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Comprehensive genomic resources related to domestication and crop improvement traits in Lima bean
Lima bean (Phaseolus lunatus L.), one of the five domesticated Phaseolus bean crops, shows a wide range of ecological adaptations along its distribution range from Mexico to Argentina. These adaptations make it a promising crop for improving food security under predicted scenarios of climate change...
Autores principales: | , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7846787/ https://www.ncbi.nlm.nih.gov/pubmed/33514713 http://dx.doi.org/10.1038/s41467-021-20921-1 |
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author | Garcia, Tatiana Duitama, Jorge Zullo, Stephanie Smolenski Gil, Juanita Ariani, Andrea Dohle, Sarah Palkovic, Antonia Skeen, Paola Bermudez-Santana, Clara Isabel Debouck, Daniel G. Martínez-Castillo, Jaime Gepts, Paul Chacón-Sánchez, Maria Isabel |
author_facet | Garcia, Tatiana Duitama, Jorge Zullo, Stephanie Smolenski Gil, Juanita Ariani, Andrea Dohle, Sarah Palkovic, Antonia Skeen, Paola Bermudez-Santana, Clara Isabel Debouck, Daniel G. Martínez-Castillo, Jaime Gepts, Paul Chacón-Sánchez, Maria Isabel |
author_sort | Garcia, Tatiana |
collection | PubMed |
description | Lima bean (Phaseolus lunatus L.), one of the five domesticated Phaseolus bean crops, shows a wide range of ecological adaptations along its distribution range from Mexico to Argentina. These adaptations make it a promising crop for improving food security under predicted scenarios of climate change in Latin America and elsewhere. In this work, we combine long and short read sequencing technologies with a dense genetic map from a biparental population to obtain the chromosome-level genome assembly for Lima bean. Annotation of 28,326 gene models show high diversity among 1917 genes with conserved domains related to disease resistance. Structural comparison across 22,180 orthologs with common bean reveals high genome synteny and five large intrachromosomal rearrangements. Population genomic analyses show that wild Lima bean is organized into six clusters with mostly non-overlapping distributions and that Mesomerican landraces can be further subdivided into three subclusters. RNA-seq data reveal 4275 differentially expressed genes, which can be related to pod dehiscence and seed development. We expect the resources presented here to serve as a solid basis to achieve a comprehensive view of the degree of convergent evolution of Phaseolus species under domestication and provide tools and information for breeding for climate change resiliency. |
format | Online Article Text |
id | pubmed-7846787 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-78467872021-02-08 Comprehensive genomic resources related to domestication and crop improvement traits in Lima bean Garcia, Tatiana Duitama, Jorge Zullo, Stephanie Smolenski Gil, Juanita Ariani, Andrea Dohle, Sarah Palkovic, Antonia Skeen, Paola Bermudez-Santana, Clara Isabel Debouck, Daniel G. Martínez-Castillo, Jaime Gepts, Paul Chacón-Sánchez, Maria Isabel Nat Commun Article Lima bean (Phaseolus lunatus L.), one of the five domesticated Phaseolus bean crops, shows a wide range of ecological adaptations along its distribution range from Mexico to Argentina. These adaptations make it a promising crop for improving food security under predicted scenarios of climate change in Latin America and elsewhere. In this work, we combine long and short read sequencing technologies with a dense genetic map from a biparental population to obtain the chromosome-level genome assembly for Lima bean. Annotation of 28,326 gene models show high diversity among 1917 genes with conserved domains related to disease resistance. Structural comparison across 22,180 orthologs with common bean reveals high genome synteny and five large intrachromosomal rearrangements. Population genomic analyses show that wild Lima bean is organized into six clusters with mostly non-overlapping distributions and that Mesomerican landraces can be further subdivided into three subclusters. RNA-seq data reveal 4275 differentially expressed genes, which can be related to pod dehiscence and seed development. We expect the resources presented here to serve as a solid basis to achieve a comprehensive view of the degree of convergent evolution of Phaseolus species under domestication and provide tools and information for breeding for climate change resiliency. Nature Publishing Group UK 2021-01-29 /pmc/articles/PMC7846787/ /pubmed/33514713 http://dx.doi.org/10.1038/s41467-021-20921-1 Text en © The Author(s) 2021 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. |
spellingShingle | Article Garcia, Tatiana Duitama, Jorge Zullo, Stephanie Smolenski Gil, Juanita Ariani, Andrea Dohle, Sarah Palkovic, Antonia Skeen, Paola Bermudez-Santana, Clara Isabel Debouck, Daniel G. Martínez-Castillo, Jaime Gepts, Paul Chacón-Sánchez, Maria Isabel Comprehensive genomic resources related to domestication and crop improvement traits in Lima bean |
title | Comprehensive genomic resources related to domestication and crop improvement traits in Lima bean |
title_full | Comprehensive genomic resources related to domestication and crop improvement traits in Lima bean |
title_fullStr | Comprehensive genomic resources related to domestication and crop improvement traits in Lima bean |
title_full_unstemmed | Comprehensive genomic resources related to domestication and crop improvement traits in Lima bean |
title_short | Comprehensive genomic resources related to domestication and crop improvement traits in Lima bean |
title_sort | comprehensive genomic resources related to domestication and crop improvement traits in lima bean |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7846787/ https://www.ncbi.nlm.nih.gov/pubmed/33514713 http://dx.doi.org/10.1038/s41467-021-20921-1 |
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