Phillip E. McClean

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.

Artificial selection for determinate growth habit in soybean

Determinacy is an agronomically important trait associated with the domestication in soybean (Glycine max). Most soybean cultivars are classifiable into indeterminate and determinate growth habit, whereas Glycine soja, the wild progenitor of soybean, is indeterminate. Indeterminate (Dt1/Dt1) and determinate (dt1/dt1) genotypes, when mated, produce progeny that segregate in a monogenic pattern. Here, we show evidence that Dt1 is a homolog (designated as GmTfl1) of Arabidopsis terminal flower 1 (TFL1), a regulatory gene encoding a signaling protein of shoot meristems. The transition from indeterminate to determinate phenotypes in soybean is associated with independent human selections of four distinct single-nucleotide substitutions in the GmTfl1 gene, each of which led to a single amino acid change. Genetic diversity of a minicore collection of Chinese soybean landraces assessed by simple sequence repeat (SSR) markers and allelic variation at the GmTfl1 locus suggest that human selection for determinacy took place at early stages of landrace radiation. The GmTfl1 allele introduced into a determinate-type (tfl1/tfl1) Arabidopsis mutants fully restored the wild-type (TFL1/TFL1) phenotype, but the Gmtfl1 allele in tfl1/tfl1 mutants did not result in apparent phenotypic change. These observations indicate that GmTfl1 complements the functions of TFL1 in Arabidopsis. However, the GmTfl1 homeolog, despite its more recent divergence from GmTfl1 than from Arabidopsis TFL1, appears to be sub- or neo-functionalized, as revealed by the differential expression of the two genes at multiple plant developmental stages and by allelic analysis at both loci.

Mesoamerican origin of the common bean (Phaseolus vulgaris L.) is revealed by sequence data

Knowledge about the origins and evolution of crop species represents an important prerequisite for efficient conservation and use of existing plant materials. This study was designed to solve the ongoing debate on the origins of the common bean by investigating the nucleotide diversity at five gene loci of a large sample that represents the entire geographical distribution of the wild forms of this species. Our data clearly indicate a Mesoamerican origin of the common bean. They also strongly support the occurrence of a bottleneck during the formation of the Andean gene pool that predates the domestication, which was suggested by recent studies based on multilocus molecular markers. Furthermore, a remarkable result was the genetic structure that was seen for the Mesoamerican accessions, with the identification of four different genetic groups that have different relationships with the sets of wild accessions from the Andes and northern Peru–Ecuador. This finding implies that both of the gene pools from South America originated through different migration events from the Mesoamerican populations that were characteristic of central Mexico.

Association mapping of iron deficiency chlorosis loci in soybean (Glycine max L. Merr.) advanced breeding lines.

Association mapping is an alternative to mapping in a biparental population. A key to successful association mapping is to avoid spurious associations by controlling for population structure. Confirming the marker/trait association in an independent population is necessary for the implementation of the marker in other genetic studies. Two independent soybean populations consisting of advanced breeding lines representing the diversity within maturity groups 00, 0, and I were screened in multi-site, replicated field trials to discover molecular markers associated with iron deficiency chlorosis (IDC), a major yield-limiting factor in soybean. Lines with extreme phenotypes were initially screened to identify simple sequence repeat (SSR) markers putatively associated with the IDC. Marker data collected from all lines were used to control for population structure and kinship relationships. Single factor analysis of variance (SFA) and mixed linear model (MLM) analyses were used to discover marker/trait associations. The MLM analyses, which include population structure, kinship or both factors, reduced the number of markers significantly associated with IDC by 50% compared with SFA. With the MLM approach, three markers were found to be associated with IDC in the first population. Two of these markers, Satt114 and Satt239, were also found to be associated with IDC in the second confirmation population. For both populations, those lines with the tolerance allele at both these two marker loci had significantly lower IDC scores than lines with one or no tolerant alleles.

Synteny mapping between common bean and soybean reveals extensive blocks of shared loci

BackgroundUnderstanding syntentic relationship between two species is critical to assessing the potential for comparative genomic analysis. Common bean (Phaseolus vulgaris L.) and soybean (Glycine max L.), the two most important members of the Phaseoleae legumes, appear to have a diploid and polyploidy recent past, respectively. Determining the syntentic relationship between these two species will allow researchers to leverage not only genomic resources but also genetic data for important agronomic traits to improve both of these species.ResultsGenetically-positioned transcript loci of common bean were mapped relative to the recent soybean 1.01 pseudochromosome assembly. In nearly every case, each common bean locus mapped to two loci in soybean, a result consistent with the duplicate polyploidy history of soybean. Blocks of synteny averaging 32 cM in common bean and 4.9 Mb in soybean were observed for all 11 common bean linkage groups, and these blocks mapped to all 20 soybean pseudochromosomes. The median physical-to-genetic distance ratio in common bean (based on soybean physical distances) was ~120 kb/cM. ~15,000 common bean sequences (primarily EST contigs and EST singletons) were electronically positioned onto the common bean map using the shared syntentic blocks as references points.ConclusionThe collected evidence from this mapping strongly supports the duplicate history of soybean. It further provides evidence that the soybean genome was fractionated and reassembled at some point following the duplication event. These well mapped syntentic relationships between common bean and soybean will enable researchers to target specific genomic regions to discover genes or loci that affect phenotypic expression in both species.

Genomics of Phaseolus Beans, a Major Source of Dietary Protein and Micronutrients in the Tropics

Common bean is grown and consumed principally in developing countries in Latin America, Africa, and Asia. It is largely a subsistence crop eaten by its producers and, hence, is underestimated in production and commerce statistics. Common bean is a major source of dietary protein, which complements carbohydrate-rich sources such as rice, maize, and cassava. It is also a rich source of minerals, such as iron and zinc, and certain vitamins. Several large germplasm collections have been established, which contain large amounts of genetic diversity, including the five domesticated Phaseolus species and wild species, as well as an incipient stock collection. The genealogy and genetic diversity of P. vulgaris are among the best known in crop species through the systematic use of molecular markers, from seed proteins and isozymes to simple sequence repeats, and DNA sequences. Common bean exhibits a high level of genetic diversity, compared with other selfing species. A hierarchical organization into gene pools and ecogeographic races has been established. There are over 15 mapping populations that have been established to study the inheritance of agronomic traits in different locations. Most linkage maps have been correlated with the core map established in the BAT93 x Jalo EEP558 cross, which includes several hundreds of markers, including Restriction Fragment Length Polymorphisms, Random Amplified Polymorphic DNA, Amplified Fragment Length Polymorphisms, Short Sequence Repeats, Sequence Tagged Sites, and Target Region Amplification Polymorphisms. Over 30 individual genes for disease resistance and some 30 Quantitative Trait Loci for a broad range of agronomic traits have been tagged. Eleven BAC libraries have been developed in genotypes that represent key steps in the evolution before and after domestication of common bean, a unique resource among crops. Fluorescence in situ hybridization provides the first links between chromosomal and genetic maps. A gene index based on some P. vulgaris 21,000 expressed sequence tags (ESTs) has been developed. ESTs were developed from different genotypes, organs, and physiological conditions. They resolve currently in some 6,500–6,800 singletons and 2,900 contigs. An additional 20,000 embryonic P. coccineus ESTs provides an additional resource. Some 1,500 M2 Targeting Local Lesions In Genomes populations exist currently. Finally, transformation methods by biolistics and Agrobacterium have been developed, which can be applied for genetic engineering. Root transformation via A. rhizogenes is also possible. Thus, the Phaseomics community has laid a solid foundation towards its ultimate goal, namely the sequencing of the Phaseolus genome. These genomic resources are a much-needed source of additional markers of known map location for marker-assisted selection and the accelerated improvement of common bean cultivars.

Genome-Wide Association Analysis Identifies Candidate Genes Associated with Iron Deficiency Chlorosis in Soybean

Iron deficiency chlorosis (IDC) is a significant yield‐limiting problem in several major soybean [Glycine max (L.) Merr.] production regions in the United States. Soybean plants display a variety of symptoms that range from a slight yellowing of the leaf to interveinal chlorosis, to stunted growth that reduces yield. The objective of this analysis was to employ single nucleotide polymorphism (SNP)‐based genome‐wide association mapping to uncover genomic regions associated with IDC tolerance. Two populations [2005 (n = 143) and 2006 (n = 141)] were evaluated in replicated, multilocation IDC trials. After controlling for population structure and individual relatedness, and selecting statistical models that minimized false positives, 42 and 88 loci, with minor allele frequency >10%, were significant in 2005 and 2006, respectively. The loci accounted for 74.5% of the phenotypic variation in IDC in2005 and 93.8% of the variation in 2006. Nine loci from seven genomic locations were significant in both years. These loci accounted for 43.7% of the variation in 2005 and 47.6% in 2006. A number of the loci discovered here mapped at or near previously discovered IDC quantitative trait loci (QTL). A total of 15 genes known to be involved in iron metabolism mapped in the vicinity (>500 kb) of significant markers in one or both populations.

BAC-end Sequence Analysis and a Draft Physical Map of the Common Bean ( Phaseolus vulgaris L.) Genome

Common bean (Phaseolus vulgaris L.) is a legume that is an important source of dietary protein in developing countries throughout the world. Utilizing the G19833 BAC library for P. vulgaris from Clemson University, 89,017 BAC-end sequences were generated giving 62,588,675 base pairs of genomic sequence covering approximately 9.54% of the genome. Analysis of these sequences in combination with 1,404 shotgun sequences from the cultivar Bat7 revealed that approximately 49.2% of the genome contains repetitive sequence and 29.3% is genic. Compared to other legume BAC-end sequencing projects, it appears that P. vulgaris has higher predicted levels of repetitive sequence, but this may be due to a more intense identification strategy combining both similarity-based matches as well as de novo identification of repeats. In addition, fingerprints for 41,717 BACs were obtained and assembled into a draft physical map consisting of 1,183 clone contigs and 6,385 singletons with ~9x coverage of the genome.

Effect of Expression of UDP-Glucose Pyrophosphorylase Ribozyme and Antisense RNAs on the Enzyme Activity and Carbohydrate Composition of Field-Grown Transgenic Potato Plants

Summary The effect of suppression of UDP-glucose pyrophosphorylase (UGPase, UTP ±-D-glucose-1-phosphate uridylyl transferase, EC 2.7.7.9) on carbohydrate metabolism in potato tubers was investigated. Constructions expressing a UGPase-specific ribozyme or a UGPase antisense RNA based on the genomic sequence, each under the control of the 35S promoter of the Cauliflower Mosaic Virus, were tested. Out of 103 plants transformed with the constructs, only 13 showed levels of UGPase activity significantly different from the control. No transgenic plants, carrying either construct, expressed an enzyme activity lower than 50-60 % of the control. Plants of seven clones were grown in the field, and UGPase activity, and the level of sugars were measured in the tubers. After storage at room temperature for one week, tubers of six of these had sucrose levels significantly (P

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.