Evolutionary studies of the soybean: the frequency and distribution of alleles among collections of Glycine Max and G. Soja of various origin

Summary Allelic frequencies at 10 loci common throughout the genus Glycine subgenus Soja were determined for 27 geographical area-species samples. The samples included 366 accessions of Glycine soja, the wild soybean, and 193 accessions of G. max, the domesticated soybean, from the USDA Soybean Germplasm Collection. The data indicate that the alleles for grey pubescence (t ₁), low seed coat peroxidase level (ep), and blunt pubescence tip (pb) probably arose as mutations during the domestication of G. max. The remaining seven loci studied(Fr, Pa ₁, Pa ₂, Fg ₁, Fg ₂, Fg ₃and Fg ₄)are polymorphic throughout the subgenus Soja; differences among collections of G. max and G. soja seem to be the result of differing selection pressures. A cluster analysis of allelic frequencies reveals two distinct groups within the subgenus corresponding to G. soja and G. max, Semi-wild accessions of G. max, while morphologically more similar to cultivated plants, clustered with samples of G. soja. The semi-wild accessions examined are thought to have arisen via hybridization between G. soja and G. max.Joint contribution: North Central Region, Agricultural Research, Science and Education Administration, U.S. Department of Agriculture, and Journal Paper No. J-9868 of the Iowa Agriculture and Home Economics Experiment Station, Ames, Iowa 50011; Project 2107.     

Mapping and use of QTLs controlling pod dehiscence in soybean

While the cultivated soybean, Glycine max (L.) Merr., is more recalcitrant to pod dehiscence (shattering-resistant) than wild soybean, Glycine soja Sieb. & Zucc., there is also significant genetic variation in shattering resistance among cultivated soybean cultivars. To reveal the genetic basis and develop DNA markers for pod dehiscence, several research groups have conducted quantitative trait locus (QTL) analysis using segregated populations derived from crosses between G. max accessions or between a G. max and G. soja accession. In the populations of G. max, a major QTL was repeatedly identified near SSR marker Sat_366 on linkage group J (chromosome 16). Minor QTLs were also detected in several studies, although less commonality was found for the magnitudes of effect and location. In G. max × G. soja populations, only QTLs with a relatively small effect were detected. The major QTL found in G. max was further fine-mapped, leading to the development of specific markers for the shattering resistance allele at this locus. The markers were used in a breeding program, resulting in the production of near-isogenic lines with shattering resistance and genetic backgrounds of Japanese elite cultivars. The markers and lines developed will hopefully contribute to the rapid production of a variety of shattering-resistant soybean cultivars.     

Heterosis of interspecific soybean hybrids for traits related to N2 fixation

Summary Three greenhouse experiments were conducted to compare the performance of soybean (Glycine max (L.) Merr.), wild soybean (G. soja Sieb. et Zucc.), and soybean x wild soybean hybrids for traits relating to N₂ fixation including nodulation, acetylene reduction, nodule leghemoglobin concentration, and nitrogen (N) accumulation and dry matter (DM) accumulation. In all three experiments G. max generally exceeded G. soja in nodulation, acetylene reduction, and N and DM accumulation while the soybean possessed higher nodule leghemoglobin concentration. In Experiment I, the mean of the hybrids did not differ significantly from the G. max parent in nodule mass, acetylene reduction activity, nodule leghemoglobin concentration, or DM accumulation. The hybrids did exceed the soybean parent in N accumulation, thus demonstrating high parent heterosis. In Experiments IIA and IIB with a more carefully chosen set of G. soja parents, high parent heterosis of individual crosses was common. Across the three experiments average high parent heterosis was 34, 28, and 28%, respectively, for nodule mass, N accumulation, and DM accumulation. If one accepts the assumption that hybrid vigor results from the accumulation of dominant alleles, then these alleles could theoretically be accumulated via selection in a homozygous genotype. If this is true than the results of the experiments reported here suggest that interspecific soybean x wild soybean crosses could serve as sources of homozygous lines which would exceed currently available soybean cultivars in nodule mass, and N and DM accumulation.This work was supported in part by the USDA Competitive Grants Program, Grant 82-CRCR-1-1039 and Cooperative Agreement 58-32U4-2-370 between the U.S. Department of Agriculture and the Agronomy Department, University of Maryland, Scientific Article No. A-4648, Contribution No. 7644 of the Maryland Agricultural Experiment Station.     

Glycine max and Glycine soja are capable of cold acclimation

Soybean has been considered a cold intolerant species; based largely upon seed germination and soil emergent evaluations. This study reports a distinct acquisition of cold tolerance, in seedlings, following short acclimation periods. Diversity in cold responses was assessed in eight cultivars of Glycine max and six accessions of G. soja. All varieties of soybean significantly increased in freezing tolerance following acclimation. This study indicates soybean seedlings are indeed capable of sensing cold and acquiring cold tolerance. Germination rates after cold imbibition were negatively correlated with maturity group, but positively correlated with cold acclimation potential in G. soja. Seed fatty acid composition was varied between the species, with Glycine soja accessions containing about 2‐times more linolenic acid (18:3) than G. max. Furthermore, high levels of linoleic acid (18:2) in seeds were positively correlated with germination rates following cold imbibition in G. soja only. We suggest that domestication has not impacted the overall ability of soybean to cold acclimate at the seedling stage and that there is little variation within the domesticated species for ability to cold acclimate. Thus, this brief comparative study reduces the enthusiasm for the “wild” species as an additional source of genetic diversity for cold tolerance.     

Differences in Ion Accumulation and Salt Tolerance among Glycine Accessions

Salinity reduces crop yield by limiting water uptake and causing ion‐specific stress. Soybean [Glycine max (L.) Merr.] is sensitive to soil salinity. However, there is variability among soybean genotypes and wild relatives for salt tolerance, suggesting that genetic improvement may be possible. The objective of this study was to identify differences in salt tolerance based on ion accumulation in leaves, stems and roots among accessions of four Glycine species. Four NaCl treatments, 0, 50, 75 and 100 mm , were imposed on G. max, G. soja, G. tomentella and G. argyrea accessions with different levels of salinity tolerance. Tolerant genotypes had less leaf scorch and a greater capacity to prevent Na⁺ and Cl^? transport from soil solution to stems and leaves than sensitive genotypes. Magnitude of leaf injury per unit increase in leaf Na⁺ or Cl^? concentrations was lower in tolerant than in susceptible accessions. Also, plant injury was associated more with Na⁺ rather than with Cl^? concentration in leaves. Salt‐tolerant accessions had greater leaf chlorophyll‐meter readings than sensitive genotypes at all NaCl concentrations. Glycine argyrea and G. tomentella accessions possessed higher salt tolerance than G. soja and G. max genotypes.     

Characterizing morphological traits and estimating genetic relationship for intermediate soybean collected from South Korea

Twenty‐two wild, 16 intermediate and 20 cultivated soybean varieties were used to analyse relationships among the species of subgenus Soja, genus Glycine using 11 morphological traits and simple sequence repeat (SSR) markers. These genotypes using eleven agronomic characteristics were divided into three clusters: cluster I included 20 G. max, cluster II included 12 intermediate, and cluster III included 22 G. soja and four intermediate lines. Genetic relationships among the species of subgenus Soja showed three distinct clusters. Cluster I consisted of 20 G. max cultivars and two intermediate type lines, and cluster II consisted of 13 intermediate type and two G. soja lines; however, cluster III consisted of 20 G. soja and one intermediate type lines. These phenotypic and genetic data suggest that the intermediate type lines could be distinguished between G. max and G. soja lines. However, the intermediate type could not be classified as a new species.     

Isozyme variation between diploid and tetraploid cytotypes of Glycine tabacina (Labill.) Benth.

Summary Glycine tabacina (Labill.) Benth. is a wild perennial species related to the cultivated soybean, G. max (L.) Merr. It is composed of diploid (2n=40) and tetraploid (2n=80) cytotypes. Currently, to differentiate the cytotypes, plants are grown out in the greenhouse and chromosome counts made on pollen mother cells. It is a laborious and time consuming process. The objective of this study was to determine whether electrophoretic techniques could be utilized to separate the cytotypes. Electrophoretic examination of seven isozyme systems from seed of 67 G. tabacina accessions revealed banding patterns that could be used to differentiate between diploid and tetraploid cytotypes in the species. Among the tetraploid accessions, the number of bands observed were always greater than the diploids. Some tetraploid banding patterns consisted of bands similar to the diploid tabacina and/or additional bands previously identified in other Glycine species. The patterns of isozyme multiplicity and variation in the tetraploid tabacinas suggests more than one mode of origin for the tetraploids.     

Association of isozyme genotypes with agronomic and seed composition traits in soybean

Summary Two crosses between Glycine max (L.) Merr. and G. soja Sieb. & Zucc. parents were used to study the association between isozyme marker loci and agronomic and seed composition traits in soybean. The parents possessed different alleles at six isozyme loci for Cross 1 (A80-244036 × PI 326581) and at eight isozyme loci for Cross 2 (A81-157007 × PI 342618A). A total of 480 BC₂F_4:6 lines from the two crosses was evaluated for 13 traits in two environments. Lines were grouped in locus classes from 0 to 5 according to the number of loci homozygous for the G. soja alleles that they possessed. Within each locus class, each isozyme genotype was represented by five random lines.Selection for G. max alleles at the isozyme loci was not effective in recovering the recurrent parent phenotype in either cross. In cross 1, however, BC₂F₄-derived lines in the 0- or 1- locus class more closely resembled the G. max parent than lines in the 4- or 5- locus classes for most of the agronomic and seed composition traits evaluated. Significant associations were found between particular isozyme genotypes and every trait analyzed. The estimated effect of genes linked to the Pgm1 locus was a delay in maturity of 6.0±3.4 days. In cross 1, the Idh2 locus was associated with a significant effect on linolenic acid content. The percentage of variation accounted for by the models of estimation varied according to the heritability of the trait. The R² was high (up to 78%) for maturity, lodging, and vining, and low (up to 21%) for seed yield. Most of the variation was associated with the BC₂F₁ family from which the lines were derived. There was little evidence that digenic epistasis was an important source of variation.Journal Paper No. J-13505 of the Iowa Agric. Home Econ. Exp. Stn., Ames, IA, Project 2475.     

Intersubgeneric Crossability in the Genus Glycine Willd.

In intersubgeneric crosses between wild perennial Glycine species of submenus Glycine and soybeans, Glycine max (L.) Merr., of subgenus Soja, all the putative hybrid pods aborted from 9 to 30 days after pollination (DAP). Spraying of 70 ppm gibberellic acid on hybridized gynoecia facilitated pod retention. Fluorescence microscopy revealed normal pollen germination and pollen tube growth in all the intersubgeneric crosses except in the G. cyrtoloba × G. max cross.     

Chromosomal location in H. chilense and expression of common bunt resistance in wheat addition lines

The inheritance of resistance to yellow mosaic virus spread by Bemisia tabaci Gen. in Glycine soja (Linn.) Seib. & Zucc. was studied following natural infection in the field condition. The resistant wild accession, Glycine soja was crossed with susceptible cultivars ‘Ankur’, ‘Bragg’, ‘PK 472’ and ‘Kalitur’ of Glycine max (Linn.) Merr. Resistance reactions of F₁ and F₂ plants, and individual F₂ plant derived F₃ families indicated that resistance was controlled by a single dominant gene. This revised version was published online in July 2006 with corrections to the Cover Date.     

Application of DNA fingerprints for identification and genetic analysis of Carica papaya and other Carica species

Summary Various DNA fingerprint probes were applied to Carica papaya and other Carica species for both identification and genetic analysis.Each of the Carica papaya cultivars is characterized by a specific DNA fingerprints pattern. Various Carica species also have specific patterns which distinguish them from one another. Band sharing levels were used to estimate the relatedness between the various Carica species.Genetic analysis of 11 progeny from a cross between the Carica papaya cultivars 17/82 and 112 suggests that application of DNA fingerprinting to Carica papaya breeding, could make the process more efficient. Genetic analysis of the DNA fingerprint bands revealed no linkage or allelic relationship among the bands analyzed, indicating that these loci are not clustered in the Carica genome.     

Random amplified polymorphic DNA (RAPD) markers variability among cultivars and landraces of common beans (Phaseolus vulgaris L.) of south-Brazil

To evaluate the variability among cultivars and landraces of common bean(Phaseolus vulgaris L.), 15 cultivars and 18 landraces of common bean (Phaseolus vulgarisL.), a undefined species of Phaseolus,two landraces of Vigna angularis L., and a landrace of soybean (Glycine maxL.), were screened with fifteen oligonucleotide primers in PCR reactions. An average of 20.3 RAPD bands were scored per primer. A total of 304 amplification products were scored of which 88.8% were polymorphic among Phaseolus genotypes. Based on the RAPD markers, four major clusters were formed. Three clusters corresponded to the soybean, to the two Vigna angularis landraces, and to the Phaseolus sp. landrace, respectively. The fourth cluster include all the landraces and cultivars of Phaseolus vulgaris. This large group could be separated into three subgroups that were correlated with the phaseolin patterns and the average seed weight of the genotypes. The analysis shows that most of the landraces collected in South Brazil (17 out of 18) belong to the Andean gene pool, and most of the cultivars (13 out of 15) belong to the Middle American gene pool. This revised version was published online in July 2006 with corrections to the Cover Date.     

A Line with Four-Seeded Pods Derived from an Interspecific Hybrid in Soybean

The cultivated soybean, Glycine max (L.) Merr., was crossed with its proposed wild progenitor, Glycine sofa (Seib. & Zucc.), to create useful genetic variability. A few plants with increased frequency of four-seeded pods were identified in a segregating generation derived from this interspecific cross. One of them had about 45 percent four-seeded pods per plant, whereas Glycine max and Glycine soja accessions used as parents in this study had only 8.0 and 5.1 per cent four-seeded pods per plant, respectively. The established line finally had 32.5 per cent four-seeded pods per plant, which is substantially higher as compared to either of the parents. Obviously, the genes which are responsible for this character are not expressed in the parental population.     

Nuclear RFLP between pepper cultivars (Capsicum annuum L.)

Summary Forty one nuclear probes, distributed across the different linkage groups of the previously published map, were used to examine restrition fragment length polymorphism between cultivated peppers. Total DNA from thirteen accessions of Capsicum annuum var. annuum and one accession of C. baccatum var. pendulum was separately cut with ten restriction enzymes. The analyses were restricted to only one enzyme per probe to reduce the polymorphism redundancy. Nei & Li's genetic distances between accessions were calculated from the 141 resultant nuclear DNA restriction fragments. The genetic variation was larger between C. annuum and C. baccatum than between C. annuum cultivars. Large fruited related accessions closely clustered together. Distances between the small fruited cultivars were larger than within the bell pepper group. A correspondence analysis performed on differences between the global RFLP patterns of each accessions of C. annuum revealed the particular genomic structure of four small fruited cultivars: Criollo de Morelos 334, H3, Perennial and Doux Long des Landes. The percentage of probes revealing at least one RFLP with at least one enzyme ranged from zero to fifty percent for all the pairwise comparisons of C. annuum accessions. 82 presumptive loci were detected with a mean number of 1.46 alleles per locus within C. annuum and 1.83 within all the accessions. This result indicates that molecular markers will be more usable in intraspecific study of C. annuum than isozyme markers.     

A cluster analysis of wild and domesticated soybean phenotypes

Summary Cluster analysis techniques were used to examine phenotypic variation within the USDA Soybean Germplasm Collection. This study included ten Plant Introductions each of the domesticated soybean, Glycine max (L). Merr., the wild soybean, G. soja Sieb. & Zucc., and a disputed species, G. gracilis Skvortz. G. max and G. soja were found to be morphologically distinct entities and G. gracilis was found to be conspecific with G. max. Because G. gracilis probably represents weedy races associated with the cultivated soybean and because gracilis phenotypes can be distinguished from G. max, the designation, G. max forma gracilis, is recommended.Joint contribution: North Central Region, Agricultural Research, Science and Education Administration, U.S. Department of Agriculture, and Journal Paper No. J-9389 of the Iowa Agriculture and Home Economics Experiment Station, Ames, Iowa 50011; Project 2107.     

Validation of molecular markers for pathogen resistance in potato

DNA markers have a large potential to improve efficiency and precision of conventional plant breeding programmes based on marker‐assisted selection (MAS). In our study, we have evaluated the predictive abilities of the SCAR marker RYSC3 and the CAPS marker GP122₅₆₄ with regard to the PVY resistance genes Ry_adg and Ry_sto, respectively, and of marker TG689 linked to H1 conferring resistance to Globodera rostochiensis and marker HC associated with high levels of G. pallida resistance. The evaluations were made in 28 cultivars and accessions and in 219 progeny genotypes descending from ten different crosses. We observed in all evaluated cultivars and accessions the expected marker patterns according to their phenotypic classification into resistant and susceptible genotypes. However, in part considerable discrepancies were observed when analysing progeny of controlled crosses involving these resistance sources, particularly with respect to H1. Based on these results, practical aspects for the efficient implementation of marker‐assisted selection are discussed, which consider the genetic origin of the material, costs aspects and methodology applied.     

Genetic diversity and differentiation of Chinese wild soybean germplasm (G. soja Sieb. & Zucc.) in geographical scale revealed by SSR markers

Wild soybean (Glycine soja), as the progenitor of soybeans (G. max), is widely distributed in China and has been collected as a supplementary germplasm pool of soybeans. In this study, 375 wild soybean accessions from a set of genebank core collection were analysed for genetic diversity by using 42 simple sequence repeat primer pairs. The mean allele number per locus was 19.62. Ten‐percent unique alleles involving 35 or 83.33% loci differentiated among the geographical regions. The mean gene diversity (h) per locus was 0.89. A very low mean coefficient of gene differentiation (G_ST = 0.08) for geographical regions and a high mean within‐region gene diversity (H_S = 0.81) were observed, indicating that most genetic diversity existed within the regions. There was an obvious relationship between genetic distance and geographical distance. The results showed multiple centers of genetic diversity for Chinese wild soybean in North China, the Huanghe River Valley, and Central China as well as the Changjiang River Valley, implicating multiple site origins of soybeans within China.     

Genotype x Bradyrhizobium japonicum strain interactions in dinitrogen fixation and agronomic traits of soybean (Glycine max L. Merr.)

Summary Bradyrhizobium japonicum strain G49 has been the only inoculum used in French soils. Soybean (Glycine max L. Merr.) cultivars were selected and tested according to their performances with this rhizobial strain. The aim of the present study was to determine the consequences of strain substitution on N₂ fixation abilities of various genotypes. Three genotypes and cultivar Weber, in combination with B. japonicum strain G49 or SMGS1, were cultivated in pots and tested for nitrogenase activity under differing nitrogen nutrition conditions. The reliability of ARA (acetylene reduction activity) measurement for assessing symbiotic nitrogen fixation under the experimental conditions used was checked. Genotypic variability for symbiotic fixation activity was observed with each strain under soil culture conditions; important genotype x strain interactions were also involved. These results were corroborated for the protein yield and other yield component performances of the various genotype-strain associations. Thus, in France, the replacement of strain G49 with another one might result in the alteration of the relative agronomic performances of the soybean cultivars, since N₂ fixation is considered as a major factor of soybean productivity.     

Chloride tolerance in soybean and perennial Glycine accessions

Diversity for chloride tolerance exists among accessions of perennial Glycine. Accessions whose tolerance thresholds exceed those of Glycine max cultivars may be useful germplasm resources. Soybean cultivars including ‘Jackson’ (sensitive) and ‘Lee’ (tolerant) and 12 accessions of perennial Glycine were evaluated for sodium chloride tolerance after 14 days in hydroponic culture at 0, 5, 10, and 15 g L^-1 NaCl. Sodium chloride had adverse effects on the growth of G. max cultivars and perennial Glycine accessions; however differential responses to salinity were observed among accessions. Considerably greater variation in sodium chloride tolerance existed among the perennial Glycine accessions than among the G. max cultivars. Sodium chloride tolerance thresholds ranged from 3.0 to 17.5 g L^-1 NaCl for the perennial accessions but only ranged from 5.2 to 8.0 g L^-1 for the cultivars, based on a Weibull model of leaf chlorosis. All G. max cultivars were severely injured or killed by NaCl at 10 g L^-1 and above. Five tolerant perennial Glycine accessions, G. argyrea 1626, G. clandestina 1388 and 1389, and G. microphylla 1143 and 1195, were significantly lower in leaf chlorosis score than any of the G. max cultivars at the 10 g L^-1 NaCl treatment. Two accessions, G. argyrea 1626 and G. clandestina 1389 were able to tolerate 15 g L^-1 NaCl with only moderate visual injury while all other accessions were severely injured or killed at this salt level. Variability for chloride tolerance observed among the perennial Glycine accessions has potential utility for developing enhanced salt tolerance in soybean. This revised version was published online in July 2006 with corrections to the Cover Date.     

Identification and validation of an over‐dominant QTL controlling soybean seed weight using populations derived from Glycine max × Glycine soja

Heterosis, or hybrid vigour, has been used to improve seed yield in several important crops for decades and it has potential applications in soybean. The discovery of over‐dominant quantitative trait loci (QTL) underlying yield‐related traits, such as seed weight, will facilitate hybrid soybean breeding via marker‐assisted selection. In this study, F₂ and F_2 : 3 populations derived from the crosses of ‘Jidou 12’ (Glycine max) × ‘ZYD2738’ (Glycine soja) and ‘Jidou 9’ (G. max) × ‘ZYD2738’ were used to identify over‐dominant QTL associated with seed weight. A total of seven QTL were identified. Among them, qSWT_13_1, mapped on chromosome 13 and linked with Satt114, showed an over‐dominant effect in two populations for two successive generations. This over‐dominant effect was further examined by six subpopulations derived from ‘Jidou12’ × ‘ZYD2738’. The seed weight for heterozygous individuals was 1.1‐ to 1.6‐fold higher than that of homozygous individuals among the six validation populations examined in different locations and years. Therefore, qSWT_13_1 may be a useful locus to improve the yield of hybrid soybean and to understand the molecular mechanism of heterosis in soybean.