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Chromosome-length genome assemblies of six legume species provide insights into genome organization, evolution, and agronomic traits for crop improvement

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Relation http://oar.icrisat.org/12189/
https://www.sciencedirect.com/science/article/pii/S2090123221002058
https://doi.org/10.1016/j.jare.2021.10.009
 
Title Chromosome-length genome assemblies of six legume species provide insights into genome organization, evolution, and agronomic traits for crop improvement
 
Creator Garg, V
Dudchenko, O
Wang, J
Khan, A W
Gupta, S
Kaur, P
Han, K
Saxena, R K
Kale, S M
Pham, M
Yu, J
Chitikineni, A
Zhang, Z
Fan, G
Lui, C
Valluri, V K
Meng, F
Bhandari, A
Liu, X
Yang, T
Chen, H
Valliyodan, B
Roorkiwal, M
Shi, C
Yang, H B
Durand, N C
Pandey, M K
Li, G
Barmukh, R
Wang, X
Chen, X
Lam, H M
Jiang, H
Zong, X
Liang, X
Liu, X
Liao, B
Guo, B
Jackson, S
Nguyen, H T
Zhuang, W
Shubo, W
Wang, X
Aiden, E L
Bennetzen, J L
Varshney, R K
 
Subject Plant Genetics
Legume Crops
 
Description 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.
 
Publisher Elsevier
 
Date 2021-11-03
 
Type Article
PeerReviewed
 
Format application/pdf
 
Language en
 
Rights cc_attribution
 
Identifier http://oar.icrisat.org/12189/1/Journal%20of%20Advanced%20Research_42_315-329_2022.pdf
Garg, V and Dudchenko, O and Wang, J and Khan, A W and Gupta, S and Kaur, P and Han, K and Saxena, R K and Kale, S M and Pham, M and Yu, J and Chitikineni, A and Zhang, Z and Fan, G and Lui, C and Valluri, V K and Meng, F and Bhandari, A and Liu, X and Yang, T and Chen, H and Valliyodan, B and Roorkiwal, M and Shi, C and Yang, H B and Durand, N C and Pandey, M K and Li, G and Barmukh, R and Wang, X and Chen, X and Lam, H M and Jiang, H and Zong, X and Liang, X and Liu, X and Liao, B and Guo, B and Jackson, S and Nguyen, H T and Zhuang, W and Shubo, W and Wang, X and Aiden, E L and Bennetzen, J L and Varshney, R K (2021) Chromosome-length genome assemblies of six legume species provide insights into genome organization, evolution, and agronomic traits for crop improvement. Journal of Advanced Research, 42. pp. 315-329. ISSN 2090-1224