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川香29水稻香味基因定位、分子标记辅助育种和基因表达分析
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摘要
水稻是全球半数多人口的主食,随着人们生活水平的日益提高,消费者对稻米品质也提出了更高要求。水稻香味是高档优质米的一个重要品质性状;香稻米质优良,香味馥郁,兼具食疗保健作用,愈来愈受到消费者的青睐和市场欢迎。本文以优良籼稻保持系川香29B(或其恢复系29R)为香味供体亲本,美国光身粳稻Lemont、R2(由Lemont选育而来)、美B、P18和G46B为受体亲本,对川香29香味性状进行了遗传分析、基因定位、分子标记辅助选择及基因芯片等多方面的分析,主要结果如下:
     1.川香29B香味遗传分析与基因定位
     1.1水稻叶片香味氢氧化钾法鉴定
     香味是感官性状,其表型鉴定受到外界气候环境诸多影响。以有香味亲本和无香味亲本为对照,对其后代分离群体用氢氧化钾法鉴定叶片香味。通过在不同时间、地点和气候环境下多年试验,发现用氢氧化钾法鉴定水稻叶片香味的最佳时机为雨过天晴后的上午,温度在20~26℃,该时期两对照亲本鉴别的准确率在99%以上,后代分离单株香与不香性状表现非常明显。
     1.2川香29B香味性状遗传分析
     川香29B/Le,29B╱R2两组合杂交种F_1种子经咀嚼米粒香味鉴定没有香味,其F_1植株叶片也均表现没有香味,即川香29B香味性状受隐性基因控制:在这两个F_2群体中,经x~2测验,无香味单株与极端香味单株分离比符合3:1,该结果由相应F_(2:3)家系香味表型进一步得到验证,表明川香29B香味性状受一对单隐性基因控制。
     1.3香味基因分子标记定位
     在均匀分布于水稻12条染色体上700对SSR引物中,有268对在29B与Lemont存在多态性,多态性频率为38.29%。其中位于第8染色体上的RM23097、RM515、RM8264、RM7049、RM7356和RM7556等标记与香味性状存在连锁。本研究开发SSR标记Aro1和Aro7在这两亲本间也存在多态性,香味基因fgr被定位在SSR标记Aro7(0.57cM)和RM515(0.71cM)之间。在29B/R2 F_2群体中,将香味基因fgr定位于RM23120(0.52 cM)和RM3459(1.23 cM)两标记之间。
     2.分子标记辅助选育香稻保持系与恢复系
     2.1香味基因连锁标记基因型鉴定
     前人报道的香味基因连锁标记RM223、和SCU-Rice-SSR-1在本研究亲本29B与Lemont中不存在多态性,RM42存在多态性但不与香味性状连锁。本研究所鉴定与香味基因连锁的8个标记在来自不同区域的13个香稻品种中基因型存在差异,因而对于香味基因的分子标记辅助选择,需要根据不同的香稻材料,确定选用的连锁标记及其对应的基因型。
     2.2水稻香味的ISSR分析
     从40条ISSR引物中筛选到的24个用于对目前生产应用较多的23份香稻与非香稻材料进行检测,共检测到208个多态性片段,扩增带的分子量在100~2200bp区间。不同引物扩增出的清晰多态条带数在5~16条之间(表2),扩增出5~9条的引物有16个,占66.7%;扩增出10~16条的引物有8个,占33.3%,平均每个引物扩增到8.67个多态性带;ISSR标记能将23份水稻完全区分开。推测ISSR标记812中多态性条带(1050bp左右)可能与水稻香味性状有关。
     2.3分子标记辅助选育香稻保持系与恢复系
     以川香29B(或其恢复系29R)为供体亲本,无香味恢复系P18和无香味保持系美B分别为受体轮回亲本,获得P18/29R的F_1和美B/29B组合的F_2。用与香味基因紧密连锁的两侧标记RM23120和RM3459在P18/29R组合中选择香味纯合基因型单株;Aro1和RM3459在美B/29B组合中选择香味纯合基因型单株;同期进行农艺性状香味表型选择和遗传背景分析。此后经过成都正季和海南南繁一年两季,连续回交;获得一批目标基因纯合且农艺性状稳定的优良香稻保持系和恢复系。
     3.水稻香味的基因芯片分析
     3.1有香味与无香味近等基因池差异基因
     从29B近等基因系(NIL)BC_6F_3群体中选择遗传背景完全相同,只在目标基因型存在差异的有香味与无香味单株,其分蘖期叶片分别等量混合用于芯片分析。在第8染色体目标区域,芯片在有香味与无香味近等基因池检测到4个差异基因:AT3G48170(gene_id)参与氨基乙酸、丝氨酸和苏氨酸新陈代谢;AT4G27070和AT5G54810参与苯基丙氨酸、酪氨酸和色氨酸生物合成;AT4G34030参与缬氨酸、亮氨酸和异亮氨酸的分化降解。其中AT3G48170即为前人报道的sk-2香味基因,也是本研究分子标记定位区域的基因。
     在分子功能(Go)和生物过程(Pathway)方面,芯片在水稻全基因组共检测到23个(不包括重复)差异基因。这些基因是一些转录启动激活、DNA控制的RNA酶活性和应激反应因子,主要参与生理生化调控和硫化物新陈代谢。进一步RT-PCR分析验证了该芯片结果的可靠性。
     3.2水稻香味机理及生化途径
     根据芯片结果,结合前人研究及生物信息学分析,发现胆碱是香味主基因sk-2调控中的重要物质。而胆碱(Choline)是维生素B复合体之一,该物质在水稻籽粒中主要存在谷壳和籽粒表面,从而找到了水稻米粒香味主要分布在表面的原因。
     在香稻材料中,BADH2基因第7外显子发生8个碱基的缺失与3个单核苷酸多态性,使终止密码子提前出现,BADH2基因不再编码甜菜碱脱氢酶(Betaine-aldehydedehydrogenase,BADH),引起甜菜碱醛(Betaine aldehyde)到甜菜碱(Glycine betaine)氧化过程的终止。生成的甜菜碱醛便在胆碱脱氢酶(choline dehydrogenase)作用下,参与反应:Betaine aldehyde+FAD+H2O<=>FADH2+Betaine,该反应与脯氨酸降解Ⅰ存在FAD与FADH2的竞争,使L-脯氨酸积累,最终引起1-吡咯啉-2-羧酸盐的产生。推测香味主成分2-乙酰-1-吡咯啉是由1-吡咯啉-2-羧酸盐通过甲基化作用一步或多步反应而来。另外,硫化合物可能与水稻香味物质的形成和调控密切相关。
Aromatic varieties constituting a small but special group of rice have gained greater importance with increase in worldwide demand for super rice.And Aroma is one of the most important characteristics for determining good quality rice.Inheritance and gene fine mapping,molecular assisted selection and gene chip analysis of aroma in rice were worked out in the paper.The main results are as following:
     1.Genetic analysis and gene fine mapping of aroma in rice
     1.1 eluting aroma from leaves with dilute KOH
     Aroma in rice is a sensory character,and it is apt to be influenced by environmental condition and other factors.Aroma evaluation with dilute KOH was constructed in different environmental conditions and different sites for many years.The best occasion for identification of aroma is the sun shines again after rain,with the temperature 20~26℃.In this condition,the contrast,aromatic and non-aromatic parents were identified with prediction of more than 99%accuracy;and the behave character of aroma in the plants from segregation population was markedly.
     1.2 Inheritance of aroma in 29B
     F_1 grains and plant-leaves from the two crosses of 29B/Lemont and 29B/R2 were non-aromatic.Each F_2 plant was self-crossed to obtain F_(2:3) family,F_3 grains were chewed to evaluate the aroma of F_(2:3) families.And the genotype of each F_2 plant was inferred from the phenotype of corresponding F_(2:3) family.Segregating ratios of F_2 non-aromatic to aromatic plants were 3:1,which indicated the inheritance of a single recessive gene in aromatic rice variety29B.
     1.3 Aroma gene fine mapping
     700 simple sequence repeat(SSR) markers well scattered on 12 chromosomes were assessed for polymorphism by comparison of parental alleles.Two hundred sixty-eight polymorphic SSRs between 29B and Le were obtained,and the percentage of polymorphism was 38.29%.The SSR markers RM23097,RM515,RM8264,RM7049, RM7356 and RM7556 were found to be linked with the aroma locus.In addition,two SSR markers Aro1 and Aro7 linked with aroma were developed.The fragrant gene fgr was mapped to the interval between Aro7(0.57 cM) and RM515(0.71 cM) in the F_2 population of 29B/Le.In the 29B/R2 F_2 population,RM23120 and RM3459 were identified to be linked with the scented locus with genetic distance of 0.52 and 1.23 cM.
     2.Molecular assisted selection for aromatic rice maintainer and restorer
     2.1 Alleles identification for Markers linked with aroma
     According to the investigations in the past,RM223,SCU-Rice- SSR-1 and RM42 were found to be linked with the aroma locus.However,in this study,RM223 and SCU-Rice- SSR-1 can't reveal the polymorphism between 29B and Le;RM42 was polymorphic between the two parents,but not linked with aroma character.In addition,the markers linked with fragrance identified in the paper were assessed for polymorphism by analysis of parental alleles in 13 scented varieties,and variation alleles were found to distinguish different genotype for each marker.
     2.2 Genetic background analysis by ISSR
     To make use of efficient molecular marker systems to reveal genetic diversity among 23 fragrance and non-fragrance cultivars from different regions,24 ISSR primers selected from 40 ISSR markers were used to analyze the cultivar groups.A total of 208 polymorphic bands were found in 23 varieties with the product from 100 to 2200bp differently.The average number of polymorphism bands per ISSR primer was8.67 with arrange from 5 to16.Genetic similarities among the 23 rice accessions ranged from 0.549 (13 and 22) to 0.887(3 and 11).The clustering analysis based on ISSR data is very identical to that varieties character of maintainer and restorer and climates which the cultivars come from.On the other hand,the polymorphic allele of ISSR marker 812 about 1050bp was assumed to be related with the aroma character.The average number of alleles per SSR locus was4.23 with arrange from 3 to 8.
     2.3 Marker assisted selection for aromatic maintainer and restorer
     The fragrance gene fgr was introduced into cultivated rice varieties P18 and Mei B by cross and continuous back crosses,respectively.In this study,we used 29B and 29R as the fgr donors and the elite but without aroma lines P18 and MeiB as recipients to develop aromatic maintainer and restorer lines of hybrid rice.The F_1 of P18/29R and F_2 of MeiB/29B were obtained and fragrance linked markers RM23120 and RM3459 were used to select fgr in MeiB/29B;Arol and RM3459 were used in P18/29R.And marker-assisted selection of rice aroma is feasible.
     3.The analysis of aroma of rice by gene chip
     3.1 Genes expressed difference between A1 and N1
     Gene chip is the new tool for biological research.In this study,cDNA gene chip technique was employed to analyze the leaf RNA expression difference between aromatic and non-aromatic nearly isogenic lines.BC_6F_3 population from 29B/G46 was developed and identified for aroma character and genetic background.The aromatic and non-aromatic plants with identical genetic background were selected and used to do cDNA microarray hybridizing.In the interval of aroma locus mapping on chromosome 8,4 genes were identified at the level of expression fold change larger than or equal to 2.AT3G48170 (gene_id) is relate to Glycine,serine and threonine metabolism,AT4G27070 and AT5G54810 are related to Phenylalanine,tyrosine and tryptophan biosynthesis,and AT3G48170 is related to Valine,leucine and isoleucine degradation.On the other hand, AT3G48170 is the BADH2 gene involved in aroma of rice.
     Gene ontology was made on 23 sites of different expression patterns,which showed that the function included transcription initiation factor activity,sigma factor activity, DNA-directed RNA polymerase activity and response to stimulus.These sites pathway was involved in the circadian rhythm and sulfur metabolism biological process.Further analysis of RT-PCR was validated the expression difference of aromatic and non-aromatic samples.
     3.2 The mechanism and biochemistry pathway of aroma in rice
     According to the analysis of the gene chip,previous studies and biological informatics, choline is the important compound in the process of the sk-2 gene controlling aroma character of rice.It is well-known that choline is one of the vitamine B compositions, which is mostly being in the chaff or the surface of rice grain.This is the result of the concentration for aroma character distributing in the surface of rice grains.
     As the BADH2 gene,aromatic varieties shows a large deletion and three single nucleotide polymorphisms(SNPs) compared to the sequence of non-aromatic varieties, and then terminates prematurely(stop codon TAA) in the exon7 of the gene.Then the function of gene losing that can't encode betaine aldehyde dehydrogenase,and betaine aldehyde is induced into the reaction of Betaine aldehyde + FAD + H20 <=> FADH2 + Betaine with the catalyzation of choline dehydrogenase;this reaction will delete FAD and produce FADH2,which restrained the reaction of proline degradationⅠ;L-proline is then accrued with the action of proline dehydrogenase and finally induce the reaction:L-proline +NAD(P)+=1-pyrroline-2-carboxylate+NAD(P)H+H+,and produce 1-pyrroline-2-carboxylate.The aroma key compound 2-acetyl-1-pyrroline may be from 1-pyrroline-2-carboxylate by methylation as their structural formulas similitude.In addition,sulfide was presumed to be relation with the form or behavior of aroma in rice.
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