Modelling temperature, photoperiod and vernalization responses of Brunonia australis (Goodeniaceae) and Calandrinia sp (Portulacaceae) to predict flowering time

Crop models for herbaceous ornamental species typically include functions for temperature and photoperiod responses, but very few incorporate vernalization, which is a requirement of many traditional crops. This study investigated the development of floriculture crop models, which describe temperature responses, plus photoperiod or vernalization requirements, using Australian native ephemerals Brunonia australis and Calandrinia sp. A novel approach involved the use of a field crop modelling tool, DEVEL2. This optimization program estimates the parameters of selected functions within the development rate models using an iterative process that minimizes sum of squares residual between estimated and observed days for the phenological event. Parameter profiling and jack-knifing are included in DEVEL2 to remove bias from parameter estimates and introduce rigour into the parameter selection process. Development rate of B. australis from planting to first visible floral bud (VFB) was predicted using a multiplicative approach with a curvilinear function to describe temperature responses and a broken linear function to explain photoperiod responses. A similar model was used to describe the development rate of Calandrinia sp., except the photoperiod function was replaced with an exponential vernalization function, which explained a facultative cold requirement and included a coefficient for determining the vernalization ceiling temperature. Temperature was the main environmental factor influencing development rate for VFB to anthesis of both species and was predicted using a linear model. The phenology models for B. australis and Calandrinia sp. described development rate from planting to VFB and from VFB to anthesis in response to temperature and photoperiod or vernalization and may assist modelling efforts of other herbaceous ornamental plants. In addition to crop management, the vernalization function could be used to identify plant communities most at risk from predicted increases in temperature due to global warming.

Haplotype analysis of vernalization loci in European barley germplasm reveals novel VRN-H1 alleles and a predominant winter VRN-H1/VRN-H2 multi-locus haplotype

In barley, variation in the requirement for vernalization (an extended period of low temperature before flowering can occur) is determined by the VRN-H1, -H2 and -H3 loci. In European cultivated germplasm, most variation in vernalization requirement is accounted for by alleles at VRN-H1 and VRN-H2 only, but the range of allelic variation is largely unexplored. Here we characterise VRN-H1 and VRN-H2 haplotypes in 429 varieties representing a large portion of the acreage sown to barley in Western Europe over the last 60 years. Analysis of genotype, intron I sequencing data and growth habit tests identified three novel VRN-H1 alleles and determined the most frequent VRN-H1 intron I rearrangements. Combined analysis of VRN-H1 and VRN-H2 alleles resulted in the classification of seventeen VRN-H1/VRN-H2 multi-locus haplotypes, three of which account for 79% of varieties. The molecular markers employed here represent powerful diagnostic tools for prediction of growth habit and assessment of varietal purity. These markers will also allow development of germplasm to test the behaviour of individual alleles with the aim of understanding the relationship between allelic variation and adaptation to specific agri-environments.

The role of BoFLC2 in cauliflower (Brassica oleracea var. botrytis L.) reproductive development

In agricultural species that are sexually propagated or whose marketable organ is a reproductive structure, management of the flowering process is critical. Inflorescence development in cauliflower is particularly complex, presenting unique challenges for those seeking to predict and manage flowering time. In this study, an integrated physiological and molecular approach was used to clarify the environmental control of cauliflower reproductive development at the molecular level. A functional allele of BoFLC2 was identified for the first time in an annual brassica, along with an allele disrupted by a frameshift mutation (boflc2). In a segregating F2 population derived from a cross between late-flowering (BoFLC2) and early-flowering (boflc2) lines, this gene behaved in a dosage-dependent manner and accounted for up to 65% of flowering time variation. Transcription of BoFLC genes was reduced by vernalization, with the floral integrator BoFT responding inversely. Overall expression of BoFT was significantly higher in early-flowering boflc2 lines, supporting the idea that BoFLC2 plays a key role in maintaining the vegetative state. A homologue of Arabidopsis VIN3 was isolated for the first time in a brassica crop species and was up-regulated by two days of vernalization, in contrast to findings in Arabidopsis where prolonged exposure to cold was required to elicit up-regulation. The correlations observed between gene expression and flowering time in controlled-environment experiments were validated with gene expression analyses of cauliflowers grown outdoors under 'natural' vernalizing conditions, indicating potential for transcript levels of flowering genes to form the basis of predictive assays for curd initiation and flowering time.

运用减法杂交、差异筛选与信使RNA差别显示聚合酶链式反应克隆冬小麦春化相关基因

对于某些一年生或二年生高等植物，春化作用是诱导其成花的一个重要的环境因子。冬小麦春化进程中存在着一个核酸代谢的关键期，利用分子生物学技术分离特异表达的基因是研究春化诱导成花机理的一个突破口。 利用TRIzol试剂快速提取冬小麦燕大1817(Triticum aestivum L. cv Yanda 1817)未春化、春化4d、春化20d、5d脱春化的胚芽中的总RNA，去除污染的DNA后，将引物P_1(5'TTTTTTTTTTTCA3')、P_2(5'TTTTTTTTTTCC3')与10个碱基的随机引物OPF_1-OPF_(20)、OPG_1-OPG_(20)组成80个引物对，对不同来源的RNA进行差别显示，共显示了大约10,000种mRNA，结果发现了两个仅在春化20d这一关键期表达而在未春化、春化4d、5d脱春化时不表达的春化相关基因(VRG)VRG49与VRG54。Northern分析进一步表明这两个基因仅与春化20d的冬小麦RNA有杂交信号。将VRG49与VRG54亚克隆于pGEM-4Z载体上，利用T_7测序系统获得了VRG49和VRG54的DNA序列，它们的长度分别为307bp与169bp。 春化21d的冬小麦京冬1号(T. aestivum L. cv Jingdong No. 1)胚芽的mRNA在逆转酶作用下反转录成sscDNA杂交，将过量的未春化、脱春化的mRNA与sscDNA杂交，运用磁珠法分离出未杂交上的sscDNA，以特异的sscDNA为模板，用DNA聚合酷I合成了dscDNA。通过对dscDNA内部EcoRI位点的甲基化、末端补平、EcoRI接头的安装、连接进入λgt10载体的EcoRI位置，以及运用包装系统进行体外包装，建立了库容为4 * 10~6pfu的富集低温诱导的冬小麦cDNA噬菌体文库。用来源于未春化、春化21d、脱春化的冬小麦mRNA合成3种cDNA探针，对噬菌斑进行原位杂交，结果筛选出了3个春化相关基因(VRG)VRG79、VRG111和VRG231。Dot blotting与Northern分析表明VRG79仅在冬小麦春化关键期21d表达。运用PCR方法从λgt10DNA中扩增出VRG79片断并亚克隆于PUC18载体上，通过T_7测序系统获得了VGR79的序列，其包括349个碱基。 通过Internet将VRG49、VRG54、VRG79与GenBank、EMBL、DDBJ、PBD中的序列进行同源性分析，结果发现这些基因至少是在植物中新发现的基因，对这些基因推测的一些功能也进行了讨论。

冬小麦春化作用相关基因Verc203的功能鉴定

本文应用反义基因技术对减法杂交和差异筛选所获得的春化相关基因CDNA克隆( Verc203)的功能进行鉴定。将Vcrc203插入PB1221质粒的CaMV35S启动子与GLIS基因之间构成表达载体，采用花粉管途径转基因法导入冬小麦胚，得到300粒种子。将上述处理的冬小麦种子萌发后在2-4℃处理28天，转入自然条件下栽培。以幼叶为材料提取基因组DNA，以Gus基因片断为探针，用点杂交法筛选获得转基因植株．转基因植株在自然条件下生长三个月未见抽穗， 而同样栽培条件下的对照（未经转基因处理的冬小麦，经相同条件春化处理）则全部抽穗。以Vcrc203和Gus基因的部分序列为引物，在转基因材料的基因组DNA中扩增出Vcrc203反义基因序列，Gus活性检测表明Gus基因在转基因小麦的茎尖和叶片中得到表达。上述结果表明Vcrc203的反义基因已整合到冬小麦基因组内，并得到高效表达。转基因植株的发育受到严重影响，显示Vcrc203基因可能参与了冬小麦春化作用对植物发育进程的调控．

植物克隆化基因功能分析及蛋白编码基因分离的研究

直到九十年代，以利用拟南芥菜和金鱼草突变体克隆到花器官发育基因为重要标志的植物发育研究取得了重大突破。但由于开花决定过程分子控制机理研究进展却较为缓慢。以mRNA人手利用差异筛选技术获得春化相关基因克隆(verc203，verc17)，Northem blot初步证明这些克隆对春化处理的特异性。根据反义RNA理论和技术对克隆化verc203基因功能进行研究。另外，从纯化蛋白人手，在金针菇中克隆到新的溶血性毒蛋白编码基因，并在细菌中得到表达，这一实验为利用此途径来克隆发育调控蛋白的编码基因进行了有益的技术路线探索。本研究的具体结果如下： 1． 春化相关基因(verc203)对冬小麦花发育调控 根据反义RNA的理论和技术进一步证明verc203在冬小麦开花启动和花发育过程中的可能控制作用。将verc203 DNA序列插入带有CaMV35S启动子和GUS基因的pBI221表达载体， 使之能在植物中高效表达反义RNA，并以转正义基因植株作为对照。通过花粉管途径转基因方法，得到326粒反义质粒冬小麦转化种子和1 98粒正义质粒冬小麦转化种子．所有转化处理种子和正常小麦种子萌发后，经春化处理，与未春化冬小麦植株一起培养直到对照植株达到成熟期。实验观察发现，转反义基因植株的抽穗受到明显的阻抑，开花过程大大推迟。其中表达较强的6株转基因植株甚至晚花五十多天。还发现一些表达较弱的植株尽管晚花20到30天，但花器官发育却受到影响，如，雄蕊缺失，穗发育异常等。Southemblot和PCR实验结果表明外源基因整合到转基因植株基因组。 Northrenblot以及报告基因(GUS)活性等实验证明反义基因在转反义基因植株RNA水平上得到高效表达。同时，GUS基因在蛋白质水平上得到表达。基于上述实验，有理由认为ver203基因可能是控制冬小麦春化诱导的成花启动和花发育过程中的主要基因之一。 2． 金针菇毒蛋白flammutoxin编码基因的克隆及其在细菌中的表达 利用色谱分离技术及SDS．PAGE电泳技术从金针菇(Flammuleina velutips)分离得到一种分子量为31 kDa、对人血红细胞具有溶血活性的蛋白质(flammutoxin)，通过蛋白质序列微量分析技术测得其N-端3 1个氨基酸顺序。利用氨基酸序列推测其编码基因序列信息，通过RT - PCR克隆到一个由973个核苷酸组成的编码基因，5’端93个核苷酸编码肽链序列与测得flammutoxin N-端氨基酸序列完全相同。基因序列同源性分析表明在GenBank (USA)，EMBL Database (Europe)和DDBJ (Japan)基因序列数据库中未找到与之同源的基因序列。这个基因与载体p-半乳糖苷酶部分基因编码的融合蛋白在E coli细胞中有效地得到表达。表达产物的SDS-PAGE，Western blot和溶血活性实验表明它是flammutoxin蛋白原编码基因。并对融合蛋白的溶血活性降低原因作了讨论。

小麦春化相关基因的克隆及其功能分析

一． 小麦相关基因ver203F cDNA全序列克隆与功能分析 　　根据本实验室通过差异筛选技术克隆到的与春化相关的基因cDNA verc203的序列，设计PCR 5’端PCR引物，利用RACE（rapid amplification of cDNA ends）克隆策略，得到春化相关基因ver203基因的同源基因ver203F cDNA的3’端序列，长度为1,197bp。Northern分析表明ver203F全长约为1.5 kb，且其表达具有春化处理的特异性。根据3’RACE克隆的ver203F 3 ’端核苷酸序列设计了3’端PCR引物，利用5’RACE克隆到该基因的5’端片段，经DNASIS核酸分析软件分析将5’45RACE和3’RACE DNA序列拼接合并，得到ver203F全长cDNA，从TdT加尾5’末端到poly A全长为1,561 bp，5’端起始密码子ATG上游非编码区－1～－192共了192bp，终止密码子TGA到poly A的非编码区有253bp，cDNA编码区全长1,119 bp，推测编码373氨基酸残基。国际基因序列数据库检索表明该基因序列（GenBank/EMBL/DDBJ：AB012013）与大麦茉莉酸诱导基因有部分同源性。因上推测该基因在调控开花过程中可能参与茉莉酸介导的信号传导途径，ver203F作用的发挥可能需要其它蛋白的参与，或ver203F本身就是一个受体蛋白。 　　为了研究ver203F基因的功能，将通过3’RACE克隆到的ver203F 3’端序到分别构建正义和反义植物表达载体，通过花粉管通道法、农杆菌介导的叶圆片法以及农杆菌介导的真空转化法分别转化小麦、烟草和拟南芥菜。获得转基因植株后，PCR、DNA Dob Blot、Southern Blot分析以及GUS活性检测证明外源基因已整合到转基因植株中，并得到表达。在获得的小麦、烟草和拟南芥菜转基因植株中，它们开花时间都相应地推迟，表明正常植物体内该基因在控制营养生长向生殖生长的转变中起作用。ver203F可以影响小麦和拟南茶菜花序的发育，首先无论正义还是反义都使得花序的发育受到抑制，在小麦中表现为顶部小穗退化，在拟南芥菜中表现为顶花。其次在转化正义基因的转基因拟南芥菜中，观察到产生的顶花为对称的两朵或以对称的两朵顶花基部为生长点长出丛生花，这种对称花的麦型小麦小穗中小花的表型相类似，说明ver203F基因可能在小麦小花的发育过程中也起着重要作用。 二． 春化相关基因ver17在开花过程中功能的分析 以春化处理冬小麦（京冬1号）幼苗cDNA为材料，通过减法杂交与差异筛选得到春化相关cDNA克隆verc17。为了研究该基因的功能，以包含CaMV 35S启动子的pBI221为载体，将ver17cDNA片段分别从两个方向插入pBI221的BamH I－Sma I, Xba I－BamH I间，构建正义和反义表达质粒：p17S和p17X，通过花粉管通道法转化小麦。对T0和T1两代转基因小麦的观察发现，在转化反义基因p17X的转基因小麦首先表现为抽穗推迟，其次穗的顶部和基部小穗严重退化，另外还发现转化反义基因的小麦败育现象严重（主要是花粉败育），因此推测ver17基困能可具有以下几方面的特点：a．春化诱导型表达;b．促进植物开花;c．促进穗顶端和基部花的发育，减少其退化;d．影响雄蕊的发育。

拟南芥bre突变体分析及小麦ver203F基因表达模式研究

第一部分 茎尖分生组织的中央部位是由干细胞组成，维持干细胞的动态平衡对于植物器官启动显得尤为重要。在拟南芥花序分生组织和花分生组织中分别有WUS/CLV和(WUS+LFY)/AG两个负反馈调节环控制着这一平衡，保证了花序分生组织的非决定性和花分生组织的决定性。 本文用T-DNA激活标签技术得到功能增强突变体bre，序列分析表明BRE就是干细胞特征基因WUSCHEL。定量RT-PCR表明在突变体的茎节间WUS大量表达，证实在WUS基因的调控区插入的4个35S增强子使WUS表达增强。突变体bre生长发育缓慢，茎弯曲，花器官数目改变，心皮发育加快。尤为突出的是在茎皮层直接分化出花分生组织。这些表型可能与WUS的表达增强有关。这说明WUS功能是多效的，除了在分生组织中决定干细胞命运、促进CLV和AG的表达外，还可能与生长素极性运输以及花分生组织特征基因的表达有关。 第二部分 春化作用是促进植物从营养生长向生殖生长转变的有效途径之一，作者所在实验室曾经分离到多个小麦春化相关基因。为研究春化期间它们在不同组织或不同细胞内的表达模式，首先建立并完善了RNA组织原位杂交系统。以春化相关基因ver203F为模板，采用地高辛为标记分子，借助体外转录制备RNA探针，分析了小麦胚芽和幼苗中ver203F的表达模式。结果表明：春化前和脱春化的胚芽中不表达ver203F，春化处理14天以上的胚芽幼叶表达ver203F,而且主要定位在叶的边缘分生组织细胞内，叶维管束和表皮组织未检测到转录物，胚芽鞘和茎尖分生组织中不表达。幼苗的侧芽中的幼叶有相同的表达模式。茉莉酸可以诱导ver203F的表达。．说明春化时的低温信号可能由幼叶接收，并有可能涉及到茉莉酸介导的信号转导途径。

小麦春化相关基因元件克隆分析与小麦矮化突变体的研究

一、 春化相关基因全长cDNA序列及其启动子的克隆与分析研究 通过建立小麦（Triticum aestivum. L. cv Jingdong No.1）胚芽春化cDNA文库，以春化相关基因VER2的3’端序列为探针，筛选获得全长1195 bp cDNA序列，它编码300个氨基酸。在VER2中存在植物疾病抗性反应蛋白和茉莉酸诱导凝集素两种蛋白的结构域。另外在VER2蛋白中存在核定位信号和多种磷酸酶的作用位点，VER2可能参与了多种调控途径。 以VER2基因的cDNA为探针，利用改进的池式PCR以及高密度膜杂交筛选的方法，从小麦TAC基因组文库中获得41,788 bp的基因组克隆，该序列含有11个基因，其中VER2基因位于第三个基因。VER2基因组序列含有3个内含子，4个外显子与cDNA序列100%同源。通过对转录起始点和转录终止点的分析，进一步证明从cDNA文库筛选得到的VER2基因为全长序列。 对VER2基因的上游启动子区域进行分析，发现基因上游启动子区存在三个小的重复序列，每个片段有482 bp，另有两个较大的重复序列，每个片段有2,161 bp。对上游2.8 kb启动子区（不含重复序列）的响应元件分析，其包括ABA响应元件（ABRE）、茉莉酸甲酯响应元件（Me-JARE）、胚乳特异性表达元件、参与淀粉酶合成的元件以及存在类似GA响应元件（ATAACAAAC）如ATAACATAC等等。根据VER2基因上游6 kb序列结构特点，将VER2启动子区域进行缺失突变形成10个片段，分别以GUS和GFP为报告基因构建成瞬间表达载体和植物表达载体等四类质粒。通过基因枪方法将最大片段（6 kb）驱动GFP报告基因的瞬间表达载体转入经春化处理或未春化处理的小麦幼叶中，结果发现GFP在春化处理的幼叶中表达，而在未春化处理的幼叶中不表达，说明VER2基因的启动子驱动基因转录受春化处理调控。 二、 小麦矮化突变体的研究 通过对小麦矮化突变体gaid遗传生理分析发现该突变体为半显性阻断GA信号途径，由此发现在赤霉素信号途径中，α-淀粉酶的诱导一定程度上通过某些与株高相关的基因控制。突变体gaid呈现对高浓度的脱落酸更敏感，当ABA浓度达到10-6M时，突变体的生长几乎完全受到了抑制，而野生型的生长需要ABA浓度达到10-5M时才能完全受到抑制。通过突变体gaid对乙烯等抑制型生长调节剂的响应实验研究，首次提出GA调控植物伸长生长存在两条信号途径，即GA基础水平信号途径（GA basal level signaling pathway）和GA正常水平信号途径（GA normal level signaling pathway），而乙烯以及高浓的GA合成抑制剂（如PAC）是通过第一条途径（GA基础水平信号途径）起作用。光形态建成中对植株生长的抑制作用存在独立于GA的信号途径。 突变体gaid的根系在强光照（63.5 Es-1m-2）和培养基内（低氧）的生长条件下，表现出弯曲、变短、加粗等异常性状，而随光照强度的减弱，这种根系异常生长的表型也减弱，在暗培养中则完全消失，但无论在哪种环境条件下，相对野生型对照而言，突变体的种子根短、侧根少。低浓度的ABA（10-8M）可以恢复突变体gaid根系在强光低氧条件下的正常生长发育。然而利用IAA及其极性运输的抑制剂（TIBA）、乙烯生物合成前提物（ACC）及合成抑制剂（AOA）处理突变体gaid，并没有发现突变体根系的生长发育得到恢复。 突变体gaid可能是一个新的属于小麦GA信号途径中的负调控基因（GAID）发生了突变或超表达，导致其负调控作用增强，呈现半显性的矮化突变。在与另一已知小麦GA信号途径中的负调控基因RHT的关系研究上发现，GAID可能对RHT蛋白磷酸化后的降解途径起抑制作用。通过双向电泳发现突变体gaid与野生型对照（京冬1号）在生长过程中存在差异蛋白，这将有助于对GA信号途径分子机理的深入研究。

The need for winter in the switch to flowering.

Vernalization is the process whereby the floral transition is promoted through exposure of plants to long periods of cold temperature or winter. A requirement for vernalization aligns flowering with the seasons to ensure that their reproductive phase occurs in favorable conditions. The mitotic stability of vernalization, suggestive of an epigenetic mechanism, has intrigued researchers for many years. Genetic analysis of the vernalization requirement in Arabidopsis has identified key floral repressor genes, FRI and FLC. The action of these floral repressors is antagonized by vernalization and the activity of a set of genes grouped into the autonomous floral pathway. Analysis of the vernalization pathway has defined a series of epigenetic regulators crucial for "cellular-memory" of the cold signal, whereas the autonomous pathway appears to function in part through posttranscriptional mechanisms. The mechanism of the vernalization requirement, which is now being explored in a range of plant species, should uncover the evolutionary origins of this key agronomic trait.

Control of Arabidopsis flowering: the chill before the bloom.

The timing of the floral transition has significant consequences for reproductive success in plants. Plants gauge both environmental and endogenous signals before switching to reproductive development. Many temperate species only flower after they have experienced a prolonged period of cold, a process known as vernalization, which aligns flowering with the favourable conditions of spring. Considerable progress has been made in understanding the molecular basis of vernalization in Arabidopsis. A central player in this process is FLC, which blocks flowering by inhibiting genes required to switch the meristem from vegetative to floral development. Recent data shows that many regulators of FLC alter chromatin structure or are involved in RNA processing.

Cold-induced silencing by long antisense transcripts of an Arabidopsis Polycomb target.

Transcription in eukaryotic genomes generates an extensive array of non-protein-coding RNA, the functional significance of which is mostly unknown. We are investigating the link between non-coding RNA and chromatin regulation through analysis of FLC - a regulator of flowering time in Arabidopsis and a target of several chromatin pathways. Here we use an unbiased strategy to characterize non-coding transcripts of FLC and show that sense/antisense transcript levels correlate in a range of mutants and treatments, but change independently in cold-treated plants. Prolonged cold epigenetically silences FLC in a Polycomb-mediated process called vernalization. Our data indicate that upregulation of long non-coding antisense transcripts covering the entire FLC locus may be part of the cold-sensing mechanism. Induction of these antisense transcripts occurs earlier than, and is independent of, other vernalization markers and coincides with a reduction in sense transcription. We show that addition of the FLC antisense promoter sequences to a reporter gene is sufficient to confer cold-induced silencing of the reporter. Our data indicate that cold-induced FLC antisense transcripts have an early role in the epigenetic silencing of FLC, acting to silence FLC transcription transiently. Recruitment of the Polycomb machinery then confers the epigenetic memory. Antisense transcription events originating from 3' ends of genes might be a general mechanism to regulate the corresponding sense transcription in a condition/stage-dependent manner.

Genetic variation at flowering time loci in wild and cultivated barley

The worldwide spread of barley cultivation required adaptation to agricultural environments far distant from those found in its centre of domestication. An important component of this adaptation is the timing of flowering, achieved predominantly in response to day length and temperature. Here, we use a collection of cultivars, landraces and wild barley accessions to investigate the origins and distribution of allelic diversity at four major flowering time loci, mutations at which have been under selection during the spread of barley cultivation into Europe. Our findings suggest that while mutant alleles at the PPD-H1 and PPD-H2 photoperiod loci occurred pre-domestication, the mutant vernalization non-responsive alleles utilized in landraces and cultivars at the VRN-H1 and VRN-H2 loci occurred post-domestication. The transition from wild to cultivated barley is associated with a doubling in the number of observed multi-locus flowering-time haplotypes, suggesting that the resulting phenotypic variation has aided adaptation to cultivation in the diverse ecogeographic locations encountered. Despite the importance of early-flowering alleles during the domestication of barley in Europe, we show that novel VRN alleles associated with early flowering in wild barley have been lost in domesticates, highlighting the potential of wild germplasm as a source of novel allelic variation for agronomic traits.