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Plant Polyploidy: Origin, Evolution, and Its Influence on crop domestication

Horticultural Plant Journal 2019年第6期5卷 231-239页

作者： Kang Zhang Xiaowu Wang Feng Cheng Chinese Academy of Agricultural Sciences Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of AgricultureSino-Dutch Joint Laboratory of Horticultural GenomicsInstitute of Vegetables and FlowersBeijing 100081China

The prevalence and recurrence of polyploidization in plant species make it one of the most important evolutionary events in plants, and as a result, polyploidization is an extensively investigated research field. Due to the rapid development of sequencing technologies, there is increased evidence to support that polyploidization plays an important role in the diversification of plant species, evolution of genes, and the domestication of crops. Here, we reviewed the influence of polyploidization on various aspects of plant evolution, mainly focused on polyploid origin, characteristics, subsequent genome divergence, and its impact on gene function innovation and crop domestication. The occurrence of many independent polyploidization events in plants was found to be tightly associated with the timing of extreme climate events or natural disasters on earth, leading to mass extinction while possibly facilitating increased polyploidization. Following allo-polyploidization, a distinct phenomenon known as sub-genome dominance occurred during sub-genome evolution, which was found to be associated with the methylation of transposons. Extensive gene fractionations(lost) following polyploidization were reported in almost all paleo-polyploids, and the evolutionary fates of multi-copy genes, such as sub-/neo-functionalization, were further proposed to illustrate their underlying mechanisms. Moreover,polyploidization was found to significantly impact species diversification, with subsequent effects on crop domestication and the development of traits with agronomic importance. Based on the progress of plant polyploidization studies, we discussed several main topics that might further improve our understanding of polyploid evolution and that are likely contribute to the application of polyploidization in crop breeding in the near future.

关键词： polyploidization genome evolution sub-genome gene function innovation crop domestication

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domestication of Marama Bean in Arid Namibia: Challenges and Opportunities in a Climate Changing Agroecology

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American Journal of Climate Change 2024年第1期13卷 14-30页

作者： Percy Maruwa Chimwamurombe Erold Naomab Department of Biology Chemistry and Physics School of Natural and Applied Sciences Faculty of Health Natural Resources and Applied Sciences Namibia University of Science and Technology Windhoek Namibia Office of the Vice Chancellor Namibia University of Science and Technology Windhoek Namibia

Tylosema esculentum (Burch.) A. Schreib. (Marama bean), referred to as marama in sections of this article, is an obligate outcrossing native plant with a yield potential of 2 ton/hectare which grows naturally in the deep sandy soils of the Kalahari Desert. It has adapted to the low precipitation levels in that agro-ecosystem. Marama serves as a staple food for the San and Bantus in that area. In Namibia, in the past you could find wild stands of marama in the Khomas region, Omaheke region, and the Otjozondjupa region without must struggle. It is renowned for its brown seeds, which are rich in high-quality oils and proteins. The tuberous root contains a significant amount of starch. The objective of domesticating orphaned marama is to provide farmers in this climate change-prone region with a viable alternative for food and nutrition security. This program, initiated in 2008 with an open-minded mindset, required swift implementation using harsh and occasionally unconventional methods. To introduce indigenous tools for resource-poor farmers, the domestication program prioritized the utilization of farmer-participatory methodologies. It was crucial to integrate old and new approaches to ensure learning from past and present experiences, leading to innovative solutions. There is little research and development of native crops in Africa because most of the currently cultivates crops were brought for use from abroad. Only a few numbers of indeginous African crops can be named. The arid Kalahari region, susceptible to climate change, necessitates the revival of indigenous crops like marama, which are resilient and well-adapted to the region’s conditions and have thrived for centuries. In many discussions regarding the health and nutrition of Africa, the recommendation to consume traditional foods to avoid exposure to modern foods, which may not be genetically compatible, is frequently emphasized. Regardless of their validity, these opinions must be acknowledged, and steps need to be taken to ensure a positive legacy for

关键词： crop Improvement crop domestication Drought Tolerance Food Security Genetic Improvement Marama Bean Tylosema esculentum

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

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Journal of Genetics and Genomics 2022年第9期49卷 833-846页

作者： Wei Li Jianan Liu Hongyu Zhang Ze Liu Yu Wang Longsheng Xing Qiang He Huilong Du School of Life Sciences Institute of Life Sciences and Green DevelopmentHebei UniversityBaodingHebei 071000China

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,pangenomics 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.

关键词： Plant pan-genome Genomic evolution crop domestication Graph-based genome

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