Genome Evolution Due to Allopolyploidization in Wheat

The wheat group has evolved through allopolyploidization, namely, through hybridization among species from the plant genera Aegilops and Triticum followed by genome doubling. This speciation process has been associated with ecogeographical expansion and with domestication. In the past few decades, we have searched for explanations for this impressive success. Our studies attempted to probe the bases for the wide genetic variation characterizing these species, which accounts for their great adaptability and colonizing ability. Central to our work was the investigation of how allopolyploidization alters genome structure and expression. We found in wheat that allopolyploidy accelerated genome evolution in two ways: (1) it triggered rapid genome alterations through the instantaneous generation of a variety of cardinal genetic and epigenetic changes (which we termed “revolutionary” changes), and (2) it facilitated sporadic genomic changes throughout the species’ evolution (i.e., evolutionary changes), which are not attainable at the diploid level. Our major findings in natural and synthetic allopolyploid wheat indicate that these alterations have led to the cytological and genetic diploidization of the allopolyploids. These genetic and epigenetic changes reflect the dynamic structural and functional plasticity of the allopolyploid wheat genome. The significance of this plasticity for the successful establishment of wheat allopolyploids, in nature and under domestication, is discussed.     

Rapid Production of Multiple Independent Lines of Fertile Transgenic Wheat (Triticum aestivum)

Improvement of wheat (Triticum aestivum) by biotechnological approaches is currently limited by a lack of efficient and reliable transformation methodology. In this report, we detail a protocol for transformation of a highly embryogenic wheat cultivar, Bobwhite. Calli derived from immature embryos, 0.5 to 1 mm long, were bombarded with microprojectiles coated with DNA containing as marker genes the bar gene, encoding phosphinothricin-resistance, and the gene encoding [beta]-glucuronidase (GUS), each under control of a maize ubiquitin promoter. The bombardment was performed 5 d after embryo excision, just after initiation of callus proliferation. The ability of plantlets to root in the presence of 1 or 3 mg/L of bialaphos was the most reliable selection criteria used to identify transformed plants. Stable transformation was confirmed by marker gene expression assays and the presence of the bar sequences in high molecular weight chromosomal DNA of the resultant plants. Nine independent lines of fertile transgenic wheat plants have been obtained thus far, at a frequency of 1 to 2 per 1000 embryos bombarded. On average, 168 d elapsed between embryo excision for bombardment and anthesis of the T0 plants. The transmission of both the resistance phenotype and bar DNA to the T1 generation verified that germline transformation had occurred.     

硬粒小麦基因组中疑似硒蛋白生物信息分析

目的：用生物信息学的方法对硬粒小麦基因组中疑似硒蛋白的氨基酸序列进行综合分析,进一步找寻其为硒蛋白的生物信息依据,并初步分析推断其功能。方法：利用Vector NTI等多种生物信息学工具对硬粒小麦AYl46587．1序列中发现的疑似硒蛋白编码序列进行综合分析研究。结果：发现2段目标编码序列具有与某些蛋白酶相似的生物信息学特征,并推测其蛋白编码具有目前未知的机理。结论：推断AYl46587．1序列中存在编码未知硒蛋白的编码段,其编码的硒蛋白参与硬粒小麦胚芽生长发育时期能量调节。     

Whole Genome Association Mapping of Plant Height in Winter Wheat (Triticum aestivum L.)

The genetic architecture of plant height was investigated in a set of 358 recent European winter wheat varieties plus 14 spring wheat varieties based on field data in eight environments. Genotyping of diagnostic markers revealed the Rht-D1b mutant allele in 58% of the investigated varieties, while the Rht-B1b mutant was only present in 7% of the varieties. Rht-D1 was significantly associated with plant height by using a mixed linear model and employing a kinship matrix to correct for population stratification. Further genotyping data included 732 microsatellite markers, resulting in 770 loci, of which 635 markers were placed on the ITMI map plus a set of 7769 mapped SNP markers genotyped with the 90 k iSELECT chip. When Bonferroni correction was applied, a total of 153 significant marker-trait associations (MTAs) were observed for plant height and the SSR markers (−log₁₀ (P-value) ≥4.82) and 280 (−log₁₀ (P-value) ≥5.89) for the SNPs. Linear regression between the most effective markers and the BLUEs for plant height indicated additive effects for the MTAs of different chromosomal regions. Analysis of syntenic regions in the rice genome revealed closely linked rice genes related to gibberellin acid (GA) metabolism and perception, i.e. GA20 and GA2 oxidases orthologous to wheat chromosomes 1A, 2A, 3A, 3B, 5B, 5D and 7B, ent-kaurenoic acid oxidase orthologous to wheat chromosome 7A, ent-kaurene synthase on wheat chromosome 2B, as well as GA-receptors like DELLA genes orthologous to wheat chromosomes 4B, 4D and 7A and genes of the GID family orthologous to chromosomes 2B and 5B. The data indicated that besides the widely used GA-insensitive dwarfing genes Rht-B1 and Rht-D1 there is a wide spectrum of loci available that could be used for modulating plant height in variety development.     

硬粒小麦基因组中硒蛋白存在性分析研究

目的：用生物信息的方法对硬粒小麦基因组中硒蛋白存在性进行分析研究。方法：利用SECISearch工具将Genebank中收录的11029条硬粒小麦核酸序列逐个分析,找出具有符合硒蛋白特有茎环结构的序列,以已经发表的衣藻中硒蛋白为参照对象,利用VectorNTI软件对匹配序列进行生物信息分析,研究硬粒小麦硒蛋白存在性。结果：发现AY146587．1序列的互补序列中存在一个表达区与衣藻硒蛋白具有较高的结构相似性（该序列区长度为288bp,对应的SECIS在其下游6071bp处）,很有可能是硬粒小麦硒蛋白（或同源蛋白）编码区。结论：获得硬粒小麦中可能与硒蛋白相关的核酸序列。     

The Vascular System of the Spikelet in Wheat (Triticum aestivum)

The lower three florets in a spikelet of wheat cv. Aotea werefound to be supplied by the principal vascular bundles of therachilla, while the system of more distal florets consistedof subvascular elements derived from the vascular cylinder formedat the disc of insertion of these florets. This pattern appearedto be the same in all spikelets irrespective of position, apartfrom the terminal one, nor was it altered by raising the supplyof nitrogen. The apparent constancy of the vascular system iscontrasted with considerable variability in the number of grain-bearingflorets depending on genotype and environment. If a floret isconnected directly with the main vascular system and if assimilatesare not limiting, then competition for assimilates does notappear to be the main factor preventing grain formation.     

Detection in Vivo of Very Rapid Red Light-Induced Calcium-Sensitive Protein Phosphorylation in Etiolated Wheat (Triticum aestivum) Leaf Protoplasts

Etiolated wheat (Triticum aestivum cv Mercia) leaf protoplasts respond to brief red-light irradiation by increasing in volume over a 10-min incubation period (M.E. Bossen, H.A. Dassen, R.E. Kendrick, W.J. Vredenberg [1988] Planta 174: 94-100). When the calcium-sensitive dye Fluo-3 was incorporated into these protoplasts, red-light irradiation initiated calcium transients lasting about 2 min (P.S. Shacklock, N.D. Read, A.J. Trewavas [1992] Nature 358: 153-155). Release of calcium in the protoplasts by photolysis of incorporated 1-{2-amino-5-[1-hydroxy-1-(2-nitro-4, 5-methylenedioxyphenyl)-methyl]-phenoxy}-2-(2[prime]-amino-5[prime]-methylp henoxy)-ethane-N,N, N[prime],N[prime] -tetraccetic acid, tetrasodium salt (caged calcium) or caged inositol trisphosphate frequently induced transient increases in intracellular calcium levels, although the kinetics of these changes showed variation between experiments. Upon exposure to red light, a pronounced increase in the phosphorylation of a 70-kD and to a lesser extent a 60-kD peptide was observed, commencing within 15 s and continuing for up to 2 min. Simultaneous far-red and red irradiation attenuated the response. Upon release of incorporated caged calcium by cage photolysis, the labeling of these two peptides was greatly increased. When incorporated caged inositol trisphosphate was photolyzed, only the labeling of the 70-kD peptide was enhanced. Phosphorylation of the 70-kD peptide was also increased when extracellular calcium was elevated, but it decreased with increasing extracellular EGTA. These data thus provide direct evidence for the operation of an in vivo transduction sequence involving red light-dependent, calcium-sensitive protein phosphorylation.     

Mineral Ion Transport in the Embryos of Germinating Wheat (Triticum aestivum)

The germinating wheat embryo contains two mineral ion pumps.One is a H⁺/K⁺ antiport system located in the scutellum andthe other is a H⁺/anion symport, or possibly an anion/OH⁺ antiportsystem located in the embryo axis. The scutellum pump closelyresembles that found in other plant tissues; its affinity constantfor K⁺ is about 0.03 mM and its activity is energy dependentThe embryo axis pump is able to transport K⁺ in place of H⁺and appears to be a general monovalent cation/anion symportsystem. The scutellum pumping activity is stimulated by GA and the GAaction is inhibited by ABA. GA stimulates H⁺ more than K⁺ transport,electrochemical neutrality always being maintained by aniontransport. In contrast to reports about IAA-stimulated ion transportin other plant tissues, there is no evidence that the GA actionin the scutellum is dependent upon active protein synthesis.     

Whole Genome Association Mapping of Fusarium Head Blight Resistance in European Winter Wheat (Triticum aestivum L.)

A total of 358 recent European winter wheat varieties plus 14 spring wheat varieties were evaluated for resistance to Fusarium head blight (FHB) caused by Fusarium graminearum and Fusarium culmorum in four separate environments. The FHB scores based on FHB incidence (Type I resistance)×FHB severity (Type II resistance) indicated a wide phenotypic variation of the varieties with BLUE (best linear unbiased estimation) values ranging from 0.07 to 33.67. Genotyping with 732 microsatellite markers resulted in 782 loci of which 620 were placed on the ITMI map. The resulting average marker distance of 6.8 cM allowed genome wide association mapping employing a mixed model. Though no clear population structure was discovered, a kinship matrix was used for stratification. A total of 794 significant (−log₁₀(p)-value≥3.0) associations between SSR-loci and environment-specific FHB scores or BLUE values were detected, which included 323 SSR alleles. For FHB incidence and FHB severity a total of 861 and 877 individual marker-trait associations (MTA) were detected, respectively. Associations for both traits co-located with FHB score in most cases. Consistent associations detected in three or more environments were found on all chromosomes except chromosome 6B, and with the highest number of MTA on chromosome 5B. The dependence of the number of favourable and unfavourable alleles within a variety to the respective FHB scores indicated an additive effect of favourable and unfavourable alleles, i.e. genotypes with more favourable or less unfavourable alleles tended to show greater resistance to FHB. Assessment of a marker specific for the dwarfing gene Rht-D1 resulted in strong effects. The results provide a prerequisite for designing genome wide breeding strategies for FHB resistance.     

Principles of Genome Evolution in the Drosophila melanogaster Species Group

That closely related species often differ by chromosomal inversions was discovered by Sturtevant and Plunkett in 1926. Our knowledge of how these inversions originate is still very limited, although a prevailing view is that they are facilitated by ectopic recombination events between inverted repetitive sequences. The availability of genome sequences of related species now allows us to study in detail the mechanisms that generate interspecific inversions. We have analyzed the breakpoint regions of the 29 inversions that differentiate the chromosomes of Drosophila melanogaster and two closely related species, D. simulans and D. yakuba, and reconstructed the molecular events that underlie their origin. Experimental and computational analysis revealed that the breakpoint regions of 59% of the inversions (17/29) are associated with inverted duplications of genes or other nonrepetitive sequences. In only two cases do we find evidence for inverted repetitive sequences in inversion breakpoints. We propose that the presence of inverted duplications associated with inversion breakpoint regions is the result of staggered breaks, either isochromatid or chromatid, and that this, rather than ectopic exchange between inverted repetitive sequences, is the prevalent mechanism for the generation of inversions in the melanogaster species group. Outgroup analysis also revealed evidence for widespread breakpoint recycling. Lastly, we have found that expression domains in D. melanogaster may be disrupted in D. yakuba, bringing into question their potential adaptive significance.     

Rapid Birth–Death Evolution Specific to Xenobiotic Cytochrome P450 Genes in Vertebrates

Genes vary greatly in their long-term phylogenetic stability and there exists no general explanation for these differences. The cytochrome P450 (CYP450) gene superfamily is well suited to investigating this problem because it is large and well studied, and it includes both stable and unstable genes. CYP450 genes encode oxidase enzymes that function in metabolism of endogenous small molecules and in detoxification of xenobiotic compounds. Both types of enzymes have been intensively studied. My analysis of ten nearly complete vertebrate genomes indicates that each genome contains 50–80 CYP450 genes, which are about evenly divided between phylogenetically stable and unstable genes. The stable genes are characterized by few or no gene duplications or losses in species ranging from bony fish to mammals, whereas unstable genes are characterized by frequent gene duplications and losses (birth–death evolution) even among closely related species. All of the CYP450 genes that encode enzymes with known endogenous substrates are phylogenetically stable. In contrast, most of the unstable genes encode enzymes that function as xenobiotic detoxifiers. Nearly all unstable CYP450 genes in the mouse and human genomes reside in a few dense gene clusters, forming unstable gene islands that arose by recurrent local gene duplication. Evidence for positive selection in amino acid sequence is restricted to these unstable CYP450 genes, and sites of selection are associated with substrate-binding regions in the protein structure. These results can be explained by a general model in which phylogenetically stable genes have core functions in development and physiology, whereas unstable genes have accessory functions associated with unstable environmental interactions such as toxin and pathogen exposure. Unstable gene islands in vertebrates share some functional properties with bacterial genomic islands, though they arise by local gene duplication rather than horizontal gene transfer.     

冬小麦植物铁载体分泌的杂种效应

缺铁是石灰性土壤常见的植物营养问题之一.禾本科植物种或基因型的植物铁载体分泌能力与耐缺铁有关,提高植物铁载体分泌能力是改良缺铁的土壤上植物铁aestivum L.) 3个杂交种及其4个亲本在缺铁营养液中植物铁载体的分泌及杂种的效应.植物铁载体的分泌率通过根分泌物对新形成的Fe(OH)3的活化能力进行测定, 在缺铁症出现时每隔2、3天测定1次.在缺铁条件下,所有基因型都分泌较多的植物铁载体,并且随缺铁症状的发展分泌量增加.杂交种具有对缺铁更敏感的反馈系统,在缺铁条件下,杂交种比亲本分泌铁载体的速度更快、量更高.通过分析杂交种和亲本的关系,认为可以通过对亲本分泌植物铁载体能力和配合力的选择,利用杂种优势来提高小麦铁的利用效率.     

冬小麦植物铁载体分泌的杂种效应

缺铁是石灰性土壤常见的植物营养问题之一。禾本科植物种或基因型的植物铁载体分泌能力与耐缺铁有关 ,提高植物铁载体分泌能力是改良缺铁的土壤上植物铁营养的关键措施之一。在水培条件下分析了冬小麦(TriticumaestivumL .) 3个杂交种及其 4个亲本在缺铁营养液中植物铁载体的分泌及杂种的效应。植物铁载体的分泌率通过根分泌物对新形成的Fe(OH) 3 的活化能力进行测定 ,在缺铁症出现时每隔 2、3天测定 1次。在缺铁条件下 ,所有基因型都分泌较多的植物铁载体 ,并且随缺铁症状的发展分泌量增加。杂交种具有对缺铁更敏感的反馈系统 ,在缺铁条件下 ,杂交种比亲本分泌铁载体的速度更快、量更高。通过分析杂交种和亲本的关系 ,认为可以通过对亲本分泌植物铁载体能力和配合力的选择 ,利用杂种优势来提高小麦铁的利用效率。     

Developmental Base Temperature in Different Phenological Phases of Wheat (Triticum aestivum)

The linear relationship between temperature and developmentrate has been widely recognized and it has been suggested thatthermal units (the summation of daily mean temperature abovea base temperature) can predict the phenological developmentof a crop. The aim of this paper was to determine the base temperaturefor different phenological phases of wheat. Two mediterraneanwheat cultivars and five sowing dates were used to obtain differentmean temperatures during development and different developmentalrates. The linear regression of development rate against meantemperatures for each period indicated that there were no uniquebase temperatures for all stages of the life span and valuesclose to 4°C and to 9·5°C were found to be bestfits for base temperatures before and after the terminal spikeletstage of both cultivars. A model to predict wheat developmentwas validated with another data set, which included differentwheat cultivars and sowing dates. Estimates of the error indevelopmental prediction by using a single base temperatureof 0°C is discussed as a function of separate developmentstages. Key words: Wheat development, base temperature, thermal time, Triticum aestivum     

Evidence on the Saltatory Origin of the G Genome in Wheat: the Description of a Triticum timopheevi-like Mutant

A spontaneously occurring somatic mutant of Triticum turgidumdicoccoides showed close morphological resemblance to T. timopheevi(AAGO). The hybrid between the mutant and the T. turgidum dicoccoides‘ mother’ plant was completely sterile, with verylow pollen fertility (0·33 percent). It exhibited a reasonablyhigh frequency of trivalents and quadrivalents at first metaphaseof meiosis, indicating that the mutation involved substantiallevels of chromosome rearrangement. The hybrid between the mutantand T. timopheevi had reasonably high fertility (53·5per cent) and high pollen fertility (86·6 per cent) andalmost regular bivalent formation at first metaphase of meiosis. It is proposed that T. timopheevi could have arisen in consequenceof somatic macromutation from T. turgidum dicoccoides givingrise to spontaneous speciation. The G genome of T. timopheeviis possibly monophyletic in origin, arising from rearrangementof chromosomes of the B genome of tetraploid wheat. Triticum turgidum dicoccoides, wheat, G genome, mutant