Paul Gepts

Races of common bean (Phaseolus vulgaris, Fabaceae)

Evidence for genetic diversity in cultivated common bean (Phaseolus vulgaris) is reviewed. Multivariate statistical analyses of morphological, agronomic, and molecular data, as well as other available information on Latin American landraces representing various geographical and ecological regions of their primary centers of domestications in the Americas, reveal the existence of two major groups of germplasm: Middle American and Andean South American, which could be further divided into six races. Three races originated in Middle America (races Durango, Jalisco, and Mesoamerica) and three in Andean South America (races Chile, Nueva Granada, and Peru). Their distinctive characteristics and their relationships with previously reported gene pools are discussed.RésuméSe presenta una revisión sobre la evidencia de variabilidad genética en el fríjol cultivado (Phaseolus vulgaris). De acuerdo con los análisis estadísticos multivariados de datos morfológicos, agronómicos y moleculares y con información adicional disponible sobre variedades criollas de América Latina que representan varias regiones ecológicas y geográficas de sus centros primarios de domesticación en las Américas, se establece la existencia de los dos grupos principales de germoplasma: los de Mesoamérica y de los Andes suramericanos; los cuales pueden ser divididos en seis razas. Tres razas se originaron en Mesoamérica (razas Durango, Jalisco y Mesoamérica) y tres los Andes suramericanos (razas Chile, Nueva Granada y Perú). Se discuten sus características distintivas y sus relaciones con otros acervos de genes reportados anteriormente.

A reference genome for common bean and genome-wide analysis of dual domestications

Common bean (Phaseolus vulgaris L.) is the most important grain legume for human consumption and has a role in sustainable agriculture owing to its ability to fix atmospheric nitrogen. We assembled 473 Mb of the 587-Mb genome and genetically anchored 98% of this sequence in 11 chromosome-scale pseudomolecules. We compared the genome for the common bean against the soybean genome to find changes in soybean resulting from polyploidy. Using resequencing of 60 wild individuals and 100 landraces from the genetically differentiated Mesoamerican and Andean gene pools, we confirmed 2 independent domestications from genetic pools that diverged before human colonization. Less than 10% of the 74 Mb of sequence putatively involved in domestication was shared by the two domestication events. We identified a set of genes linked with increased leaf and seed size and combined these results with quantitative trait locus data from Mesoamerican cultivars. Genes affected by domestication may be useful for genomics-enabled crop improvement.

Phaseolin-protein Variability in Wild Forms and Landraces of the Common Bean(Phaseolus vulgaris): Evidence for Multiple Centers of Domestication

A sample of 106 wild forms and 99 landraces of common bean (Thaseolus vulgaris) from Middle America and the Andean region of South America were screened for variability in phaseolin seed protein using one-dimensional sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS/PAGE) and two-dimensional isoelectric focusing SDS/PAGE. The Middle American wild forms exhibited phaseolin patterns similar to the ‘S’ pattern described previously in cultivated forms, as well as a wide variety of additional banding patterns—‘M’ (Middle America) types—not encountered among common bean cultivars. The Andean wild forms showed only the ‘T’ phaseolin pattern, also described previously among cultivated forms. Landraces from Middle America showed ‘S’ or ‘S’-like patterns with the exception of 2 lines with ‘T’ phaseolin. In Andean South America, a majority of landraces had the ‘T’ phaseolin. Additional types represented in that region were (in decreasing order of frequency) the ‘S’ and ‘C’ types (already described among cultivated forms) as well as the ‘H’ (Huevo de huanchaco) and ‘A’ (Ayacucho), (new patterns previously undescribed among wild and cultivated beans). In each region—Middle America and Andean South America—the seeds of landraces with ‘T’ phaseolin were significantly larger than those of landraces with ‘S’ phaseolin. No significant differences in seed size were observed among landraces with ‘T,’ ‘C,’ ‘H,’ and ‘A’ phaseolin types of the Andean region. Our data favor 2 primary areas of domestication, one in Middle America leading to small-seeded cultivars with ‘S’ phaseolin patterns and the other in the Andes giving rise to large-seeded cultivars with ‘T’ (and possibly ‘C,’ ‘H,’ and ‘A’) phaseolin patterns.

Towards an integrated linkage map of common bean. 4. Development of a core linkage map and alignment of RFLP maps

Abstract Three RFLP maps, as well as several RAPD maps have been developed in common bean (Phaseolus vulgaris L.). In order to align these maps, a core linkage map was established in the recombinant inbred population BAT93×Jalo EEP558 (BJ). This map has a total length of 1226 cM and comprises 563 markers, including some 120 RFLP and 430 RAPD markers, in addition to a few isozyme and phenotypic marker loci. Among the RFLPs mapped were markers from the University of California, Davis (established in the F2 of the BJ cross), University of Paris-Orsay, and University of Florida maps. These shared markers allowed us to establish a correspondence between the linkage groups of these three RFLP linkage maps. In total, the general map location (i.e., the linkage group membership and approximate location within linkage groups) has been determined for some 1070 markers. Approaches to align this core map with other current or future maps are discussed.

Towards an integrated linkage map of common bean 1. Development of genomic DNA probes and levels of restriction fragment length polymorphism

SummaryTwo genomic libraries were established to provide markers to develop an integrated map combining molecular markers and genes for qualitative and quantitative morpho-agronomic traits in common bean. Contrasting characteristics were observed for the two libraries. While 89% of the PstI clones were classified as single-copy sequences, only 21% of the EcoRIBamHI clones belonged in that category. Clones of these two libraries were hybridized against genomic DNA of nine genotypes chosen according to their divergent evolutionary origin and contrasting agronomic traits. Eight restriction enzymes were used in this study. PstI clones revealed 80–90% polymorphism between the Andean and Middle American gene pools and 50–60% polymorphism within these gene pools. However, under the same conditions only 30% of the EcoRI-BamHI clones showed polymorphism between the Middle American and Andean gene pools. Hybridization with PstI clones to EcoRI-, EcoRV-, or HindIII-digested genomic DNA resulted in a cumulative frequency of polymorphism of approximately 80%. Hybridizations to BamHI-, HaeIII-, HinfI-, PstI-, and XbaI-digested genomic DNA detected no additional polymorphisms not revealed by the former three enzymes. In the PstI library, a positive correlation was observed between the average size of hybridizing restriction fragments and the frequency of polymorphism detected by each restriction enzyme. This relationship is consistent with the higher proportion of insertion/deletion events compared with the frequency of nucleotide substitutions observed in that library.

Tagging and mapping of genes and QTL and molecular marker-assisted selection for traits of economic importance in bean and cowpea

Bean/Cowpea Collaborative Research Support Program (B/C CRSP) scientists have successfully developed integrated consensus maps of the 11 linkage groups (LGs) in both bean (Phaseolus vulgaris L.) and cowpea (Vigna unguiculata L. Walp). The bean map is approximately 1200 cM with some 500 markers and an additional 500 markers shared with other bean maps. The cowpea map spans 2670 cM with over 400 markers. In addition to molecular markers, both maps include map locations of defense genes and phenotypic traits for disease and insect resistance, seed size, color and storage proteins, pod color and those traits associated with the domestication syndrome in bean. Since the bean and cowpea maps were developed independently, LGs with the same number probably refer to non-syntenic groups. Map locations of major resistance genes in bean are revealing gene clusters on LGs B1, B4, B7, and B11 for resistance to bean rust, anthracnose, common bacterial blight and white mold. Gene tagging and marker-assisted selection for disease resistance has progressed to a point where the indirect selection for resistance to a number of major diseases is now routine in bean breeding programs both in the US and overseas. # 2003 Elsevier Science B.V. All rights reserved.

Agriculture: Feeding the future

Humanity depends on fewer than a dozen of the approximately 300,000 species of flowering plants for 80% of its caloric intake. And we capitalize on only a fraction of the genetic diversity that resides within each of these species. This is not enough to support our food system in the future. Food availability must double in the next 25 years to keep pace with population and income growth around the world. Already, food-production systems are precarious in the face of intensifying demand, climate change, soil degradation and water and land shortages. Farmers have saved the seeds of hundreds of crop species and hundreds of thousands of ‘primitive’ varieties (local domesticates called landraces), as well as the wild relatives of crop species and modern varieties no longer in use. These are stored in more than 1,700 gene banks worldwide. Maintaining the 11 international gene-bank collections alone costs about US

Allozyme diversity in wild Phaseolus vulgaris: further evidence for two major centers of genetic diversity

18 million a year.

Current perspectives and the future of domestication studies

SummaryAllozyme analysis was performed on 83 wild Phaseolus vulgaris accessions, representing a wide geographical distribution from Mesoamerica to Argentina, to determine levels of genetic diversity and geographic patterns of variability at nine polymorphic isozyme loci. The collection can be divided into two major groups, one consisting of accessions from Mexico, Central America, Colombia and Peru, and the other consisting of accessions from Peru and Argentina. One accession from northern Peru is distinct from the two major groups, and may delineate a transition zone between the two divergent groups. The level of genetic diversity within wild P. vulgaris (Ht=0.132) is comparable with those found in other Phaseolus species. There was no significant within-accession gene diversity (Hs=0.006); however, there is a moderate level of genetic diversity (Dst=0.126) between accessions. Our results are consistent with previous studies on the genetic diversity of wild P. vulgaris using phaseolin, the major seed storage protein of beans.

Asymmetry of gene flow and differential geographical structure of molecular diversity in wild and domesticated common bean (Phaseolus vulgaris L.) from Mesoamerica.

It is difficult to overstate the cultural and biological impacts that the domestication of plants and animals has had on our species. Fundamental questions regarding where, when, and how many times domestication took place have been of primary interest within a wide range of academic disciplines. Within the last two decades, the advent of new archaeological and genetic techniques has revolutionized our understanding of the pattern and process of domestication and agricultural origins that led to our modern way of life. In the spring of 2011, 25 scholars with a central interest in domestication representing the fields of genetics, archaeobotany, zooarchaeology, geoarchaeology, and archaeology met at the National Evolutionary Synthesis Center to discuss recent domestication research progress and identify challenges for the future. In this introduction to the resulting Special Feature, we present the state of the art in the field by discussing what is known about the spatial and temporal patterns of domestication, and controversies surrounding the speed, intentionality, and evolutionary aspects of the domestication process. We then highlight three key challenges for future research. We conclude by arguing that although recent progress has been impressive, the next decade will yield even more substantial insights not only into how domestication took place, but also when and where it did, and where and why it did not.