上饶早梨‘六月雪’和‘黄皮消’全基因组重测序分析
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摘要
以上饶早梨Pyrus pyrifolia 2个品种‘六月雪’‘Liuyuexue’和‘黄皮消’‘Huangpixiao’试管苗为材料,进行全基因组重测序分析。结果表明:2个样本的总单核苷酸多态位点(SNP)数量分别为6 171 357和6 140 603个,编码区内无义突变位点(nsSNP)分别为335 659和332 280个。对nsSNP的常见变异(common variant, CV)分析发现,共有2 282个nsSNP关联了2 067个基因。2个样本的总插入缺失位点(INDEL)分别为800 388和799 603个,其中15 509和15 274个位于编码区,共5 115个差异INDEL关联到了3 682个基因,烟草花叶病毒(tobacco mosaic virus)耐药蛋白N,抗病蛋白等关键基因发生变异。差异nsSNP和差异INDEL富集得到的基因本体术语(GO terms)一致。本实验结果可为上饶早梨2个品种‘六月雪’和‘黄皮消’ SNP和INDEL相关标记的开发、优异基因的挖掘提供参考。
A whole genome re-sequencing analysis was carried out with plantlets for two cultivars('Liuyuexue' and 'Huangpixiao') of early pear(Pyrus pyrifolia) in Shangrao using a common variant analysis for nsSNPs(nonsynonymous mutations single-nucleotide polymorphism).Results showed a total number of single-nucleotide polymorphisms(SNP) in the two samples of 6 171 357 for 'Liuyuexue' and 6 140 603 for 'Huangpixiao',and a total number of nsSNP within the coding region of 335 659 for 'Liuyuexue' and 332 280 for'Huangpixiao '.Using the common variant analysis for nsSNPs,2 282 nsSNPs were found associated with2 067 genes.The total indel numbers of the two samples were 800 388 for 'Liuyuexue' and 799 603 for'Huangpixiao'.In the coding area,15 509 indels for 'Liuyuexue' and 15 274 indels for 'Huangpixiao' were obtained,and 5 115 differential indels were associated with 3 682 genes.Key genes of the tobacco mosaic virus resistant protein N and the disease resistant protein as well as others were mutated.Enriched gene ontology(GO) terms of differential nsSNPs and differential indels were consistent.Results of this study could provide important references for the development of SNP and indel related markers and the extraction of excellent genes for the two cultivars('Liuyuexue' and 'Huangpixiao') of early pear in Shangrao.
A whole genome re-sequencing analysis was carried out with plantlets for two cultivars('Liuyuexue' and 'Huangpixiao') of early pear(Pyrus pyrifolia) in Shangrao using a common variant analysis for nsSNPs(nonsynonymous mutations single-nucleotide polymorphism).Results showed a total number of single-nucleotide polymorphisms(SNP) in the two samples of 6 171 357 for 'Liuyuexue' and 6 140 603 for 'Huangpixiao',and a total number of nsSNP within the coding region of 335 659 for 'Liuyuexue' and 332 280 for'Huangpixiao '.Using the common variant analysis for nsSNPs,2 282 nsSNPs were found associated with2 067 genes.The total indel numbers of the two samples were 800 388 for 'Liuyuexue' and 799 603 for'Huangpixiao'.In the coding area,15 509 indels for 'Liuyuexue' and 15 274 indels for 'Huangpixiao' were obtained,and 5 115 differential indels were associated with 3 682 genes.Key genes of the tobacco mosaic virus resistant protein N and the disease resistant protein as well as others were mutated.Enriched gene ontology(GO) terms of differential nsSNPs and differential indels were consistent.Results of this study could provide important references for the development of SNP and indel related markers and the extraction of excellent genes for the two cultivars('Liuyuexue' and 'Huangpixiao') of early pear in Shangrao.
引文
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[9]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,2015,51(9):1400-1404.YUAN Jinhong,LI Junhua,HUANG Xiaocheng,et al.Advance of SNP analysis based on whole genome resequencing in crop gene mapping[J].Plant Physiol J,2015,51(9):1400-1404.
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[12]莫文娟,袁德义,段经华,等.新高系梨9个品种SSR标记分析[J].浙江林学院学报,2009,26(5):639-645.MO Wenjuan,YUAN Deyi,DUAN Jinghua,et al.Simple sequence repeat analysis on pear cultivars in Niitaka line[J].J Zhejiang For Coll,2009,26(5):639-645.
[13]YAMAMOTO T,TERAKAMI S.Genomics of pear and other Rosaceae fruit trees[J].Breed Sci,2016,66(1):148-159.
[14]周贺,李浩男,蔡斌华,等.砂梨果皮转录组SNP位点发掘及其功能注释分析[J].青岛农业大学学报(自然科学版),2014,31(2):105-111.ZHOU He,LI Haonan,CAI Bihua,et al.SNP mining and functional annotation in transcriptome of sand pear[J].JQingdao Agric Univ Nat Sci,2014,31(2):105-111.
[15]李节法.赤霉素促进梨果实库强的转录组学和蛋白质组学研究[D].上海:上海交通大学,2015.LI Jiefa.Transcriptome and Proteomics Study of Gibberellin Promoting Pear Fruit Storehouse Strength[D].Shanghai Shanghai Jiao Tong University,2015.
[16]WU Jun,LI Leiting,LI Meng,et al.High-density genetic linkage map construction and identification of fruit-related QTLs in pear using SNP and SSR markers[J].J Exp Bot,2014,65(20):5771-5781.
[17]MONTANARI S,SAEED M,KN魧BEL M,et al.Identification of Pyrus single nucleotide polymorphisms(SNPs)and evaluation for genetic mapping in European pear and interspecific Pyrus hybrids[J].PLoS One,2013,8(10)e77022.doi:10.1371/journal.pone.0077022.
[18]TERAKAMI S,NISHITANI C,YAMAMOTO T.Development of SNP markers for marker-assisted selection in pear[J].Acta Hortic,2013,976(976):463-469.
[19]ROBINSON M D,Mc CARTHY D J,SMYTH G K.EdgeR:a bioconductor package for differential expression analysis of digital gene expression data[J].Bioinformatics,2010,26(1):139-140.
[20]LANGMEAD B,SALZBERG S L.Fast gapped-read alignment with Bowtie 2[J].Nat Method,2013,9(4):357-359.
[21]DePRISTO M A,BANKS E,POPLIN R,et al.A framework for variation discovery and genotyping using next-generation DNA sequencing data[J].Nat Genet,2011,43(5):491-498.
[22]WANG Kai,LI Mingyao,HAKONARSON H.ANNOVAR:functional annotation of genetic variants from highthroughput sequencing data[J].Nucleic Acid Res,2010,38(16):e164.doi:10.1093/nar/gkq603.
[23]SILVA J,SCHEFFLER B,SANABRIA Y,et al.Identification of candidate genes in rice for resistance to sheath blight disease by whole genome sequencing[J].Theor Appl Genet,2012,124(1):63-74.
[24]DU Zhou,ZHOU Xin,LING Yi,et al.Agrigo:a GO analysis toolkit for the agricultural community[J].Nucl Acid Res,2010,38(Web Server issue):W64-W70.doi:10.1093/nar/gkq310.
[25]KOBOLDT D C,ZHANG Qunyuan,LARSON D E,et al.VarScan 2:somatic mutation and copy number alteration discovery in cancer by exome sequencing[J].Genome Res,2012,22(3):568-576.
[26]OLSHEN A B,VENKATRAMAN E S,LUCITO R,et al.Circular binary segmentation for the analysis of array-based DNA copy number data[J].Biostatistics,2004,5(4):557-572.
[27]SU Zhenqiang,NING Baitang,FANG Hong,et al.Next-generation sequencing and its applications in molecular diagnostics[J].Exp Rev Mol Diagn,2011,11(3):333-343.
[28]SCHMID K J,S魻RENSEN T R,STRACKE R,et al.Large-scale identification and analysis of genome-wide singlenucleotide polymorphisms for mapping in Arabidopsis thaliana[J].Genome Res,2003,13(6A):1250-1257.
[29]HUANG Xuehui,WEI Xinghua,SANG Tao,et al.Genome-wide association studies of 14 agronomic traits in rice landraces[J].Nat Genet,2010,42(11):961-967.
[30]CABEZAS J A,IB魣譙EZ J,LIJAVETZKY D,et al.A 48 SNP set for grapevine cultivar identification[J].BMC Plant Biol,2011,11(1):153.
[31]LAI Jinsheng,LI Ruiqiang,XU Xun,et al.Genome-wide patterns of genetic variation among elite maize inbred lines[J].Nat Genet,2010,42(11):1027-1030.
[32]BAI Hui,CAO Yinghao,QUAN Jianzhang,et al.Identifying the genome-wide sequence variations and developing new molecular markers for genetics research by re-sequencing a landrace cultivar of foxtail millet[J].PLoS One2013,8(9):e73514.
[33]LIN Tao,ZHU Guangtao,ZHANG Junhong,et al.Genomic analyses provide insights into the history of tomato breeding[J].Nat Genet,2014,46(11):1220-1226.
[34]ZHOU Zhengkui,JIANG Yu,WANG Zheng,et al.Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean[J].Nat Biotechnol,2015,33(4):408-414.
[35]张彦威,李伟,张礼凤,等.基于重测序的大豆新品种齐黄34的全基因组变异挖掘[J].中国油料作物学报,2016,38(2):150-158.ZHANG Yanwei,LI Wei,ZHANG Lifeng,et al.Genome-wide variations of soybean cultivar Qihuang 34 by whole genome re-sequencing[J].Chin J Oil Crop Sci,2016,38(2):150-158.
[36]田义轲,王彩虹,白牡丹,等.基于梨贝壳杉烯氧化酶基因PpKO序列的功能性SNP标记[J].园艺学报,2012,39(10):1876-1884.TIAN Yike,WANG Caihong,BAI Mudan,et al.Development of functional SNP markers anchored PpKO gene in pear[J].Acta Hortic Sin,2012,39(10):1876-1884.
[2]徐芬芬,樊生树,叶利民.采收期和贮藏温度对上饶早梨保鲜效果的影响[J].保鲜与加工,2016,16(3):11-15.XU Fenfen,FAN Shengshu,YE Limin.Effects of harvest time and storage temperature on the fresh-keeping effect of Shangrao early pears[J].Storage Process,2016,16(3):11-15.
[3]洪森荣,张铭心,董雅凤,等.上饶早梨嫩梢热处理嫁接苗脱毒效果分析[J].分子植物育种,2017,15(8):3388-3392.HONG Senrong,ZHANG Mingxin,DONG Yafeng,et al.Virus-free effect analysis of grafted seedlings using heat-treated young shoots of early pear in Shangrao[J].Mol Plant Breed,2017,15(8):3388-3392.
[4]尹明华,周宇瑶,杨星鹏,等.上饶早梨主栽品种病毒种类分析及其茎尖脱毒技术效率比较[J].浙江农业学报,2017,29(1):89-100.YIN Minghua,ZHOU Yuyao,YANG Xingpeng,et al.Analysis of virus species in main cultivars of early pear in Shangrao and the efficiency of their shoot tip virus-free techniques[J].Acta Agric Zhejiang,2017,29(1):89-100.
[5]夏华炎,徐路,肖虹,等.上饶早梨主栽品种离体快繁体系的建立[J].南方农业学报,2016,47(9):1547-1552.XIA Huayan,XU Lu,XIAO Hong,et al.Establishment of in vitro propagation system of main cultivars of Shangrao early pear[J].J Southern Agric,2016,47(9):1547-1552.
[6]尹明华,周宇瑶,苏爱芳,等.上饶早梨道地性农家种遗传多样性与亲缘关系的荧光AFLP分子标记分析[J]基因学与应用生物学,2016,35(11):3178-3188.YIN Minghua,ZHOU Yuyao,SU Aifang,et al.Analysis of genetic diversity and genetic relationships of local genuine landraces of early pear in Shangrao by fluorescence AFLP molecular markers[J].Genomics Appl Biol,2016,35(11)3178-3188.
[7]尹明华,何林森,朱奇志,等.上饶早梨品种鉴定及再生苗遗传稳定性SSR检测[J].分子植物育种,2016,14(11):3120-3129.YIN Minghua,HE Linsen,ZHU Qizhi,et al.Identification of early pear main cultivars in Shangrao and genetic stability SSR analysis of their regenerated plants[J].Mol Plant Breed,2016,14(11):3120-3129.
[8]洪森荣,周宇瑶,黄慧.上饶早梨离体保存库再生苗遗传稳定性的同工酶分析[J].基因组学与应用生物学,2016,35(12):3552-3561.HONG Senrong,ZHOU Yuyao,HUANG Hui.Isoenzyme analysis of genetic stability of the plantlets regenerated from conservation bank in vitro of early pear in Shangrao[J].Genomics Appl Biol,2016,35(12):3552-3561.
[9]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,2015,51(9):1400-1404.YUAN Jinhong,LI Junhua,HUANG Xiaocheng,et al.Advance of SNP analysis based on whole genome resequencing in crop gene mapping[J].Plant Physiol J,2015,51(9):1400-1404.
[10]QI Jianjian,LIU Xin,SHEN Di,et al.A genomic variation map provides insights into the genetic basis of cucumber domestication and diversity[J].Nat Genet,2013,45(12):1510-1515.
[11]WU Jun,WANG Zhiwen,SHI Zebin,et al.The genome of pear(Pyrus bretschneideri Rehd.)[J].Genome Res,201223(2):396-408.
[12]莫文娟,袁德义,段经华,等.新高系梨9个品种SSR标记分析[J].浙江林学院学报,2009,26(5):639-645.MO Wenjuan,YUAN Deyi,DUAN Jinghua,et al.Simple sequence repeat analysis on pear cultivars in Niitaka line[J].J Zhejiang For Coll,2009,26(5):639-645.
[13]YAMAMOTO T,TERAKAMI S.Genomics of pear and other Rosaceae fruit trees[J].Breed Sci,2016,66(1):148-159.
[14]周贺,李浩男,蔡斌华,等.砂梨果皮转录组SNP位点发掘及其功能注释分析[J].青岛农业大学学报(自然科学版),2014,31(2):105-111.ZHOU He,LI Haonan,CAI Bihua,et al.SNP mining and functional annotation in transcriptome of sand pear[J].JQingdao Agric Univ Nat Sci,2014,31(2):105-111.
[15]李节法.赤霉素促进梨果实库强的转录组学和蛋白质组学研究[D].上海:上海交通大学,2015.LI Jiefa.Transcriptome and Proteomics Study of Gibberellin Promoting Pear Fruit Storehouse Strength[D].Shanghai Shanghai Jiao Tong University,2015.
[16]WU Jun,LI Leiting,LI Meng,et al.High-density genetic linkage map construction and identification of fruit-related QTLs in pear using SNP and SSR markers[J].J Exp Bot,2014,65(20):5771-5781.
[17]MONTANARI S,SAEED M,KN魧BEL M,et al.Identification of Pyrus single nucleotide polymorphisms(SNPs)and evaluation for genetic mapping in European pear and interspecific Pyrus hybrids[J].PLoS One,2013,8(10)e77022.doi:10.1371/journal.pone.0077022.
[18]TERAKAMI S,NISHITANI C,YAMAMOTO T.Development of SNP markers for marker-assisted selection in pear[J].Acta Hortic,2013,976(976):463-469.
[19]ROBINSON M D,Mc CARTHY D J,SMYTH G K.EdgeR:a bioconductor package for differential expression analysis of digital gene expression data[J].Bioinformatics,2010,26(1):139-140.
[20]LANGMEAD B,SALZBERG S L.Fast gapped-read alignment with Bowtie 2[J].Nat Method,2013,9(4):357-359.
[21]DePRISTO M A,BANKS E,POPLIN R,et al.A framework for variation discovery and genotyping using next-generation DNA sequencing data[J].Nat Genet,2011,43(5):491-498.
[22]WANG Kai,LI Mingyao,HAKONARSON H.ANNOVAR:functional annotation of genetic variants from highthroughput sequencing data[J].Nucleic Acid Res,2010,38(16):e164.doi:10.1093/nar/gkq603.
[23]SILVA J,SCHEFFLER B,SANABRIA Y,et al.Identification of candidate genes in rice for resistance to sheath blight disease by whole genome sequencing[J].Theor Appl Genet,2012,124(1):63-74.
[24]DU Zhou,ZHOU Xin,LING Yi,et al.Agrigo:a GO analysis toolkit for the agricultural community[J].Nucl Acid Res,2010,38(Web Server issue):W64-W70.doi:10.1093/nar/gkq310.
[25]KOBOLDT D C,ZHANG Qunyuan,LARSON D E,et al.VarScan 2:somatic mutation and copy number alteration discovery in cancer by exome sequencing[J].Genome Res,2012,22(3):568-576.
[26]OLSHEN A B,VENKATRAMAN E S,LUCITO R,et al.Circular binary segmentation for the analysis of array-based DNA copy number data[J].Biostatistics,2004,5(4):557-572.
[27]SU Zhenqiang,NING Baitang,FANG Hong,et al.Next-generation sequencing and its applications in molecular diagnostics[J].Exp Rev Mol Diagn,2011,11(3):333-343.
[28]SCHMID K J,S魻RENSEN T R,STRACKE R,et al.Large-scale identification and analysis of genome-wide singlenucleotide polymorphisms for mapping in Arabidopsis thaliana[J].Genome Res,2003,13(6A):1250-1257.
[29]HUANG Xuehui,WEI Xinghua,SANG Tao,et al.Genome-wide association studies of 14 agronomic traits in rice landraces[J].Nat Genet,2010,42(11):961-967.
[30]CABEZAS J A,IB魣譙EZ J,LIJAVETZKY D,et al.A 48 SNP set for grapevine cultivar identification[J].BMC Plant Biol,2011,11(1):153.
[31]LAI Jinsheng,LI Ruiqiang,XU Xun,et al.Genome-wide patterns of genetic variation among elite maize inbred lines[J].Nat Genet,2010,42(11):1027-1030.
[32]BAI Hui,CAO Yinghao,QUAN Jianzhang,et al.Identifying the genome-wide sequence variations and developing new molecular markers for genetics research by re-sequencing a landrace cultivar of foxtail millet[J].PLoS One2013,8(9):e73514.
[33]LIN Tao,ZHU Guangtao,ZHANG Junhong,et al.Genomic analyses provide insights into the history of tomato breeding[J].Nat Genet,2014,46(11):1220-1226.
[34]ZHOU Zhengkui,JIANG Yu,WANG Zheng,et al.Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean[J].Nat Biotechnol,2015,33(4):408-414.
[35]张彦威,李伟,张礼凤,等.基于重测序的大豆新品种齐黄34的全基因组变异挖掘[J].中国油料作物学报,2016,38(2):150-158.ZHANG Yanwei,LI Wei,ZHANG Lifeng,et al.Genome-wide variations of soybean cultivar Qihuang 34 by whole genome re-sequencing[J].Chin J Oil Crop Sci,2016,38(2):150-158.
[36]田义轲,王彩虹,白牡丹,等.基于梨贝壳杉烯氧化酶基因PpKO序列的功能性SNP标记[J].园艺学报,2012,39(10):1876-1884.TIAN Yike,WANG Caihong,BAI Mudan,et al.Development of functional SNP markers anchored PpKO gene in pear[J].Acta Hortic Sin,2012,39(10):1876-1884.