胡萝卜始花期、主薹高和单株种子量的QTL分析
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摘要
以‘松滋野生’胡萝卜和橘色栽培品种‘Amsterdam’构建的回交重组自交系为试材,深入分析‘松滋野生’染色体片段对后代植株始花期、主薹高及单株种子量的遗传影响。试验结果表明,始花期在两年间均为偏正态分布,而主薹高均呈正态分布,单株种子量仅在2015年表现为正态分布。方差分析表明,3个性状在基因型间、年份间、基因型×年份间存在极显著差异。基于最新胡萝卜基因组数据构建了一张含有2 027个Bin(共154 776个SNP标记),总图距为1 436.433 c M,平均图距0.709 c M的遗传图谱。QTL定位分别获得了2、4、2个与始花期、主薹高和单株种子量相关位点,表型贡献率在14.6%~23.8%之间,其中始花期位点DIF5-1和主薹高位点MSL5-1位置重叠。
A set of backcross inbred lines(BILs)crossed by a wild carrot species‘Songzi'with an orange cultivar‘Amsterdam'were used to deeply analyze the genetic influence of‘Songzi'chromosome fragments on date of initial flowering(DIF),main stalk length(MSL),and seed weight per plant(SWP). The experimental results suggested that MSL was normal distributed in 2014 and 2015,but DIF was on the contrary,and that SWP was only normal distributed in 2015. ANOVA analysis indicated that there was significant difference among BILs genotypes,years,and genotypes × years. Based on the last carrot genome resequencing data,a genetic map consisted of 2 027 Bins and 154 776 SNPs was developed,and the total genetic distance was 1 436.433 cM with an average interval of 0.709 cM between Bin markers. Two,four and two QTLs associated with DIF,MSL and SWP were discovered,respectively,with 14.6%–23.8% phenotypic variance. DIF5-1 locus was overlapped with MSL5-1 locus.
A set of backcross inbred lines(BILs)crossed by a wild carrot species‘Songzi'with an orange cultivar‘Amsterdam'were used to deeply analyze the genetic influence of‘Songzi'chromosome fragments on date of initial flowering(DIF),main stalk length(MSL),and seed weight per plant(SWP). The experimental results suggested that MSL was normal distributed in 2014 and 2015,but DIF was on the contrary,and that SWP was only normal distributed in 2015. ANOVA analysis indicated that there was significant difference among BILs genotypes,years,and genotypes × years. Based on the last carrot genome resequencing data,a genetic map consisted of 2 027 Bins and 154 776 SNPs was developed,and the total genetic distance was 1 436.433 cM with an average interval of 0.709 cM between Bin markers. Two,four and two QTLs associated with DIF,MSL and SWP were discovered,respectively,with 14.6%–23.8% phenotypic variance. DIF5-1 locus was overlapped with MSL5-1 locus.
引文
Alessandro M S,Galmarini C R,Iorizzo M,Simon P W.2013.Molecular mapping of vernalization requirement and fertility restoration genes in carrot.Theoretical and Applied Genetics,126:415-423.
Bai L,Zhang G,Zhou Y,Zhang Z,Wang W,Du Y,Song C P.2009.Plasma membrane-associated praline-rich extension-like receptor kinase 4,a novel regulator of Ca2+signalling,is required for abscisic acid responses in Arabidopsis thaliana.The Plant Journal,60:314-327.
Boiteux L S,Belter J G,Roberts P A,Simon P W.2000.RAPD linkage map of the genomic region encompassing the rootknot nematode(Meloidogyne javanica)resistance locus in carrot.Theoretical and Applied Genetics,100:439-446.
Briard M,Le Clerc V,Grzebelus D,Senalik D,Simon P W.2000.Modified protocols for rapid carrot genomic DNA extraction and AFLPTM analysis using silver stain or radioisotopes.Plant Molecular Biology Reporter,18:235-241.
Cavagnaro P F,Chung S M,Manin S,Yildiz M,Ali A,Alessandro M S,Iorizzo M,Senalik D A,Simon P W.2011.Microsatellite isolation and marker development in carrot-genomic distribution,linkage mapping,genetic diversity analysis and marker transferability across Apiaceae.BMC Genomics,12:386.
Cavagnaro P F,Iorizzo M,Yildiz M,Senalik D,Parsons J,Ellison S,Simon P W.2014.A gene-derived SNP-based high resolution linkage map of carrot including the location of QTL conditioning root and leaf anthocyanin pigmentation.BMC Genomics,15:1118.
De Pristo M A,Banks E,Poplin R,Garimella K V,Maguire J R,Hartl C,Philippakis A A,del Angel G,Rivas M A,Hanna M,Mc Kenna A,Fennell T J,Kernytsky A M,Sivachenko A Y,Cibulskis K,Gabriel S B,Altshuler D,Daly M J.2011.A framework for variation discovery and genotyping using next-generation DNA sequencing data.Nature Genetics,43:491-498.
Fang Zhi-yuan.2017.Vegetables breeding in China.Beijing:China Agriculture Press.(in Chinese)方智远.2017.中国蔬菜育种学.北京:中国农业出版社.
Finkelstein R R,Gampala S S L,Rock C D.2002.Abscisic acid signaling in seeds and seedlings.The Plant Cell,14:15-45.
Fujita Y,Nakashima K,Yoshida T,Katagiri T,Kidokoro S,Kanamori N,Kobayashi M.2009.Three Sn RK2 protein kinases are the main positive regulators of abscisic acid signaling in response to water stress in Arabidopsis.Plant and Cell Physiology,50:2123-2132.
Gray D,Steckel J R A,1983a.Some effects of umbel order and harvest date on carrot seed variability and seedling performance.Journal of Horticultural Science,58:73-82.
Gray D,Steckel J R A,1983b.Seed quality in carrots:the effects of seed crop plant density,harvest date and seed grading on seed and seedling variability.Journal of Horticultural Science,58:393-401.
Grzebelus D,Iorizzo M,Senalik D,Ellison S,Cavagnaro P F,Macko-Podgorni A,Heller-Uszynska K,Kilian A,Nothnagel T,Allender C,Simon P W,Baranski R.2014.Diversity,genetic mapping,and signatures of domestication in the carrot(Daucus carota L.)genome,as revealed by Diversity Arrays Technology(DAr T)markers.Molecular Breeding,33:625-637.
Huang X,Feng Q,Qian Q,Zhao Q,Wang L,Wang A,Guan J,Fan D,Weng Q,Huang T,Dong G,Sang T,Han B.2009.High-throughput genotyping by whole-genome resequencing.Genome Research,19:1068-1076.
Iorizzo M,Ellison S,Senalik D,Zeng P,Satapoomin P,Huang J,Bowman M,Iovene M,Sanseverino W,Cavagnaro P,Yildiz M,Spooner D M,Simon P W.2016.A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution.Nature Genetics,doi:10.1038/ng.3565.
Liu H,Stone S L.2010 Abscisic acid increases Arabidopsis ABI5 transcription factor levels by promoting KEG E3 ligase self-ubiquitination and proteasomal degradation.Plant Cell,22:2630-2641.
Nakashima K,Fujita Y,Kanamori N,Katagiri T,Umezawa T,Kidokoro S,Shinozaki K.2009.Three Arabidopsis Sn RK2 protein kinases,SRK2D/Sn RK2.2,SRK2E/Sn RK2.6/OST1 and SRK2I/Sn RK2.3,involved in ABA signaling are essential for the control of seed development and dormancy.Plant and Cell Physiology,50:1345-1363.
Nakashima K,Yamaguchi-Shinozaki K.2013.ABA signaling in stress-response and seed development.Plant Cell Reports,32:959-970.
Ou Cheng-gang,Deng Bo-tao,Bao Sheng-you,Zhao Zhi-wei,Hu Hong,Zhuang Fei-yun,Mao Shu-min.2010.QTL mapping for contents of main carotenes and lycopene in carrot(Daucus carota L.).Hereditas,32:1290-1295.(in Chinese)欧承刚,邓波涛,鲍生有,赵志伟,胡鸿,庄飞云,茅淑敏.2010.胡萝卜(Daucus carota L.)中主要胡萝卜素和番茄红素含量的QTL分析.遗传,32:1290-1295.
Ou C G,Mao J H,Liu L J,Li C J,Ren H F,Zhao Z W,Zhuang F Y.2017.Characterizing genes associated with flowering time in carrot(Daucus carota L.)using transcriptome analysis.Plant Biology,19:286-297.
Ou Cheng-gang,Sun Ting-ting,Liu Xin-yan,Li Cheng-jiang,Xu Dong-hui,Zhao Zhi-wei,Zhuang Fei-yun.2017.Fine mapping of main carotenoids contents in carrot root.Acta Horticulturae Sinica,44:288-296.(in Chinese)欧承刚,孙婷婷,刘新艳,李成江,徐东辉,赵志伟,庄飞云.2017.胡萝卜根中主要类胡萝卜素含量相关QTL的精细定位.园艺学报,44:288-296.
Rubatzky V E,Quiros C F,Simon P W.1999.Carrots and related vegetable Umbelliferae.New York:CABI Publishing.
Song Y H,Smith R W,To B J,Millar A J,Imaizumi T.2012.FKF1 conveys timing information for CONSTANS stabilization in photoperiodic flowering.Science,336:1045-1049.
Stein M,Nothnagel T.1995.Some remarks on carrot breeding(Daucus carota sativus Hoffm.).Plant Breeding,114:1-11.
Stone S L,Williams L A,Farmer L M,Vierstra R D,Callis J.2006.KEEP ON GOING,a RING E3 ligase essential for Arabidopsis growth and development,is involved in abscisic acid signaling.The Plant Cell,18:3415-3428.
ühlken C,Horvath B,Stadler R,Sauer N,Weingartner M.2014.MAIN‐LIKE1 is a crucial factor for correct cell division and differentiation in Arabidopsis thaliana.The Plant Journal,78:107-120.
van Ooijen J W.2006.Join Map 4.0:software for the calculation of genetic linkage maps in experimental populations.Wageningen,Netherlands:Kyazma B.V.
Wang S,Basten C J,Zeng Z B.2011.Windows QTL Cartographer 2.5.Raleigh,NC:Department of Statistics,North Carolina State University.
Zhuang Fei-yun,Zhu De-wei.2007.Descriptions and data standard for carrot(Daucus carota L.).Beijing:China Agriculture Press.(in Chinese)庄飞云,朱德慰.2007.胡萝卜种质资源描述规范和数据标准.北京:中国农业出版社.
Bai L,Zhang G,Zhou Y,Zhang Z,Wang W,Du Y,Song C P.2009.Plasma membrane-associated praline-rich extension-like receptor kinase 4,a novel regulator of Ca2+signalling,is required for abscisic acid responses in Arabidopsis thaliana.The Plant Journal,60:314-327.
Boiteux L S,Belter J G,Roberts P A,Simon P W.2000.RAPD linkage map of the genomic region encompassing the rootknot nematode(Meloidogyne javanica)resistance locus in carrot.Theoretical and Applied Genetics,100:439-446.
Briard M,Le Clerc V,Grzebelus D,Senalik D,Simon P W.2000.Modified protocols for rapid carrot genomic DNA extraction and AFLPTM analysis using silver stain or radioisotopes.Plant Molecular Biology Reporter,18:235-241.
Cavagnaro P F,Chung S M,Manin S,Yildiz M,Ali A,Alessandro M S,Iorizzo M,Senalik D A,Simon P W.2011.Microsatellite isolation and marker development in carrot-genomic distribution,linkage mapping,genetic diversity analysis and marker transferability across Apiaceae.BMC Genomics,12:386.
Cavagnaro P F,Iorizzo M,Yildiz M,Senalik D,Parsons J,Ellison S,Simon P W.2014.A gene-derived SNP-based high resolution linkage map of carrot including the location of QTL conditioning root and leaf anthocyanin pigmentation.BMC Genomics,15:1118.
De Pristo M A,Banks E,Poplin R,Garimella K V,Maguire J R,Hartl C,Philippakis A A,del Angel G,Rivas M A,Hanna M,Mc Kenna A,Fennell T J,Kernytsky A M,Sivachenko A Y,Cibulskis K,Gabriel S B,Altshuler D,Daly M J.2011.A framework for variation discovery and genotyping using next-generation DNA sequencing data.Nature Genetics,43:491-498.
Fang Zhi-yuan.2017.Vegetables breeding in China.Beijing:China Agriculture Press.(in Chinese)方智远.2017.中国蔬菜育种学.北京:中国农业出版社.
Finkelstein R R,Gampala S S L,Rock C D.2002.Abscisic acid signaling in seeds and seedlings.The Plant Cell,14:15-45.
Fujita Y,Nakashima K,Yoshida T,Katagiri T,Kidokoro S,Kanamori N,Kobayashi M.2009.Three Sn RK2 protein kinases are the main positive regulators of abscisic acid signaling in response to water stress in Arabidopsis.Plant and Cell Physiology,50:2123-2132.
Gray D,Steckel J R A,1983a.Some effects of umbel order and harvest date on carrot seed variability and seedling performance.Journal of Horticultural Science,58:73-82.
Gray D,Steckel J R A,1983b.Seed quality in carrots:the effects of seed crop plant density,harvest date and seed grading on seed and seedling variability.Journal of Horticultural Science,58:393-401.
Grzebelus D,Iorizzo M,Senalik D,Ellison S,Cavagnaro P F,Macko-Podgorni A,Heller-Uszynska K,Kilian A,Nothnagel T,Allender C,Simon P W,Baranski R.2014.Diversity,genetic mapping,and signatures of domestication in the carrot(Daucus carota L.)genome,as revealed by Diversity Arrays Technology(DAr T)markers.Molecular Breeding,33:625-637.
Huang X,Feng Q,Qian Q,Zhao Q,Wang L,Wang A,Guan J,Fan D,Weng Q,Huang T,Dong G,Sang T,Han B.2009.High-throughput genotyping by whole-genome resequencing.Genome Research,19:1068-1076.
Iorizzo M,Ellison S,Senalik D,Zeng P,Satapoomin P,Huang J,Bowman M,Iovene M,Sanseverino W,Cavagnaro P,Yildiz M,Spooner D M,Simon P W.2016.A high-quality carrot genome assembly provides new insights into carotenoid accumulation and asterid genome evolution.Nature Genetics,doi:10.1038/ng.3565.
Liu H,Stone S L.2010 Abscisic acid increases Arabidopsis ABI5 transcription factor levels by promoting KEG E3 ligase self-ubiquitination and proteasomal degradation.Plant Cell,22:2630-2641.
Nakashima K,Fujita Y,Kanamori N,Katagiri T,Umezawa T,Kidokoro S,Shinozaki K.2009.Three Arabidopsis Sn RK2 protein kinases,SRK2D/Sn RK2.2,SRK2E/Sn RK2.6/OST1 and SRK2I/Sn RK2.3,involved in ABA signaling are essential for the control of seed development and dormancy.Plant and Cell Physiology,50:1345-1363.
Nakashima K,Yamaguchi-Shinozaki K.2013.ABA signaling in stress-response and seed development.Plant Cell Reports,32:959-970.
Ou Cheng-gang,Deng Bo-tao,Bao Sheng-you,Zhao Zhi-wei,Hu Hong,Zhuang Fei-yun,Mao Shu-min.2010.QTL mapping for contents of main carotenes and lycopene in carrot(Daucus carota L.).Hereditas,32:1290-1295.(in Chinese)欧承刚,邓波涛,鲍生有,赵志伟,胡鸿,庄飞云,茅淑敏.2010.胡萝卜(Daucus carota L.)中主要胡萝卜素和番茄红素含量的QTL分析.遗传,32:1290-1295.
Ou C G,Mao J H,Liu L J,Li C J,Ren H F,Zhao Z W,Zhuang F Y.2017.Characterizing genes associated with flowering time in carrot(Daucus carota L.)using transcriptome analysis.Plant Biology,19:286-297.
Ou Cheng-gang,Sun Ting-ting,Liu Xin-yan,Li Cheng-jiang,Xu Dong-hui,Zhao Zhi-wei,Zhuang Fei-yun.2017.Fine mapping of main carotenoids contents in carrot root.Acta Horticulturae Sinica,44:288-296.(in Chinese)欧承刚,孙婷婷,刘新艳,李成江,徐东辉,赵志伟,庄飞云.2017.胡萝卜根中主要类胡萝卜素含量相关QTL的精细定位.园艺学报,44:288-296.
Rubatzky V E,Quiros C F,Simon P W.1999.Carrots and related vegetable Umbelliferae.New York:CABI Publishing.
Song Y H,Smith R W,To B J,Millar A J,Imaizumi T.2012.FKF1 conveys timing information for CONSTANS stabilization in photoperiodic flowering.Science,336:1045-1049.
Stein M,Nothnagel T.1995.Some remarks on carrot breeding(Daucus carota sativus Hoffm.).Plant Breeding,114:1-11.
Stone S L,Williams L A,Farmer L M,Vierstra R D,Callis J.2006.KEEP ON GOING,a RING E3 ligase essential for Arabidopsis growth and development,is involved in abscisic acid signaling.The Plant Cell,18:3415-3428.
ühlken C,Horvath B,Stadler R,Sauer N,Weingartner M.2014.MAIN‐LIKE1 is a crucial factor for correct cell division and differentiation in Arabidopsis thaliana.The Plant Journal,78:107-120.
van Ooijen J W.2006.Join Map 4.0:software for the calculation of genetic linkage maps in experimental populations.Wageningen,Netherlands:Kyazma B.V.
Wang S,Basten C J,Zeng Z B.2011.Windows QTL Cartographer 2.5.Raleigh,NC:Department of Statistics,North Carolina State University.
Zhuang Fei-yun,Zhu De-wei.2007.Descriptions and data standard for carrot(Daucus carota L.).Beijing:China Agriculture Press.(in Chinese)庄飞云,朱德慰.2007.胡萝卜种质资源描述规范和数据标准.北京:中国农业出版社.