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.
• Background and Aims The actual number of domestications of a crop is one of the key questions in domestication studies. Answers to this question have generally been based on relationships between ...wild progenitors and domesticated descendants determined with anonymous molecular markers. In this study, this question was investigated by determining the number of instances a domestication phenotype had been selected in a crop species. One of the traits that appeared during domestication of common bean (Phaseolus vulgaris) is determinacy, in which stems end with a terminal inflorescence. It has been shown earlier that a homologue of the arabidopsis TFL1 gene -PvTFL1y -controls determinacy in a naturally occurring variation of common bean. • Methods Sequence variation was analysed for PvTFL1y in a sample of 46 wild and domesticated accessions that included determinate and indeterminate accessions. • Key Results Indeterminate types - wild and domesticated -showed only synonymous nucleotide substitutions. Determinate types - observed only among domesticated accessions - showed, in addition to synonymous substitutions, non-synonymous substitutions, indels, a putative intron-splicing failure, a retrotransposon insertion and a deletion of the entire locus. The retrotransposon insertion was observed in 70 % of determinate cultivars, in the Americas and elsewhere. Other determinate mutants had a more restricted distribution in the Americas only, either in the Andean or in the Mesoamerican gene pool of common bean. • Conclusions Although each of the determinacy haplotypes probably does not represent distinct domestication events, they are consistent with the multiple (seven) domestication pattern in the genus Phaseolus. The predominance of determinacy in the Andean gene pool may reflect domestication of common bean prior to maize introduction in the Andes.
Common bean (Phaseolus vulgaris L.) is an important legume crop worldwide. However, abiotic and biotic stress limits bean yields to <600 kg ha−1 in low-income countries. Current low yields result in ...food insecurity, while demands for increased yields to match the rate of population growth combined with the threat of climate change are significant. Novel and significant advances in genetic improvement using untapped genetic diversity available in crop wild relatives and closely related species must be further explored. A meeting was organized by the Global Crop Diversity Trust to consider strategies for common bean improvement. This review resulted from that meeting and considers our current understanding of the genetic resources available for common bean improvement and the progress that has been achieved thus far through introgression of genetic diversity from wild relatives of common bean, and from closely related species, including: P. acutifolius, P. coccineus, P. costaricensis and P. dumosus. Newly developed genomic tools and their potential applications are presented. A broad outline of research for use of these genetic resources for common bean improvement in a ten-year multi-disciplinary effort is presented.
Common bean (Phaseolus vulgaris) is an important grain legume and there has been a recent resurgence in interest in its relative, tepary bean (P. acutifolius), owing to this species' ability to ...better withstand abiotic stresses. Genomic resources are scarce for this minor crop species and a better knowledge of the genome-level relationship between these two species would facilitate improvement in both. High-throughput genotyping has facilitated large-scale single nucleotide polymorphism (SNP) identification leading to the development of molecular markers with associated sequence information that can be used to place them in the context of a full genome assembly.
Transcript-based SNPs were identified from six common bean and two tepary bean accessions and a subset were used to generate a 768-SNP Illumina GoldenGate assay for each species. The tepary bean assay was used to assess diversity in wild and cultivated tepary bean and to generate the first gene-based map of the tepary bean genome. Genotypic analyses of the diversity panel showed a clear separation between domesticated and cultivated tepary beans, two distinct groups within the domesticated types, and P. parvifolius was confirmed to be distinct. The genetic map of tepary bean was compared to the common bean genome assembly to demonstrate high levels of collinearity between the two species with differences limited to a few intra-chromosomal rearrangements.
The development of the first set of genomic resources specifically for tepary bean has allowed for greater insight into the structure of this species and its relationship to its agriculturally more prominent relative, common bean. These resources will be helpful in the development of efficient breeding strategies for both species and will facilitate the introgression of agriculturally important traits from one crop into the other.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Aim
The conservation and effective use of crop genetic diversity are crucial to overcome challenges related to human nutrition and agricultural sustainability. Farmers’ traditional varieties ...(“landraces”) are major sources of genetic variation. The degree of representation of crop landrace diversity in ex situ conservation is poorly understood, partly due to a lack of methods that can negotiate both the anthropogenic and environmental determinants of their geographic distributions. Here, we describe a novel spatial modelling and ex situ conservation gap analysis modelling framework for crop landraces, using common bean (Phaseolus vulgaris L.) as a case study.
Location
The Americas.
Methods
The modelling framework includes five main steps: (a) determining relevant landrace groups using literature to develop and test classification models; (b) modelling the potential geographic distributions of these groups using occurrence (landrace presences) combined with environmental and socioeconomic predictor data; (c) calculating geographic and environmental gap scores for current genebank collections; (d) mapping ex situ conservation gaps; and (e) compiling expert inputs.
Results
Modelled distributions and conservation gaps for the two genepools of common bean (Andean and Mesoamerican) were robustly predicted and align well with expert opinions. Both genepools are relatively well conserved, with Andean ex situ collections representing 78.5% and Mesoamerican 98.2% of their predicted geographic distributions. Modelling revealed additional collection priorities for Andean landraces occur primarily in Chile, Peru, Colombia and, to a lesser extent, Venezuela. Mesoamerican landrace collecting priorities are concentrated in Mexico, Belize and Guatemala.
Conclusions
The modelling framework represents an advance in tools that can be deployed to model the geographic distributions of cultivated crop diversity, to assess the comprehensiveness of conservation of this diversity ex situ and to highlight geographic areas where further collecting may be conducted to fill gaps in ex situ conservation.
A name given by Molina in 1782 and again in 1810 to a new Phaseolus species after a food legume crop grown for millennia mostly in the western part of the Quechua realm in South America refers to ...that crop (in the text of his essay) as well as to a weed (in his short Latin description), thus raising taxonomical uncertainty. Obviously, a taxonomical epithet cannot refer to two different botanical entities within the same genus. An example of that uncertainty was the naming of a specimen likely of Macroptilium lathyroides collected in northern Colombia and kept in the negative series of Berlin-Dahlem at the Field Museum. That crop spread so widely and fast that it received several names that Molina and a fortiori Philippi should have considered.
Background and Aims Improved understanding of the secondary gene pools of crops is essential for advancing genetic gain in breeding programmes. Common bean, Phaseolus vulgaris, is a staple crop with ...several wild relatives in its secondary gene pool. The year-long bean, P. dumosus, an important crop in Guatemala, is considered particularly closely related to P. vulgaris and a potential source of novel variation. However, the genetic diversity and relationship to other Phaseolus species of P. dumosus remain unclear. Methods We conducted the first comprehensive investigation of P. dumosus genetic diversity using both nuclear and chloroplast genome markers. Our nuclear marker set included over 700 markers present within the Phaseolus DArT (Diversity Arrays Technology) array, which we applied to P. dumosus and other relatives of P. vulgaris (including every secondary gene pool species: P. acutifolius, P. albescens, P. coccineus and P. costaricensis). Key Results Phaseolus dumosus arose from hybridization of P. vulgaris and P. coccineus, followed by at least two later hybridizations with sympatric congener populations. Existing P. dumosus collections have low genetic diversity. Conclusions The under-utilized crop P. dumosus has a complex hybrid origin. Further sampling in the region in which it arose may uncover additional germplasm for introgressing favourable traits into crops within the P. vulgaris gene pool.
Lima bean
(Phaseolus lunatus
L.) is the second most important domesticated species of
Phaseolus
in the world and it could be a valuable alternative resource for food security and quality. Worldwide, ...and in Latin America especially, Lima bean may also contribute to sustainability in the face of climate change. Currently, many experts on conservation, domestication, genetic improvement, and plant-rhizosphere relationships of Lima bean have been working alone or in small groups. This situation has limited the progress and reach of their research and demonstrated the need to connect Lima bean researchers worldwide. To increase collaboration between experts in the study of Lima bean, we present the International Lima Bean Network (ILBN). The main objectives of ILBN are to deepen the knowledge on this species and to promote its use around the world. The success of ILBN will depend on the collaboration of the international scientific community interested in the study of Lima bean. Therefore, we are inviting people from different sectors of society (researchers, producers, companies, NGOs, governments) to participate in this initiative. To learn more, you can visit
https://www.cicy.mx/sitios/red-internacional-frijol-lima
The genus
Phaseolus
, native to the Americas, is composed of more than eighty wild species, five of which were domesticated in pre-Columbian times. Since the beginning of domestication events in this ...genus, ample opportunities for gene flow with wild relatives have existed. The present work reviews the extent of gene flow in the genus
Phaseolus
in primary and secondary areas of domestication with the aim of illustrating how this evolutionary force may have conditioned ecological fitness and the widespread adoption of cultigens. We focus on the biological bases of gene flow in the genus
Phaseolus
from a spatial and time perspective, the dynamics of wild-weedy-crop complexes in the common bean and the Lima bean, the two most important domesticated species of the genus, and the usefulness of genomic tools to detect inter and intraspecific introgression events. In this review we discuss the reproductive strategies of several
Phaseolus
species, the factors that may favor outcrossing rates and evidence suggesting that interspecific gene flow may increase ecological fitness of wild populations. We also show that wild-weedy-crop complexes generate genetic diversity over which farmers are able to select and expand their cultigens outside primary areas of domestication. Ultimately, we argue that more studies are needed on the reproductive biology of the genus
Phaseolus
since for most species breeding systems are largely unknown. We also argue that there is an urgent need to preserve wild-weedy-crop complexes and characterize the genetic diversity generated by them, in particular the genome-wide effects of introgressions and their value for breeding programs. Recent technological advances in genomics, coupled with agronomic characterizations, may make a large contribution.
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