Chromosome-length genome assemblies of six legume species provide insights into genome organization, evolution, and agronomic traits for crop improvement
| Autor: | Zhikang Zhang, Henry T. Nguyen, Baozhu Guo, Kai Han, Wan Shubo, Chen Hua, Rajeev K. Varshney, Vinodkumar Valluri, Aditi Bhandari, Chengcheng Shi, Fanbo Meng, Tao Yang, Jinpeng Wang, Weijian Zhuang, Xin Liu, Annapurna Chitikineni, Erez Lieberman Aiden, Boshou Liao, Scott A. Jackson, Rutwik Barmukh, Hong Bin Yang, Xiaoping Chen, Xuanqiang Liang, Xingjun Wang, Rachit K. Saxena, Neva C. Durand, Saurabh Gupta, Huifang Jiang, Melanie Pham, Xuxiao Zong, X. D. Liu, Guangyi Fan, Aamir W. Khan, Babu Valliyodan, Jigao Yu, Parwinder Kaur, Hon-Ming Lam, Guowei Li, Vanika Garg, Manish Roorkiwal, Christopher Lui, Manish K. Pandey, Xiyin Wang, Olga Dudchenko, Sandip Kale, Jeffrey L. Bennetzen |
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| Rok vydání: | 2022 |
| Předmět: |
Crops
Agricultural Genome evolution Multidisciplinary business.industry Drought tolerance Chromosome Mapping food and beverages Sequence assembly Fabaceae Quantitative trait locus Biology Genome Cicer Chromosomes Biotechnology Crop Plant Breeding Humans Soybeans business Genome Plant Legume Genome-Wide Association Study Genomic organization |
| Zdroj: | Journal of Advanced Research. 42:315-329 |
| ISSN: | 2090-1232 |
| DOI: | 10.1016/j.jare.2021.10.009 |
| Popis: | Introduction Legume crops are an important source of protein and oil for human health and in fixing atmospheric N2 for soil enrichment. With an objective to accelerate much-needed genetic analyses and breeding applications, draft genome assemblies were generated in several legume crops; many of them are not high quality because they are mainly based on short reads. However, the superior quality of genome assembly is crucial for a detailed understanding of genomic architecture, genome evolution, and crop improvement. Objectives Present study was undertaken with an objective of developing improved chromosome-length genome assemblies in six different legumes followed by their systematic investigation to unravel different aspects of genome organization and legume evolution. Methods We employed in situ Hi-C data to improve the existing draft genomes and performed different evolutionary and comparative analyses using improved genome assemblies. Results We have developed chromosome-length genome assemblies in chickpea, pigeonpea, soybean, subterranean clover, and two wild progenitor species of cultivated groundnut (A. duranensis and A. ipaensis). A comprehensive comparative analysis of these genome assemblies offered improved insights into various evolutionary events that shaped the present-day legume species. We highlighted the expansion of gene families contributing to unique traits such as nodulation in legumes, gravitropism in groundnut, and oil biosynthesis in oilseed legume crops such as groundnut and soybean. As examples, we have demonstrated the utility of improved genome assemblies for enhancing the resolution of “QTL-hotspot” identification for drought tolerance in chickpea and marker-trait associations for agronomic traits in pigeonpea through genome-wide association study. Genomic resources developed in this study are publicly available through an online repository, ‘Legumepedia’. Conclusion This study reports chromosome-length genome assemblies of six legume species and demonstrates the utility of these assemblies in crop improvement. The genomic resources developed here will have significant role in accelerating genetic improvement applications of legume crops. |
| Databáze: | OpenAIRE |
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