高等植物基因组测序回顾与展望

全基因组序列测定为揭示植物重要性状形成的分子和遗传机制提供了强大工具,基因组学研究正开始指引着农作物新品种培育向定向化和精确化转变.在新一代测序技术的带动下,植物全基因组测序的热潮已经到来.对迄今开展的高等植物基因组测序工作进行简要回顾,并对未来的研究热点进行展望.     

Current status and future possibilities of molecular genetics techniques in <Emphasis Type="Italic">Brassica napus</Emphasis>

As PCR methods have improved over the last 15 years, there has been an upsurge in the number of new DNA marker tools, which has allowed the generation of high-density molecular maps for all the key Brassica crop types. Biotechnology and molecular plant breeding have emerged as a significant tool for molecular understanding that led to a significant crop improvement in the Brassica napus species. Brassica napus possess a very complicated polyploidy-based genomics. The quantitative trait locus (QTL) is not sufficient to develop effective markers for trait introgression. In the coming years, the molecular marker techniques will be more effective to determine the whole genome impairing desired traits. Available genetic markers using the single-nucleotide sequence (SNP) technique and high-throughput sequencing are effective in determining the maps and genome polymorphisms amongst candidate genes and allele interactions. High-throughput sequencing and gene mapping techniques are involved in discovering new alleles and gene pairs, serving as a bridge between the gene map and genome evaluation. The decreasing cost for DNA sequencing will help in discovering full genome sequences with less resources and time. This review describes (1) the current use of integrated approaches, such as molecular marker technologies, to determine genome arrangements and interspecific outcomes combined with cost-effective genomes to increase the efficiency in prognostic breeding efforts. (2) It also focused on functional genomics, proteomics and field-based breeding practices to achieve insight into the genetics underlying both simple and complex traits in canola.     

高通量测序技术在动植物研究领域中的应用

高通量测序是核酸测序研究的一次革命性技术创新, 该技术以极低的单碱基测序成本和超高的数据产出量为特征, 为基因组学和后基因组学研究带来了新的科研方法和解决方案. 在动植物研究领域, 高通量测序引领了一次具有里程碑意义的科学研究模式革新, 科研人员可利用该技术在基因组、转录组和表观基因组等领域展开多层次多方面多水平研究. 本文就高通量测序技术应用于动植物基因组学和功能基因组学研究进展进行了系统阐述, 并对当前高通量测序技术的现状和热点及未来的发展趋势作了深入剖析和讨论.     

Recent progression and future perspectives in cotton genomic breeding

Upland cotton is an important global cash crop for its long seed fibers and high edible oil and protein content.Progress in cotton genomics promotes the advancement of cotton genetics,evolutionary studies,functional genetics,and breeding,and has ushered cotton research and breeding into a new era.Here,we summarize high-impact genomics studies for cotton from the last 10 years.The diploid Gossypium arboreum and allotetraploid Gossypium hirsutum are the main focus of most genetic and genomic studi...     

TILLING by Sequencing (TbyS) for targeted genome mutagenesis in crops

TILLING (Targeting Induced Local Lesions in Genomes) by Sequencing (TbyS) refers to the application of high-throughput sequencing technologies to mutagenised TILLING populations as a tool for functional genomics. TbyS can be used to identify and characterise induced variation in genes (controlling traits of interest) within large mutant populations, and is a powerful approach for the study and harnessing of genetic variation in crop breeding programmes. The extension of existing TILLING platforms by TbyS will accelerate crop functional genomics studies, in concert with the rapid increase in genome editing capabilities and the number and quality of sequenced crop plant genomes. In this mini-review, we provide an overview of the growth of TbyS and its potential applications to crop molecular breeding.     

Plant genomics in Africa: present and prospects

Plants are the world’s most consumed goods. They are of high economic value and bring many health benefits. In most countries in Africa, the supply and quality of food will rise to meet the growing population’s increasing demand. Genomics and other biotechnology tools offer the opportunity to improve subsistence crops and medicinal herbs in the continent. Significant advances have been made in plant genomics, which have enhanced our knowledge of the molecular processes underlying both plant quality and yield. The sequencing of complex genomes of African plant species, facilitated by the continuously evolving next-generation sequencing technologies and advanced bioinformatics approaches, has provided new opportunities for crop improvement. This review summarizes the achievements of genome sequencing projects of endemic African plants in the last two decades. We also present perspectives and challenges for future plant genomic studies that will accelerate important plant breeding programs for African communities. These challenges include a lack of basic facilities, a lack of sequencing and bioinformatics facilities, and a lack of skills to design genomics studies. However, it is imperative to state that African countries have become key players in the plant genome revolution and genome derived-biotechnology. Therefore, African governments should invest in public plant genomics research and applications, establish bioinformatics platforms and training programs, and stimulate university and industry partnerships to fully deploy plant genomics, particularly in the fields of agriculture and medicine.     

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。     

Plant pan-genomics: recent advances,new challenges,and roads ahead

Pan-genomics can encompass most of the genetic diversity of a species or population and has proved to be a powerful tool for studying genomic evolution and the origin and domestication of species, and for providing information for plant improvement. Plant genomics has greatly progressed because of improvements in sequencing technologies and the rapid reduction of sequencing costs. Nevertheless, pan-genomics still presents many challenges, including computationally intensive assembly methods, high costs with large numbers of samples, ineffective integration of big data, and difficulty in applying it to downstream multi-omics analysis and breeding research. In this review, we summarize the definition and recent achievements of plant pan-genomics, computational technologies used for pan-genome construction, and the applications of pan-genomes in plant genomics and molecular breeding. We also discuss challenges and perspectives for future pan-genomics studies and provide a detailed pipeline for sample selection, genome assembly and annotation, structural variation identification, and construction and application of graph-based pan-genomes. The aim is to provide important guidance for plant pan-genome research and a better understanding of the genetic basis of genome evolution, crop domestication, and phenotypic diversity for future studies.     

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。     

主要农作物细胞质雄性不育系育性恢复基因研究进展

提升作物产量、抗逆性和品质的主要手段之一是利用杂种优势,其中细胞质雄性不育/恢复(CMS/Rf)系统是应用最广的雄性不育系统。研究细胞质雄性不育系育性恢复机理是“三系”法选育的重要分子遗传学基础。目前,各个作物已经创制了不同类型的不育系。随着分子技术、基因组学和测序技术的深入,大量育性恢复基因已被定位,且部分已被克隆和功能鉴定。针对主要作物中恢复基因的遗传模式,分子标记定位、克隆及CMS/Rf系统在杂交育种中的应用进行了系统总结。希望本文能为今后恢复系分子标记辅助选育,或利用转基因、基因编辑手段创制新恢复系提供思路。     

Pigeonpea genomics initiative (PGI): an international effort to improve crop productivity of pigeonpea (Cajanus cajan L.)

Pigeonpea (Cajanus cajan), an important food legume crop in the semi-arid regions of the world and the second most important pulse crop in India, has an average crop productivity of 780 kg/ha. The relatively low crop yields may be attributed to non-availability of improved cultivars, poor crop husbandry and exposure to a number of biotic and abiotic stresses in pigeonpea growing regions. Narrow genetic diversity in cultivated germplasm has further hampered the effective utilization of conventional breeding as well as development and utilization of genomic tools, resulting in pigeonpea being often referred to as an ‘orphan crop legume’. To enable genomics-assisted breeding in this crop, the pigeonpea genomics initiative (PGI) was initiated in late 2006 with funding from Indian Council of Agricultural Research under the umbrella of Indo-US agricultural knowledge initiative, which was further expanded with financial support from the US National Science Foundation’s Plant Genome Research Program and the Generation Challenge Program. As a result of the PGI, the last 3 years have witnessed significant progress in development of both genetic as well as genomic resources in this crop through effective collaborations and coordination of genomics activities across several institutes and countries. For instance, 25 mapping populations segregating for a number of biotic and abiotic stresses have been developed or are under development. An 11X-genome coverage bacterial artificial chromosome (BAC) library comprising of 69,120 clones have been developed of which 50,000 clones were end sequenced to generate 87,590 BAC-end sequences (BESs). About 10,000 expressed sequence tags (ESTs) from Sanger sequencing and ca. 2 million short ESTs by 454/FLX sequencing have been generated. A variety of molecular markers have been developed from BESs, microsatellite or simple sequence repeat (SSR)-enriched libraries and mining of ESTs and genomic amplicon sequencing. Of about 21,000 SSRs identified, 6,698 SSRs are under analysis along with 670 orthologous genes using a GoldenGate SNP (single nucleotide polymorphism) genotyping platform, with large scale SNP discovery using Solexa, a next generation sequencing technology, is in progress. Similarly a diversity array technology array comprising of ca. 15,000 features has been developed. In addition, >600 unique nucleotide binding site (NBS) domain containing members of the NBS-leucine rich repeat disease resistance homologs were cloned in pigeonpea; 960 BACs containing these sequences were identified by filter hybridization, BES physical maps developed using high information content fingerprinting. To enrich the genomic resources further, sequenced soybean genome is being analyzed to establish the anchor points between pigeonpea and soybean genomes. In addition, Solexa sequencing is being used to explore the feasibility of generating whole genome sequence. In summary, the collaborative efforts of several research groups under the umbrella of PGI are making significant progress in improving molecular tools in pigeonpea and should significantly benefit pigeonpea genetics and breeding. As these efforts come to fruition, and expanded (depending on funding), pigeonpea would move from an ‘orphan legume crop’ to one where genomics-assisted breeding approaches for a sustainable crop improvement are routine.     

Advances in the research of celery,an important Apiaceae vegetable crop

Celery (Apium graveolens L.), one of the most important vegetables in Apiaceae family, is cultivated worldwide and utilized in food and cosmetic industries because it is an excellent source of vitamins, phenolic compounds, volatile oils and other nutrients. Celery extracts possess various medicinal properties, such as antibacterial, anti-inflammatory and lowering blood glucose and serum lipid levels. With the rapid advancements in molecular biology and sequencing technology, studies on celery have been performed. Numerous molecular markers and regulatory genes have been discovered and applied to improve celery. Research advances, including genetic breeding, genomics research, function genes and chemical composition, regarding celery are reviewed in this paper. Further exploration and application trends are briefly described. This review provides a reference for basic and applied research on celery, an important Apiaceae vegetable crop.     

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.     

A special issue on ＂Plant Molecular Biology＂

The use of molecular biology and genomics tools in plant biology research has greatly expanded our understandingof the molecular mechanisms that underlie plant development and physiology.The successful establishment of researchresources such as mutant populations has led to progress in a variety of fields,including plant reproductive develop-ment,signal transduction,hormone functions,defense responses and epigenetic control.In the future these advanceswill potentially facilitate crop improvement through molecular breeding.     

三维基因组学在动物遗传育种中的研究进展*

三维基因组学是近年兴起的研究基因组三维空间和结构的学科,是在基因组序列、基因结构及其调控元件的基础上对基因组序列在细胞核内的三维空间结构,及其对基因复制、转录、修复和调控等生物过程中的功能进行的研究。随着高通量测序技术的出现和改进,三维基因组学相关研究也得到快速发展。重点介绍三维基因组的发展历程、研究技术、结构层次,并总结近年来三维基因组学在动物遗传育种方面的应用。     

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。     

高通量测序在病原微生物耐药方面的应用进展

高通量测序是一种高效、准确、价廉的新型测序技术,随着近年来的不断推广,逐渐进入不同的研究领域。目前,多重耐药菌的感染给患者和社会增加了巨大负担,耐药机制和抗菌药物的研发是科学研究的热点之一。高通量测序技术也开始在病原微生物耐药方面发挥了巨大作用,尤其是在耐药机制研究方面,解决了一些用现有的技术无法解决的问题。本文从病原菌鉴定、耐药机制、药物新靶标、耐药菌流行病学以及用药指导等方面阐述了高通量测序在病原微生物耐药方面的应用及进展,重点讨论了耐药机制和抗菌药物新靶标进展以及现阶段存在的问题。高通量测序技术不断发展,尤其是进入病原微生物研究领域后延伸出新的研究技术和方法,随着相关的生物信息学的进步,此项技术应用将会更加广泛。