基于基因组学的作物种质资源研究:现状与展望

作物种质资源工作涉及面很广,包括种质资源的收集、编目、保护、繁种更新、分发利用与信息系统建立等基础性工作,作物起源、驯化与传播、种质分类、民族植物学与传统知识研究等基础研究,遗传多样性评价、重要性状表型鉴定、种质资源基因型鉴定、基因发掘和种质创新等应用基础研究。经过近百年的努力,种质资源的基础性工作已卓有成效,作物种质资源保护与共享利用体系基本建立。但由于主要基于形态学的传统研究思路和方法存在很多先天不足,种质资源基础研究和应用基础研究一直举步维艰,效率低下。随着分子标记技术和第二代测序技术的快速发展,基因组学理论和方法不断深入到种质资源研究的多个层面,使种质资源保护和创新利用发生了研究思路和方法学上的变革。基因组学研究成果为种质资源的有效收集和保护提供了理论指导,也为阐明作物起源和演化、全面评估种质资源结构多样性提供了核心理论和技术,同时大幅度提高了基因发掘和种质创新效率。特别是全基因组测序、重测序和简化基因组测序技术不断成熟,使在全基因组水平上比较不同种质资源基因组变异成为可能;在此基础上,可阐明农作物起源以及驯化、改良和传播对种质资源形成的影响,明确现有种质资源和野外种质资源群体结构和遗传多样性,提出种质资源异地保存和原生境保护的最佳策略;结合表型鉴定数据,利用连锁分析和关联分析等基因组学方法,可高效发掘种质资源中蕴含的新基因和有利等位基因,提出其利用途径和具体方案,并在种质创新过程中充分利用基因组学研究成果提高创新效率。文章评述了基因组学在种质资源研究中的应用现状,特别是在种质资源基因型鉴定、异地保存和原生境保护、作物起源与进化研究、结构多样性分析、新基因发掘和种质创新等方面的应用情况及其发展趋势。提出了今后的发展方向和工作重点,强调把基因组学理论和方法与作物种质资源研究紧密结合,为种质资源的有效保护和高效利用提供强有力的理论、技术、材料与信息支撑。

Genomics-Based Crop Germplasm Research: Advances and Perspectives

The scale of activities related to crop germplasm is massive, including basic work (germplasm collecting, documentation, multiplication, conservation, regeneration, distribution and information system establishment, etc.), basic research (studies on crop origin, domestication and dispersal, germplasm classification, ethnobotany, indigenous knowledge, etc.), and applied basic research (genetic diversity assessment, precise phenotypic evaluation of important traits, germplasm genotyping, gene discovery and allele mining, germplasm enhancement etc.). With the efforts in the last century, the basic work on crop germplasm has been very fruitful and the system of crop germplasm conservation and utilization has been established in the world. Because the traditional ideas and methodologies based on morphology had their innate disadvantages, however, the basic research and the applied basic research had developed along at an agonizingly slow pace before genomics appeared. With rapid development of molecular marker technology and next-generation sequencing technology, theories and techniques of genomics have extended to multi-faceted germplasm research, resulting in revolutionary changes of conception and methodology in germplasm conservation, in-depth research and utilization. The achievements made in genomics provide not only theoretical guidance to collecting and conservation of crop germplasm, but also core theories and techniques to clarify crop origin and evolution. Meanwhile, genomics has the power to promote the efficiency of gene discovery and germplasm enhancement. Especially, the rapid development of whole genome sequencing, genome re-sequencing and simplified genome sequencing enable comparisons of genomic variation in different germplasms at the whole-genomic level. Further, crop origin can be illustrated and effects of domestication, improvement and dispersal on germplasm can be clarified. Population structure and genetic diversity of crop germplasm preserved in genebanks and existing in the wild can be evaluated in depth, generating huge amounts of information useful in designing optimum strategies of ex situ preservation and in situ conservation of crop genetic resources. Through integrating phenotypic data, new genes and their favorable alleles can be mined by using various approaches such as linkage mapping and association analysis. In addition, germplasm enhancement can also be benefited from the advances in genomics through the use of alleles discovered and other molecular marker-based techniques such as marker-assisted selection and genomic selection. This paper reviews the advances of genomics-based crop germplasm research, especially the applications of genomics in germplasm genotyping, ex situ and in situ conservation, crop origin and evolution research, structural diversity assessment, gene discovery and allele mining, and germplasm enhancement etc. Finally, future development directions and priorities in the field are proposed, which emphasize the close combination of genomics and crop germplasm research to provide a strong support to effective conservation and efficient utilization of crop germplasm in terms of theories, techniques, materials and information.