Comprehensive genomic resources related to domestication and crop improvement traits in Lima bean

Tatiana Garcia, Jorge Duitama (), Stephanie Smolenski Zullo, Juanita Gil, Andrea Ariani, Sarah Dohle, Antonia Palkovic, Paola Skeen, Clara Isabel Bermudez-Santana, Daniel G. Debouck, Jaime Martínez-Castillo, Paul Gepts and Maria Isabel Chacón-Sánchez ()
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Tatiana Garcia: Universidad Nacional de Colombia
Jorge Duitama: Universidad de los Andes
Stephanie Smolenski Zullo: University of California
Juanita Gil: Universidad de los Andes
Andrea Ariani: University of California
Sarah Dohle: University of California
Antonia Palkovic: University of California
Paola Skeen: Universidad Nacional de Colombia
Clara Isabel Bermudez-Santana: Universidad Nacional de Colombia
Daniel G. Debouck: Centro Internacional de Agricultura Tropical
Jaime Martínez-Castillo: Centro de Investigación Científica de Yucatán
Paul Gepts: University of California
Maria Isabel Chacón-Sánchez: Universidad Nacional de Colombia

Nature Communications, 2021, vol. 12, issue 1, 1-17

Abstract: Abstract 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.

Date: 2021
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Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-20921-1

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DOI: 10.1038/s41467-021-20921-1

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