Prospects for crop production under drought: research priorities and future directions

The efficient use of water supplies requires a systems approach that encompasses all aspects of making water available and its use within society that must recognise global issues. Increasing the efficiency of water use within agricultural systems is an essential priority in many regions including the Mediterranean. This review examines the research priorities, the prospects for crop and soil management and plant breeding and biotechnology that are needed to achieve high stable yield under drought in the Mediterranean. Research must combine the latest genomics resources including quantitative genetics, genomics and biomathematics with an ecophysiological understanding of the interactions between crop plant genotypes and the growing environment to better inform crop improvement.     

Applying modelling experiences from the past to shape crop systems biology: the need to converge crop physiology and functional genomics

Functional genomics has been driven greatly by emerging experimental technologies. Its development as a scientific discipline will be enhanced by systems biology, which generates novel, quantitative hypotheses via modelling. However, in order to better assist crop improvement, the impact of developing functional genomics needs to be assessed at the crop level, given a projected diminishing effect of genetic alteration on phenotypes from the molecule to crop levels. This review illustrates a recently proposed research field, crop systems biology, which is located at the crossroads of crop physiology and functional genomics, and intends to promote communications between the two. Past experiences with modelling whole-crop physiology indicate that the layered structure of biological systems should be taken into account. Moreover, modelling not only plays a role in data synthesis and quantitative prediction, but certainly also in heuristics and system design. These roles of modelling can be applied to crop systems biology to enhance its contribution to our understanding of complex crop phenotypes and subsequently to crop improvement. The success of crop systems biology needs commitments from scientists along the entire knowledge chain of plant biology, from molecule or gene to crop and agro-ecosystem.     

WheatGenome.info: an integrated database and portal for wheat genome information

Bread wheat (Triticum aestivum) is one of the most important crop plants, globally providing staple food for a large proportion of the human population. However, improvement of this crop has been limited due to its large and complex genome. Advances in genomics are supporting wheat crop improvement. We provide a variety of web-based systems hosting wheat genome and genomic data to support wheat research and crop improvement. WheatGenome.info is an integrated database resource which includes multiple web-based applications. These include a GBrowse2-based wheat genome viewer with BLAST search portal, TAGdb for searching wheat second-generation genome sequence data, wheat autoSNPdb, links to wheat genetic maps using CMap and CMap3D, and a wheat genome Wiki to allow interaction between diverse wheat genome sequencing activities. This system includes links to a variety of wheat genome resources hosted at other research organizations. This integrated database aims to accelerate wheat genome research and is freely accessible via the web interface at http://www.wheatgenome.info/.     

作物组学数据库的比较和应用

组学研究是生命科学研究的重要组成部分,是从整体角度研究全部组分及其相互关系的学科。组学数据库收集整理了与组学研究相关的所有信息,为组学研究提供了全面的数据基础。其中,作物组学数据库主要是以作物为对象建立的组学数据库,尤其是几大主要粮食作物的组学测序及信息挖掘,提升了作物科学的基础研发和生产水平,使我国粮食储备迈上一个新的台阶。本文以水稻、玉米和小麦为代表,通过搜集它们在组学研究中常用的数据库,概述了作物基因组学、转录组学、蛋白质组学、代谢组学及表型组学的主要研究内容,阐述了作物组学数据库在作物科学研究中的发展现状,揭示了在高通量信息时代下多种组学数据库的交叉及综合利用已经成为作物科学研究发展的重要方向和手段。     

How Can We Use Genomics to Improve Cereals with Rice as a Reference Genome?

Rice serves as a model crop for cereal genomics. The availability of complete genome sequences, together with various genomic resources available for both rice and Arabidopsis, have revolutionized our understanding of the genetic make-up of crop plants. Both macrocolinearity revealed by comparative mapping and microcolinearity revealed by sequence comparisons among the grasses indicate that sequencing and functional analysis of the rice genome will have a significant impact on other cereals in terms of both genomic studies and crop improvement. The availability of mutants, introgression libraries, and advanced transformation techniques make functional genomics in rice and other cereals more manageable than ever before. A wide array of genetic markers, including anchor markers for comparative mapping, SSRs and SNPs are widely used in genetic mapping, germplasm evaluation and marker assisted selection. An integrated database that combines genome information for rice and other cereals is key to the effective utilization of all genomics resources for cereal improvement. To maximize the potential of genomics for plant breeding, experiments must be further miniaturized and costs must be reduced. Many techniques, including targeted gene disruption or allele substitution, insertional mutagenesis, RNA interference and homologous recombination, need to be refined before they can be widely used in functional genomic analysis and plant breeding.     

The <Emphasis Type="Italic">GCP molecular marker toolkit</Emphasis>, an instrument for use in breeding food security crops

Crop genetic resources carry variation useful for overcoming the challenges of modern agriculture. Molecular markers can facilitate the selection of agronomically important traits. The pervasiveness of genomics research has led to an overwhelming number of publications and databases, which are, nevertheless, scattered and hence often difficult for plant breeders to access, particularly those in developing countries. This situation separates them from developed countries, which have better endowed programs for developing varieties. To close this growing knowledge gap, we conducted an intensive literature review and consulted with more than 150 crop experts on the use of molecular markers in the breeding program of 19 food security crops. The result was a list of effectively used and highly reproducible sequence tagged site (STS), simple sequence repeat (SSR), single nucleotide polymorphism (SNP), and sequence characterized amplified region (SCAR) markers. However, only 12 food crops had molecular markers suitable for improvement. That is, marker-assisted selection is not yet used for Musa spp., coconut, lentils, millets, pigeonpea, sweet potato, and yam. For the other 12 crops, 214 molecular markers were found to be effectively used in association with 74 different traits. Results were compiled as the GCP Molecular Marker Toolkit, a free online tool that aims to promote the adoption of molecular approaches in breeding activities.     

Plant translational genomics: from model species to crops

Plant genomic research now faces the ultimate challenge to develop applications in crop plants which implies the translation of gene functions from a model to a crop which is the field of ‘Plant translational genomics’. In this paper we discuss the perspectives of the candidate gene approach (CGA) as a tool for translational genomics in the ‘whole genome’ era. Factors to be considered for a successful application of the CGA in crops such as the type of crop, the complexity of the trait and the type of genes involved are discussed. Several crop traits that require improvement such as tolerance to stress, pod shatter in Brassicaceae and Fusarium resistance, are evaluated with regard to the potential of a CGA as a tool for crop improvement     

Bioinformatics: harvesting information for plant and crop science

Bioinformatics is an integral aspect of plant and crop science research. Developments in data management and analytical software are reviewed with an emphasis on applications in functional genomics. This includes information resources for Arabidopsis and crop species, and tools available for analysis and visualisation of comparative genomic data. Approaches used to explore relationships between plant genes and expressed sequences are compared, including use of ontologies. The impact of bioinformatics in forward and reverse genetics is described, together with the potential from data mining. The role of bioinformatics is explored in the wider context of plant and crop science.     

水稻功能基因组学研究

水稻是迄今为止第一个被测序的农作物。随着水稻基因组测序计划的完成,以功能基因组学研究为标志的后基因组时代已经到来。综述了水稻功能基因组学的工作进展与方法,主要包括:表达序列标签(EST)c、DNA微阵列和DNA芯片、蛋白质组学、生物信息学和反向遗传学等新方法。     

Recent Progress Using High-throughput Sequencing Technologies in Plant Molecular Breeding

High-throughput sequencing is a revolutionary technological innovation in DNA sequencing.This technology has an ultra-low cost per base of sequencing and an overwhelmingly high data output.High-throughput sequencing has brought novel research methods and solutions to the research fields of genomics and post-genomics.Furthermore,this technology is leading to a new molecular breeding revolution that has landmark significance for scientific research and enables us to launch multi-level,multi-faceted,and multi-extent studies in the fields of crop genetics,genomics,and crop breeding.In this paper,we review progress in the application of high-throughput sequencing technologies to plant molecular breeding studies.     

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.     

Genetic improvement of Purslane (Portulaca oleracea L.) and its future prospects

Common purslane (Portulaca oleracea), also known as pigweed, fatweed, pusle, and little hogweed, is an annual succulent herb in the family Portulacaceae that is found in most corners of the globe. From the ancient ages purslane has been treated as a major weed of vegetables as well as other crops. However, worldwide researchers and nutritionists have studied this plant as a potential vegetable crop for humans as well as animals. Purslane is a nutritious vegetable with high antioxidant properties and recently has been recognized as the richest source of α-linolenic acid, essential omega-3 and 6 fatty acids, ascorbic acid, glutathione, α-tocopherol and β-carotene. The lack of vegetable sources of ω-3 fatty acids has resulted in a growing level of attention to introduce purslane as a new cultivated vegetable. In the rapid-revolutionizing worldwide atmosphere, the ability to produce improved planting material appropriate to diverse and varying rising conditions is a supreme precedence. Though various published reports on morphological, physiological, nutritional and medicinal aspects of purslane are available, research on the genetic improvement of this promising vegetable crop are scant. Now it is necessary to conduct research for the genetic improvement of this plant. Genetic improvement of purslane is also a real scientific challenge. Scientific modernization of conventional breeding with the advent of advance biotechnological and molecular approaches such as tissue culture, protoplast fusion, genetic transformation, somatic hybridization, marker-assisted selection, qualitative trait locus mapping, genomics, informatics and various statistical representation have opened up new opportunities of revising the relationship between genetic diversity, agronomic performance and response to breeding for varietal improvement. This review is an attempt to amalgamate the assorted scientific information on purslane propagation, cultivation, varietal improvement, nutrient analyses, medicinal uses and to describe prospective research especially for genetic improvement of this crop.     

分子标记在绿豆遗传连锁图谱构建和基因定位研究中的应用

绿豆(Vigna radiata(L.)Wilczek)作为一种医食两用作物,不仅是重要的食物资源,在改善土壤环境、提高农民收入等方面也发挥着重要作用。然而,相对于大宗作物而言,绿豆基础研究薄弱,基因组研究更是落后。近年来,分子标记技术迅速发展,在绿豆基因组学研究中发挥了重要的作用。国内外利用分子标记技术已构建了超过20张绿豆遗传连锁图谱。一些优良基因尤其是与抗性相关的基因被鉴定或精细定位,为绿豆分子标记辅助选择打下基础,加快了抗性新品种的培育进程。本研究通过对分子标记技术在绿豆遗传连锁图谱构建、重要功能基因的定位等方面的应用进行综述,以期为绿豆遗传育种研究及功能基因组学分析提供参考。     

Lotus japonicus as a platform for legume research

The major role of 'model plants' is to provide knowledge and technologies obtained in related systems to researchers studying crop plants. Lotus japonicus was chosen as a model system first for legume genetics and then for legume genomics. A large number of L. japonicus mutants that have alterations in legume-specific phenomena have been generated and phenotypically characterized, and genomics has drastically accelerated the molecular characterization of these mutants. Substantial resources of information and experimental materials, including genomic and cDNA sequences, corresponding DNA libraries and high-density linkage maps demonstrate that L. japonicus is an excellent model system. Transfer of knowledge from L. japonicus to other legumes, especially crop legumes, is a matter for urgent consideration.