework for analyzing nextgeneration DNA sequencing data[J].Genome research，2010，20(9)：1297-1303.[20]LI H，HANDSAKER B，WYSOKER A，et al.The sequence alignment/map format and SAMtools[J].Bioinformatics，2009，25(16)：2078-2079.[21]KUMAR S，STECHER G，LI M，et al.MEGA X：Molecular evolutionary genetics analysis across computing platforms[J].Molecular Biology and Evolution,2018,35(6)：1547-1549.[22]ALEXANDER D H，NOVEMBRE J，LANGE K，et al.Fast modelbased estimation of ancestry in unrelated individuals[J].Genome Research，2009，19(9)：1655-1664.[23]ALKES L P，NICK J P，PLENGE R M，et al.Principal components analysis corrects for stratification in genomEwide association studies[J].Nature Genetics，2006,38(8):904-909.[24]申爱民,李永辉,蔡伟,等.河南省茄子育种现状及展望[J].中国瓜菜,2017,30(1):3-7.[25]LIU J，HUANG S，SUN M，et al.An improved allelEspecific PCR primer design method for SNP marker analysis and its application[J].Plant Methods，2012，8(1):34.[26]宋拉拉,赵丹,苏丹,等.基于简化基因组测序(SLAF-seq)对贵州辣椒品种亲缘关系分析[J].分子植物育种,2021,19(23):7995-8004.[27]WEI Q Z，WANG Y Z，QIN X D，et al.An SNPbased saturated genetic map and QTL analysis of fruit related traits in cucumber using specific length amplified fragment(SLAF) sequencing[J].BMC Genomics,2014（15）:1158.[28]赵海悦.基于简化基因组测序对人参遗传多样性分析及SNP位点的开发及验证[D].北京:中国农业科学院,2021.[29]ZHANG Y X，WANG L H，XIN H G，et al.Construction of a highdensity genetic map for sesame based on large scale marker development by specific length amplified fragment (SLAF) sequencing[J].BMC Plant Biology,2013，13(17):2636-2646.[30]王柏柯,李宁,唐亚萍,等.基于简化基因组测序技术的番茄雄性不育基因定位[J].西北农林科技大学学报(自然科学版），2017，45(6)：177-184.[31]张爱民,阳文龙,方红曼,等.作物种质资源研究态势分析[J].植物遗传资源学报，2018，19(3)：377-382.[32]张宏斌,吕东,赵明,等.基于全基因组SNP分子标记分析青海云杉遗传结构[J].植物研究,2022,42(3):373-382.[33]林珲,黄建都,陈继兵,等.茄子种质资源遗传多样性SRAP分析[J].分子植物育种,2019,17(19):6535-6542.
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备注/Memo
第一作者简介：李静（1998-），女，硕士研究生，研究方向为蔬菜遗传育种。Email：1580674703@qq.com.责任作者：赵凯（1981-），男，博士，副教授，现主要从事蔬菜遗传育种等研究工作。Email：343810456@qq.com.基金项目：国家自然科学基金资助项目（32160715）；云南省科技计划重点资助项目(202102AE090005)；云南泸西县蔬菜产业科技特派团资助项目（202204BI090006）。收稿日期：2022-10-12