黄瓜MADS-box基因家族生物信息学分析及CsMADS-box AGL62的克隆
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摘要
分别以全雌系D1104-2-4、强雌系D1158♀-2、雌雄异花同株D0528-2为母本,与1个雌雄异花同株父本D0708-2杂交获得杂种一代,调查开花初期、根瓜期、盛果期3个时期雌性相关农艺性状,筛选出差异显著的组合进行转录组测序分析进而分析黄瓜杂交组合间MADS-box家族的差异基因。结果表明:以全雌系D1104-2-4为母本的杂种一代C15-114在雌花数、雌花节率上均具有超亲优势,3个杂交组合F1均具有早熟的中亲优势。转录组分析结果发现,以全雌系D1104-2-4为母本的杂种一代基因表达情况显著的偏向母本,挑选的37个黄瓜MADS-box家族基因只有6个与母本有表达差异,17个与父本有表达差异。生物信息学分析并命名了1个差异最显著的基因Cs MADS-box AGL62,该基因全长745 bp,编码187个氨基酸,编码的蛋白属于线粒体中不稳定的亲水性跨膜蛋白,NCBI比对结果表明该蛋白是1个转录因子,系统进化分析发现其与甜瓜中AGL62同源性最高,在黄瓜中该蛋白和其他黄瓜AGL62亚型属于同一分支并且属于I型。
The gynoecious line ‘D1104-2-4',pistillate line ‘D1158♀-2' and monoecious line ‘D0528-2' were used as female parents,and the hybrid generation was obtained by crossing with monoecious line ‘D0708-2' as male parent.The paper investigated the female related agronomic characters at 3 periods including early blooming stage,fruiting early stage and fruiting period; then screened the significantly different combination to carry out trans-criptional sequence;and finally analyzed the differential genes of MADS-box family among cucumber hybrid combinations.The results showed that the F1 generation with ‘D1104-2-4' as female parent had super parent advantage on the numbers of female flower and female flower node rate.And F1 of all 3 hybrid combinations had the early maturing mid-parent advantage.The results of transcriptional analysis showed that the F1 gene expression in the whole gynoecious line ‘D1104-2-4' combination was significantly biased to the maternal parent,and only 6 of 37 cucumber MADS-box family genes were different from the female parent,and 17 of them were differ in expression with male parent.Bioinformatics analyzed and named a significantly differential expre ss gene CsMADS-box AGL62 that encodes 187 amino acids in the whole length of 745 bp.The encoded protein was belonged to an unstable hydrophilic transmembrane protein in the mitochondria.The NCBI alignment results showed that this protein was a transcription factor.Systematic analysis found this protein had the highest homology to AGL62 in muskmelon.In cucumber,this gene was belonged to the same branch with the other cucumber AGL62 subtypes and belonged to type I.
The gynoecious line ‘D1104-2-4',pistillate line ‘D1158♀-2' and monoecious line ‘D0528-2' were used as female parents,and the hybrid generation was obtained by crossing with monoecious line ‘D0708-2' as male parent.The paper investigated the female related agronomic characters at 3 periods including early blooming stage,fruiting early stage and fruiting period; then screened the significantly different combination to carry out trans-criptional sequence;and finally analyzed the differential genes of MADS-box family among cucumber hybrid combinations.The results showed that the F1 generation with ‘D1104-2-4' as female parent had super parent advantage on the numbers of female flower and female flower node rate.And F1 of all 3 hybrid combinations had the early maturing mid-parent advantage.The results of transcriptional analysis showed that the F1 gene expression in the whole gynoecious line ‘D1104-2-4' combination was significantly biased to the maternal parent,and only 6 of 37 cucumber MADS-box family genes were different from the female parent,and 17 of them were differ in expression with male parent.Bioinformatics analyzed and named a significantly differential expre ss gene CsMADS-box AGL62 that encodes 187 amino acids in the whole length of 745 bp.The encoded protein was belonged to an unstable hydrophilic transmembrane protein in the mitochondria.The NCBI alignment results showed that this protein was a transcription factor.Systematic analysis found this protein had the highest homology to AGL62 in muskmelon.In cucumber,this gene was belonged to the same branch with the other cucumber AGL62 subtypes and belonged to type I.
引文
路洪凤.2014.黄瓜早花基因的QTL定位[博士论文].北京:中国农业科学院.
沈辰,熊露,韩书庆,马娟娟,吴建寨.2017.我国果菜类蔬菜生产与流通形势分析.中国蔬菜,(9):7-11.
张则婷,李学宝.2007.Mads-box基因在植物发育中的功能.植物生理学报,43(2):218-222.
Becker A,Theissen G.2003.The major clades of mads-box genes and their role in the development and evolution of flowering plants.Molecular Phylogenetics&Evolution,29(3):464-489.
Bemer M,Wolters-Arts M,Grossniklaus U,Angenent G C.2008.The mads domain protein diana acts together with agamous-like80 to specify the central cell in Arabidopsis ovules.Plant Cell,20(8):2088-2101.
De Bodt S,Raes J,Florquin K,Rombauts S,RouzéP,Thei?en G,van de Peer Y.2003.Genomewide structural annotation and evolutionary analysis of the type I MADS-box genes in plants.Journal of Molecular Evolution,56(5):573-586.
Dreni L,Zhang D.2016.Flower development:the evolutionary history and functions of the agl6 subfamily MADS-box genes.Journal of Experimental Botany,67(6):1625-1638.
Gan D F,Jiao W U,Zhuang D,Liang D D,Zhan M D,Hao F L.2014.Cloning and expression analysis of ap1-ful type madsbox gene in cucumber(Cucumis sativus L.).Journal of Nuclear Agricultural Sciences,8:1585-1590.
Hehenberger E,Kradolfer D,K?hler C.2012.Endosperm cellularization defines an important developmental transition for embryo development.Development,139(11):2031-2039.
Henschel K,Kofuji R,Hasebe M,Saedler H,Münster T,Thei?en G.2002.Two ancient classes of mikc-type mads-box genes are present in the moss physcomitrella patens.Molecular Biology&Evolution,19(6):801-814.
Kang I H,Steffen J G,Portereiko M F,Lloyd A,Drews G N.2008.The agl62 mads domain protein regulates cellularization during endosperm development in Arabidopsis.Plant Cell,20(3):635-647.
Lin C S,Hsu C T,Liao D C,Chang W J,Chou M L,Huang Y T.2015.Transcriptome-wide analysis of the MADS-box gene family in the orchid Erycina pusilla.Plant Biotechnology Journal,14(1):284-298.
Lu K,Li T,He J,Chang W,Zhang R,Liu M,Yu M,Fan Y,Ma J,Sun W,Qu C,Liu L,Li N,Liang Y,Wang R,Qian W,Tang Z,Xu X,Lei B,Zhang K,Li J.2018.qprimerDB:a thermodynamics-based gene-specific qPCR primer database for147 organisms.Nucleic Acids Research,46(Database issue):D1229-D1236.
Masiero S,Colombo L,Grini P E,Schnittger A,Kater M M.2011.The emerging importance of type I MADS-box transcription factors for plant reproduction.Plant Cell,23(3):865-872.
Oliveira R R D,Cesarino I,Mazzafera P,Dornelas M C.2014.Flower development in Coffea arabica L.:new insights into MADS-box genes.Plant Reproduction,27(2):79-94.
ParenicováL,de Folter S,Kieffer M,Horner D S,Favalli C,Busscher J,Cook H E,Ingram R M,Kater M M,Davies B,Angenent G C,Colombo L.2003.Molecular and phylogenetic analyses of the complete MADS-box transcription factor family in Arabidopsis:new openings to the MADS world.Plant Cell,15:1538-1551.
Zeng X,Liu H,Du H,Wang S,Yang W,Chi Y.2018.Soybean MADS-box gene GmAGL1 promotes flowering via the photoperiod pathway.Bmc Genomics,19(1):51-67.
沈辰,熊露,韩书庆,马娟娟,吴建寨.2017.我国果菜类蔬菜生产与流通形势分析.中国蔬菜,(9):7-11.
张则婷,李学宝.2007.Mads-box基因在植物发育中的功能.植物生理学报,43(2):218-222.
Becker A,Theissen G.2003.The major clades of mads-box genes and their role in the development and evolution of flowering plants.Molecular Phylogenetics&Evolution,29(3):464-489.
Bemer M,Wolters-Arts M,Grossniklaus U,Angenent G C.2008.The mads domain protein diana acts together with agamous-like80 to specify the central cell in Arabidopsis ovules.Plant Cell,20(8):2088-2101.
De Bodt S,Raes J,Florquin K,Rombauts S,RouzéP,Thei?en G,van de Peer Y.2003.Genomewide structural annotation and evolutionary analysis of the type I MADS-box genes in plants.Journal of Molecular Evolution,56(5):573-586.
Dreni L,Zhang D.2016.Flower development:the evolutionary history and functions of the agl6 subfamily MADS-box genes.Journal of Experimental Botany,67(6):1625-1638.
Gan D F,Jiao W U,Zhuang D,Liang D D,Zhan M D,Hao F L.2014.Cloning and expression analysis of ap1-ful type madsbox gene in cucumber(Cucumis sativus L.).Journal of Nuclear Agricultural Sciences,8:1585-1590.
Hehenberger E,Kradolfer D,K?hler C.2012.Endosperm cellularization defines an important developmental transition for embryo development.Development,139(11):2031-2039.
Henschel K,Kofuji R,Hasebe M,Saedler H,Münster T,Thei?en G.2002.Two ancient classes of mikc-type mads-box genes are present in the moss physcomitrella patens.Molecular Biology&Evolution,19(6):801-814.
Kang I H,Steffen J G,Portereiko M F,Lloyd A,Drews G N.2008.The agl62 mads domain protein regulates cellularization during endosperm development in Arabidopsis.Plant Cell,20(3):635-647.
Lin C S,Hsu C T,Liao D C,Chang W J,Chou M L,Huang Y T.2015.Transcriptome-wide analysis of the MADS-box gene family in the orchid Erycina pusilla.Plant Biotechnology Journal,14(1):284-298.
Lu K,Li T,He J,Chang W,Zhang R,Liu M,Yu M,Fan Y,Ma J,Sun W,Qu C,Liu L,Li N,Liang Y,Wang R,Qian W,Tang Z,Xu X,Lei B,Zhang K,Li J.2018.qprimerDB:a thermodynamics-based gene-specific qPCR primer database for147 organisms.Nucleic Acids Research,46(Database issue):D1229-D1236.
Masiero S,Colombo L,Grini P E,Schnittger A,Kater M M.2011.The emerging importance of type I MADS-box transcription factors for plant reproduction.Plant Cell,23(3):865-872.
Oliveira R R D,Cesarino I,Mazzafera P,Dornelas M C.2014.Flower development in Coffea arabica L.:new insights into MADS-box genes.Plant Reproduction,27(2):79-94.
ParenicováL,de Folter S,Kieffer M,Horner D S,Favalli C,Busscher J,Cook H E,Ingram R M,Kater M M,Davies B,Angenent G C,Colombo L.2003.Molecular and phylogenetic analyses of the complete MADS-box transcription factor family in Arabidopsis:new openings to the MADS world.Plant Cell,15:1538-1551.
Zeng X,Liu H,Du H,Wang S,Yang W,Chi Y.2018.Soybean MADS-box gene GmAGL1 promotes flowering via the photoperiod pathway.Bmc Genomics,19(1):51-67.