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.
Lima bean (Phaseolus lunatus L.) is one of the five domesticated Phaseolus bean crops, which are essential sources of dietary proteins for human consumption. Compared to common bean (P. vulgaris), it shows a wider range of ecological adaptations along its distribution range from Mexico to Argentina. These adaptations and its phenotypic plasticity make Lima bean a promising crop for improving food security under predicted scenarios of climate change in Latin America and elsewhere. Lima bean is also an excellent model to study convergent evolution of the adaptive domestication syndrome due to its dual domestication in Mesoamerica and the Andes. Combining long and short read sequencing technologies with a dense genetic map from a biparental population, we obtained the first chromosome-level genome assembly for Lima bean. Annotation of 28,326 gene models showed high diversity among 1,917 genes with conserved domains related to disease resistance. Structural comparison across 21,180 orthologs with common bean revealed high genome synteny and two large intrachromosomal rearrangements. Speciation between P. lunatus and P. vulgaris occurred about six million years ago according to nucleotide evolution between these orthologs. Population genomic analysis of GBS data for 482 wild and domesticated accessions from the Mesoamerican and Andean gene pools provided novel evidence on population structure at a finer geographical scale. Results 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. A new wild cluster of diversity was found in the Colombian Andes and a separate genetic cluster was observed for Mesoamerican landraces of the Peninsula of Yucatan in Mexico. This study also documents genome wide patterns of selection and haplotype introgression events among gene pools. Analysis of RNA-seq data obtained from wild and domesticated accessions at two different pod developmental stages revealed 4,275 differentially expressed genes, which could be related to pod dehiscence and seed development. We expect that the present resources serve as a solid basis to achieve a comprehensive view of the degree of convergent evolution of Phaseolus species under domestication and provide new tools and information for breeding for climate change resiliency of different domesticated species.
The domestication process in Lima bean (Phaseolus lunatus L.) involves at least two independent events, within the Mesoamerican and Andean gene pools. Both processes produced similar phenotypic changes in landraces, making Lima bean an excellent model to understand convergent evolution. Despite recent research efforts, the mechanisms of adaptation followed by Mesoamerican and Andean landraces are largely unknown. The genes related to these adaptations can be selected by identification of selective sweeps within gene pools. Most of the previous genetic analyses in Lima bean have relied on Single Nucleotide Polymorphism (SNP) loci and have ignored transposable elements (TEs) which are a major source of variation in plant genomes. The current availability of high-throughput sequencing technologies enables the collection of whole-genome resequencing (WGS) data to approach intraspecies population dynamics of TEs. The present research collected WGS data from 60 wild and domesticated Lima bean accessions to generate the most complete characterization developed to date of transposable elements and SNP loci in the Lima bean genome. We generated an updated annotation of 223,780 transposable elements in the Lima bean genome. Furthermore, we identified genes and variable TEs affected by selective sweeps. Combining three different approaches, selective sweeps were predicted to generate a set of domestication candidate genes. A small percentage of genes under selection (1.6%) were shared among gene pools, suggesting that domestication followed different genetic avenues in both gene pools. Up to 25% of the genes with previously reported selective sweeps in common bean were also detected in Lima bean. We also built a catalog of 39,459 TEs with presence-absence variation (PAV). The fact that 75% of these TEs were located close to genes shows their potential to affect gene functions in Lima bean. The genetic structure inferred from variable TEs was consistent with that obtained from SNP markers, suggesting that TE dynamics can be related to the demographic history of wild and domesticated Lima bean and its adaptive processes, in particular selection processes during domestication.
The domestication process in lima bean (Phaseolus lunatus L.) involves two independent events, within the Mesoamerican and Andean gene pools. This makes lima bean an excellent model to understand convergent evolution. The mechanisms of adaptation followed by Mesoamerican and Andean landraces are largely unknown. Genes related to these adaptations can be selected by identification of selective sweeps within gene pools. Previous genetic analyses in lima bean have relied on Single Nucleotide Polymorphism (SNP) loci, and have ignored transposable elements (TEs). Here we show the analysis of whole-genome sequencing data from 61 lima bean accessions to characterize a genomic variation database including TEs and SNPs, to associate selective sweeps with variable TEs and to predict candidate domestication genes. A small percentage of genes under selection are shared among gene pools, suggesting that domestication followed different genetic avenues in both gene pools. About 75% of TEs are located close to genes, which shows their potential to affect gene functions. The genetic structure inferred from variable TEs is consistent with that obtained from SNP markers, suggesting that TE dynamics can be related to the demographic history of wild and domesticated lima bean and its adaptive processes, in particular selection processes during domestication.
Lima bean (Phaseolus lunatus L.) is the second most important domesticated species of Phaseolus in the world and could represent a precious alternative for food security and quality, as well as play a major role for sustainability in the face of climate change in Latin America and worldwide. Currently, many experts on conservation, domestication, genetic improvement, and plant-rhizosphere relationship of Lima bean have been working alone or in small groups. This situation has limited obtaining a greater benefit from their research and strongly prompts the study of the Lima bean worldwide. To increase the collaboration between experts in the study of the Lima bean, we present the Lima Bean International Network (LBIN). The main objectives of LBIN are to deepen the knowledge on this species and to promote its use worldwide. The success of LBIN will depend on the collaboration of the international scientific community interested in the study of Lima bean. Hence, we invite people from different sectors of society (researchers, producers, companies, NGOs, governments) to participate in this initiative. To get more information, you can visit https://www.cicy.mx/sitios/red-internacional-frijol-lima
Lima bean (Phaseolus lunatus L.) is the second most important domesticated species of Phaseolus in the world and could represent a precious alternative for food security and quality, as well as play a major role for sustainability in the face of climate change in Latin America and worldwide. Currently, many experts on conservation, domestication, genetic improvement, and plant-rhizosphere relationship of Lima bean have been working alone or in small groups. This situation has limited obtaining a greater bene t from their research and strongly prompts the study of the Lima bean worldwide. To increase the collaboration between experts in the study of the Lima bean, we present the Lima Bean International Network (LBIN). The main objectives of LBIN are to deepen the knowledge on this species and to promote its use worldwide. The success of LBIN will depend on the collaboration of the international scienti c community interested in the study of Lima bean. Hence, we invite people from different sectors of society (researchers, producers, companies, NGOs, governments) to participate in this initiative. To get more information, you can visit https://www.cicy.mx/sitios/red-internacional-frijol-lima
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