基于简化基因组的花生InDel标记开发和功能解析
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摘要
InDel在基因组中的分布密度仅次于SNP,可作为动植物群体遗传分析、分子辅助育种等研究领域的有效分子标记。花生是世界范围内重要的油料作物之一。目前,花生栽培种全基因组已经公布,为准确挖掘花生基因组信息提供了重要参考。本研究通过169份花生核心种质的GBS(Genotyping-by-sequencing)测序和比对,共获得大小分布在1～14 bp范围内的10401个InDels。染色体Arahy.16上分布的InDels最多,达741个;而在染色体Arahy.08上分布的最少,有263个。参考基因组注释信息,仅有1167个InDels分布在功能基因相关区域。经GO注释,InDel分子功能主要包括催化活性(catalytic activity)和结合(binding);生物过程主要涉及代谢过程(metabolic process)、单组织过程(single-organism process)和细胞过程(cellular process)。经KEGG通路分析发现,InDels所在的基因区域的功能主要与代谢相关。本研究开发出全基因组水平的InDel标记,并做了相应功能分类和注释,为进一步分子验证和利用提供丰富的基因资源。
Insertion/deletion(InDel)is the second largest molecular markers,which provide the valuable reference for population genetic and marker-assisted selection study.Peanut is one of the most important oil crops worldwide.The whole genome sequence of cultivated peanut has been released and therefore provided the important genome reference.In this study,we focus on InDels detection in peanut genome based on 169 peanut core collections.10401 InDels ranged from 1 to 14 bp have been detected by double digest genotypingby sequencing(ddGBS).The largest number of InDels distributed on Arahy.16,while the smallest number of In Dels found on Arahy.08.Obviously,the coding regions of these InDels showed the specific functions,including catalytic activity and binding compared with other regions.The KEGG analysis suggested that InDels were mainly detected in the metabolism process.These InDels will provide the important genetic resources for the further validation.
Insertion/deletion(InDel)is the second largest molecular markers,which provide the valuable reference for population genetic and marker-assisted selection study.Peanut is one of the most important oil crops worldwide.The whole genome sequence of cultivated peanut has been released and therefore provided the important genome reference.In this study,we focus on InDels detection in peanut genome based on 169 peanut core collections.10401 InDels ranged from 1 to 14 bp have been detected by double digest genotypingby sequencing(ddGBS).The largest number of InDels distributed on Arahy.16,while the smallest number of In Dels found on Arahy.08.Obviously,the coding regions of these InDels showed the specific functions,including catalytic activity and binding compared with other regions.The KEGG analysis suggested that InDels were mainly detected in the metabolism process.These InDels will provide the important genetic resources for the further validation.
引文
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[6]李斯更,沈镝,刘博,邱杨,张晓辉,张忠华,王海平,李锡香.基于黄瓜基因组重测序的InDel标记开发及其应用.植物遗传资源学报,2013,14(2):278-283LiSG,ShenD,LiuB,QiuY,ZhangXH,ZhangZH,Wang H P,Li X X.Development and application of cucumber InDel markers based on genome re-sequencing.Journal of Plant Genetic Resources,2013,14(2):278-283
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[9]张浩.中国栽培花生(Arachis hypogaea L.)遗传多样性分析与核心种质构建.广州:仲恺农业工程学院,2013Zhang H.Construction of core collections and genetic diversity analysisofarachishypogaeacultivarinChina.Guangzhou:Zhongkai University of Agriculture and Engineering,2013
[10]王娟,李春娟,闫彩霞,赵小波,单世华.栽培种花生ddGBS测序中酶切组合的选择.花生学报,2017,46(4):48-51Wang J,Li C J,Yan C X,Zhao X B,Shan S H.The screening of ddGBS restriction enzyme combinations in peanut.Journal of Peanut Science,2017,46(4):48-51
[11]Li H,Durbin R.Fast and accurate short read alignment with Burrows-Wheelertransform.Bioinformatics,2009,25(14):1754-1760
[12]Li H,Handsaker B,Wysoker A,Fennell T,Ruan J,Homer N,Marth G,Abecasis G,Durbin R.1000 genome project data processing subgroup.The sequence alignment/map format and SAMTOOLS.Bioinformatics,2009,25(16):2078-2079
[13]Mckenna A,Hanna M,Banks E,Sivachenko A,Cibulskis K,Kernytsky A,GarimellaK,AltshulerD,GabrielS,DalyM,DePristoM A.TheGenome Analysis Toolkit:AMapReduce framework for analyzing next-generation DNA sequencing data.Genome Research,2010,20(9):1297-1303
[14]Bertioli D J,Cannon S B,Froenicke L,Huang G,Farmer A D,CannonEK,LiuX,GaoD,ClevengerJ,DashS,Ren L,MoretzsohnMC,ShirasawaK,HuangW,VidigalB,Abernathy B,Chu Y,Niederhuth C E,Umale P,Araújo A C,Kozik A,KimKD,BurowMD,VarshneyRK,WangX,ZhangX,BarkleyN,Guimar?esPM,IsobeS,GuoB,Liao B,StalkerH T,SchmitzRJ,SchefflerBE,Leal-BertioliS C,XunX,JacksonS A,MichelmoreR,Ozias-AkinsP.The genome sequences of Arachis duranensis and Arachis ipaensis,thediploidancestorsofcultivatedpeanut.NatureGenetics,2016,48(4):438-446
[15]Meng S,Yang X L,Dang P M,Cui S L,Mu G J,Chen C Y,LiuLF.Evaluationofinsertion-deletionmarkerssuitablefor genetic diversity studies and marker-trait correlation analyses in cultivated peanut(Arachis hypogaea L.).Genetics&Molecular Research Gmr,2016,doi:10.4238/gmr.15038207
[16]Liu L F,Dang P M,Chen C Y.Development and utilization of InDelmarkerstoidentifypeanut(Arachishypogaea)disease resistance.Frontiers in Plant Science,2015,6:988
[17]Mahmood S.Genome-wide characterization of insertion/deletion variationsandmarkerdevelopmentinoilseedrape(Brassica napusL.)byvalorizingresequencinggenomedata.Wuhan:Huazhong Agricultural University,2016
[18]吴磊,王丹,苏文悦,郭长虹,束永俊.利用比较基因组学开发山羊草属InDel分子标记.作物学报,2012,38(7):1334-1338Wu L,Wang D,Su W Y,Guo C H,Shu Y J.Developing InDel markers from aegilops genus based on comparative genomics.Acta Agronomica Sinica,2012,38(7):1334-1338
[2]Varshney R K,Nayak S N,May G D,Jackson S A.Nextgenerationsequencingtechnologiesandtheirimplicationsfor crop genetics and breeding.Trends in Biotechnology,2009,27(9):522-530
[3]杨洁.InDel标记的研究和应用进展.生物多样性,2016,24(2):237-243Yang J.Progress in research and application of InDel markers.Biodiversity Science,2016,24(2):237-243
[4]Alkan C,Coe B P,Eichler E E.Genome structural variation discovery and genotyping.Nature Reviews Genetics,2011,12(5):363-376
[5]郭广君,孙茜,刘金兵,潘宝贵,刁卫平,戈伟,高长洲,王述彬.基于辣椒基因组重测序的InDel标记开发及应用.江苏农业学报,2015,31(6):1400-1406Guo G J,Sun Q,Liu J B,Pan B G,Diao W P,Ge W,Gao C Z,WangSB.DevelopmentandapplicationofpepperInDel markersbasedongenomere-sequencing.JiangsuJournalof Agricultural Sciences,2015,31(6):1400-1406
[6]李斯更,沈镝,刘博,邱杨,张晓辉,张忠华,王海平,李锡香.基于黄瓜基因组重测序的InDel标记开发及其应用.植物遗传资源学报,2013,14(2):278-283LiSG,ShenD,LiuB,QiuY,ZhangXH,ZhangZH,Wang H P,Li X X.Development and application of cucumber InDel markers based on genome re-sequencing.Journal of Plant Genetic Resources,2013,14(2):278-283
[7]刘栓桃,张志刚,司立英,王荣花,李巧云,王立华,赵智中,梁水美,张全芳,步迅.基于InDels标记的大白菜育种材料的亲缘关系鉴定.植物遗传资源学报,2018,19(4):657-667LiuST,ZhangZG,SiL Y,WangRH,LiQ Y,WangL H,ZhaoZZ,LiangSM,ZhangQF,BuX.Identificationof geneticrelationshipsofchinesecabbageinbredlinesusing InDelsmarkers.JournalofPlantGeneticResources,2018,19(4):657-667
[8]Elshire R J,Glaubitz J C,Sun Q,Poland J A,Kawamoto K,BucklerES,ElshireRJ.Arobust,simpleGenotyping-bySequencing(GBS)approachforhighdiversityspecies.PLoS One,2013,6(5):e19379
[9]张浩.中国栽培花生(Arachis hypogaea L.)遗传多样性分析与核心种质构建.广州:仲恺农业工程学院,2013Zhang H.Construction of core collections and genetic diversity analysisofarachishypogaeacultivarinChina.Guangzhou:Zhongkai University of Agriculture and Engineering,2013
[10]王娟,李春娟,闫彩霞,赵小波,单世华.栽培种花生ddGBS测序中酶切组合的选择.花生学报,2017,46(4):48-51Wang J,Li C J,Yan C X,Zhao X B,Shan S H.The screening of ddGBS restriction enzyme combinations in peanut.Journal of Peanut Science,2017,46(4):48-51
[11]Li H,Durbin R.Fast and accurate short read alignment with Burrows-Wheelertransform.Bioinformatics,2009,25(14):1754-1760
[12]Li H,Handsaker B,Wysoker A,Fennell T,Ruan J,Homer N,Marth G,Abecasis G,Durbin R.1000 genome project data processing subgroup.The sequence alignment/map format and SAMTOOLS.Bioinformatics,2009,25(16):2078-2079
[13]Mckenna A,Hanna M,Banks E,Sivachenko A,Cibulskis K,Kernytsky A,GarimellaK,AltshulerD,GabrielS,DalyM,DePristoM A.TheGenome Analysis Toolkit:AMapReduce framework for analyzing next-generation DNA sequencing data.Genome Research,2010,20(9):1297-1303
[14]Bertioli D J,Cannon S B,Froenicke L,Huang G,Farmer A D,CannonEK,LiuX,GaoD,ClevengerJ,DashS,Ren L,MoretzsohnMC,ShirasawaK,HuangW,VidigalB,Abernathy B,Chu Y,Niederhuth C E,Umale P,Araújo A C,Kozik A,KimKD,BurowMD,VarshneyRK,WangX,ZhangX,BarkleyN,Guimar?esPM,IsobeS,GuoB,Liao B,StalkerH T,SchmitzRJ,SchefflerBE,Leal-BertioliS C,XunX,JacksonS A,MichelmoreR,Ozias-AkinsP.The genome sequences of Arachis duranensis and Arachis ipaensis,thediploidancestorsofcultivatedpeanut.NatureGenetics,2016,48(4):438-446
[15]Meng S,Yang X L,Dang P M,Cui S L,Mu G J,Chen C Y,LiuLF.Evaluationofinsertion-deletionmarkerssuitablefor genetic diversity studies and marker-trait correlation analyses in cultivated peanut(Arachis hypogaea L.).Genetics&Molecular Research Gmr,2016,doi:10.4238/gmr.15038207
[16]Liu L F,Dang P M,Chen C Y.Development and utilization of InDelmarkerstoidentifypeanut(Arachishypogaea)disease resistance.Frontiers in Plant Science,2015,6:988
[17]Mahmood S.Genome-wide characterization of insertion/deletion variationsandmarkerdevelopmentinoilseedrape(Brassica napusL.)byvalorizingresequencinggenomedata.Wuhan:Huazhong Agricultural University,2016
[18]吴磊,王丹,苏文悦,郭长虹,束永俊.利用比较基因组学开发山羊草属InDel分子标记.作物学报,2012,38(7):1334-1338Wu L,Wang D,Su W Y,Guo C H,Shu Y J.Developing InDel markers from aegilops genus based on comparative genomics.Acta Agronomica Sinica,2012,38(7):1334-1338