Soybean (Glycine max) is one of the most important crop plants for seed protein and oil content, and for its capacity to fix atmospheric nitrogen through symbioses with soil-borne microorganisms. We sequenced the 1.1-gigabase genome by a whole-genome shotgun approach and integrated it with physical and high-density genetic maps to create a chromosome-scale draft sequence assembly. We predict 46,430 protein-coding genes, 70% more than Arabidopsis and similar to the poplar genome which, like soybean, is an ancient polyploid (palaeopolyploid). About 78% of the predicted genes occur in chromosome ends, which comprise less than one-half of the genome but account for nearly all of the genetic recombination. Genome duplications occurred at approximately 59 and 13 million years ago, resulting in a highly duplicated genome with nearly 75% of the genes present in multiple copies. The two duplication events were followed by gene diversification and loss, and numerous chromosome rearrangements. An accurate soybean genome sequence will facilitate the identification of the genetic basis of many soybean traits, and accelerate the creation of improved soybean varieties.

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Genome sequence of the palaeopolyploid soybean

Polyploidy and genome evolution in plants.

The importance of hybridization in plant speciation and evolution has been debated for decades, with opposing views of hybridization as either a creative evolutionary force or evolutionary noise. Hybrid speciation may occur at either the homoploid (i.e., between two species of the same ploidy) or the polyploid level, each with its attendant genetic and evolutionary consequences. Whereas allopolyploidy (i.e., resulting from hybridization and genome doubling) has long been recognized as an important mode of plant speciation, the implications of genome duplication have typically not been taken into account in most fields of plant biology. Recent developments in genomics are revolutionizing our views of angiosperm genomes, demonstrating that perhaps all angiosperms have likely undergone at least one round of polyploidization and that hybridization has been an important force in generating angiosperm species diversity. Hybridization and polyploid formation continue to generate species diversity, with several n...

The Role of Hybridization in Plant Speciation

Polyploidy has long been recognized as a major force in angiosperm evolution. Recent genomic investigations not only indicate that polyploidy is ubiquitous among angiosperms, but also suggest several ancient genome-doubling events. These include ancient whole genome duplication (WGD) events in basal angiosperm lineages, as well as a proposed paleohexaploid event that may have occurred close to the eudicot divergence. However, there is currently no evidence for WGD in Amborella, the putative sister species to other extant angiosperms. The question is no longer "What proportion of angiosperms are polyploid?", but "How many episodes of polyploidy characterize any given lineage?" New algorithms provide promise that ancestral genomes can be reconstructed for deep divergences (e.g., it may be possible to reconstruct the ancestral eudicot or even the ancestral angiosperm genome). Comparisons of diversification rates suggest that genome doubling may have led to a dramatic increase in species richness in several angiosperm lineages, including Poaceae, Solanaceae, Fabaceae, and Brassicaceae. However, additional genomic studies are needed to pinpoint the exact phylogenetic placement of the ancient polyploidy events within these lineages and to determine when novel genes resulting from polyploidy have enabled adaptive radiations.

Polyploidy and angiosperm diversification

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.

/pdf/a-reference-genome-for-common-bean-and-genome-wide-analysis-g1x7c0gfie.pdf

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

Using plant EST collections, we obtained 1392 potential gene duplicates across 8 plant species: Zea mays, Oryza sativa, Sorghum bicolor, Hordeum vulgare, Solanum tuberosum, Lycopersicon esculentum,...

Mining EST databases to resolve evolutionary events in major crop species

The germination and sporulation of Colletotrichum acutatum were characterized over time on strawberry leaves (cv. Tristar) and plastic coverslips incubated at 26 degrees C under continuous wetness. Conidia germinated within 3 h after inoculation and formed melanized appressoria with pores by 9 h after inoculation. Host penetration was not observed up to 7 days after inoculation. Production of secondary conidia on conidial and hyphal phialides began within 6 h after inoculation. Secondary conidiation was responsible for up to a threefold increase in the total number of conidia within 7 days after inoculation. Primary conidia and hyphae began to collapse 48 h after inoculation, whereas melanized appressoria remained intact. These findings suggest that appressoria and secondary conidia of C. acutatum produced on symptomless strawberry foliage may be significant sources of inoculum for fruit infections.

Germination and Sporulation of Colletotrichum acutatum on Symptomless Strawberry Leaves

Strawberry leaves (cv. Tristar) inoculated with Colletotrichum acuta-tum conidia were incubated at 10, 15, 20, 25, 30, and 35°C under continuous wetness, and at 25°C under six intermittent wetness regimes. The number of conidia and appressoria was quantified on excised leaf disks. In order to assess pathogen survival, inoculated leaves were frozen and incubated to induce acervular development. Germination, secondary3 conidiation, and appressorial development were significantly (P ≤ 0.05) affected by temperature and wetness treatments. Under continuous wetness, the optimum temperature range for conidial germination was 23.0 to 27.7°C, whereas the optimum temperature for appressorial development ranged from 17.6 to 26.5°C. Secondary conidiation showed an optimum temperature range of 21.3 to 32.7°C and was most abundant between 12 and 36 h after inoculation. Conidial germination, appressorial production, and secondary conidiation were favored by increasing wetness duration and more than 4 h of wetne...

Influence of Temperature and Wetness Duration on Conidia and Appressoria of Colletotrichum acutatum on Symptomless Strawberry Leaves

Batzer, J. C., Gleason, M. L., Weldon, B., Dixon, P. M., and Nutter, F. W., Jr. 2002. Evaluation of postharvest removal of sooty blotch and flyspeck on apples using sodium hypochlorite, hydrogen peroxide with peroxyacetic acid, and soap. Plant Dis. 86:1325-1332. Postharvest dips of apples (Malus × domestica) in commercial disinfestants were used to remove signs of the flyspeck (FS) pathogen, Schizothyrium pomi, and the sooty blotch (SB) complex (Peltaster fructicola, Leptodontium elatius, and Geastrumia polystigmatis). Apples were dipped for 7 or 15 min in buffered sodium hypochlorite (Agclor 310 plus Decco 312 Buffer) at 200, 400, 500, 600, or 800 ppm chlorine, a mixture of hydrogen peroxide and peroxyacetic acid (Tsunami 100) at 60 ppm/80 ppm, 120 ppm/160 ppm, or 360 ppm/480 ppm, respectively, or soap (Kleen 440), then brushed and rinsed for 30 s on a commercial grading line. Disease severity was assessed as percent diseased area using a quantitative rating system, and by counting the number of colonies of three mycelial types of SB and FS. Percent diseased area on apples was converted to USDA apple grade ratings and retail values. Both assessment methods provided similar results, but the percent-diseased-area method was less labor intensive. A 7-min dip in 800 ppm chlorine resulted in a mean increase from 25 and 55% to 100% Extra Fancy grade for ‘Jonathan’ and ‘Golden Delicious’ apples, respectively, and increased market value by 31 and 14%, respectively. The 7-min, 200-ppm chlorine dip resulted in an increase from 28 and 45% to 92.5 and 96.5% Extra Fancy after treatment for ‘Jonathan’ and ‘Golden Delicious’, respectively. Blemishes were removed more effectively from ‘Jonathan’ and ‘McIntosh’ apples than from ‘Golden Delicious’. Mycelial types of the sooty blotch and flyspeck fungi were removed differentially by the disinfestant dip treatments.

https://apsjournals.apsnet.org/doi/pdfplus/10.1094/PDIS.2002.86.12.1325

Evaluation of Postharvest Removal of Sooty Blotch and Flyspeck on Apples Using Sodium Hypochlorite, Hydrogen Peroxide with Peroxyacetic Acid, and Soap

Three forecasting models for Stewart's disease (Pantoea stewartii subsp. stewartii) of corn (Zea mays) were examined for their ability to accurately predict the prevalence of Stewart's disease in Iowa at the county level. The Stevens Model, which is used as a predictor of the early wilt phase of Stewart's disease, the Stevens-Boewe Model, which predicts the late leaf blight phase of Stewart's disease, and the Iowa State Model that is used to predict the prevalence of Stewart's disease, all use mean air temperatures for December, January, and February for a preplant prediction of Stewart's disease risk in a subsequent season. Models were fitted using weighted binary logistic regression with Stewart's disease prevalence data and air temperature data for 1972 to 2003. For each model, the years 1972 to 1999 (n = 786 county-years) were used for model development to obtain parameter coefficients. All three models indicated an increased likelihood for Stewart's disease occurring in growing seasons preceded by warmer winters. Using internal bootstrap validation, the Stevens Model had a maximum error between predicted and calibrated probabilities of 10%, whereas the Stevens-Boewe and Iowa State models had maximum errors of 1% or less. External validation for each model, using air temperature and seed corn inspection data between 2000 and 2003 (n = 154 county-years), indicated that overall accuracy to predict Stewart's disease at the county level was between 62 and 66%. However, both the Stevens and Stevens-Boewe models were overly optimistic in predicting that Stewart's disease would not occur within specific counties, as the sensitivity for these two models was quite low (18 and 43%, respectively). The Iowa State Model was substantially more sensitive (67%). The results of this study suggest that the Iowa State Model has increased predictive ability beyond statewide predictions for estimating the risk of Stewart's disease at the county level in Iowa.

https://apsjournals.apsnet.org/doi/pdfplus/10.1094/PD-90-1353

P. M. Dixon

Papers

Mining EST databases to resolve evolutionary events in major crop species

Germination and Sporulation of Colletotrichum acutatum on Symptomless Strawberry Leaves

Influence of Temperature and Wetness Duration on Conidia and Appressoria of Colletotrichum acutatum on Symptomless Strawberry Leaves

Evaluation of Postharvest Removal of Sooty Blotch and Flyspeck on Apples Using Sodium Hypochlorite, Hydrogen Peroxide with Peroxyacetic Acid, and Soap

Comparison of Models for Forecasting of Stewart's Disease of Corn in Iowa