Nucleotide diversity of the upstream region of the putative MADS-box gene controlling soybean maturity

MADS-box genes are involved in plant reproductive development. However, the role of gene nucleotide diversity in soybean flowering and maturity remains unknown. Therefore, in this study, the distribution of DNA polymorphisms in the putative MADS-box gene located near the quantitative trait loci (QTL) for flowering time and maturity was targeted for association analysis using Glycine max (cultivated soybean) and Glycine soja (wild soybean). Sixteen single nucleotide polymorphisms identified in the upstream region of the putative MADS-box gene around QTL Pod mat 13-7 and Fflr 4-2 on chromosome 7 were found to be highly associated with maturity in soybean. The genetic diversity between cultivated soybeans and the wild relative was comparable, although the early maturity group (EMG) was less diverse than the late maturity group (LMG) of the cultivated soybean. Population size changes of the MADS-box gene in this soybean germplasm appeared to result from non-random selection. A selective pressure seemed to act on this gene in the EMG, while the LMG and G. soja were in genetic equilibrium. Neutrality tests and the constructed neighbor-joining tree indicate that the EMG of G. max has experienced strong artificial selection for its domestication and genetic improvement.     

The salt resistance of wild soybean (Glycine soja Sieb. et Zucc. ZYD 03262) under NaCl stress is mainly determined by Na+ distribution in the plant

Understanding the salt resistance mechanism of wild soybean is important in improving salt tolerance of cultivated soybean. Therefore, we comparatively analyzed effects of NaCl on photosynthesis, antioxidant enzyme activity, and ion distribution in a cultivated (Glycine. max) and a wild (Glycine soja) soybean to study the salt resistance mechanism of the G. soja. The results showed that more Na⁺ was accumulated in the G. soja roots than in the G. max roots, but the Na⁺ in the G. soja leaves was much less than that observed in the G. max leaves. The Na⁺ concentrations in the G. soja leaves were not high enough to affect the photosynthetic apparatus, which was demonstrated by less inhibition of photosynthetic activity, stomatal conductance, carboxylation efficiency in the G. soja leaves than in the G. max leaves after treated with different concentrations of NaCl. Meanwhile, there were no significant changes in intercellular CO₂ concentration, maximum PSII quantum yield, and relative water content in the G. soja leaves after NaCl treatment, while they significantly decreased in the G. max leaves. The non-photochemical quenching and the activities of superoxide dismutase (EC 1.15.1.1) and ascorbate peroxidase (EC 1.11.1.11) in the G. soja leaves increased with the increasing of NaCl concentrations, whereas only the activity of superoxide dismutase increased in G. max leaves. Based on these results, we suggested that the G. soja is able to accumulate higher levels of Na⁺ in its roots, and prevent the transportation of Na⁺ to leaves to protect photosynthetic apparatus from salt damage.     

Inducibly-formed isoflavonoids from leaves of soybean

Isoformononetin, glyceollins I, II and 2-isopentenyl-3,6a,9-trihydroxypterocarpan (glyceocarpin) accumulated in soybean (Glycine max) leaves after treatment with aqueous sodium iodoacetate or a cell suspension of the bacterium, Pseudomonas pisi. These compounds were also accompanied by two previously unreported pterocarpans, glyceofuran its 9-O-methyl derivative. Glyceocarpin is described for the first time as a plant product.     

Physiological regulation of seed soaking with soybean isoflavones on drought tolerance of Glycine max and Glycine soja

In this study, the Glycine max Jackson cultivar (the relatively drought-sensitive) and the Glycine soja BB52 accession (the drought-tolerant one) were used as the experimental materials. Effects of seed soaking with exogenous soybean isoflavones (daidzin or genistin) on seed germination, and seedlings photosynthesis, relative electrolytic leakage, content of thiobarbituric acid reactive substances , and anti-oxidative activities were investigated under drought stress conditions. The results showed that, treatments of seed soaking with daidzin or genistin could improve seed germination, and alleviate cell damage, enhance anti-oxidative activities and photosynthesis in drought-stressed seedlings, therefore displayed mitigated effects on soybean drought injury, especially for the drought-sensitive G. max Jackson cultivar. Thus seed soaking with exogenous soybean isoflavones may be a usable approach to enhance drought tolerance of cultivated soybean in practice.     

Study of the biosafety of genetically modified soybean in the center of its origin and diversity in the Far East of the Russian Federation

Wild soybean (Glycine soja Sieb. and Zucc.) is the nearest relative of cultivated soybean (G. max (L.) Merr.). Study of the population genetic structure of wild-growing relatives of genetically modified (GM) plants in the centers of their origin is one of the main procedures before introduction of GM crops in these areas. We studied the genetic variability of nine wild-growing soya populations of Primorskii krai using RAPD analysis. The level of genetic variability of G. soja was considerably higher than that of G. max. We analyzed phylogenetic relationships in the genus Glycine subgenus Soja using RAPD markers. Our data confirm the validity of allocation to G. gracilis of the rank of species.     

Nodulation and Competition for Nodulation of Selected Soybean Genotypes among Bradyrhizobium japonicum Serogroup 123 Isolates

Twenty recently obtained field isolates of Bradyrhizobium japonicum serogroup 123 were tested for their nodule mass production on the standard commercial soybean (Glycine max (L.) Merr. cv. Williams) and on two soybean plant introduction (PI) genotypes previously determined to restrict nodulation by strain USDA 123. Four of the field isolates showed similar restricted nodulation on the two genotypes, while all 20 isolates produced a normal amount of nodules on G. max cv. Williams. Serological analyses with adsorbed fluorescent antibodies showed that members of the 123 serotype ranked low in nodulation of the two PIs, in contrast to members of serotypes 127 and 129. Competition studies on the PIs indicated that isolates which were restricted were not competitive for nodule occupancy against strain USDA 110. However, unrestricted isolates of serogroup 123 were very competitive against USDA 110. On G. max cv. Williams, all serogroup 123 isolates tested were very competitive against USDA 110.     

Development of a radioimmunoassay for the soybean phytoalexin glyceollin I

A radioimmunoassay for glyceollin I, the major phytoalexin produced by soybean (Glycine max [L.] Merr.), has been developed. Antibodies were raised in rabbits against a glyceollin I-bovine serum albumin conjugate. The antisera were used to establish a radioimmunoassay for glyceollin I using [¹²⁵I]glyceollin I as the tracer. A logit plot of a standard concentration series yielded a straight line in the range of 1 to 100 picomoles (0.34-34 nanograms) of glyceollin I. The structurally related pterocarpan phytoalexins, glyceollins II and III, glyceollidin II and glycinol, which also accumulate in infected soybean tissue, show a low cross-reactivity in the radioimmunoassay (0.5-5% at 50% displacement of the tracer). Two related isoflavones present constitutively in soybean tissue, daidzein and genistein, have cross-reactivities of less than 0.84% and 1.1%, respectively. The radioimmunoassay permitted the quantitative determination of glyceollin I in 15-micrometer microtome sections of soybean hypocotyl tissue infected with zoospores of Phytophthora megasperma f. sp. glycinea.     

Uncovering signatures of selection in the soybean genome using SSR diversity near QTLs of agronomic importance

The cultivated soybean [Glycine max (L.) Merr.] is widely considered to descend from the wild soybean (G. soja Sieb. & Zucc.). This study was designed to evaluate the genetic variability and differentiation between G. soja and G. max, and to detect signatures of the selection that may have occurred during the domestication process from G. soja to G. max. A total of 192 G. soja accessions and 104 G. max accessions were genotyped using eight selected simple sequence repeat (SSR) markers assigned to three SSR groups. Four SSRs in group A were not located near any known QTL. Three SSRs in group B were associated with seed protein content, and an SSR in group C was associated with resistance to Sclerotinia stem rot. The number of alleles per locus and the level of genetic variability in G. soja were higher than those in G. max. A total of 122 out of 125 alleles were present in G. soja, but only 59 alleles were detected in G. max. The average gene diversity was 0.74 in G. soja and 0.64 in G. max. Four SSRs near QTLs of agronomic importance showed strong genetic differentiation and shift change in high frequency alleles in groups B and C between G. soja and G. max, revealing selection signatures that may reflect the domestication events and recent selective breeding. With reduced diversity in G. max, some undomesticated genes from G. soja should be prime candidates for introgression to increase the pool of diversity in G. max.     

Genetic variants in root architecture-related genes in a Glycine soja accession,a potential resource to improve cultivated soybean

Background

Root system architecture is important for water acquisition and nutrient acquisition for all crops. In soybean breeding programs, wild soybean alleles have been used successfully to enhance yield and seed composition traits, but have never been investigated to improve root system architecture. Therefore, in this study, high-density single-feature polymorphic markers and simple sequence repeats were used to map quantitative trait loci (QTLs) governing root system architecture in an inter-specific soybean mapping population developed from a cross between Glycine max and Glycine soja.

Results

Wild and cultivated soybean both contributed alleles towards significant additive large effect QTLs on chromosome 6 and 7 for a longer total root length and root distribution, respectively. Epistatic effect QTLs were also identified for taproot length, average diameter, and root distribution. These root traits will influence the water and nutrient uptake in soybean. Two cell division-related genes (D type cyclin and auxin efflux carrier protein) with insertion/deletion variations might contribute to the shorter root phenotypes observed in G. soja compared with cultivated soybean. Based on the location of the QTLs and sequence information from a second G. soja accession, three genes (slow anion channel associated 1 like, Auxin responsive NEDD8-activating complex and peroxidase), each with a non-synonymous single nucleotide polymorphism mutation were identified, which may also contribute to changes in root architecture in the cultivated soybean. In addition, Apoptosis inhibitor 5-like on chromosome 7 and slow anion channel associated 1-like on chromosome 15 had epistatic interactions for taproot length QTLs in soybean.

Conclusion

Rare alleles from a G. soja accession are expected to enhance our understanding of the genetic components involved in root architecture traits, and could be combined to improve root system and drought adaptation in soybean.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1334-6) contains supplementary material, which is available to authorized users.     

Leaf flavonoids of Glycine subgenus Glycine in relation to systematics

A survey of leaf flavonoids and isoflavonoids in several taxa of the genus Glycne subgenus Glycine was undertaken to see if this would help interpret inter- and intraspecific relationships in the genus. C-Glycosylflavones based on apigenin were found in Glycine tomentelia, G. tabacina and G. falcata. Glycosides of quercetin and kaempferol were also detected in G. tabacina. In the cultivated soybean, G. max, and its wild annual relative, G. soja, only quercetin and kaempferol glycosides have been reported. Interspecific hybrids of Glycine species sometimes show additive flavonoid patterns in F₁ hybrid leaf tissue. All perennial wild species analysed including Glycine canescens and G. latifolia have the isoflavonoids genistin (genesitein 7-O-glucoside), daidzein and coumestrol in the leaves.     

Induction of cyclic electron flow around photosystem 1 and state transition are correlated with salt tolerance in soybean

We investigated the role of cyclic electron flow around photosystem 1 (CEF1) and state transition (ST) in two soybean cultivars that differed in salt tolerance. The CEF1 and maximum photochemical efficiency (F_v/F_m) were determined under control and NaCl (50 mM) stress and the NaCl-induced light-harvesting complex 2 (LHC2) phosphorylation in vitro was analysed in light and dark. NaCl induced the increase of CEF1 more greatly in wild soybean Glycine cyrtoloba (cv. ACC547) than in cultivated soybean Glycine max (cv. Melrose). The F_v/F_m was reduced less in G. cyrtoloba than in G. max after 10-d NaCl stress. In G. cyrtoloba, the increase of CEF1 was associated with enhancement of LHC2 phosphorylation in thylakoid membrane under both dark and light. However, in G. max the NaCl treatment decreased the LHC2 phosphorylation. Treatment with photosynthetic electron flow inhibitors (DCMU, DBMIB) inhibited LHC2 phosphorylation more in G. max than in G. cyrtoloba. Thus the NaCl-induced up-regulation in CEF1 and ST might contribute to salt resistance of G. cyrtoloba.     

Single nucleotide mutation leading to an amino acid substitution in the variant <Emphasis Type="Italic">Tik</Emphasis> soybean Kunitz trypsin inhibitor (SKTI) identified in Chinese wild soybean (<Emphasis Type="Italic">Glycine soja</Emphasis> Sieb. &; Zucc.)

The wild soybean (Glycine soja), which is the progenitor of cultivated soybean (Glycine max), is expected to offer more information about genetic variability and more useful mutants for evolutionary research and breeding applications. Here, a total of 1,600 wild soybean samples from China were investigated for genetic variation with regard to the soybean Kunitz trypsin inhibitor (SKTI). A new mutant SKTI, Tik, was identified. It was found to be a Tia-derived codominant allele caused by a transversion point mutation from C to G at nucleotide +171, leading to an alteration of one codon (AAC → AAG) and a corresponding amino acid substitution (Asn → Lys) at the ninth residue. Upon examination of this variant and others previously found in wild soybeans, it became clear that SKTI has undergone high-level evolutionary differentiation. There were more abundant polymorphisms in the wild than in the cultivated soybean.     

Nodulation, Nitrogen Fixation, and Hydrogen Oxidation by Pigeon Pea Bradyrhizobium spp. in Symbiotic Association with Pigeon Pea, Cowpea, and Soybean

The pigeon pea strains of Bradyrhizobium CC-1, CC-8, UASGR(S), and F4 were evaluated for nodulation, effectiveness for N₂ fixation, and H₂ oxidation with homologous and nonhomologous host plants. Strain CC-1 nodulated Macroptilium atropurpureum, Vigna unguiculata, Glycine max, and G. soja but did not nodulate Pisum sativum, Phaseolus vulgaris, Trigonella foenum-graecum, and Trifolium repens. Strain F4 nodulated G. max cv. Peking and PI 434937 (Malayan), but the symbioses formed were poor. Similarly, G. max cv. Peking, cv. Bragg, PI 434937, PR 13-28-2-8-7, and HM-1 were nodulated by strain CC-1, and symbioses were also poor. G. max cv. Williams and cv. Clark were not nodulated. H₂ uptake activity was expressed with pigeon pea and cowpea, but not with soybean. G. max cv. Bragg grown in Bangalore, India, in local soil not previously exposed to Bradyrhizobium japonicum formed nodules with indigenous Bradyrhizobium spp. Six randomly chosen isolates, each originating from a different nodule, formed effective symbioses with pigeon pea host ICPL-407, nodulated PR 13-28-2-8-7 soybean forming moderately effective symbioses, and did not nodulate Williams soybean. These results indicate the six isolates to be pigeon pea strains although they originated from soybean nodules. Host-determined nodulation of soybean by pigeon pea Bradyrhizobium spp. may depend upon the ancestral backgrounds of the cultivars. The poor symbioses formed by the pigeon pea strains with soybean indicate that this crop should be inoculated with B. japonicum for its cultivation in soils containing only pigeon pea Bradyrhizobium spp.     

Influence of Heterodera glycines on Interspecific and Intraspecific Competition Associated with Glycine max and Chenopodium album

The influence of Heterodera glycines (soybean cyst nematode) on the interspecific and intraspecific competition associated with Glycine max (soybean) and Chenopodium album (common lambsquarters) was studied in 1988 and 1989 in three de Wit replacement series experiments in growth chambers and microplots. Glycine max was grown alone (1 plant/experimental unit), in intraspecific competition (2 plants/experimental unit), in interspecific competition with C. album, and in presence or absence of H. glycines. No significant effects of H. glycines and C. album on G. max growth were observed 14 days after planting. By 42 days after planting, both H. glycines and C. album had a negative (P = 0.05) influence on the growth of G. max. Relative crowding coefficients for G. max were lower and deviated (P = 0.05 and P = 0.001) from 1.0 in the presence of H. glycines, compared to that of C. album and early emerged C. album in the absence of the nematode, respectively. Glycine max, therefore, became less competitive than C. album. There was a trend that the presence of H. glycines decreased the competitiveness of G. max on measures of the aggressivity and relative mixture response. Heterodera glycines decreased the aggressivity of G. max (ca. 150-350%) and increased the relative effects of intraspecific interference on G. max (ca. 10-50%) and interspecific interference (ca. 60-350%) after 42 days of plant growth, compared with plants grown in the absence of H. glycines. No H. glycines x C. album interactions were detected. Observations showed that H. glycines and early emerged C. album inhibited the growth of G. max 5-13%, as measured by plant dry weight.     

QTL affecting fitness of hybrids between wild and cultivated soybeans in experimental fields

The objective of this study was to identify quantitative trait loci (QTL) affecting fitness of hybrids between wild soybean (Glycine soja) and cultivated soybean (Glycine max). Seed dormancy and seed number, both of which are important for fitness, were evaluated by testing artificial hybrids of G. soja × G. max in a multiple‐site field trial. Generally, the fitness of the F₁ hybrids and hybrid derivatives from self‐pollination was lower than that of G. soja due to loss of seed dormancy, whereas the fitness of hybrid derivatives with higher proportions of G. soja genetic background was comparable with that of G. soja. These differences were genetically dissected into QTL for each population. Three QTLs for seed dormancy and one QTL for total seed number were detected in the F₂ progenies of two diverse cross combinations. At those four QTLs, the G. max alleles reduced seed number and severely reduced seed survival during the winter, suggesting that major genes acquired during soybean adaptation to cultivation have a selective disadvantage in natural habitats. In progenies with a higher proportion of G. soja genetic background, the genetic effects of the G. max alleles were not expressed as phenotypes because the G. soja alleles were dominant over the G. max alleles. Considering the highly inbreeding nature of these species, most hybrid derivatives would disappear quickly in early self‐pollinating generations in natural habitats because of the low fitness of plants carrying G. max alleles.     

The use of laser capture microdissection to study the infection of Glycine max (soybean) by Heterodera glycines (soybean cyst nematode)

The soybean cyst nematode (Heterodera glycines) is an obligate parasite of soybean (Glycine max). It is the most destructive pathogen of G. max, accounting for approximately 0.46–0.82 billion dollars in crop losses, annually, in the U.S. Part of the infection process involves H. glycines establishing feeding sites (syncytia) that it derives its nourishment from throughout its lifecycle. Microscopic methods (i.e., laser capture microdissection [LCM]) that faithfully dissect out those feeding sites are important improvements to the study of this significant plant pathogen. Our isolation of developing feeding sites during an incompatible or a compatible reaction is providing new ways by which this important plant-pathogen interaction can be studied. We have used these methods to create cDNA libraries, clone genes and perform microarray analyses. Importantly, it is providing insight not only into how the root is responding at the organ level to H. glycines, but also how the syncytium is responding during its maturation into a functional feeding site.Key words: soybean, Glycine max, soybean cyst nematode, SCN, Heterodera glycines, microarray, gene expression, plant pathogen, parasite, laser capture microdissection     

The genetic diversity and population structure of wild soybean evaluated by chloroplast and nuclear gene sequences

Glycine soja, also called wild soybean, is the wild ancestor of domesticated soybean (Glycine max), and one of the world's major cultivated crops. Wild soybean is a valuable resource for the breeding of cultivated soybean and harbors useful genes or agronomic traits. To use and conserve this valuable resource, we conducted a study to evaluate the genetic diversity and population structure of wild soybean using the sequencing data of two nuclear loci (AF105221 and PhyB) and one chloroplast locus (trnQ-rps16) of more than 600 individuals representing 53 populations throughout the natural distribution range. The results showed that most of the variation was found within the populations and groups, but significant genetic differentiation was also detected among different eco-geographical groups. Correlations between genetic and geographical distance at all the loci were consistent with the isolation by distance gene flow model. G. soja exhibited the highest genetic diversity in middle and downstream of Yangzi River (MDYR) region, followed by North East China (NEC), and was the lowest in North West China (NWC). We concluded that both in situ and ex situ conservation strategies required for wild soybean populations, especially which are native to MDYR and NEC regions.