Wild Soybean Species Research Articles

Discovery and genome-wide characterization of a novel miniature inverted repeat transposable element reveal genome-specific distribution in Glycine.

Miniature inverted repeat transposable elements (MITEs) are a dynamic component responsible for genome evolution. Tourist MITEs are derived from and mobilized by elements from the harbinger superfamily. In this study, a novel family of Tourist-like MITE was characterized in wild soybean species Glycine falcata. The new GftoMITE1 was initially discovered as an insertional polymorphism of the centromere-specific histone H3 (CenH3) gene in G. falcata. Using polymerase chain reaction, cloning and sequencing approaches, we showed a high number of copies of the GftoMITE1 family. Extensive bioinformatic analyses revealed the genome-level distribution and locus-specific mapping of GftoMITE1 members in Glycine species. Our results provide the first extensive characterization of the GftoMITE1 family and contribute to the understanding of the evolution of MITEs in the Glycine genus. Genome-specific GftoMITE1 was prominent in perennial wild soybean species, but not in annual cultivated soybean (Glycine max) or its progenitor (Glycine soja). We discuss that the GftoMITE1 family reveals a single rapid amplification in G. falcata and could have potential implications for gene regulation and soybean breeding as an efficient genetic marker for germplasm utilization in the future.

Mapping Quantitative Trait Loci for Soybean Seedling Shoot and Root Architecture Traits in an Inter-Specific Genetic Population.

Wild soybean species (Glycine soja Siebold & Zucc.) comprise a unique resource to widen the genetic base of cultivated soybean [Glycine max (L.) Merr.] for various agronomic traits. An inter-specific mapping population derived from a cross of cultivar Williams 82 and PI 483460B, a wild soybean accession, was utilized for genetic characterization of root architecture traits. The objectives of this study were to identify and characterize quantitative trait loci (QTL) for seedling shoot and root architecture traits, as well as to determine additive/epistatic interaction effects of identified QTLs. A total of 16,469 single nucleotide polymorphisms (SNPs) developed for the Illumina beadchip genotyping platform were used to construct a high resolution genetic linkage map. Among the 11 putative QTLs identified, two significant QTLs on chromosome 7 were determined to be associated with total root length (RL) and root surface area (RSA) with favorable alleles from the wild soybean parent. These seedling root traits, RL (BARC_020495_04641 ~ BARC_023101_03769) and RSA (SNP02285 ~ SNP18129_Magellan), could be potential targets for introgression into cultivated soybean background to improve both tap and lateral roots. The RL QTL region harbors four candidate genes with higher expression in root tissues: Phosphofructokinase (Glyma.07g126400), Snf7 protein (Glyma.07g127300), unknown functional gene (Glyma.07g127900), and Leucine Rich-Repeat protein (Glyma.07g127100). The novel alleles inherited from the wild soybean accession could be used as molecular markers to improve root system architecture and productivity in elite soybean lines.

The Soybean Laccase Gene Family: Evolution and Possible Roles in Plant Defense and Stem Strength Selection.

Laccase is a widely used industrial oxidase for food processing, dye synthesis, paper making, and pollution remediation. At present, laccases used by industries come mainly from fungi. Plants contain numerous genes encoding laccase enzymes that show properties which are distinct from that of the fungal laccases. These plant-specific laccases may have better potential for industrial purposes. The aim of this work was to conduct a genome-wide search for the soybean laccase genes and analyze their characteristics and specific functions. A total of 93 putative laccase genes (GmLac) were identified from the soybean genome. All 93 GmLac enzymes contain three typical Cu-oxidase domains, and they were classified into five groups based on phylogenetic analysis. Although adjacent members on the tree showed highly similar exon/intron organization and motif composition, there were differences among the members within a class for both conserved and differentiated functions. Based on the expression patterns, some members of laccase were expressed in specific tissues/organs, while some exhibited a constitutive expression pattern. Analysis of the transcriptome revealed that some laccase genes might be involved in providing resistance to oomycetes. Analysis of the selective pressures acting on the laccase gene family in the process of soybean domestication revealed that 10 genes could have been under artificial selection during the domestication process. Four of these genes may have contributed to the transition of the soft and thin stem of wild soybean species into strong, thick, and erect stems of the cultivated soybean species. Our study provides a foundation for future functional studies of the soybean laccase gene family.

Comparing performance of Aphis glycines Matsumura fed on two novel hosts relative to Glycine max (L.) Merrill

Abstract The soybean aphid, Aphis glycines Matsumura, is an important pest of soybean. During some years with occurrences of heavy aphid infestations in field, A. glycines can cause serious damage to soybeans. A. glycines has a heteroecious and holocyclic life cycle, with migration occurring between the primary and secondary hosts during each year. The primary hosts of A. glycines are Rhamnus spp., and the secondary hosts are soybean, Glycine max (L.) Merrill, and wild soybean species, Glycine soja Sieb & Zucc. In this study, A. glycines were fed on detached leaves and live plants of Trifolium repens L. and Metaplexis japonica (Thunb.) Makino, and their survival, development and reproduction were studied at five constant temperatures. These data were compared to those of controls fed on the known host plant G. max. When A. glycines were fed on detached leaves of T. repens and M. japonica, they showed vigorous development and reproduction. The novel and striking results were that: (1) A. glycines could not thrive on live plants of M. japonica, and only a few nymphs were deposited. (2) When A. glycines were fed on live plants of vegetative stage T. repens, adult longevity and fecundity were as long as 11.64 ± 1.17 days and as great as 12.92 ± 1.23 nymphs per adult, respectively. This work provides important evidence that M. japonica is not a host of A. glycines, but T. repens is probably an important host for this aphid.

Soybean aphid, Aphis glycines (Hemiptera: Aphididae), developmental and reproductive capacity on white clover, Trifolium repens (Rosales: Leguminosae), in northeast China

Nymphs of Aphis glycines Matsumura were individually reared to adults in the laboratory on detached leaf discs of Trifolium repens L. (white clover) mounted on agar medium. Adults of A. glycines were fed T. repens within small clip cages in the field. Development, reproduction and intrinsic rates of increase of A. glycines were studied. These data were compared to those of controls fed known host plants including cultivated soybean Glycine max (L.) Merr. and the wild soybean species Glycine soja Sieb & Zucc. The results demonstrated that nymphs of A. glycines successfully developed into adults and reproduced efficiently when reared on T. repens in the laboratory. The lower development temperature threshold for nymphs fed T. repens was estimated as 8.27 °C, and the effective cumulative temperature for A. glycines development from nymph to adult was 90.91 degree-days. Adults of A. glycines could also survive on T. repens in the field, but only a few nymphs were produced.

Structural and Functional Characterization of the VQ Protein Family and VQ Protein Variants from Soybean.

Proteins containing the FxxxVQxhTG or VQ motif interact with WRKY transcription factors. Although VQ proteins have been reported in several plants, knowledge about their structures, functions and evolution is still very limited. Here, we report structural and functional analysis of the VQ protein family from soybean. Like Arabidopsis homologues, soybean VQ proteins bind only Group I and IIc WRKY proteins and a substantial number of their genes are responsive to stress-associated phytohormones. Overexpression of some soybean VQ genes in Arabidopsis had strong effects on plant growth, development, disease resistance and heat tolerance. Phylogenetic analysis, sequence alignment and site-directed mutagenesis revealed that the region immediately upstream of the FxxxVQxhTG motif also affects binding to WRKY proteins. Consistent with a larger WRKY-binding VQ domain, soybean VQ22 protein from cultivated soybean contains a 4-amino acid deletion in the region preceding its VQ motif that completely abolishes its binding to WRKY proteins. By contrast, the 4-amino acid deletion is absent in the VQ22 protein from wild soybean species (Glycine soja). Overexpression of wild soybean VQ22 in cultivated soybean inhibited growth, particularly after cold treatment. Thus, the mutation of soybean VQ22 is associated with advantageous phenotypes and may have been positively selected during evolution.

Genetic differentiation in relation to seed weights in wild soybean species (Glycine soja Sieb. & Zucc.)

Seed weight is one of the most important botanical and phylogenetic characteristics. The study objective was to understand whether there is genetic difference in different seed weights of wild soybean (Glycine soja Sieb. & Zucc.). A total of 563 wild soybean samples, which belonged separately to genebank germplasm accessions (220 samples), one regional population samples (293 plants) and one natural population (150 plants), were analyzed using microsatellite markers. Of four size classes, the smallest seed size type had the highest coefficient of variation in seed weight; small and large seed types had relatively great genetic differences. In the national genebank germplasm accessions, genetic diversity gradually decreased from quantitatively dominant small and middling seed types to less frequent large seed types. In the regional and natural populations, generally, small to middling seed sizes had higher genetic diversity than the smallest and larger seed sizes. Cluster analysis revealed genetic differences in seed size traits. The semi-wild type (Glycine gracilis Skvortzow) was the most genetically differentiated from other seed sizes. However, it was also clearly shown that the phylogenic genetic differentiation among seed sizes was less than the genetic differentiation among geographical habitat populations in the wild soybean species.

Genetic characterization and gene flow in different geographical-distance neighbouring natural populations of wild soybean (Glycine soja Sieb. & Zucc.) and implications for protection from GM soybeans

To design appropriate strategies for ex situ and in situ conservation of wild soybean and safeguard the biosafety of the wild soybean gene pool when genetically modified soybeans are grown, it is important to understand its genetic characteristics, and to quantify gene flow and kinship within and between neighboring populations. We analyzed 9 pairs of neighboring populations of wild soybeans using 20 pairs of nuclear SSR markers. Results showed that Chinese wild soybean natural populations had outcrossing rates of 0–3.5% and that most populations contained many kinship families. The kinship families could be attributed to the accumulation of outcrossed offspring within populations during the history of population colonization. Wild soybean is very sensitive to environmental selection, which results in genetic differentiation of populations, and the emergence of specific alleles. We used an index τ to explain why genetic differences would exist between the pairwise populations; the interpopulation genetic differentiation chiefly consisted in the differences of allele frequencies over the genome. We found long-distance dispersal (1.5 km) of wild soybean seeds in a land ecosystem. There was close correlation between genetic and geographical distance among natural populations of Chinese wild soybean. Within a distance of 50 km, there was greater gene flow when the distance between populations was shorter. These findings have implications for ex situ and in situ conservation in an ecogeographical region, and also for protection of the gene pool from contamination by GM soybeans in wild soybean species.

Genetic diversity and geographical peculiarity of Tibetan wild soybean (Glycine soja)

Tibet is the highest Plateau in China and the world, however wild soybean has been found in its southeastern fringe region adjacent to the northwest of Yunnan Province. Tibetan wild soybean was distributed only in the Gongrigabuqu-River Gorge in southeast Tibet. This regional plant species belong to the flora of Himalayan-Hengduan Mountains, which comprises composite elements of ancient arcto-tertiary flora, tropical and semitropical flora. To date, few studies have been carried out on Tibetan wild soybean. Studying Tibetan wild soybean together with other regional ones helps to understand the history of the origin and dissemination of wild soybean species in China. Here we reported the status of genetic diversity in Tibetan wild soybean and the genetic relationship between Tibetan and other regional wild soybeans revealed by nuclear SSR markers. The results showed that the Tibetan wild soybean sample was significantly differentiated from other regional ones, as characterized by the lowest mean allelic richness (\( {\hat{\text{r}}} \) = 1.40) and gene diversity (He = 0.130) and the highest ratios of regionally unique alleles (63.26%) and fixed alleles (46.94%). These genetic attributes suggested that Tibetan wild soybean may have undergone severe adaptation selection for the plateau climate and ecogeographical conditions, and had less genetic exchange with inland populations. The regional population south of the Changjiang River (Central and South China) showed higher genetic richness. UPGMA cluster analysis revealed two large geographical groups, Tibetan and inland, and revealed closer relationship among the eastern populations, which suggested that the dissemination of this species in the eastern part of China might be rapider.

Cyclic electron flow around photosystem 1 is required for adaptation to salt stress in wild soybean species Glycine cyrtoloba ACC547

A wild soybean species Glycine cyrtoloba ACC547 was found to possess a high salinity resistance trait. It maintained higher net photosynthetic rate (PN) and maximal photochemical efficiency (Fv/Fm) than the soybean Glycine max cultivar Melrose under salt stress. Saline treatment enlarged the post-illumination transient increase in chlorophyll fluorescence in ACC547 much more than that in Melrose, indicating that its cyclic electron flow around photosystem 1 (CEF1) was accelerated more by salt stress. Additionally, ACC547 maintained higher nonphotochemical dissipation of excitation energy than Melrose under salt stress. It is suggested that the salinity resistance of ACC547 might be due to the CEF1-coupled dissipation of excess excitation energy.

Response of three Glycine species to salt stress

Responses of leaf area, biomass, photosynthetic gas exchange and ion contents to four NaCl treatments, 0, 17, 51, and 85 mM NaCl, were examined for three wild soybean species ( Glycine soja, Glycine tomentella and Glycine tabacina). In G. soja, NaCl treatment for 2 months reduced the photosaturated photosynthetic rate ( A max), leaf area and biomass of NaCl treated plants relative to control treatments. Reductions were larger at higher NaCl concentrations. Similar changes were found in G. tabacina, however, the reductions were less than those in G. soja. In G. tomentella, significant reductions in A max and biomass were found in 51 and 85 mM NaCl treated plants, but not in 17 mM concentrations. Results imply that the three species have differentiated in their sensitivity to salinity, with G. soja being the most sensitive, G. tabacina intermediate, and G. tomentella the least sensitive. The three species also differed in leaf tissue concentrations of Na and K. A negative correlation between Na accumulation in leaf tissue and salt tolerance was found that contrasted to a positive correlation between K concentration in leaf tissue and salt tolerance.

Photosynthetic Gas Exchange and Chlorophyll a Fluorescence of Three Wild Soybean Species in Response to NaCl Treatments

Responses of photosynthetic gas exchange and chlorophyll (Chl) a fluorescence of three wild soybeans, Glycine soja, G. tomentella, and G. tabacina occurring in different habitats of Taiwan, to four NaCl treatments, 0S, LS, MS, and HS (i.e. 0, 17, 51, and 85 mM NaCl) were compared. In G. soja following exposure to NaCl treatment for one month, the photon saturated photosynthetic rate (PN), the ratio of variable to maximum fluorescence (Fv/Fm), the quantum yield of photosystem 2 (ΦPS2), and the electron transport rate (ETR) decreased dramatically. These reductions increased with increasing concentration of NaCl treatment. Plants of MS and HS treatments did not survive after extending the treatment to two months. Reductions in PN, ΦPS2, and ETR (but not in Fv/Fm) were found in G. tabacina after two months of exposure to MS and HS treatments, but the reduction was not as severe as that in G. soja. In G. tomentella, significant reductions in PN and gs were found only in HS plants after two months of treatment, but no significant differences in Fv/Fm, ΦPS2, and ETR were found among plants of the four treatments. Thus the three wild soybeans in Taiwan have differentiated in their photosynthetic susceptibility to salinity, G. tomentella being the least susceptible, G. soja the most sensitive, and G. tabacina the intermediate. Different mechanisms are attributed to the inhibition effect of salinity on photosynthesis of the three species.

Detection of Polymorphic DNA and Taxonomic Relationships Among 10 Wild Perennial Soybean Species Using Specific and Arbitrary Nucleotide Primers

Polymorphic DNA in complex genomes of agronomic crops can be detected using specific nucleotide and arbitrary primers and the polymerase chain reaction (PCR). Nineteen accessions representing 10 species of the wild perennial soybean were evaluated using 4 sets of specific primers and 3 sets of random amplified polymorphic DNAs (RAPD) primers. The potential of the RAPD assays was further increased by combining two primers in a single PCR. The fragments generated by the two assays discriminated 10 wild species by banding profiles. The size of the amplified DNA fragments ranged from 100 to 2100 base pairs. The resolved PCR products yielded highly characteristic and homogeneous DNA fingerprints. The fingerprints were useful not only for investigating genetic variability but also for further characterizing the wild soybean species by detecting inter- and intra-specific polymorphisms, constructing dendrograms defining the phylogenetic relationships among these species, and identifying molecular markers for the construction of genetic linkage maps. Furthermore, unique markers distinguishing particular species were also identified. Thus, it is expected that PCR will have great relevance for taxonomic studies.