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The CGIAR crop improvement (CI) programs, unlike commercial CI programs, which are mainly geared to profit though meeting farmers’ needs, are charged with meeting multiple objectives with target populations that include both farmers and the community at large. We compiled the opinions from >30 experts in the private and public sector on key strategies, methodologies, and activities that could the help CGIAR meet the challenges of providing farmers with improved varieties while simultaneously meeting the goals of: (i) nutrition, health, and food security; (ii) poverty reduction, livelihoods, and jobs; (iii) gender equality, youth, and inclusion; (iv) climate adaptation and mitigation; and (v) environmental health and biodiversity. We review the crop improvement processes starting with crop choice, moving through to breeding objectives, production of potential new varieties, selection, and finally adoption by farmers. The importance of multidisciplinary teams working towards common objectives is stressed as a key factor to success. The role of the distinct disciplines, actors, and their interactions throughout the process from crop choice through to adoption by farmers is discussed and illustrated., This document arose from the urgent need to join forces (across nations and research disciplines) and stand together to improve the prospects for the most vulnerable population on the globe whose well-being depends on agricultural production. Here, we learn from the past, and draft future strategic guidelines that will facilitate efforts of the CGIAR institutions (https://www.cgiar.org/) to enhance the livelihoods of the less privileged through crop improvement.

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 is an important crop for improving food security in Latin America and elsewhere. Here, the authors assemble its genome, conduct population genomics analysis using genotyping-by-sequencing data, and identify differentially expressed genes between two pod developmental stages.

Crop landraces have unique local agroecological and societal functions and offer important genetic resources for plant breeding. Recognition of the value of landrace diversity and concern about its erosion on farms have led to sustained efforts to establish ex situ collections worldwide. The degree to which these efforts have succeeded in conserving landraces has not been comprehensively assessed. Here we modelled the potential distributions of eco-geographically distinguishable groups of landraces of 25 cereal, pulse and starchy root/tuber/fruit crops within their geographic regions of diversity. We then analysed the extent to which these landrace groups are represented in genebank collections, using geographic and ecological coverage metrics as a proxy for genetic diversity. We find that ex situ conservation of landrace groups is currently moderately comprehensive on average, with substantial variation among crops; a mean of 63% ± 12.6% of distributions is currently represented in genebanks. Breadfruit, bananas and plantains, lentils, common beans, chickpeas, barley and bread wheat landrace groups are among the most fully represented, whereas the largest conservation gaps persist for pearl millet, yams, finger millet, groundnut, potatoes and peas. Geographic regions prioritized for further collection of landrace groups for ex situ conservation include South Asia, the Mediterranean and West Asia, Mesoamerica, sub-Saharan Africa, the Andean mountains of South America and Central to East Asia. With further progress to fill these gaps, a high degree of representation of landrace group diversity in genebanks is feasible globally, thus fulfilling international targets for their ex situ conservation. ispartof: NATURE PLANTS vol:8 issue:5 pages:491-+ ispartof: location:England status: published

Phaseolus species are globally important food security crops. Drought and low soil fertility are primary constraints to Phaseolus production in developing nations. Root phenes have important roles in soil resource capture and plant performance. We profiled root phenotypes in 30 wild and seven domesticated Phaseolus taxa in laboratory and greenhouse environments. Our results reveal that substantial variation for root phenotypes exists among and within Phaseolus taxa, notably for phenes such as basal root number, basal root whorl number, root hair length, root hair density, metaxylem vessel number, and total cross-sectional area. Wild taxa display greater genetic variation for root architecture and anatomy and possess desirable phenotypes that are either not found or are not sufficiently expressed in domesticated accessions. Consequently, wild taxa represent an important resource for breeding programs to improve abiotic stress tolerance. Root phenotypes were also associated with the environment in the region of origin, suggesting that they have adaptive value. We speculate that significant variation in root phenotypes across different Phaseolus species is related to their abiotic stress tolerance and are valuable for breeding programs focused on improving edaphic stress tolerance.

Background 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. Results 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. Conclusions 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. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2499-3) contains supplementary material, which is available to authorized users.

† 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.

International audience; Grain legumes contribute significantly to total world food production. Legumes are the primary source of dietary proteins in many developing countries, where protein hunger and malnutrition are widespread. Grain legumes germplasm constitute similar to 15% of the 7.4 M accessions preserved globally. Nearly, 78% of the CGIAR's, 0.217 M accessions, have been characterized, compared to 34% of national genebank collections. Interestingly, limited data on grain quality are available as the primary focus has been on morpho-agronomic traits. Clearly, more resources should be targeted on biochemical evaluation to identify nutritionally rich and genetically diverse germplasm. The formation of core and mini core collections has provided crop breeders with a systematic yet manageable entry point into global germplasm resources. These subsets have been reported for most legumes and have proved useful in identifying new sources of variation. They may however not eliminate the need to evaluate entire collections, particularly for very rare traits. Molecular characterization and association mapping will further aid to insights into the structure of legume diversity and facilitate greater use of collections. The use of high resolution elevational climate models has greatly improved our capacity to characterize plant habitats and species' adaptive responses to stresses. Evidence suggests that there has been increased use of wild relatives as well as new resources resulting from mutagenesis to enhance the genetic base of legume cultigens.