Wild Crop Relatives: Genomic and Breeding Resources

Common beans (Phaseolus vulgaris L.) originated in the New World and are the grain legume of greatest production for direct human consumption. Common bean production is subject to frequent droughts in highland Mexico, in the Pacific coast of Central America, in northeast Brazil, and in eastern and southern Africa from Ethiopia to South Africa. This article reviews efforts to improve common bean for drought tolerance, referring to genetic diversity for drought response, the physiology of drought tolerance mechanisms, and breeding strategies. Different races of common bean respond differently to drought, with race Durango of highland Mexico being a major source of genes. Sister species of P. vulgaris likewise have unique traits, especially P. acutifolius which is well adapted to dryland conditions. Diverse sources of tolerance may have different mechanisms of plant response, implying the need for different methods of phenotyping to recognize the relevant traits. Practical considerations of field management are discussed including: trial planning; water management; and field preparation.

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Phenotyping common beans for adaptation to drought.

The South American continent is composed of several biogeographical regions harbouring the highest biodiversity on the globe, encompassing five of the world’s biodiversity ‘hot spots’. Nonetheless, the patterns and processes responsible for shaping its astonishing species diversity are largely unknown. Here, we present a review of current South American phylogeographical knowledge based on published articles on this topic. An appraisal of the literature reveals emerging phylogeographical patterns in the biota of South America. The striking phylogeographical divergence observed among organism lineages in South American studies is suggestive of high levels of undocumented species diversity. The interplay between Pleistocene climatic oscillations and Pliocene/Miocene orogenic events has contributed to shaping the current diversity and distribution of modern lineages in both the tropical and temperate regions of South America. Although older divergence times were observed for a range of species, most herpetofauna underwent an intraspecific lineage split much earlier than other organisms. The geographical ranges of species associated with forest habitats were reduced mainly during glacial cycles, whereas species associated with open vegetation domains have shown variable responses to climatic oscillations. The results suggest a highly complex mosaic of phylogeographical patterns in South America. We suggest future research directions to promote a better understanding of the origin and maintenance of the South American biota.

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Phylogeographical patterns shed light on evolutionary process in South America.

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.

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

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.

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

Landraces of common bean (Phaseolus vulgaris L.) pertaining to the Andean gene pool are remarkably diverse in plant and grain morphology and agroecological adaptation. The objectives of this study were to determine the genetic structure of a large sample of Andean landraces, and to establish a correspondence between Andean landraces and wild bean populations that might have served as the source of domesticated bean. A total of 182 landraces representing the three recognized races of Andean bean and including many popping bean types were analyzed using amplified fragment length polymorphism (AFLP) technology with multiple correspondence analysis (MCA) and unweighted pair group method with arithmetic mean (UPGMA). Twenty-nine wild bean accessions representing the diversity of wild bean in South America and Middle America were also included. Two sets of primers were used to generate 189 polymorphic AFLP. The graph of the results of MCA indicated that most landrace accessions formed a single undifferentiated group, and analysis by UPGMA combined with bootstrapping confirmed this. A small number of outliers presented bands that suggested introgression from Mesoamerican beans. Among wild bean populations from South America, those from Bolivia graphed in closest proximity to the cultivated bean, suggesting that Bolivia might have been an important primary domestication site. The narrow genetic base of Andean beans emphasizes the need to broaden the genetic base of the Andean gene pool.

Diversity and Origin of Andean Landraces of Common Bean

The taxonomic classification of the wild Lima bean complex needs to be assessed to select species for use in breeding programs and to identify genetic resources for conservation. The objectives of this study were to determine the genetic relationships among, and the phylogeny of, wild Lima bean (Phaseolus lunatus L.) and related species (P. augusti Harms, P. bolivianus Piper, P. pachyrrhizoides Harms, and P. rosei Piper) from South America and to identify specific genetic reserves for conservation. These relationships were investigated by means of amplified restriction fragment length polymorphism (AFLPs) on total genomic DNA. The 122 accessions formed a cluster that was distant from common bean (P. vulgaris L.), confirming earlier morphology and hybridology data. Two gene pools of wild Lima beans were confirmed. One was widely distributed in neotropical lowlands, while the other was restricted to the western Andes, in Ecuador and northern Peru. The study also revealed the existence of a third group of wild Lima bean distributed in the Departments of Boyaca and Cundinamarca, Colombia. The three species P. augusti, P. bolivianus, and P. pachyrrhizoides differed very little, certainly not sufficiently to merit a separate taxonomic ranking at the species level. The accessions could be grouped instead according to four geographic origins: Ecuador and northern Peru; Department of Junin, Peru; Departments of Cuzco and Apurimac, Peru; and Bolivia and northwestern Argentina. Results from this study should result in a better selection of parental materials in breeding programs and point to areas where germplasm collections and conservation are needed.

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AFLP Fingerprinting of Phaseolus lunatus L. and Related Wild Species from South America

The Amazon river dolphin, genus Inia, is endemic to the major river basins of northern South America. No previous studies have focused on the genetic structure of this genus. In this work, 96 DNA samples from specimens of this genus were collected in the Orinoco basin (four rivers), the Putumayo River, a tributary of the Colombian Amazon and the Mamore, and the Tijamuchi and Ipurupuru rivers in theBolivian Amazon. These samples were used to amplify a fragment of 400 bp of the mitochondrial DNA (mtDNA) control region. In addition, 38 of these samples were also used to sequence 600 bp of the mitochondrial cytochrome b gene. The analysis of the population structure subdivision with an analysis of molecular variance (AMOVA) revealed important aspects about the genetic structure of Inia groups fromthese three geographically separate regions. By comparing the control region DNA and cytochrome b sequences, distinct types of nonshared haplotypes were observed. The net genetic divergence of control region sequences was 6.53% between the Orinoco and Bolivian rivers, 5.32% between the Putumayo and Bolivian rivers, and 2.50% between the Orinoco and Putumayo rivers. For the cytochrome b gene, these values were 2.48%, 2.98%, and 0.06%, respectively. The nucleotide sequences were analyzed phylogenetically using several genetic distance matrices and applying neighbor-joining, maximum likelihood, and maximum parsimony procedures. The results support the proposal to subdivide the Inia genus into at least two evolutionarily significant units: one confined to the Bolivian river basin and the other widely distributed across the Amazon and Orinoco basins.

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Molecular Identification of Evolutionarily Significant Units in the Amazon River Dolphin Inia sp. (Cetacea: Iniidae)

Introduction Gene flow is the spread of genetic material among populations and may constitute an important evolutionary force to create genetic variability. We study possible cases of gene flow in accessions of Phaseolus vulgaris L. collected in the Central Valley of Costa Rica (Araya et al. 2001), The present study aims to establish the movement of genes in the complex wild/weed/cultivated of this crop model as a result of cross pollinations. We focus on intemiediate, weedy forms in order to (1) find evidence of gene flow, and (2) quantify its importance and direction.

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E. Gaitan

Papers

Diversity and Origin of Andean Landraces of Common Bean

AFLP Fingerprinting of Phaseolus lunatus L. and Related Wild Species from South America

Molecular Identification of Evolutionarily Significant Units in the Amazon River Dolphin Inia sp. (Cetacea: Iniidae)

Monitoring gene flow between wild relatives and landraces of common bean in Costa Rica.