Evolution of genetic diversity during the domestication of common-bean (Phaseolus vulgaris L.)

Phylogeny and disparate selection signatures suggest two genetically independent domestication events in pea (Pisum L.)

Domestication is considered a model of adaptation that can be used to draw conclusions about the modus operandi of selection in natural systems. Investigating domestication may give insights into how plants react to different intensities of human manipulation, which has direct implication for the continuing efforts of crop improvement. Therefore, scientists of various disciplines study domestication-related questions to understand the biological and cultural bases of the domestication process. We employed restriction site-associated DNA sequencing (RAD-seq) of 494 Pisum sativum (pea) samples from all wild and domesticated groups to analyze the genetic structure of the collection. Patterns of ancient admixture were investigated by analysis of admixture graphs. We used two complementary approaches, one diversity based and one based on differentiation, to detect the selection signatures putatively associated with domestication. An analysis of the subpopulation structure of wild P. sativum revealed five distinct groups with a notable geographic pattern. Pisum abyssinicum clustered unequivocally within the P. sativum complex, without any indication of hybrid origin. We detected 32 genomic regions putatively subjected to selection: 29 in P. sativum ssp. sativum and three in P. abyssinicum. The two domesticated groups did not share regions under selection and did not display similar haplotype patterns within those regions. Wild P. sativum is structured into well-diverged subgroups. Although Pisum sativum ssp. humile is not supported as a taxonomic entity, the so-called 'southern humile' is a genuine wild group. Introgression did not shape the variation observed within the sampled germplasm. The two domesticated pea groups display distinct genetic bases of domestication, suggesting two genetically independent domestication events.

Homogenized Phylogeographic Structure across the Indo-Burma Ranges of a Large Monoecious Fig, Ficus altissima Blume

As well as bountiful natural resources, the Indo-Burma biodiversity hotspot features high rates of habitat destruction and fragmentation due to increasing human activity; however, most of the Indo-Burma species are poorly studied. The exploration of plants closely associated with human activity will further assist us to understand our influence in the context of the ongoing extinction events in the Anthropocene. This study, based on widely and intensively sampled F. altissima across Indo-Burma and the adjacent south China ranges, using both the chloroplast psbA-trnH spacer and sixteen newly developed nuclear microsatellite markers (nSSRs), aims to explore its spatial genetic structure. The results indicated low chloroplast haplotype diversity and a moderate level of nuclear genetic diversity. Although limited seed flow was revealed by psbA-trnH, no discernible phylogeographic structure was shown due to the low resolution of cpDNA markers and dominance of an ancestral haplotype. From the nSSRs data set, phylogeographic structure was homogenized, most likely due to extensive pollen flow mediated by pollinating fig wasps. Additionally, human cultivation and human-mediated transplanting further confounded the analyses of population structure. No geographic barriers are evident across the large study range, with F. altissima constituting a single population, and extensive human cultivation is likely to have had beneficial consequences for protecting the genetic diversity of F. altissima.

Diversity and Distribution of Viruses Infecting Wild and Domesticated Phaseolus spp. in the Mesoamerican Center of Domestication

Viruses are an important disease source for beans. In order to evaluate the impact of virus disease on Phaseolus biodiversity, we determined the identity and distribution of viruses infecting wild and domesticated Phaseolus spp. in the Mesoamerican Center of Domestication (MCD) and the western state of Nayarit, Mexico. We used small RNA sequencing and assembly to identify complete or near-complete sequences of forty-seven genomes belonging to nine viral species of five genera, as well as partial sequences of two putative new endornaviruses and five badnavirus- and pararetrovirus-like sequences. The prevalence of viruses in domesticated beans was significantly higher than in wild beans (97% vs. 19%; p < 0.001), and all samples from domesticated beans were positive for at least one virus species. In contrast, no viruses were detected in 80-83% of the samples from wild beans. The Bean common mosaic virus and Bean common mosaic necrosis virus were the most prevalent viruses in wild and domesticated beans. Nevertheless, Cowpea mild mottle virus, transmitted by the whitefly Bemisia tabaci, has the potential to emerge as an important pathogen because it is both seed-borne and a non-persistently transmitted virus. Our results provide insights into the distribution of viruses in cultivated and wild Phaseolus spp. and will be useful for the identification of emerging viruses and the development of strategies for bean viral disease management in a center of diversity.

Gene Flow in Phaseolus Beans and Its Role as a Plausible Driver of Ecological Fitness and Expansion of Cultigens

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.

Exploration of the Yield Potential of Mesoamerican Wild Common Beans From Contrasting Eco-Geographic Regions by Nested Recombinant Inbred Populations

Genetic analyses and utilization of wild genetic variation for crop improvement in common bean (Phaseolus vulgaris L.) have been hampered by yield evaluation difficulties, identification of advantageous variation, and linkage drag. The lack of adaptation to cultivation conditions and the existence of highly structured populations make association mapping of diversity panels not optimal. Joint linkage mapping of nested populations avoids the later constraint, while populations crossed with a common domesticated parent allow the evaluation of wild variation within a more adapted background. Three domesticated by wild backcrossed-inbred-line populations (BC₁S₄) were developed using three wild accessions representing the full range of rainfall of the Mesoamerican wild bean distribution crossed to the elite drought tolerant domesticated parent SEA 5. These populations were evaluated under field conditions in three environments, two fully irrigated trials in two seasons and a simulated terminal drought in the second season. The goal was to test if these populations responded differently to drought stress and contained progenies with higher yield than SEA 5, not only under drought but also under water-watered conditions. Results revealed that the two populations derived from wild parents of the lower rainfall regions produced lines with higher yield compared to the domesticated parent in the three environments, i.e., both in the drought-stressed environment and in the well-watered treatments. Several progeny lines produced yields, which on average over the three environments were 20% higher than the SEA 5 yield. Twenty QTLs for yield were identified in 13 unique regions on eight of the 11 chromosomes of common bean. Five of these regions showed at least one wild allele that increased yield over the domesticated parent. The variation explained by these QTLs ranged from 0.6 to 5.4% of the total variation and the additive effects ranged from -164 to 277 kg ha^-1, with evidence suggesting allelic series for some QTLs. Our results underscore the potential of wild variation, especially from drought-stressed regions, for bean crop improvement as well the identification of regions for efficient marker-assisted introgression.

Root and shoot variation in relation to potential intermittent drought adaptation of Mesoamerican wild common bean (Phaseolus vulgaris L.)

BACKGROUND

Wild crop relatives have been potentially subjected to stresses on an evolutionary time scale prior to domestication. Among these stresses, drought is one of the main factors limiting crop productivity and its impact is likely to increase under current scenarios of global climate change. We sought to determine to what extent wild common bean (Phaseolus vulgaris) exhibited adaptation to drought stress, whether this potential adaptation is dependent on the climatic conditions of the location of origin of individual populations, and to what extent domesticated common bean reflects potential drought adaptation.

METHODS

An extensive and diverse set of wild beans from across Mesoamerica, along with a set of reference Mesoamerican domesticated cultivars, were evaluated for root and shoot traits related to drought adaptation. A water deficit experiment was conducted by growing each genotype in a long transparent tube in greenhouse conditions so that root growth, in addition to shoot growth, could be monitored.

RESULTS

Phenotypic and landscape genomic analyses, based on single-nucleotide polymorphisms, suggested that beans originating from central and north-west Mexico and Oaxaca, in the driest parts of their distribution, produced more biomass and were deeper-rooted. Nevertheless, deeper rooting was correlated with less root biomass production relative to total biomass. Compared with wild types, domesticated types showed a stronger reduction and delay in growth and development in response to drought stress. Specific genomic regions were associated with root depth, biomass productivity and drought response, some of which showed signals of selection and were previously related to productivity and drought tolerance.

CONCLUSIONS

The drought tolerance of wild beans consists in its stronger ability, compared with domesticated types, to continue growth in spite of water-limited conditions. This study is the first to relate bean response to drought to environment of origin for a diverse selection of wild beans. It provides information that needs to be corroborated in crosses between wild and domesticated beans to make it applicable to breeding programmes.

Genotyping-by-Sequencing Reveals Molecular Genetic Diversity in Italian Common Bean Landraces

The common bean (Phaseolus vulgaris L.) is one of the main legumes worldwide and represents a valuable source of nutrients. Independent domestication events in the Americas led to the formation of two cultivated genepools, namely Mesoamerican and Andean, to which European material has been brought back. In this study, Italian common bean landraces were analyzed for their genetic diversity and structure, using single nucleotide polymorphism (SNP) markers derived from genotyping-by-sequencing (GBS) technology. After filtering, 11,866 SNPs were obtained and 798 markers, pruned for linkage disequilibrium, were used for structure analysis. The most probable number of subpopulations (K) was two, consistent with the presence of the two genepools, identified through the phaseolin diagnostic marker. Some landraces were admixed, suggesting probable hybridization events between Mesoamerican and Andean material. When increasing the number of possible Ks, the Andean germplasm appeared to be structured in two or three subgroups. The subdivision within the Andean material was also observed in a principal coordinate analysis (PCoA) plot and a dendrogram based on genetic distances. The Mesoamerican landraces showed a higher level of genetic diversity compared to the Andean landraces. Calculation of the fixation index (FST) at individual SNPs between the Mesoamerican and Andean genepools and within the Andean genepool evidenced clusters of highly divergent loci in specific chromosomal regions. This work may help to preserve landraces of the common bean from genetic erosion, and could represent a starting point for the identification of interesting traits that determine plant adaptation.

Deciphering rhizosphere microbiome assembly of wild and modern common bean (Phaseolus vulgaris) in native and agricultural soils from Colombia

BACKGROUND

Modern crop varieties are typically cultivated in agriculturally well-managed soils far from the centers of origin of their wild relatives. How this habitat expansion impacted plant microbiome assembly is not well understood.

RESULTS

Here, we investigated if the transition from a native to an agricultural soil affected rhizobacterial community assembly of wild and modern common bean (Phaseolus vulgaris) and if this led to a depletion of rhizobacterial diversity. The impact of the bean genotype on rhizobacterial assembly was more prominent in the agricultural soil than in the native soil. Although only 113 operational taxonomic units (OTUs) out of a total of 15,925 were shared by all eight bean accessions grown in native and agricultural soils, this core microbiome represented a large fraction (25.9%) of all sequence reads. More OTUs were exclusively found in the rhizosphere of common bean in the agricultural soil as compared to the native soil and in the rhizosphere of modern bean accessions as compared to wild accessions. Co-occurrence analyses further showed a reduction in complexity of the interactions in the bean rhizosphere microbiome in the agricultural soil as compared to the native soil.

CONCLUSIONS

Collectively, these results suggest that habitat expansion of common bean from its native soil environment to an agricultural context had an unexpected overall positive effect on rhizobacterial diversity and led to a stronger bean genotype-dependent effect on rhizosphere microbiome assembly.

Evolution of SSR diversity from wild types to U.S. advanced cultivars in the Andean and Mesoamerican domestications of common bean (Phaseolus vulgaris)

Progress in common bean breeding requires the exploitation of genetic variation among market classes, races and gene pools. The present study was conducted to determine the amount of genetic variation and the degree of relatedness among 192 selected common bean advanced cultivars using 58 simple-sequence-repeat markers (SSR) evenly distributed along the 11 linkage groups of the Phaseolus reference map. All the lines belonged to commercial seed type classes that are widely grown in the USA and include both dry bean and snap beans for the fresh and processing markets. Through population structure, principal components analyses, cluster analysis, and discriminant analysis of principal components (DAPC), Andean and Mesoamerican genotypes as well as most American commercial type classes could be distinguished. The genetic relationship among the commercial cultivars revealed by the SSR markers was generally in agreement with known pedigree data. The Mesoamerican cultivars were separated into three major groups-black, small white, and navy accessions clustered together in a distinct group, while great northern and pinto clustered in another group, showing mixed origin. The Andean cultivars were distributed in two different groups. The kidney market classes formed a single group, while the green bean accessions were distributed between the Andean and Mesoamerican groups, showing inter-gene pool genetic admixture. For a subset of 24 SSR markers, we compared and contrasted the genetic diversity of the commercial cultivars with those of wild and domesticated landrace accessions of common bean. An overall reduction in genetic diversity was observed in both gene pools, Andean and Mesoamerican, from wild to landraces to advanced cultivars. The limited diversity in the commercial cultivars suggests that an important goal of bean breeding programs should be to broaden the cultivated gene pool, particularly the genetic diversity of specific commercial classes, using the genetic variability present in common bean landraces.

The western Mediterranean region provided the founder population of domesticated narrow-leafed lupin

This study revealed that the western Mediterranean provided the founder population for domesticated narrow-leafed lupin and that genetic diversity decreased significantly during narrow-leafed lupin domestication. The evolutionary history of plants during domestication profoundly shaped the genome structure and genetic diversity of today's crops. Advances in next-generation sequencing technologies allow unprecedented opportunities to understand genome evolution in minor crops, which constitute the majority of plant domestications. A diverse set of 231 wild and domesticated narrow-leafed lupin (Lupinus angustifolius L.) accessions were subjected to genotyping-by-sequencing using diversity arrays technology. Phylogenetic, genome-wide divergence and linkage disequilibrium analyses were applied to identify the founder population of domesticated narrow-leafed lupin and the genome-wide effect of domestication on its genome. We found wild western Mediterranean population as the founder of domesticated narrow-leafed lupin. Domestication was associated with an almost threefold reduction in genome diversity in domesticated accessions compared to their wild relatives. Selective sweep analysis identified no significant footprints of selection around domestication loci. A genome-wide association study identified single nucleotide polymorphism markers associated with pod dehiscence. This new understanding of the genomic consequences of narrow-leafed lupin domestication along with molecular marker tools developed here will assist plant breeders more effectively access wild genetic diversity for crop improvement.

The population genetics of cultivation: domestication of a traditional Chinese medicine, Scrophularia ningpoensis Hemsl. (Scrophulariaceae)

BACKGROUND

Domestic cultivation of medicinal plants is an important strategy for protecting these species from over harvesting. Some species of medicinal plants have been brought into cultivation for more than hundreds years. Concerns about severe loss of genetic diversity and sustainable cultivation can potentially limit future use of these valuable plants. Genetic studies with comprehensive sampling of multiple medicinal species by molecular markers will allow for assessment and management of these species. Here we examine the population genetic consequences of cultivation and domestication in Scrophularia ningpoensis Hemsl. We used chloroplast DNA and genomic AFLP markers to clarify not only the effects of domestication on genetic diversity, but also determine the geographic origins of cultivars and their genetic divergence from native populations. These results will allow both better management of cultivated populations, but also provide insights for crop improvement.

RESULTS

Twenty-one cpDNA haplotypes of S. ningpoensis were identified. Wild populations contain all haplotypes, whereas only three haplotypes were found in cultivated populations with wild populations having twice the haplotype diversity of cultivated populations. Genetic differentiation between cultivated populations and wild populations was significant. Genomic AFLP markers revealed similar genetic diversity patterns. Furthermore, Structure analysis grouped all wild populations into two gene pools; two of which shared the same gene pool with cultivated S. ningpoensis. The result of Neighbor-Joining analysis was consistent with the structure analysis. In principal coordinate analysis, three cultivated populations from Zhejiang Province grouped together and were separated from other cultivated populations.

CONCLUSIONS

These results suggest that cultivated S. ningpoensis has experienced dramatic loss of genetic diversity under anthropogenic influence. We postulate that strong artificial selection for medicinal quality has resulted in genetic differentiation between cultivated and wild populations. Furthermore, it appears that wild populations in Jiangxi-Hunan area were involved in the origin of cultivated S. ningpoensis.

Sequence-related amplified polymorphism (SRAP) markers: A potential resource for studies in plant molecular biology(1.)

In the past few decades, many investigations in the field of plant biology have employed selectively neutral, multilocus, dominant markers such as inter-simple sequence repeat (ISSR), random-amplified polymorphic DNA (RAPD), and amplified fragment length polymorphism (AFLP) to address hypotheses at lower taxonomic levels. More recently, sequence-related amplified polymorphism (SRAP) markers have been developed, which are used to amplify coding regions of DNA with primers targeting open reading frames. These markers have proven to be robust and highly variable, on par with AFLP, and are attained through a significantly less technically demanding process. SRAP markers have been used primarily for agronomic and horticultural purposes, developing quantitative trait loci in advanced hybrids and assessing genetic diversity of large germplasm collections. Here, we suggest that SRAP markers should be employed for research addressing hypotheses in plant systematics, biogeography, conservation, ecology, and beyond. We provide an overview of the SRAP literature to date, review descriptive statistics of SRAP markers in a subset of 171 publications, and present relevant case studies to demonstrate the applicability of SRAP markers to the diverse field of plant biology. Results of these selected works indicate that SRAP markers have the potential to enhance the current suite of molecular tools in a diversity of fields by providing an easy-to-use, highly variable marker with inherent biological significance.

Developing market class specific InDel markers from next generation sequence data in Phaseolus vulgaris L

Next generation sequence data provides valuable information and tools for genetic and genomic research and offers new insights useful for marker development. This data is useful for the design of accurate and user-friendly molecular tools. Common bean (Phaseolus vulgaris L.) is a diverse crop in which separate domestication events happened in each gene pool followed by race and market class diversification that has resulted in different morphological characteristics in each commercial market class. This has led to essentially independent breeding programs within each market class which in turn has resulted in limited within market class sequence variation. Sequence data from selected genotypes of five bean market classes (pinto, black, navy, and light and dark red kidney) were used to develop InDel-based markers specific to each market class. Design of the InDel markers was conducted through a combination of assembly, alignment and primer design software using 1.6× to 5.1× coverage of Illumina GAII sequence data for each of the selected genotypes. The procedure we developed for primer design is fast, accurate, less error prone, and higher throughput than when they are designed manually. All InDel markers are easy to run and score with no need for PCR optimization. A total of 2687 InDel markers distributed across the genome were developed. To highlight their usefulness, they were employed to construct a phylogenetic tree and a genetic map, showing that InDel markers are reliable, simple, and accurate.

Domestication bottlenecks limit genetic diversity and constrain adaptation in narrow-leafed lupin (Lupinus angustifolius L.)

In contrast to most widespread broad-acre crops, the narrow-leafed lupin (Lupinus angustifolius L.) was domesticated very recently, in breeding programmes isolated in both space and time. Whereas domestication was initiated in Central Europe in the early twentieth century, the crop was subsequently industrialized in Australia, which now dominates world production. To investigate the ramifications of these bottlenecks, the genetic diversity of wild (n = 1,248) and domesticated populations (n = 95) was characterized using diversity arrays technology, and adaptation studied using G × E trials (n = 31) comprising all Australian cultivars released from 1967 to 2004 (n = 23). Principal coordinates analysis demonstrates extremely limited genetic diversity in European and Australian breeding material compared to wild stocks. AMMI analysis indicates that G × E interaction is a minor, albeit significant effect, dominated by strong responses to local, Western Australian (WA) optima. Over time Australian cultivars have become increasingly responsive to warm, intermediate rainfall environments in the northern WA grainbelt, but much less so to cool vegetative phase eastern environments, which have considerably more yield potential. G × E interaction is well explained by phenology, and its interaction with seasonal climate, as a result of varying vernalization responses. Yield differences are minimized when vegetative phase temperatures fully satisfy the vernalization requirement (typical of eastern Australia), and maximized when they do not (typical of WA). In breeding for WA optima, the vernalization response has been eliminated and there has been strong selection for terminal drought avoidance through early phenology, which limits yield potential in longer season eastern environments. Conversely, vernalization-responsive cultivars are more yield-responsive in the east, where low temperatures moderately extend the vegetative phase. The confounding of phenology and vernalization response limits adaptation in narrow-leafed lupin, isolates breeding programmes, and should be eliminated by widening the flowering time range in a vernalization-unresponsive background. Concomitantly, breeding strategies that will widen the genetic base of the breeding pool in an ongoing manner should be initiated.

Impact of human management on the genetic variation of wild pepper, Capsicum annuum var. glabriusculum

Management of wild peppers in Mexico has occurred for a long time without clear phenotypic signs of domestication. However, pre-domestication management could have implications for the population's genetic richness. To test this hypothesis we analysed 27 wild (W), let standing (LS) and cultivated (C) populations, plus 7 samples from local markets (LM), with nine polymorphic microsatellite markers. Two hundred and fifty two alleles were identified, averaging 28 per locus. Allele number was higher in W, and 15 and 40% less in LS and C populations, respectively. Genetic variation had a significant population structure. In W populations, structure was associated with ecological and geographic areas according to isolation by distance. When LM and C populations where included in the analysis, differentiation was no longer apparent. Most LM were related to distant populations from Sierra Madre Oriental, which represents their probable origin. Historical demography shows a recent decline in all W populations. Thus, pre-domestication human management is associated with a significant reduction of genetic diversity and with a loss of differentiation suggesting movement among regions by man. Measures to conserve wild and managed populations should be implemented to maintain the source and the architecture of genetic variation in this important crop relative.

Investigation of the domestication of common bean (Phaseolus vulgaris) using multilocus sequence data

Multilocus sequence data collected from domesticated and related wild relatives provides a rich source of information on the effect of human selection on the diversity and adaptability of a species to complex environments. To evaluate the domestication history of common bean (Phaseolus vulgaris L.), multilocus sequence data from landraces representing the various races within the Middle American (MA) and Andean gene pools was evaluated. Across 13 loci, nucleotide diversity was similar between landraces and wild germplasm in both gene pools. The diversity data were evaluated using the approximate Bayesian computation approach to test multiple domestication models and estimate population demographic parameters. A model with a single domestication event coupled with bidirectional migration between wild and domesticated genotypes fitted the data better than models consisting of two or three domestication events in each genepool. The effective bottleneck population size was ~50% of the base population in each genepool. The bottleneck began ~8200 and ~8500 years before present and ended at ~6300 and ~7000 years before present in MA and Andean gene pools respectively. Linkage disequilibrium decayed to a greater extent in the MA genepool. Given the (1) geographical adaptation bottleneck in each wild gene pool, (2) a subsequent domestication bottleneck within each gene pool, (3) differentiation into gene-pool specific races and (4) variable extents of linkage disequilibrium, association mapping experiments for common bean would more appropriately be performed within each genepool.

SNP marker diversity in common bean (Phaseolus vulgaris L.)

Single nucleotide polymorphism (SNP) markers have become a genetic technology of choice because of their automation and high precision of allele calls. In this study, our goal was to develop 94 SNPs and test them across well-chosen common bean (Phaseolus vulgaris L.) germplasm. We validated and accessed SNP diversity at 84 gene-based and 10 non-genic loci using KASPar technology in a panel of 70 genotypes that have been used as parents of mapping populations and have been previously evaluated for SSRs. SNPs exhibited high levels of genetic diversity, an excess of middle frequency polymorphism, and a within-genepool mismatch distribution as expected for populations affected by sudden demographic expansions after domestication bottlenecks. This set of markers was useful for distinguishing Andean and Mesoamerican genotypes but less useful for distinguishing within each gene pool. In summary, slightly greater polymorphism and race structure was found within the Andean gene pool than within the Mesoamerican gene pool but polymorphism rate between genotypes was consistent with genepool and race identity. Our survey results represent a baseline for the choice of SNP markers for future applications because gene-associated SNPs could themselves be causative SNPs for traits. Finally, we discuss that the ideal genetic marker combination with which to carry out diversity, mapping and association studies in common bean should consider a mix of both SNP and SSR markers.

From forest to field: perennial fruit crop domestication

PREMISE OF THE STUDY

Archaeological and genetic analyses of seed-propagated annual crops have greatly advanced our understanding of plant domestication and evolution. Comparatively little is known about perennial plant domestication, a relevant topic for understanding how genes and genomes evolve in long-lived species, and how perennials respond to selection pressures operating on a relatively short time scale. Here, we focus on long-lived perennial crops (mainly trees and other woody plants) grown for their fruits.

KEY RESULTS

We reviewed (1) the basic biology of long-lived perennials, setting the stage for perennial domestication by considering how these species evolve in nature; (2) the suite of morphological features associated with perennial fruit crops undergoing domestication; (3) the origins and evolution of domesticated perennials grown for their fruits; and (4) the genetic basis of domestication in perennial fruit crops.

CONCLUSIONS

Long-lived perennials have lengthy juvenile phases, extensive outcrossing, widespread hybridization, and limited population structure. Under domestication, these features, combined with clonal propagation, multiple origins, and ongoing crop-wild gene flow, contribute to mild domestication bottlenecks in perennial fruit crops. Morphological changes under domestication have many parallels to annual crops, but with key differences for mating system evolution and mode of reproduction. Quantitative trait loci associated with domestication traits in perennials are mainly of minor effect and may not be stable across years. Future studies that take advantage of genomic approaches and consider demographic history will elucidate the genetics of agriculturally and ecologically important traits in perennial fruit crops and their wild relatives.

Molecular insights into the evolution of crop plants

The domestication and improvement of crop plants have long fascinated evolutionary biologists, geneticists, and anthropologists. In recent years, the development of increasingly powerful molecular and statistical tools has reinvigorated this now fast-paced field of research. In this paper, we provide an overview of how such tools have been applied to the study of crop evolution. We also highlight lessons that have been learned in light of a few long-standing and interrelated hypotheses concerning the origins of crop plants and the nature of the genetic changes underlying their evolution. We conclude by discussing compelling evolutionary genomic approaches that make possible the efficient and unbiased identification of genes controlling crop-related traits and provide further insight into the actual timing of selection on particular genomic regions.

Microsatellite characterization of Andean races of common bean (Phaseolus vulgaris L.)

The Andean gene pool of common bean (Phaseolus vulgaris L.) has high levels of morphological diversity in terms of seed color and size, growth habit and agro-ecological adaptation, but previously was characterized by low levels of molecular marker diversity. Three races have been described within the Andean gene pool: Chile, Nueva Granada and Peru. The objective of this study was to characterize a collection of 123 genotypes representing Andean bean diversity with 33 microsatellite markers that have been useful for characterizing race structure in common beans. The genotypes were from both the primary center of origin as well as secondary centers of diversity to which Andean beans spread and represented all three races of the gene pool. In addition we evaluated a collection of landraces from Colombia to determine if the Nueva Granada and Peru races could be distinguished in genotypes from the northern range of the primary center. Multiple correspondence analyses of the Andean race representatives identified two predominant groups corresponding to the Nueva Granada and Peru races. Some of the Chile race representatives formed a separate group but several that had been defined previously as from this race grouped with the other races. Gene flow was more notable between Nueva Granada and Peru races than between these races and the Chile race. Among the Colombian genotypes, the Nueva Granada and Peru races were identified and introgression between these two races was especially notable. The genetic diversity within the Colombian genotypes was high, reaffirming the importance of this region as an important source of germplasm. Results of this study suggest that the morphological classification of all climbing beans as Peru race genotypes and all bush beans as Nueva Granada race genotypes is erroneous and that growth habit traits have been mixed in both races, requiring a re-adjustment in the concept of morphological races in Andean beans.

Generation means analysis of climbing ability in common bean (Phaseolus vulgaris L.)

Climbing common bean (Phaseolus vulgaris L.) genotypes have among the highest yield potential of all accessions found in the species. Genetic improvement of climbing beans would benefit from an understanding of the inheritance of climbing capacity (made up of plant height [PH] and internode length [IL] traits). The objective of this study was to determine the inheritance of climbing capacity traits in 3 crosses made within and between gene pools (Andean x Andean [BRB32 x MAC47], Mesoamerican x Mesoamerican [Tío Canela x G2333], and Mesoamerican x Andean [G2333 x G19839]) using generation means analysis. For each population, we used 6 generations (P(1), P(2), F(1), F(2), BC(1)P(1), and BC(1)P(2)) that were evaluated at 2 growth stages (40 and 70 days after planting). Results showed the importance of additive compared with the dominant-additive portion of the genetic model. Broad-sense heritabilities for the traits varied from 62.3% to 85.6% for PH and from 66.5% to 83.7% for IL. The generation means analysis and estimates of heritability suggested that the inheritance of PH and IL in climbing beans is relatively simple.

Microsatellite marker diversity in common bean (Phaseolus vulgaris L.)

A diversity survey was used to estimate allelic diversity and heterozygosity of 129 microsatellite markers in a panel of 44 common bean (Phaseolus vulgaris L.) genotypes that have been used as parents of mapping populations. Two types of microsatellites were evaluated, based respectively on gene coding and genomic sequences. Genetic diversity was evaluated by estimating the polymorphism information content (PIC), as well as the distribution and range of alleles sizes. Gene-based microsatellites proved to be less polymorphic than genomic microsatellites in terms of both number of alleles (6.0 vs. 9.2) and PIC values (0.446 vs. 0.594) while greater size differences between the largest and the smallest allele were observed for the genomic microsatellites than for the gene-based microsatellites (31.4 vs. 19.1 bp). Markers that showed a high number of alleles were identified with a maximum of 28 alleles for the marker BMd1. The microsatellites were useful for distinguishing Andean and Mesoamerican genotypes, for uncovering the races within each genepool and for separating wild accessions from cultivars. Greater polymorphism and race structure was found within the Andean gene pool than within the Mesoamerican gene pool and polymorphism rate between genotypes was consistent with genepool and race identity. Comparisons between Andean genotypes had higher polymorphism (53.0%) on average than comparisons among Mesoamerican genotypes (33.4%). Within the Mesoamerican parental combinations, the intra-racial combinations between Mesoamerica and Durango or Jalisco race genotypes showed higher average rates of polymorphism (37.5%) than the within-race combinations between Mesoamerica race genotypes (31.7%). In multiple correspondance analysis we found two principal clusters of genotypes corresponding to the Mesoamerican and Andean gene pools and subgroups representing specific races especially for the Nueva Granada and Peru races of the Andean gene pool. Intra population diversity was higher within the Andean genepool than within the Mesoamerican genepool and this pattern was observed for both gene-based and genomic microsatellites. Furthermore, intra-population diversity within the Andean races (0.356 on average) was higher than within the Mesoamerican races (0.302). Within the Andean gene pool, race Peru had higher diversity compared to race Nueva Granada, while within the Mesoamerican gene pool, the races Durango, Guatemala and Jalisco had comparable levels of diversity which were below that of race Mesoamerica.

Extensive ribosomal DNA amplification during Andean common bean (Phaseolus vulgaris L.) evolution

The extent of 5S and 45S ribosomal DNA (rDNA) variation was investigated in wild and domesticated common beans (Phaseolus vulgaris) chosen to represent the known genetic diversity of the species. 5S and 45S rDNA probes were localized on mitotic chromosomes of 37 accessions by fluorescent in situ hybridization (FISH). The two 5S rDNA loci were largely conserved within the species, whereas a high variation in the number of 45S rDNA loci and changes in position of loci and number of repeats per locus were observed. Domesticated accessions from the Mesoamerican gene pool frequently had three 45S rDNA loci per haploid genome, and rarely four. Domesticated accessions from Andean gene pool, particularly from the race Peru, showed six, seven, eight or nine loci, but seven loci were found in all three races of this gene pool. Between three and eight loci were observed in accessions resulting from crosses between Andean and Mesoamerican genotypes. The presence of two to eight 45S rDNA loci in wild common beans from different geographic locations indicates that the 45S rDNA amplification observed in the Andean lineage took place before domestication. Our data suggest that ectopic recombination between terminal chromosomal regions might be the mechanism responsible for this variation.

A single domestication for potato based on multilocus amplified fragment length polymorphism genotyping

The cultivated potato, Solanum tuberosum, ultimately traces its origin to Andean and Chilean landraces developed by pre-Colombian cultivators. These Andean landraces exhibit tremendous morphological and genetic diversity, and are distributed throughout the Andes, from western Venezuela to northern Argentina, and in southern Chile. The wild species progenitors of these landraces have long been in dispute, but all hypotheses center on a group of approximately 20 morphologically very similar tuber-bearing (Solanum section Petota) wild taxa referred to as the S. brevicaule complex, distributed from central Peru to northern Argentina. We present phylogenetic analyses based on the representative cladistic diversity of 362 individual wild (261) and landrace (98) members of potato (all tuber-bearing) and three outgroup non-tuber-bearing members of Solanum section Etuberosum, genotyped with 438 robust amplified fragment length polymorphisms. Our analyses are consistent with a hypothesis of a "northern" (Peru) and "southern" (Bolivia and Argentina) cladistic split for members of the S. brevicaule complex, and with the need for considerable reduction of species in the complex. In contrast to all prior hypotheses, our data support a monophyletic origin of the landrace cultivars from the northern component of this complex in Peru, rather than from multiple independent origins from various northern and southern members.

A genome-wide analysis of differentiation between wild and domesticated Phaseolus vulgaris from Mesoamerica

Lack of introgression or divergent selection may be responsible for the maintenance of phenotypic differences between sympatric populations of crops and their wild progenitors. To distinguish between these hypotheses, amplified fragment length polymorphism markers were located on a molecular linkage map of Phaseolus vulgaris relative to genes for the domestication syndrome and other traits. Diversity for these same markers was then analyzed in two samples of wild and domesticated populations from Mesoamerica. Differentiation between wild and domesticated populations was significantly higher in parapatric and allopatric populations compared to sympatric populations. It was also significantly higher near genes for domestication compared to those away from these genes. Concurrently, the differences in genetic diversity between wild and domesticated populations were strongest around such genes. These data suggest that selection in the presence of introgression appears to be a major evolutionary factor maintaining the identity of wild and domesticated populations in sympatric situations. Furthermore, alleles from domesticated populations appear to have displaced alleles in sympatric wild populations, thus leading to a reduction in genetic diversity in such populations. These results also provide a possible experimental framework for assessing the long-term risk of transgene escape and the targeting of transgenes inside the genome to minimize the survival of these transgenes into wild populations following introduction by gene flow.

Domestication patterns in common bean (Phaseolus vulgaris L.) and the origin of the Mesoamerican and Andean cultivated races

Chloroplast DNA polymorphisms were studied by PCR sequencing and PCR-restriction fragment length polymorphism in 165 accessions of domesticated landraces of common bean from Latin America and the USA, 23 accessions of weedy beans, and 134 accessions of wild beans covering the entire geographic range of wild Phaseolus vulgaris. Fourteen chloroplast haplotypes were identified in wild beans, only five of which occur also in domesticated beans. The chloroplast data agree with those obtained from analyses based on morphology and isozymes and with other DNA polymorphisms in supporting independent domestications of common bean in Mesoamerica and the Andean region and in demonstrating a founder effect associated with domestication in each region. Andean landraces have been classified into three different racial groups, but all share the same chloroplast haplotype. This suggests that common bean was domesticated once only in South America and that the races diverged post-domestication. The haplotype found in Andean domesticated beans is confined to the southern part of the range of wild beans, so Andean beans were probably domesticated somewhere within this area. Mesoamerican landraces have been classified into four racial groups. Our limited samples of Races Jalisco and Guatemala differ from the more widespread and commercially important Races Mesoamerica and Durango in types and/or frequencies of haplotypes. All four Mesoamerican races share their haplotypes with local wild beans in parts of their ranges. Independent domestications of at least some of the races in Mesoamerica and/or conversion of some locally adapted wild beans to cultigens by hybridization with introduced domesticated beans, followed by introgression of the "domestication syndrome" seem the most plausible explanations of the chloroplast and other molecular data.

Possible effects of (trans)gene flow from crops on the genetic diversity from landraces and wild relatives

Gene flow is a potential concern associated with the use of transgenic crops because it could affect genetic diversity of related landraces and wild relatives. This concern has taken on added importance with the looming introduction of transgenic crops in centers of crop domestication (Mexico, China) and those producing pharmaceutical compounds. For gene flow to take place among cultivars and their wild relatives, several steps have to be fulfilled, including the presence of cultivars or wild relatives within pollen or seed dispersal range, the ability to produce viable and fertile hybrids, at least partial overlap in flowering time, actual gene flow by pollen or seed, and the establishment of crop genes in the domesticated or wild recipient populations. In contrast with domestication genes, which often make crops less adapted to natural ecosystems, transgenes frequently represent gains of function, which might release wild relatives from constraints that limit their fitness. In most sexually reproducing organisms, the chromosomal region affected by selection of a single gene amounts to a small percentage of the total genome size. Because of gene flow, the level of genetic diversity present in the domesticated gene pool becomes a crucial factor affecting the genetic diversity of the wild gene pool. For some crops, such as cotton and maize, the introduction of transgenic technologies has led to a consolidation of the seed industry and a reduction in the diversity of the elite crop gene pool. Thus, diversity in improved varieties grown by farmers needs to be monitored. Several areas deserve further study, such as the actual magnitude of gene flow and its determinants in different agroecosystems, the long-term effects of gene flow on genetic diversity both across gene pools and within genomes, the expression of transgenes in new genetic backgrounds, and the effects of socio-economic factors on genetic diversity.

A single domestication for maize shown by multilocus microsatellite genotyping

There exists extraordinary morphological and genetic diversity among the maize landraces that have been developed by pre-Columbian cultivators. To explain this high level of diversity in maize, several authors have proposed that maize landraces were the products of multiple independent domestications from their wild relative (teosinte). We present phylogenetic analyses based on 264 individual plants, each genotyped at 99 microsatellites, that challenge the multiple-origins hypothesis. Instead, our results indicate that all maize arose from a single domestication in southern Mexico about 9,000 years ago. Our analyses also indicate that the oldest surviving maize types are those of the Mexican highlands with maize spreading from this region over the Americas along two major paths. Our phylogenetic work is consistent with a model based on the archaeological record suggesting that maize diversified in the highlands of Mexico before spreading to the lowlands. We also found only modest evidence for postdomestication gene flow from teosinte into maize.

Identification of an ancestral resistance gene cluster involved in the coevolution process between Phaseolus vulgaris and its fungal pathogen Colletotrichum lindemuthianum

The recent cloning of plant resistance (R) genes and the sequencing of resistance gene clusters have shed light on the molecular evolution of R genes. However, up to now, no attempt has been made to correlate this molecular evolution with the host-pathogen coevolution process at the population level. Cross-inoculations were carried out between 26 strains of the fungal pathogen Colletotrichum lindemuthianum and 48 Phaseolus vulgaris plants collected in the three centers of diversity of the host species. A high level of diversity for resistance against the pathogen was revealed. Most of the resistance specificities were overcome in sympatric situations, indicating an adaptation of the pathogen to the local host. In contrast, plants were generally resistant to allopatric strains, suggesting that R genes that were efficient against exotic strains but had been overcome locally were maintained in the plant genome. These results indicated that coevolution processes between the two protagonists led to a differentiation for resistance in the three centers of diversity of the host. To improve our understanding of the molecular evolution of these different specificities, a recombinant inbred (RI) population derived from two representative genotypes of the Andean (JaloEEP558) and Mesoamerican (BAT93) gene pools was used to map anthracnose specificities. A gene cluster comprising both Andean (Co-y; Co-z) and Mesoamerican (Co-9) host resistance specificities was identified, suggesting that this locus existed prior to the separation of the two major gene pools of P. vulgaris. Molecular analysis revealed a high level of complexity at this locus. It harbors 11 restriction fragment length polymorphisms when R gene analog (RGA) clones are used. The relationship between the coevolution process and diversification of resistance specificities at resistance gene clusters is discussed.

Genetic divergence among common bean cultivars from different races based on RAPD markers

The genetic divergence of 27 common bean (Phaseolus vulgaris L.) cultivars from different races was evaluated using RAPD markers. The association of this divergence with some indirect variability estimates obtained in field experiments was also assessed. Genetic distances were calculated using Sorensen-Dice's similarity coefficient, displayed in a dendrogram (UPGMA method), and by projection in two-dimensional space. Analysis of molecular variance (AMOVA) was used to evaluate the distribution of variance between and within domestication centers. RAPD marker genetic diversity within these centers was also calculated. The correlations between estimates of genetic distances obtained with RAPD markers and estimates of Mahalanobis' generalized distances, specific combination ability, and midparent heterosis obtained from morpho-agronomical traits were also determined. RAPD markers were efficient in separating cultivars according to domestication centers. However, only for Middle American domestication center was there good agreement between the grouping obtained and the proposed classification of races. The genetic divergence obtained with these markers was similar to that provided by morpho-agronomical traits. RAPD markers, however, were not efficient in predicting the specific combination ability and midparent heterosis expressed in crosses.

Genetic Diversity and Pathogenic Variation of Colletotrichum lindemuthianum in the Three Centers of Diversity of Its Host, Phaseolus vulgaris

ABSTRACT Population subdivision of Colletotrichum lindemuthianum, the causal agent of anthracnose, was studied in three regions located in three centers of diversity of its host, Phaseolus vulgaris. Random amplified polymorphic DNA (RAPD) markers, restriction endonuclease analysis of the amplified ribosomal internal transcribed spacer region, and virulence on a set of 12 cultivars were used to assess the genetic diversity of C. lindemuthianum strains isolated in Mexican, Ecuadorian, and Argentinean wild common bean populations. The three regions were significantly differentiated for molecular markers. For these markers, Mexico was the most polymorphic and the most distant from Ecuador and Argentina. The majority of the RAPD alleles present in Ecuador and Argentina were found in Mexico, suggesting that Andean populations have been derived from the Mesoamerican center. Pathogenicity tests on a set of 12 cultivars showed that all but one of the Mexican strains were virulent exclusively on Mesoamerican cultivars. Argentinean strains were virulent preferentially on southern Andes cultivars, and the Ecuadorian strains, except for one strain, were avirulent on all cultivars. These results suggest an adaptation of strains on cultivars of the same geographic origin. Thus, based on molecular and virulence markers, C. lindemuthianum strains isolated from wild common bean populations were divided into three groups corresponding to host gene pools.

Colombian Common and Lima Beans: Views on their Origin and Evolutionary Significance

<p>This article reviews the geographical distribution of wild common and lima beans in the Neotropics, their morphological and ecological attributes, and their biochemical and molecular variation along their ranges. These facts reveal the organization of the genetic diversity into three major gene pools, with one being considered ancestral, and additional subdivisions within the derived ones. The relationships between the ancestral branch and related species are discussed. Colombia appears to he more than a place of contact between gene pools of cultivated materials, but the transit place of the ancestral branches, and a possible place of domestication as well. </p><p> </p><p><strong>Los Fríjoles Colombianos Lima y Común: Puntos de Vista de su Origen y el Significado de su Evolución</strong></p><p>Se presenta una revisión de la distribución geográfica de las formas silvestres del frijol común y del frijol lima en el Neotrópico, de sus características morfológicas y ecológicas, y de la variación bioquímica y molecular a lo largo de esta distribución. Estos hechos muestran que la diversidad genética viene organizada en tres acervos o grupos de genes, uno de ellos siendo ancestral, y con subdivisiones adicionales dentro de los acervos derivados. Se discuten las relaciones filogenéticas entre este ramal ancestral y las especies afines. Más que lugar de contacto entre acervos de materiales cultivados, Colombia aparece como corredor biológico donde transitaron las ramas ancestrales, y como lugar de posible domesticación.</p><p> </p><p> </p>