摘要
人工驯化为农业发展提供了原始驱动力,也深刻地改变了许多动植物的遗传背景。伴随组学大数据理论和技术体系的发展,作物基因组研究已迈入泛基因组时代。借助泛基因组的研究思路,通过多基因组间的比较和整合,能够评估物种遗传信息上界和下界,认知物种的遗传多样性全貌。此外,将泛基因组与染色体大尺度结构变异、群体高通量测序及多层次组学数据相结合,可以进行更为深入的性状-遗传机制解析。大豆(Glycine max(L.)Merr.)是重要的粮油经济作物,大豆产能关乎国家粮食安全。对大豆遗传背景形成、重要农艺性状关键位点的解析,是实现更高效的大豆育种改良的前提。本文首先对泛基因组学的核心问题进行了阐述,解释了从头组装/比对组装、迭代式组装和图基因组等泛基因组研究策略的演变历程和各自特征;接着对作物泛基因组研究的热点问题进行了概括,并且以大豆为例详细阐释了包括类群选择、泛基因组构建、数据挖掘等方面在内的泛基因组研究的开展思路,着重说明染色体结构变异在大豆演化/驯化历程中的贡献及其在农艺性状遗传基础挖掘上的价值;最后讨论了图泛基因组在数据整合、结构变异计算方面的应用前景。本文对作物泛基因组未来的发展趋势进行了展望,以期为作物基因组学及数据科学研究提供参考。
Artificial domestication provided the original motivation to the blooming of agriculture,following with the dramatic change of the genetic background of crops and livestock.According to theory and technology upgradation that contributing to the omics,we appreciate using the pan-genome instead of single reference genome for crop study.By comparison and integration of multiple genomes under the guidance of pan-genome theory,we can estimate the genomic information range of a species,leading to a global understanding of its genetic diversity.Combining pan-genome with large size chromosomal structural variations,high throughput population resequencing,and multi-omics data,we can profoundly study the genetic basis behind species traits we focus on.Soybean is one of the most important commercial crops over the world.It is also essential to our food security.Dissecting the formation of genetic diversity and the causal loci of key agricultural traits of soybean will make the modern soybean breeding more efficiently.In this review,we summarize the core idea of pan-genome and clarified the characteristics of construction strategies of pan-genome such as de novo/mapping assembly,iterative assembly and graph-based genome.Then we used the soybean pan-genome work as a case study to introduce the general way to study pan-genome.We highlighted the contribution of structural variation(SV)to the evolution/domestication of soybean and its value in understanding the genetic bases of agronomy traits.By those,we approved the value of graph-based pan-genome for data integration and SV calculation.Future research directions are also discussed for crop genomics and data science.
作者
刘羽诚
申妍婷
田志喜
Yucheng Liu;Yanting Shen;Zhixi Tian(Key Laboratory of Seed Innovation,Institute of Genetics and Development of Biology,Chinese Academy of Sciences,Beijing 100101,China;University of Chinese Academy of Sciences,Beijing 101408,China)
出处
《遗传》
CAS
CSCD
北大核心
2024年第3期183-198,共16页
Hereditas（Beijing)
基金
国家自然科学基金项目(编号:32201775,U22A20473)
中国科学院稳定支持青年团队计划(编号:YSBR-078)资助。
关键词
大豆
泛基因组
结构变异
演化
驯化
soybean
pan-genome
structural variation
evolution
domestication
