Rian Lee

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.

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.

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.

Demographic factors shaped diversity in the two gene pools of wild common bean Phaseolus vulgaris L.

Wild common bean (Phaseolus vulgaris L.) is distributed throughout the Americas from Mexico to northern Argentina. Within this range, the species is divided into two gene pools (Andean and Middle American) along a latitudinal gradient. The diversity of 24 wild common bean genotypes from throughout the geographic range of the species was described by using sequence data from 13 loci. An isolation–migration model was evaluated using a coalescent analysis to estimate multiple demographic parameters. Using a Bayesian approach, Andean and Middle American subpopulations with high percentage of parentages were observed. Over all loci, the Middle American gene pool was more diverse than the Andean gene pool (πsil=0.0089 vs 0.0068). The two subpopulations were strongly genetically differentiated over all loci (Fst=0.29). It is estimated that the two current wild gene pools diverged from a common ancestor ∼111 000 years ago. Subsequently, each gene pool underwent a bottleneck immediately after divergence and lasted ∼40 000 years. The Middle American bottleneck population size was ∼46% of the ancestral population size, whereas the Andean was 26%. Continuous asymmetric gene flow was detected between the two gene pools with a larger number of migrants entering Middle American gene pool from the Andean gene pool. These results suggest that because of the complex population structure associated with the ancestral divergence, subsequent bottlenecks in each gene pool, gene pool-specific domestication and intense selection within each gene pool by breeders; association mapping would best be practised within each common bean gene pool.

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.

Population structure and genetic differentiation among the USDA common bean (Phaseolus vulgaris L.) core collection

Genetic diversity data were collected from a large population of common bean (Phaseolus vulgaris L.) landraces representing the United States Department of Agriculture core collection. The data were based on microsatellite data from all linkage groups. A procedure was developed to determine if we collected sufficient marker data to adequately estimated pairwise diversity. The diversity data were used to define populations using distance and model-based approaches. Genetic differentiation and genetic isolation by distance data were collected. Diversity was also compared for markers linked and unlinked to domestication loci. Using a model-based approach, the landraces were divided into the traditional Middle American and Andean gene pools. Diversity was greater for the Middle American gene pool. Six Middle American and three Andean subpopulations were defined, and the Middle American subpopulations exhibited strong geographic identity. Unlike other studies, seed size varied considerably with subpopulations, and a number of the subpopulations contained landraces from multiple common bean races. All of the subpopulations were highly differentiated, with the Middle American subpopulations showing the greatest differentiation. Genetic isolation by distance was observed among the Middle American and Andean subpopulations but not among subpopulations within a gene pool. Within each gene pool, diversity was lower for markers linked to domestication loci.

Genome-Wide Association Study Identifies Candidate Loci Underlying Agronomic Traits in a Middle American Diversity Panel of Common Bean

Common bean (Phaseolus vulgaris L.) breeding programs aim to improve both agronomic and seed characteristics traits. However, the genetic architecture of the many traits that affect common bean production are not completely understood. Genome‐wide association studies (GWAS) provide an experimental approach to identify genomic regions where important candidate genes are located. A panel of 280 modern bean genotypes from race Mesoamerica, referred to as the Middle American Diversity Panel (MDP), were grown in four US locations, and a GWAS using >150,000 single‐nucleotide polymorphisms (SNPs) (minor allele frequency [MAF] ≥ 5%) was conducted for six agronomic traits. The degree of inter‐ and intrachromosomal linkage disequilibrium (LD) was estimated after accounting for population structure and relatedness. The LD varied between chromosomes for the entire MDP and among race Mesoamerica and Durango–Jalisco genotypes within the panel. The LD patterns reflected the breeding history of common bean. Genome‐wide association studies led to the discovery of new and known genomic regions affecting the agronomic traits at the entire population, race, and location levels. We observed strong colocalized signals in a narrow genomic interval for three interrelated traits: growth habit, lodging, and canopy height. Overall, this study detected ∼30 candidate genes based on a priori and candidate gene search strategies centered on the 100‐kb region surrounding a significant SNP. These results provide a framework from which further research can begin to understand the actual genes controlling important agronomic production traits in common bean.

Sequence-Based Introgression Mapping Identifies Candidate White Mold Tolerance Genes in Common Bean.

Sequenced‐based introgression mapping rapidly maps QTL to a physical location A highly polymorphic candidate gene associated with apoptosis maps in the WM7.1 QTL A highly polymorphic gene associated with effector recognition maps in the WM8.3 QTL