Next-generation sequencing of flow-sorted wheat chromosome 5D reveals lineage-specific translocations and widespread gene duplications

Background

The ~17 Gb hexaploid bread wheat genome is a high priority and a major technical challenge for genomic studies. In particular, the D sub-genome is relatively lacking in genetic diversity, making it both difficult to map genetically, and a target for introgression of agriculturally useful traits. Elucidating its sequence and structure will therefore facilitate wheat breeding and crop improvement.

Results

We generated shotgun sequences from each arm of flow-sorted Triticum aestivum chromosome 5D using 454 FLX Titanium technology, giving 1.34× and 1.61× coverage of the short (5DS) and long (5DL) arms of the chromosome respectively. By a combination of sequence similarity and assembly-based methods, ~74% of the sequence reads were classified as repetitive elements, and coding sequence models of 1314 (5DS) and 2975 (5DL) genes were generated. The order of conserved genes in syntenic regions of previously sequenced grass genomes were integrated with physical and genetic map positions of 518 wheat markers to establish a virtual gene order for chromosome 5D.

Conclusions

The virtual gene order revealed a large-scale chromosomal rearrangement in the peri-centromeric region of 5DL, and a concentration of non-syntenic genes in the telomeric region of 5DS. Although our data support the large-scale conservation of Triticeae chromosome structure, they also suggest that some regions are evolving rapidly through frequent gene duplications and translocations.

Sequence accessions

EBI European Nucleotide Archive, Study no. ERP002330

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-1080) contains supplementary material, which is available to authorized users.     

披碱草属(Elymus L.)两个物种之订正

披碱草属Elymus L．是小麦族Triticeae Dumort．中最大的属,全世界共有150多个种,广泛分布于 温带地区。我国约有80余种(包括鹅观草属Roegneria C．Koch),是披碱草属的重要分布区和多样性分 化中心。由于披碱草属植物种类繁多、分布广泛、生境多样以及形态变异较为复杂,导致该属在分类上 存在许多问题。同时,由于地域的局限和地区间交流的缺乏,致使同一种披碱草属植物被不同的学者多 次发表及同物异名现象的出现。本文对E．antiquus和E．burchan-buddae这两个曾多次被订名的披碱草 属物种进行了分类订正。     

麦类作物原位杂交影响因素的研究

为了更好地利用原位杂交技术进行麦类作物外源染色体的检测和基因定位,对麦类作物原位杂交的影响因素进行了研究。（１）利用缺口转译法对克隆的ＤＮＡ 片段进行生物素标记,即节省时间,又可以获得较高的标记效率;对麦类作物的基因组ＤＮＡ,宜采用随机寡核苷酸引物标记法进行生物素标记,适当延长标记时间可以提高标记效率。（２）共变性法比较适宜麦类作物的原位杂交,分别变性法如掌握不当易使染色体产生膨胀现象,变性温度过高也会使黑麦（Ｓｅｃａｌｅ ｃｅｒｅａｌ）染色体的轮廓模糊不清。（３）应根据麦类作物亲本之间的亲缘关系决定封阻ＤＮＡ 的使用浓度,并利用生物素标记的簇毛麦（Ｈａｙｎａｌｄｉａ ｖｉｌｌｏｓａ）基因组ＤＮＡ 为探针,从普通小麦（Ｔｒｉｔｉｃｕｍ ａｅｓｔｉｖｕｍ ）－簇毛麦双二倍体的染色体中识别了簇毛麦的染色体。（４）麦类作物的原位杂交受洗脱强度的影响很大,利用甲酰胺进行洗脱可以获得背景清晰的原位杂交带型。随着原位杂交技术分辨率的不断提高,该技术还将用于单拷贝基因的染色体定位     

Assessing genetic diversity of Elymus sibiricus (Poaceae: Triticeae) populations from Qinghai-Tibet Plateau by ISSR markers

Inter-simple sequence repeats (ISSR) markers were used to assess the genetic diversity and population structure in eight populations of Elymus sibiricus L. from the southeast of Qinghai-Tibet Plateau of China. Of the 100 primers screened, 13 produced highly reproducible ISSR bands. Using these primers, 193 discernible DNA fragments were generated with 149 (77.2%) being polymorphic, indicating considerable genetic variation at the species level. In contrast, there were relatively low levels of polymorphism at the population level with the percentage of polymorphic bands (PPB) ranging from 44.04 to 54.92%. The mean gene diversity (H_E) was estimated to be 0.181 within populations (range 0.164–0.200), and 0.274 at the species level. A high level of genetic differentiation among populations was detected based on Nei's genetic diversity analysis (33.1%), Shannon's index analysis (34.5%), Bayesian method (33.2%) and AMOVA analysis (42.5%). No significant statistical differences (analysis of molecular variance [AMOVA], P = 0.08) in ISSR variation were found between the sample collection regions. However, among populations (42.5% of the variance) and within populations (57.5% of the variance), there were significant differences (P < 0.001). Populations shared high levels of genetic identity. This pattern of genetic variation was different from that for most of inbreeding Triticeae species reported. In addition, a geographical pattern of population differentiation, where the populations from south and north of sampling sites were clearly separated from each other, was revealed by both the cluster and principal coordinates analyses. Generally, the result of this study indicates that E. sibiricus contains high molecular variation in its populations. The implications of these results for the conservation of the species are discussed.     

Genomic influence on somatic embryogenesis in the Triticeae

Somatic embryogenesis is generally accepted to be under genetic control. The influence of genome interactions is not well understood given the difficulties of obtaining the appropriate vegetal material. Synthetic alloploids in which genomes from two species are fused together are suitable subject material to analyse this factor. In the Triticeae tribe amphiploids can be easily synthesised, which provides the opportunity to carry on this type of study. Crossing three autotetraploids, Hordeum chilense (HHHH), Triticum tauschii (DDDD) and Secale cereale (RRRR), we obtained three tetraploid amphiploids, ×Tritordeum (HHDD), ×Triticale (DDRR) and ×Hordecale (HHRR). Somatic embryogenesis from immature inflorescence and flag leaves were scored on parents and amphiploids. Immature inflorescences had a higher embryogenic response than the flag leaves. The amphiploids showed higher regeneration ability than their parents. The best genomic combination was the tetraploid triticale DDRR for every inflorescence and flag leaf size tested, followed by HHDD and HHRR. Heterosis was found to be the main genetic factor affecting the in vitro culture response although there are clear differences among the three amphiploids tested. Received: 11 February 1998 / Revision received: 8 April 1998 / Accepted: 22 November 1998     

Effect of leaf structure and water status on carbon isotope discrimination in field-grown durum wheat

The relationships between leaf and kernel carbon isotope discriminations (Δ) and several leaf structural parameters that are indicators of photosynthetic capacity were studied in durum wheat grown in the field under three water regimens. A set of 144 genotypes were cultivated in two rain-fed trials, and 125 of these were grown under supplementary irrigation before heading. Total chlorophyll and nitrogen (N) contents, the dry mass per unit leaf area (LDM, the reciprocal of specific leaf area) and carbon isotope discrimination (Δ) were measured in penultimate leaves and Δ of mature kernels was also analysed. Both LDM and N per unit area showed significant (P≤ 0.001) negative correlation (r=–0.60 and r=–0.36, respectively) with leaf Δ in the wettest trial. Little or no correlation was found for any structural parameter and leaf Δ in the rain-fed trials. In contrast, in the two rain-fed trials LDM was the parameter with the strongest positive correlation (P≤ 0.001) with kernel Δ (r= 0.47 and 0.30) and grain yield (r= 0.43 and 0.29), whereas no correlation was found in the irrigation trial. These correlations, rather than representing a causal link between the amount of photosynthetic tissue and Δ, were probably indirect associations caused by a parallel effect of water status and phenology on leaf structure, grain Δ and yield. Correlations across trials (i.e. environments) between leaf structure and either Δ and yield were very high, although also spurious. Our results suggest that LDM should be used to cull segregating population differences in leaf Δ based on the internal photosynthetic capacity only in the absence of drought. Selecting for kernel Δ and grain yield on the basis of LDM is worthwhile for rain-fed trials.     

新疆多年生小麦族植物染色体数的观察

本文对1987年采集于新疆的多年生小麦族(Triticeae Dum. )属种进行了细胞学观察。该地区多年生小麦族各属种的染色体数目变化范围是从2n=14到2n=84,前者主要存在于大麦属(Hordeum)、新麦草属(Psathyrostachys),而后者全部集中于赖草属(Leymus).其中染色体数目为2n=28和2n=42的频率最高,主要存在于鹅冠草属(Roegneria)和披碱草属(Elymus)。Roegneria gobicola, Roegneria kuqaensis, Roegneria tahelacona, Roegneria zhoasuensis的染色体数为首次报道。     

鹅观草属三个种的形态变异与核型的研究

本文通过对鹅观草属的三个种:鹅观草(Roegneria kamoji Ohwi)、纤毛鹅观草(R. ciliars (Trin.) Nevski)和竖立鹅观草(R. japonensis(Honda)Keng)的形态学比较和核型分析研究了该三个种的系统关系。R. kamoji与R. ciliaris、R. japonensis形态上的差异明显,而后二个种差异甚小,难以进行划分。R. kamoji的核型公式为:2n=6x=42=30m+8sm+4SAT;R. ciliaris为:2n=4x=28=18m+6sm+4SAT;R. japonensis为:2n=4x=28=18m+6sm+4SAT。t-测验的结果表明R. ciliaris与R. japonensis的核型无显著差异。因此笔者认为R. ciliaris和R. japonensis应合并为一种系内的分类群。     

Dehydrins: Emergence of a biochemical role of a family of plant dehydration proteins

A number of proteins have been identified that typically accumulate in plants in response to any environmental stimulus that has a dehydrative component or is temporally associated with dehydration. This includes drought, low temperature, salinity and seed maturation. Among the induced proteins, dehydrins (late embryogenesis abundant [LEA] D-II family) have been the most commonly observed, yet we still have an incomplete knowledge of their fundamental biochemical role in the cell. Current research trends are changing this situation: immunolocalization and in vitro biochemical analyses are, through analogies to other more fully characterized proteins and molecules, shaping our understanding. In brief, dehydrins may be structure stabilizers with detergent and chaperone-like properties and an array of nuclear and cytoplasmic targets. Recent progress on the mapping of dhn genes and the inheritance of freezing tolerance in barley and other Triticeae species tentatively points to dehydrins as key components of dehydration tolerance.