Genomics and crop response to global change: what have we learned?

Global change poses major challenges for research in fields ranging from crop improvement to water and fertilizer management. Plant genomics is often promoted as a likely source of breakthroughs in understanding plant response to temperature and water stress. This special issue includes papers that range from consideration of gene-to-phenotype associations to papers at the system scale that examine successes and problems with linking physiology and genomics for global change research. Key themes covered include “How genomics can contribute to global change research,” “Genomics and basic understanding of crop responses to the environment,” and “What can field-level physiology bring to genomic research?”. Extrapolation from the model species arabidopsis [Arabidopsis thaliana (L.) Heynh.] has proven more problematic than anticipated, but new techniques and advances in gene sequencing of crop species helps compensate for such difficulties. Physiological research complements genomics by bringing an understanding of the response of the whole plant or crop to differing environments. Physiology also leads to an appreciation of how macro-scale processes such as photosynthesis and partitioning add biological meaning to genotype-by-environment interactions that are significant statistically but otherwise are not meaningful. Furthermore, physiologists have traditionally measured phenotypes in careful detail, and they have a clear role in adding precision to research on gene-to-phenotype associations. Research on crop response to global change has much to gain from strengthened collaboration between genomics and field-level crop physiology.     

Integration of genomics approach with traditional breeding towards improving abiotic stress adaptation: drought and aluminum toxicity as case studies

Traditional breeding efforts are expected to be greatly enhanced through collaborative approaches incorporating functional, comparative and structural genomics. Potential benefits of combining genomic tools with traditional breeding have been a source of widespread interest and resulted in numerous efforts to achieve the desired synergy among disciplines. The International Center for Tropical Agriculture (CIAT) is applying functional genomics by focusing on characterizing genetic diversity for crop improvement in common bean (Phaseolus vulgaris L.), cassava (Manihot esculenta Crantz), tropical grasses, and upland rice (Oriza sativa L.). This article reviews how CIAT combines genomic approaches, plant breeding, and physiology to understand and exploit underlying genetic mechanisms of abiotic stress adaptation for crop improvement. The overall CIAT strategy combines both bottom-up (gene to phenotype) and top-down (phenotype to gene) approaches by using gene pools as sources for breeding tools. The strategy offers broad benefits by combining not only in-house crop knowledge, but publicly available knowledge from well-studied model plants such as arabidopsis [Arabidopsis thaliana (L.) Heynh.]. Successfully applying functional genomics in trait gene discovery requires diverse genetic resources, crop phenotyping, genomics tools integrated with bioinformatics and proof of gene function in planta (proof of concept). In applying genomic approaches to crop improvement, two major gaps remain. The first gap lies in understanding the desired phenotypic trait of crops in the field and enhancing that knowledge through genomics. The second gap concerns mechanisms for applying genomic information to obtain improved crop phenotypes. A further challenge is to effectively combine different genomic approaches, integrating information to maximize crop improvement efforts. Research at CIAT on drought tolerance in common bean and aluminum resistance in tropical forage grasses (Brachiaria spp.) is used to illustrate the opportunities and constraints in breeding for adaptation to abiotic stresses.     

Introgressive Hybridization in Potato Revealed by Novel Cytogenetic and Genomic Technologies

Potato is the third most important food crop in the world and is crucial to ensure food security. However, increasing biotic and abiotic stresses jeopardize its stable production. Fortunately, breeders count on a rich pool of wild relatives that provide sources for disease resistance and tolerance to environmental stresses. To use such traits effectively, breeders require tools that facilitate exploration and exploitation of the genetic diversity of potato wild relatives. Introgression programs to incorporate such alien chromatin into the crop have so far relied on cytogenetic and genetic studies to tap desired traits from these wild resources. The available genetic and cytogenetic tools, supplemented with more recent genomic technologies, can assist in the use of potato relatives in pre-breeding. This information can also facilitate cisgenesis and genome editing to improve potato cultivars. Despite the abundant and rapidly growing genomic information of potato, that of its wild relatives is still limited.     

作物遗传学发展历程回顾与玉米育种目标的前瞻

遗传学的发展是依据性状表现在亲子间传递关系来建立遗传理论及法则,然后从解析遗传基因的核苷酸分子结构来验证遗传理论及法则。育种学是应用遗传原理,依据人类需要,选择并固定在某一特定生育环境最佳性状表现的遗传组合个体或品种,采用分子方法及关联分析来定义影响某一特定性状表现的遗传基因及遗传机制。未来对基因组学基因功能整体运作协调配合的了解,将提高育种的选择效率,并获得适应某一特定生育环境的最佳作物品种。     

花生基因组资源的开发及应用

花生是世界主要的油料作物,但由于花生本身的遗传特性,导致其基因组资源的开发和利用存在较大难度。花生的高度闭花授粉、初级基因库遗传基础狭窄以及栽培种与二倍体近缘野生种之间的杂交不亲和性,导致花生栽培种的分子遗传多样性偏低,成为花生分子遗传改良的主要瓶颈。然而,近五年来,花生基因组资源开发迅速,分子标记的开发、遗传和物理图谱的构建、表达序列标签（ESTs）的产生、突变体资源的创建和功能基因组学平台的构建促进了QTL的鉴定以及与农艺性状相关的耐/抗生物和非生物胁迫基因的挖掘。本文概述了当前花生基因组资源的研究现状,并对下一步的发展方向进行了展望。     

基因编辑技术及其水稻中的发展和应用

CRISPR/Cas系统作为一种新兴的基因编辑系统,以其简单、高效、特异性高等特点已广泛应用于植物功能基因组研究和品种改良.在本文中,首先,我们系统总结了CRISPR/Cas技术及其衍生技术在植物中的开发和优化;其次,重点介绍了基于基因组编辑技术的水稻种质和品种改良的最新进展,并描述了基于基因编辑技术的水稻育种新策略,...     

In-vitro Androgenesis in Rice: Advantages,Constraints and Future Prospects

In vitro androgenesis is an important component of plant biotechnology when the pollen grains are forced to switch from their normal pollen developmental pathway towards an embryogenic route. Haploid and doubled haploid produced through androgenesis have long been recognized as a valuable tool in plant breeding as it can shorten the breeding cycle, fix agronomic characters in homozygous state and enhance the selection efficiency of useful recessive agronomic traits. Recently, doubled haploids have been largely recognized as an important component of crop improvement through genome mapping, quantitative trait locus analysis, and genetic mutation, and as targets for genetic transformation programs. Thus, this review is focused mainly on various facets of doubled haploid in the chief staple food crop rice and sights its recent applications in plant breeding, genetics and genomics.     

禾本科新型模式植物二穗短柄草的研究进展

二穗短柄草 (Brachypodium distachyum) 植株矮小,生育期短,基因组大小仅为水稻的0.71倍;和水稻相比,在进化上它与小麦等温季型禾谷类作物的亲缘关系更近,是目前较为理想的禾谷类作物模式植物.在短短几年中人们对这一模式植物在细胞遗传学、基因组学以及遗传转化等方面进行了大量研究.对已取得的研究进展进行了全面总结和综述,以期为禾谷类作物尤其是温季型禾谷类作物的相关研究提供参考.     

我国水稻分子生物学发展及展望

水稻是最重要的主粮之一,也是禾谷类作物基因组研究的模式作物。经过几十年的努力,我国科学家在水稻遗传学和功能基因组学领域取得了一系列创新性的成就,特别是在水稻理想株型、育性、广谱抗病、耐冷耐热、耐盐和养分高效利用方面的分子遗传机理解析,以及分子设计育种理论方面,开创了以水稻为模式作物研究复杂性状基因调控网络的新领域。展望了我国未来水稻分子生物学发展的趋势。     

Application of resequencing to rice genomics,functional genomics and evolutionary analysis

Rice is a model system used for crop genomics studies. The completion of the rice genome draft sequences in 2002 not only accelerated functional genome studies, but also initiated a new era of resequencing rice genomes. Based on the reference genome in rice, next-generation sequencing (NGS) using the high-throughput sequencing system can efficiently accomplish whole genome resequencing of various genetic populations and diverse germplasm resources. Resequencing technology has been effectively utilized in evolutionary analysis, rice genomics and functional genomics studies. This technique is beneficial for both bridging the knowledge gap between genotype and phenotype and facilitating molecular breeding via gene design in rice. Here, we also discuss the limitation, application and future prospects of rice resequencing.     

Breeding and biotechnological efforts in Jatropha curcas L. for sustainable yields

Jatropha is a non-edible, important bioenergy plant, which can grow in marginalized land. The seeds possess about 36% oil and this would be converted into biodiesel or biojet-fuel. Jatropha provides an option for sustainable feed and fuel production due to its inherent qualities including hardy nature, drought tolerance and surviving with limited amount of water, tolerance to unfavorable conditions and excessive moisture. However, heterozygosity, low productivity and poor understanding of its genome are the major impediments to elite line development. Further, classical breeding and advanced technological investments remain limited owing to long juvenile phase and breeding cycles. Scientific technologies that lead to identification of elite genotypes and development of high yielding elite Jatropha lines and effective methods of detoxification of seeds needs immediate priority. Efficient tissue culture system, doubled haploids (DH) and genomic tools are increasingly made available to improve the seed yield and its oil quantity through the development of geminivirus disease resistant lines. The application of advanced, sequencing technologies has presented a repertoire of genomic information for this important yet orphan crop. In the present investigation, we highlight the achievements made in Jatropha towards development of high yielding, virus resistant elite lines and hybrids with yield potential ranging from 3 to 5 tons per hectare in a year, which is a first ever report in the world. We also developed potential biotechnological tools such as genetic transformation, genome editing and next generation genomics tools including linkage maps and QTLs for accelerating breeding efforts through marker assisted selection. Because of our concerted and continuous efforts during the past 15 years, we have overcome all the obstacles and developed high yielding, disease resistant hybrids/lines, advanced cultivation technologies with thorough knowledge on Agronomy of the Jatropha crop. The Jatropha cultivation technology developed for the first time in the world, could open up new avenues for higher yield productivity of commercial viability.     

Advances in Functional Genomics and Genetic Modification of Potato

The challenges facing potato breeding have actually changed very little over the years with resistance to pests and pathogens remaining high on the agenda together with improvements in storability, reduction in blemishes, and novelty and consistency in cooking/processing qualities. The need to expand the range of targets for potato improvement is being driven by requirements for reduced agrochemical usage and by predictions of the effects of changing climates. Thus fertiliser and water use efficiency are moving up the political agenda. Genetic variation present in germplasm collections needs to be harnessed to provide the genes and alleles required. This paper provides examples of the functional genomics tools and approaches being developed and deployed to provide new options for advancing the breeding of next generation crops. Whilst genetic modification (GM) approaches remain contentious in Europe, this paper will also provide some recent examples of the range of potential impacts that GM approaches could make. It will also consider the value of so-called intragenic or cisgenic approaches to potato genetic engineering.     

水稻基因设计育种的研究进展与展望

 分子标记、基因工程（转基因技术）和基因组学的研究成果为实现对基因型的直接选择和农作物新品种设计育种提供了可能。设计育种旨在控制所有重要农艺性状基因的所有等位性变异。通过精细遗传定位、高饱和染色体片段系的构建和表型鉴定,可以实现设计育种。鉴于一系列可以得到的标记技术、软件工具以及已定位和克隆的水稻基因、已建立的基因 表型（G P）数据关联信息,设计育种目标已成为现实。主要介绍了设计育种、分子育种及一些基本技术,当前重点应用的基因功能研究与水稻功能基因分子利用的研究进展,并对水稻基因设计育种的前景进行了展望。     

生防菌株Bacillus velezensis Z全基因组测序分析

生防菌株Bacillus velezensis Z对胡椒瘟病等多种植物病害具有良好的生防效果;全基因组测序能够为其分子机理研究和开发应用提供信息基础。本研究开展该菌株全基因组测序,并进行比较基因组学和抑菌次生代谢产物合成基因簇预测研究。结果表明:B.velezensisZ菌株的基因组中含有1条4054780bp大小的环形染色体DNA和1个17 122 bp大小的环形质粒,总基因组的GC含量为46.24%,共编码基因4173个;包含27个rRNA,86个tRNA基因,34个sRNA;含有串联重复序列179个,其中13个微卫星DNA,138个小卫星DNA;通过比较基因组学分析,结果发现该菌株与贝莱斯芽孢杆菌模式菌株FZB42同源性极高,与枯草芽孢杆菌模式菌株168之间具有一定的遗传距离;同时发现B. velezensis Z基因组中共编码次生代谢产物合成基因簇13个,其中8个与表面活性素(surfactin)、泛革素(fengycin)、溶杆菌素(bacilysin)、macrolactinH、bacillaene、difficidin、plantazolicin、amylocyclici...     

Agrobacterium-Mediated Transformation of Rice: Constraints and Possible Solutions

Genetic transformation of rice(Oryza sativa L.) by introducing beneficial traits is now a central research instrument in plant physiology and a practical tool for plant improvement. Many approaches are verified for stable introduction of foreign genes into the plant genome. The review examined the different constraints that limit the success of rice genetic transformation via Agrobacterium-mediated approach and suggested possible solutions. Explant identification, gene transfer technique and construct to tailor the integration, transgene expression without collateral to genetic damage and transformant selection are among the technical challenges affecting the rice transformation. Despite the contests, Agrobacteriummediated transformation system has been a better option for producing transgenic rice varieties because of its exact T-DNA processing and simple integration of low copy-number transgene. This information is necessary for improving the transformation system for recalcitrant rice varieties.     

肯尼亚与中国茶业比较

本文从植物遗传改良等因素比较了肯尼亚与中国的茶产业。中国茶区辽阔,生态条件多样化,各地分别适宜种植不同类型的茶树品种;而肯尼亚则受到较大制约。中国茶区分布在亚热带和温带的高海拔地区和平原地区,肯尼亚茶区则限于气温凉爽、雨量充沛而且降雨量分布均匀的高海拔地区。茶原产于中国,而且有数千年的茶树栽培历史。肯尼亚和中国两国的历史和气候条件不同,茶树品种的适应性亦有差异,种茶“传统”和生态条件使肯尼亚开发利用的茶树品种具有保守性,其茶树历史起源与印度类似。随着肯尼亚茶树品种的演变及挑战性的显现,有必要对其经验和教训进行回顾。本文同时概述了两国在茶产业管理结构、挑战性和茶树遗传改良的机遇,对两国在茶业技术及生物科学进步等有关信息交流等方面开展研讨。     

基于遗传位置的水稻与玉米重要农艺性状QTL比较研究

 收集整理了水稻与玉米15个共有性状已发表的QTL定位信息,依据QTL遗传位置信息整合遗传图谱,开展了水稻与玉米基因组QTL水平的比较研究工作。结果表明：1）任一性状QTL的定位频率在染色体上的不同区域内是不同的,存在着若干“热点区域”。QTL定位频率较高的区域,往往能够反映不同遗传背景、不同环境条件下这一区域对特定性状的强表达。在这些区段内,有较高的概率找到控制这一性状遗传率较高的QTL。2）几个不同性状QTL的热点区域常常发生重合,这可能是控制不同性状的基因在染色体上密集排列紧密连锁成一个基因簇造成的;也可能是一个基因影响了多个性状,即一因多效的结果。这些同时对几个性状产生影响的活跃区域,对作物的遗传改良有较大利用价值。