Consistent effects of independent domestication events on the plant microbiota.

The effect of plant domestication on plant-microbe interactions remains difficult to prove. In this study, we provide evidence of a domestication effect on the composition and abundance of the plant microbiota. We focused on the genus Phaseolus, which underwent four independent domestication events within two species (P. vulgaris and P. lunatus), providing multiple replicates of a process spanning thousands of years. We targeted Phaseolus seeds to identify a link between domesticated traits and bacterial community composition as Phaseolus seeds have been subject to large and consistent phenotypic changes during these independent domestication events. The seed bacterial communities of representative plant accessions from subpopulations descended from each domestication event were analyzed under controlled and field conditions. The results showed that independent domestication events led to similar seed bacterial community signatures in independently domesticated plant populations, which could be partially explained by selection for common domesticated plant phenotypes. Our results therefore provide evidence of a consistent effect of plant domestication on seed microbial community composition and abundance and offer avenues for applying knowledge of the impact of plant domestication on the plant microbiota to improve microbial applications in agriculture.

Selection signatures and population dynamics of transposable elements in lima bean.

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.

Consequences of introgression and gene flow on the genetic structure and diversity of Lima bean (Phaseolus lunatus L.) in its Mesoamerican diversity area.

We evaluated the role of gene flow and wild-crop introgression on the structure and genetic diversity of Lima bean (Phaseolus lunatus) in the Yucatan Peninsula, an important Mesoamerican diversity area for this crop, using a genotyping-by-sequencing approach (15,168 SNP markers) and two scales. At the local scale, STRUCTURE and NGSEP analyses showed predominantly crop-to-wild introgression, but also evidence of a bidirectional gene flow in the two wild-weedy-crop complexes studied (Itzinté and Dzitnup). The ABBA-BABA tests showed a higher introgression in Itzinté (the older complex) than in Dzitnup (the younger one); at the allelic level, the wild-crop introgression in Itzinté was similar in both directions, in Dzitnup it was higher from crop-to-wild; and at the chromosomal level, introgression in Itzinté was from wild-to-crop, whereas in Dzitnup it occured in the opposite direction. Also, we found H E values slightly higher in the domesticated accessions than in the wild ones, in both complexes (Itzinté: wild = 0.31, domesticated = 0.34; Dzinup: wild = 0.27, domesticated = 0.36), but %P and π estimators were higher in the wild accessions than in the domesticated ones. At a regional scale, STRUCTURE and MIGRATE showed a low gene flow, predominantly from crop-to-wild; and STRUCTURE, Neighbor-Joining and PCoA analyses indicated the existence of two wild groups and one domesticated group, with a marked genetic structure based in the existence of domesticated MI and wild MII gene pools. Also, at the regional scale, we found a higher genetic diversity in the wild accessions than in the domesticated ones, in all estimators used (e.g., H E = 0.27 and H E = 0.17, respectively). Our results indicate that gene flow and introgression are playing an important role at the local scale, but its consequences on the structure and genetic diversity of the Lima bean are not clearly reflected at the regional scale, where diversity patterns between wild and domesticated populations could be reflecting historical events.

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 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.

Darwin y la domssticación de plantas en las américas: el caso del maíz y el fríjol / Darwin and Plant Domestication in the Americas: The Case of Maize and Bean

En este artículo se revisan los aportes que diversos autores, contemporáneos y posteriores a Darwin, han realizado sobre el estudio del origen de las plantas domesticadas, en especial al tema del origen geográfico de los cultivos. Posteriormente se revisa cómo la evidencia arqueológica junto con la evidencia genética han ayudado a comprender el origen de tres de los cultivos americanos más antiguos e importantes en épocas precolombinas y actuales: el maíz, el fríjol común y el fríjol Lima. Estos cultivos presentan patrones contrastantes de domesticación, mientras el maíz es producto de un solo evento de domesticación, el fríjol común y el fríjol Lima son cada uno de ellos resultado de domesticaciones múltiples e independientes. Se discute la relevancia del fenómeno de las domesticaciones múltiples en nuestra comprensión del origen del síndrome de domesticación y los aportes que la disciplina conocida como evolución de cultivos, junto con otras disciplinas, puede realizar para un mejor entendimiento de los procesos de adaptación en las poblaciones naturales y para acelerar el mejoramiento y la adopción de nuevos cultivos al servicio de la humanidad.

In the present article, the main contributions that Darwin and other scholars, contemporary and posterior to him, made on the subject of plant domestication, in special the geography of crop origins, are reviewed. The article also reviews recent studies where the archaeological and genetic evidence have complemented each other to give a better understanding of the origin of three of the oldest and most important pre-Columbian and current crops: maize, common bean and Lima bean. These crops are examples of contrasting domestication patterns: a single domestication event in the case of maize and multiple and independent domestication events in the case of the common and Lima bean. Finally, the relevance of the phenomenon of multiple domestication in the study of the origin of the domestication syndrome is discussed along with the contribution that the discipline known as Crop Evolution can make in advancing our knowledge about adaptation processes in wild populations and the future of genetic improvement and adoption of new crops relevant for human welfare.