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四篇Science文章公布最新小麦基因组序列

科研动态2014-07-21

导读:正值美国著名遗传学家、世界“绿色革命”的先驱Norman Borlaug诞辰100周年之际,科学家们成功获得了几近完整的小麦基因组序列信息,这是小麦基因组研究的一个重要里程碑,为今后培育高产且持续性的小麦品种奠定了坚实的基础,意义深远。

       小麦是全球最重要的粮食作物之一,提供了20%人类所需的热量。2010年英国科学家宣布他们绘制出了小麦基因组草图,但这一序列并不完整。

       在7月17日Science杂志上,两个研究组分别公布了Chinese Spring小麦品种的每个染色体臂的基因组序列,以及小麦染色体3B基因组序列,另外两个研究小组整理了发育中的普通小麦谷物组织的RNA产物,以及现代普通小麦的系统发育历史。这些成果将给我们呈递几近完整的小麦基因组序列信息。

       这些研究成果由国际小麦基因组测序协作组织(IWGSC)联合其它实验室完成,国际小麦测序协作组织成立于2005年,由小麦种植者团体、植物科学家、公共或私人育种者联合建立的一个国际性合作机构,有来自全世界57个国家的1000多个成员。其目标是获取并公布高质量的面包小麦基因组序列信息,为小麦基础科学研究奠定基础,从而推动育种学者进行小麦品种改良。

       到2050年,世界人口预计会从七十亿增加到九十亿,在可用耕地越来越少的情况下,要满足全球对粮食持续增长的需求,就要培育出高产量的主要农作物。小麦、水稻和玉米是世界粮食供应的三大支柱,其中小麦是欧洲、印度、中国和非洲等地主要的食物来源。然而近年来由于气候变暖,灾害频发,全球的小麦产量受到严重威胁,解析这种植物的基因组,将有助于培育更高质量的小麦品种。

       普通小麦来源于三个祖先,其基因组是三个基因组的复合体特别复杂,普通小麦的基因组大小是人类基因组的五倍,可能是迄今为止测序了的最复杂的基因组。

       在第一篇文章中,IWGSC德国的科学家针对早熟小麦(Triticum aestivum)展开了研究,他们对这一小麦品种的每个染色体臂进行了分离,测序及组装。沿着这些染色体臂,研究人员能够精确定位超过12万个基因,它们中有许多与在农业上重要的像谷物品质、对病虫害的抵抗性或非生物胁迫耐受性等特性有关。

        其次,法国的科学家们公布了小麦参考序列,这一序列是小麦21条染色体中最大的序列:染色体3B。从中研究人员确认了数千个重要基因标记。由于小麦基因组是高度重复的,并有非常频繁的插入,因此即使是组装一个染色体也是困难的。

        这项研究采用了BAC-to-BAC测序方法,这种方法基于细菌人工染色体(Bacterial Artificial Chromosome,BAC)文库构建,BAC末端测序技术通过测定插入片段两端的序列,能够迅速而精确地进行序列拼装,并确定基因组序列结构的多态性,如倒置和易位等,在基因组全序列测序中有着举足轻重的作用。

       利用这种方法,研究人员完成了这一染色体的组装,并为测序所剩下的20条染色体建立了一个模板。应用这一相同的策略,明年可能会完成另外几条普通小麦染色体的测序。

       还有来自奥斯陆大学等处的一个研究组通过草图序列在小麦基因组的历史与进化方面以及籽粒发育相关基因进行研究,指出了当今的普通小麦基因组是多轮杂交事件的一个产物,并显示了对全基因组数据集的分析如何能协助厘清基因演化的复杂模式。

       最后还有一组研究人员对来自发育中的普通小麦谷物组织的RNA产物进行了编目以了解该3种亚基因组是如何促成现代普通小麦基因组对其基因表达的影响的。

       掌握了基于单条染色体的全基因组序列资源,植物育种家便有了新的高质量工具,可以用来加速育种计划、鉴定控制复杂性状的基因,如产量、谷物质量、病害、抗虫、以及非生物逆境胁迫等。他们从而能培育出新一代更加高产和更有持续性的小麦品种,在不断变化的环境中满足人口增长的需求。 

参考文献
 
Structural and functional partitioning of bread wheat chromosome 3B

Structural and functional partitioning of bread wheat chromosome 3B

We produced a reference sequence of the 1-gigabase chromosome 3B of hexaploid bread wheat. By sequencing 8452 bacterial artificial chromosomes in pools, we assembled a sequence of 774 megabases carrying 5326 protein-coding genes, 1938 pseudogenes, and 85% of transposable elements. The distribution of structural and functional features along the chromosome revealed partitioning correlated with meiotic recombination. Comparative analyses indicated high wheat-specific inter- and intrachromosomal gene duplication activities that are potential sources of variability for adaption. In addition to providing a better understanding of the organization, function, and evolution of a large and polyploid genome, the availability of a high-quality sequence anchored to genetic maps will accelerate the identification of genes underlying important agronomic traits.

Genome interplay in the grain transcriptome of hexaploid bread wheat

Genome interplay in the grain transcriptome of hexaploid bread wheat

Allohexaploid bread wheat (Triticum aestivum L.) provides approximately 20% of calories consumed by humans. Lack of genome sequence for the three homeologous and highly similar bread wheat genomes (A, B, and D) has impeded expression analysis of the grain transcriptome. We used previously unknown genome information to analyze the cell type–specific expression of homeologous genes in the developing wheat grain and identified distinct co-expression clusters reflecting the spatiotemporal progression during endosperm development. We observed no global but cell type– and stage-dependent genome dominance, organization of the wheat genome into transcriptionally active chromosomal regions, and asymmetric expression in gene families related to baking quality. Our findings give insight into the transcriptional dynamics and genome interplay among individual grain cell types in a polyploid cereal genome.

A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome

A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome

An ordered draft sequence of the 17-gigabase hexaploid bread wheat (Triticum aestivum) genome has been produced by sequencing isolated chromosome arms. We have annotated 124,201 gene loci distributed nearly evenly across the homeologous chromosomes and subgenomes. Comparative gene analysis of wheat subgenomes and extant diploid and tetraploid wheat relatives showed that high sequence similarity and structural conservation are retained, with limited gene loss, after polyploidization. However, across the genomes there was evidence of dynamic gene gain, loss, and duplication since the divergence of the wheat lineages. A high degree of transcriptional autonomy and no global dominance was found for the subgenomes. These insights into the genome biology of a polyploid crop provide a springboard for faster gene isolation, rapid genetic marker development, and precise breeding to meet the needs of increasing food demand worldwide.

Ancient hybridizations among the ancestral genomes of bread wheat

Ancient hybridizations among the ancestral genomes of bread wheat

The allohexaploid bread wheat genome consists of three closely related subgenomes (A, B, and D), but a clear understanding of their phylogenetic history has been lacking. We used genome assemblies of bread wheat and five diploid relatives to ana

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