禾草模式植物二穗短柄草的研究进展

二穗短柄草（Brachypodium distachyon）是近来开发的一种温带禾草模式植物。它具有与粮食作物相同的许多生物学特性,可作为研究粮食作物生物学特性的模式实验植物。不同采集地的二穗短柄草具有高度的表观变异性,可帮助研究人员对这些生物学特性从表观到遗传的深入研究。二穗短柄草与其他重要经济作物如小麦、大麦及其他潜在能源植物一样同属于早熟禾亚科,使其成为研究这些重要经济作物无可非议的模式植物。近来,由于二穗短柄草基因组序列及其相关注释的完成,功能基因组学和其他实验技术手段的不断进步,二穗短柄草可为其他禾草类植物提供序列分析、基因表达和功能研究等诸多便利。本文综述了利用二穗短柄草作为模式植物来进行比较基因组学、生物学研究、转化和T—DNA突变等方面的最新研究进展。     

Brachypodium distachyon. A New Model System for Functional Genomics in Grasses

A new model for grass functional genomics is described based on Brachypodium distachyon, which in the evolution of the Pooideae diverged just prior to the clade of "core pooid" genera that contain the majority of important temperate cereals and forage grasses. Diploid ecotypes of B. distachyon (2n = 10) have five easily distinguishable chromosomes that display high levels of chiasma formation at meiosis. The B. distachyon nuclear genome was indistinguishable in size from that of Arabidopsis, making it the simplest genome described in grasses to date. B. distachyon is a self-fertile, inbreeding annual with a life cycle of less than 4 months. These features, coupled with its small size (approximately 20 cm at maturity), lack of seed-head shatter, and undemanding growth requirements should make it amenable to high-throughput genetics and mutant screens. Immature embryos exhibited a high capacity for plant regeneration via somatic embryogenesis. Regenerated plants display very low levels of albinism and have normal fertility. A simple transformation system has been developed based on microprojectile bombardment of embryogenic callus and hygromycin selection. Selected B. distachyon ecotypes were resistant to all tested cereal-adapted Blumeria graminis species and cereal brown rusts (Puccinia reconditia). In contrast, different ecotypes displayed resistance or disease symptoms following challenge with the rice blast pathogen (Magnaporthe grisea) and wheat/barley yellow stripe rusts (Puccinia striformis). Despite its small stature, B. distachyon has large seeds that should prove useful for studies on grain filling. Such biological characteristics represent important traits for study in temperate cereals.     

Genome-wide survey of alternative splicing in the grass Brachypodium distachyon: a emerging model biosystem for plant functional genomics

A draft sequence of the genome of Brachypodium distachyon, the emerging grass model, was recently released. This represents a unique opportunity to determine its functional diversity compared to the genomes of other model species. Using homology mapping of assembled expressed sequence tags with chromosome scale pseudomolecules, we identified 128 alternative splicing events in B. distachyon. Our study identified that retention of introns is the major type of alternative splicing events (53%) in this plant and highlights the prevalence of splicing site recognition for definition of introns in plants. We have analyzed the compositional profiles of exon-intron junctions by base-pairing nucleotides with U1 snRNA which serves as a model for describing the possibility of sequence conservation. The alternative splicing isoforms identified in this study are novel and represent one of the potentially biologically significant means by which B. distachyon controls the function of its genes. Our observations serve as a basis to understand alternative splicing events of cereal crops with more complex genomes, like wheat or barley.     

短柄草与麦类作物的比较基因组学研究进展

麦类作物是人类主要的食物来源,其遗传改良对于保障世界粮食生产具有重要作用。获得麦类作物的基因组和功能基因组信息是作物遗传育种学家解析种质资源高产及抗逆机理,并准确选择目标性状、实现分子设计育种目标的有效途径。目前,二穗短柄草（Brachypodium distachyum）是早熟禾亚科中唯一完成全基因组测序的植物。以二穗短柄草为模式植物,利用比较基因组学方法获得早熟禾亚科中基因组庞大而复杂的麦类作物的相关信息,必将加速麦类作物的遗传改良进程。本文重点介绍近十年来短柄草在麦类作物比较基因组学方面的研究进展。     

Advances in cereal genomics and applications in crop breeding

Recent advances in cereal genomics have made it possible to analyse the architecture of cereal genomes and their expressed components, leading to an increase in our knowledge of the genes that are linked to key agronomically important traits. These studies have used molecular genetic mapping of quantitative trait loci (QTL) of several complex traits that are important in breeding. The identification and molecular cloning of genes underlying QTLs offers the possibility to examine the naturally occurring allelic variation for respective complex traits. Novel alleles, identified by functional genomics or haplotype analysis, can enrich the genetic basis of cultivated crops to improve productivity. Advances made in cereal genomics research in recent years thus offer the opportunities to enhance the prediction of phenotypes from genotypes for cereal breeding.     

Genomic resources in fruit plants: an assessment of current status

The availability of many genomic resources such as genome sequences, functional genomics resources including microarrays and RNA-seq, sufficient numbers of molecular markers, express sequence tags (ESTs) and high-density genetic maps is causing a rapid acceleration of genetics and genomic research of many fruit plants. This is leading to an increase in our knowledge of the genes that are linked to many horticultural and agronomically important traits. Recently, some progress has also been made on the identification and functional analysis of miRNAs in some fruit plants. This is one of the most active research fields in plant sciences. The last decade has witnessed development of genomic resources in many fruit plants such as apple, banana, citrus, grapes, papaya, pears, strawberry etc.; however, many of them are still not being exploited. Furthermore, owing to lack of resources, infrastructure and research facilities in many lesser-developed countries, development of genomic resources in many underutilized or less-studied fruit crops, which grow in these countries, is limited. Thus, research emphasis should be given to those fruit crops for which genomic resources are relatively scarce. The development of genomic databases of these less-studied fruit crops will enable biotechnologists to identify target genes that underlie key horticultural and agronomical traits. This review presents an overview of the current status of the development of genomic resources in fruit plants with the main emphasis being on genome sequencing, EST resources, functional genomics resources including microarray and RNA-seq, identification of quantitative trait loci and construction of genetic maps as well as efforts made on the identification and functional analysis of miRNAs in fruit plants.     

大麦基因组和分子育种研究进展

大麦(Hordeum vulgare L.)是世界上重要的谷类作物之一,其二倍体特性使其成为麦类作物基因组研究的重要材料。随着大量分子标记图谱、BACs文库、突变集合和DNA阵列技术的应用,大麦基因组测序工作已不断深入,越来越多的大麦基因组信息使综合分析大麦基因组结构和功能,了解基因表达网络同重要农艺性状之间的关系成为可能。就大麦基因组研究内容,如ESTs系统、物理图谱的构建、功能基因组学研究和大麦分子育种研究作简要综述,为进一步阐述大麦基因组结构和功能特性,提高大麦分子育种能力提供理论依据。     

Setaria genome sequencing: an overview

The genus Setaria includes two important C₄ Panicoid grass species, namely S. italica (cultivated) and S. viridis (weed; wild ancestor), which together represent an appropriate model system for architectural, physiological, evolutionary, and genomic studies in related grasses. It is a diploid, inbreeder, self-fertile annual cereal grass having short life cycle and minimal growth requirements. There close relatedness to biofuel crops like switch grass and napier grass further signifies their importance. Further, foxtail millet is an important food and fodder grain crop grown in arid and semi-arid regions in many parts of the world. Therefore, an increasing interest in these species has led to a gradual accumulation and development of genomic data and genetic resources. Setaria genome sequencing is an outcome of such endeavors. These sequencing efforts uncovered several distinctive attributes of Setaria genome that may help in understanding its physiology, evolution and adaptation. This will not only aid in comparative genomics studies of Setaria and related crops including bioenergy grasses but also help in rapid advancements of genomics information for developing varieties with superior traits either through marker-assisted selection (MAS) or using transgenic approaches in these crops.     

Genetic resources offer efficient tools for rice functional genomics research

Rice is an important crop and major model plant for monocot functional genomics studies. With the establishment of various genetic resources for rice genomics, the next challenge is to systematically assign functions to predicted genes in the rice genome. Compared with the robustness of genome sequencing and bioinformatics techniques, progress in understanding the function of rice genes has lagged, hampering the utilization of rice genes for cereal crop improvement. The use of transfer DNA (T‐DNA) insertional mutagenesis offers the advantage of uniform distribution throughout the rice genome, but preferentially in gene‐rich regions, resulting in direct gene knockout or activation of genes within 20–30 kb up‐ and downstream of the T‐DNA insertion site and high gene tagging efficiency. Here, we summarize the recent progress in functional genomics using the T‐DNA‐tagged rice mutant population. We also discuss important features of T‐DNA activation‐ and knockout‐tagging and promoter‐trapping of the rice genome in relation to mutant and candidate gene characterizations and how to more efficiently utilize rice mutant populations and datasets for high‐throughput functional genomics and phenomics studies by forward and reverse genetics approaches. These studies may facilitate the translation of rice functional genomics research to improvements of rice and other cereal crops.     

Rice Genomics: over the Past Two Decades and into the Future

Domestic rice (Oryza sativa L.) is one of the most important cereal crops, feeding a large number of worldwide populations. Along with various high-throughput genome sequencing projects, rice genomics has been making great headway toward direct field applications of basic research advances in understanding the molecular mechanisms of agronomical traits and utilizing diverse germplasm resources. Here, we briefly review its achievements over the past two decades and present the potential for its bright future.     

Weed genomics: new tools to understand weed biology

In spite of the large yield losses that weeds inflict on crops, we know little about the genomics of economically important weed species. Comparative genomics between plant model species and weeds, map-based approaches, genomic sequencing and functional genomics can play vital roles in understanding and dissecting weedy traits of agronomically important weed species that damage crops. Weed genomics research should increase our understanding of the evolution of herbicide resistance and of the basic genetics underlying traits that make weeds a successful group of plants. Here, we propose specific weed candidates as genomic models, including economically important plants that have evolved herbicide resistance on several occasions and weeds with good comparative genomic qualities that can be anchored to the genomics of Arabidopsis and Oryza sativa.     

T-DNA mutagenesis in Brachypodium distachyon

During the past decade, Brachypodium distachyon has emerged as an attractive experimental system and genomics model for grass research. Numerous molecular tools and genomics resources have already been developed. Functional genomics resources, including mutant collections, expression/tiling microarray, mapping populations, and genome re-sequencing for natural accessions, are rapidly being developed and made available to the community. In this article, the focus is on the current status of systematic T-DNA mutagenesis in Brachypodium. Large collections of T-DNA-tagged lines are being generated by a community of laboratories in the context of the International Brachypodium Tagging Consortium. To date, >13?000 lines produced by the BrachyTAG programme and USDA-ARS Western Regional Research Center are available by online request. The utility of these mutant collections is illustrated with some examples from the BrachyTAG collection at the John Innes Centre-such as those in the eukaryotic initiation factor 4A (eIF4A) and brassinosteroid insensitive-1 (BRI1) genes. A series of other mutants exhibiting growth phenotypes is also presented. These examples highlight the value of Brachypodium as a model for grass functional genomics.     

Multiple models for Rosaceae genomics

The plant family Rosaceae consists of over 100 genera and 3,000 species that include many important fruit, nut, ornamental, and wood crops. Members of this family provide high-value nutritional foods and contribute desirable aesthetic and industrial products. Most rosaceous crops have been enhanced by human intervention through sexual hybridization, asexual propagation, and genetic improvement since ancient times, 4,000 to 5,000 B.C. Modern breeding programs have contributed to the selection and release of numerous cultivars having significant economic impact on the U.S. and world markets. In recent years, the Rosaceae community, both in the United States and internationally, has benefited from newfound organization and collaboration that have hastened progress in developing genetic and genomic resources for representative crops such as apple (Malus spp.), peach (Prunus spp.), and strawberry (Fragaria spp.). These resources, including expressed sequence tags, bacterial artificial chromosome libraries, physical and genetic maps, and molecular markers, combined with genetic transformation protocols and bioinformatics tools, have rendered various rosaceous crops highly amenable to comparative and functional genomics studies. This report serves as a synopsis of the resources and initiatives of the Rosaceae community, recent developments in Rosaceae genomics, and plans to apply newly accumulated knowledge and resources toward breeding and crop improvement.     

Exploiting the Brachypodium Tool Box in cereal and grass research

It is now a decade since Brachypodium distachyon (Brachypodium) was suggested as a model species for temperate grasses and cereals. Since then transformation protocols, large expressed sequence tag (EST) databases, tools for forward and reverse genetic screens, highly refined cytogenetic probes, germplasm collections and, recently, a complete genome sequence have been generated. In this review, we will describe the current status of the Brachypodium Tool Box and how it is beginning to be applied to study a range of biological traits. Further, as genomic analysis of larger cereals and forage grasses genomes are becoming easier, we will re-evaluate Brachypodium as a model species. We suggest that there remains an urgent need to employ reverse genetic and functional genomic approaches to identify the functionality of key genetic elements, which could be employed subsequently in plant breeding programmes; and a requirement for a Pooideae reference genome to aid assembling large pooid genomes. Brachypodium is an ideal system for functional genomic studies, because of its easy growth requirements, small physical stature, and rapid life cycle, coupled with the resources offered by the Brachypodium Tool Box.     

Rice functional genomics research in China

Rice functional genomics is a scientific approach that seeks to identify and define the function of rice genes, and uncover when and how genes work together to produce phenotypic traits. Rapid progress in rice genome sequencing has facilitated research in rice functional genomics in China. The Ministry of Science and Technology of China has funded two major rice functional genomics research programmes for building up the infrastructures of the functional genomics study such as developing rice functional genomics tools and resources. The programmes were also aimed at cloning and functional analyses of a number of genes controlling important agronomic traits from rice. National and international collaborations on rice functional genomics study are accelerating rice gene discovery and application.     

Genome Sequencing and Identification of Gene Function in Rice

Rice is known to be one of the most important crops for human consumption. As the model cereal crop, large-scale sequencing of rice genome must play quite important roles both in theoretical research and practical application in rice breeding, which announces the opening of another new way to resolve the world food crisis. At present, the emphasis of rice genome research has been transferred from structure genomics to functional analysis. The discovery of new genes and annotation of gene function was believed to be an important issue in functional genomics research. In this article, the sequencing and functional research of the rice genome were reviewed. These results may provide some useful clues for rice genetic engineering and breeding practices.     

水稻基因组测序及基因功能的鉴定

水稻是重要的粮食作物。作为单子叶模式植物,水稻基因组的大规模测序具有巨大的理论价值和现实意义。目前已获得了籼稻“93—11”和粳稻“日本晴”高质量的基因组数据,这为在基因组水平上深入研究其生长、发育、抗病和高产等的遗传机理提供了便利,从而为进一步解决世界粮食危机提供了新的突破口和契机。随着水稻基因组计划的顺利结束,其研究重心也已由建立高分辨率的遗传、物理和转录图谱为主的结构基因组学转向基因功能的研究。结构基因组学研究获得的大量序列数据为揭示和开发功能基因开辟了广阔的前景。目前,利用图位克隆和电子克隆等方法已成功分离了多个水稻抗病、抗虫、抗逆境、抗倒伏、高产、优质等重要农艺性状相关的基因,对培育水稻新品种,促进农业的可持续发展意义重大。据估计,水稻至少拥有3．7万个非转座因子相关的蛋白编码基因。因此,完成全基因组序列测定后,重要基因功能的鉴定已成为当前基因组学研究的主要目标。反向遗传学、大规模基因功能表达谱分析和蛋白质组研究等策略已在研究水稻重要基因的功能方面发挥了重要作用。文章综述了水稻基因组测序及基因功能研究的现状,并就新基因发掘和基因功能注释的方法作了评述,期待为水稻遗传工程和育种实践提供参考。     

全基因组关联分析实现水稻粒型自然变异的分子解析

全基因组关联分析(GWAS)近年来被广泛应用于解析生物自然变异的遗传基础。但限于其遗传定位精度, 在水稻(Oryza sativa)遗传学研究中, 该方法尚无法取代传统的图位克隆法在克隆复杂性状调控基因中的作用。近期, 中国科学家在应用GWAS等大数据来克隆控制水稻粒长和粒重等复杂性状的QTL方面取得了新突破。