Semi-wild Soybean Research Articles

Creation of a semi-wild soybean with vine growth form, seed hardness and shattering resistance for drastic labor-saving cultivation in abandoned arable field, and proposals for its cultivation and utilization

Creation of a semi-wild soybean with vine growth form, seed hardness and shattering resistance for drastic labor-saving cultivation in abandoned arable field, and proposals for its cultivation and utilization

Construction of a high-density genetic map and mapping of QTLs for soybean (Glycine max) agronomic and seed quality traits by specific length amplified fragment sequencing

BackgroundSoybean is not only an important oil crop, but also an important source of edible protein and industrial raw material. Yield-traits and quality-traits are increasingly attracting the attention of breeders. Therefore, fine mapping the QTLs associated with yield-traits and quality-traits of soybean would be helpful for soybean breeders. In the present study, a high-density linkage map was constructed to identify the QTLs for the yield-traits and quality-traits, using specific length amplified fragment sequencing (SLAF-seq).ResultsSLAF-seq was performed to screen SLAF markers with 149 F8:11 individuals from a cross between a semi wild soybean, ‘Huapidou’, and a cultivated soybean, ‘Qihuang26’, which generated 400.91 M paired-end reads. In total, 53,132 polymorphic SLAF markers were obtained. The genetic linkage map was constructed by 5111 SLAF markers with segregation type of aa×bb. The final map, containing 20 linkage groups (LGs), was 2909.46 cM in length with an average distance of 0.57 cM between adjacent markers. The average coverage for each SLAF marker on the map was 81.26-fold in the male parent, 45.79-fold in the female parent, and 19.84-fold average in each F8:11 individual. According to the high-density map, 35 QTLs for plant height (PH), 100-seeds weight (SW), oil content in seeds (Oil) and protein content in seeds (Protein) were found to be distributed on 17 chromosomes, and 14 novel QTLs were identified for the first time. The physical distance of 11 QTLs was shorter than 100 Kb, suggesting a direct opportunity to find candidate genes. Furthermore, three pairs of epistatic QTLs associated with Protein involving 6 loci on 5 chromosomes were identified. Moreover, 13, 14, 7 and 9 genes, which showed tissue-specific expression patterns, might be associated with PH, SW, Oil and Protein, respectively.ConclusionsWith SLAF-sequencing, some novel QTLs and important QTLs for both yield-related and quality traits were identified based on a new, high-density linkage map. Moreover, 43 genes with tissue-specific expression patterns were regarded as potential genes in further study. Our findings might be beneficial to molecular marker-assisted breeding, and could provide detailed information for accurate QTL localization.

Comparison of Salt Tolerance in Soja Based on Metabolomics of Seedling Roots.

Soybean is an important economic crop that is continually threatened by abiotic stresses, especially salt stress. Wild soybean is an important germplasm resource for the breeding of cultivated soybean. The root system plays a very important role in plant salt tolerance. To explore the salt tolerance-related mechanisms among Soja, we have demonstrated the seedling roots' growth and metabolomics in wild soybean, semi-wild soybean, and cultivated soybean under two types of salt stress by using gas chromatography-mass spectrometry. We characterized 47 kinds of differential metabolites under neutral salt stress, and isoleucine, serine, l-allothreonine, glutamic acid, phenylalanine, asparagines, aspartic acid, pentadecanoic acid, lignoceric acid, oleic acid, galactose, tagatose, d-arabitol, dihydroxyacetone, 3-hydroxybutyric acid, and glucuronic acid increased significantly in the roots of wild soybean seedlings. However, these metabolites were suppressed in semi-wild and cultivated soybeans. Amino acid, fatty acid, sugars, and organic acid synthesis and the secondary metabolism of antioxidants increased significantly in the roots of wild soybean seedling. Under alkaline salt stress, wild soybean contained significantly higher amounts of proline, glutamic acid, aspartic acid, l-allothreonine, isoleucine, serine, alanine, arachidic acid, oleic acid, cis-gondoic acid, fumaric acid, l-malic acid, citric acid, malonic acid, gluconic acid, 5-methoxytryptamine, salicylic acid, and fluorene than semi-wild and cultivated soybeans. Our study demonstrated that carbon and nitrogen metabolism, and the tricarboxylic acid (TCA) cycle and receiver operating characteristics (especially the metabolism of phenolic substances) of the seedling roots were important to resisting salt stress and showed a regular decreasing trend from wild soybean to cultivated soybean. The metabolomics's changes were critical factors in the evolution of salt tolerance among Soja. This study provides new insights into salt tolerance in soybean, and presents quantitative parameters for a salt tolerant soybean breeding system, which is conducive to the rational use and protection of wild soybean resources.

The complete chloroplast genome sequence of semi-wild soybean, Glycine gracilis (Fabales: Fabaceae)

Semi-wild soybean, Glycine gracilis, harbors unique gene resources for the soybean breeding programs, which would help to understand the process of soybean domestication. Here, we sequenced and characterized the complete chloroplast genome sequence of the semi-wild soybean. The genome of G. gracilis has 152,218 bp in length with 35.37% GC content. It contains two inverted repeats blocks of 25,574 bp, separated by the large single-copy block of 83,175 bp and small single-copy block of 17,895 bp. A total of 111 unique genes were annotated, including 77 protein coding genes, 30 tRNA genes and 4 rRNA genes. Phylogenetic analysis of the ten sequenced Glycine chloroplast genomes revealed that the semi-wild soybean G. gracilis is closer to cultivated soybean G. max than wild soybean G. soja. The newly sequenced complete chloroplast genome of G. gracilis will provide useful resources for the further genetic characterization that would enhance the conservation of this highly endangered species.

English

This study was conducted to determine the differences and changes in trends of physiological metabolism in the process of adaptation to saline environments and artificial domestication among the subgenus Soja. Glycine max, Glycine gracilis and Glycine soja were used as the experimental material. The determination of mineral contents during different growth periods and the photosynthetic pigments, gas exchange parameters and soluble carbohydrate contents in the initial bloom stage were investigated. The results showed that, NO3, H2PO4, Cu, Zn and B contents and the photosynthetic pigments, gas exchange parameters and photosynthetic product were significantly higher in salt-tolerant wild soybean than in common wild soybean. NO3, H2PO4, SO4, K, Mg, Fe, Cu, Mo and Mn contents were significantly lower in cultivated soybean than in common wild soybean; and Ca and B were significantly higher. The photosynthetic pigments, gas exchange parameters and photosynthetic product at the initial bloom stage in cultivated soybean were significant higher than in common wild soybean and semi-wild soybean. The correlations of H2PO4, SO4, K, Mg, Mo and Mn with photosynthetic characteristic parameters significantly differed among members of Soja. Our study confirmed that mineral contents and photosynthetic characteristics among Soja had evolved towards the different environments and human requirements during long-term natural selection and artificial domestication. These findings will contribute to understanding the evolutionary trend of soybean. © 2016 Friends Science Publishers

Heterosis and combining ability estimates in isoflavone content using different parental soybean accessions: wild soybean, a valuable germplasm for soybean breeding.

Isoflavone, a group of secondary metabolites in soybean, is beneficial to human health. Improving isoflavone content in soybean seeds has become one of the most important breeding objectives. However, the narrow genetic base of soybean cultivars hampered crop improvement. Wild soybean is an extraordinarily important gene pool for soybean breeding. In order to select an optimal germplasm for breeding programs to increase isoflavone concentration, 36 F1 soybean progenies from different parental accessions (cultivars, wild, Semi-wild and Interspecific) with various total isoflavone (TIF) concentration (High, Middle, Low) were analyzed for their isoflavone content. Results showed that male parents, except for Cultivars, showed positive GCA effects. In particular, wild soybean had higher positive GCA effects for TIF concentration. Both MP and BP heterosis value declined in the hybrid in which male parents were wild soybean, semi-wild soybean, interspecific offspring and cultivar in turn. In general, combining ability and heterosis in hybrids which had relative higher TIF concentration level parents showed better performance than those which had lower TIF concentration level parents. These results indicated characteristics of isoflavone content were mainly governed by additive type of gene action, and wild relatives could be utilized for breeding of soybean cultivars with this trait. A promising combination was found as the best potential hybrid for isoflavone content improvement.

Genome Re-Sequencing of Semi-Wild Soybean Reveals a Complex Soja Population Structure and Deep Introgression

Semi-wild soybean is a unique type of soybean that retains both wild and domesticated characteristics, which provides an important intermediate type for understanding the evolution of the subgenus Soja population in the Glycine genus. In this study, a semi-wild soybean line (Maliaodou) and a wild line (Lanxi 1) collected from the lower Yangtze regions were deeply sequenced while nine other semi-wild lines were sequenced to a 3-fold genome coverage. Sequence analysis revealed that (1) no independent phylogenetic branch covering all 10 semi-wild lines was observed in the Soja phylogenetic tree; (2) besides two distinct subpopulations of wild and cultivated soybean in the Soja population structure, all semi-wild lines were mixed with some wild lines into a subpopulation rather than an independent one or an intermediate transition type of soybean domestication; (3) high heterozygous rates (0.19–0.49) were observed in several semi-wild lines; and (4) over 100 putative selective regions were identified by selective sweep analysis, including those related to the development of seed size. Our results suggested a hybridization origin for the semi-wild soybean, which makes a complex Soja population structure.

The possible origin of thick stem in Chinese wild soybean (Glycine soja)

Thicker, erect stem and enlarged seeds are characteristic of the domestication of cultivated soybeans (Glycine max) from its progenitor, wild soybean (G.soja). Wild soybeans have different stem thicknesses but the thick stem as defined here appears in a small number of small-seeded wild soybeans (≤2.0 g/100-seeds) in China. However, little attention has been paid to this phenomenon in considering the origin of thick stem in wild soybean. Here, we addressed this question through the study of a mixed field of wild, semi-wild and cultivated soybeans. Thick-stemmed samples had lower sensitivity to light period, higher mean genetic diversity (He = 0.090, H = 0.535) and higher mean multilocus outcrossing rate (tm = 9.77 %), while thin-stemmed plants were the opposite (He = 0.029, H = 0.416) and lower mean outcrossing rate (tm = 5.88 %). F statistics calculations indicated that there was genetic differentiation between the thin and thick stems. UPGM cluster analysis showed that not only were thick-stemmed wild soybeans genetically different from thin-stemmed ones, but they were also genetically closer to semi-wild soybean, to varying degrees completely dependent on seed size. These data strongly implied that the plants with thick stems had more complicated genetic backgrounds than the thin-stemmed ones, and that they were related to cultivated soybeans. This study suggests that if plants have distinctly thick stems (an average 2.5-fold thicker than other thin-stemmed plants) or stems similar to semi-wild plants and/or near to local soybeans in a natural wild population adjacent to farmlands, such plants could be cultivar-introgressive offspring.

Genetic diversity and gene flow dynamics revealed in the rare mixed populations of wild soybean (Glycine soja) and semi-wild type (Glycine gracilis) in China

Thus far, there is little knowledge of the genetic diversity, structure and gene flow dynamics in rare wild and semi-wild soybean mixed populations, and such information is vital for understanding of the origin of semi-wild soybean (Glycine gracilis) and the biosafety protection of wild soybean from transgenic soybeans. Population eco-genetic data are necessary to provide a more coherent and comprehensive understanding of the genetic events that occurred in the natural habitats of wild soybean (Glycine soja). We tested genetic diversity and structure of 11 wild mixed populations of wild soybean (Glycine soja) and semi-wild soybean (G. gracilis), 1 wild soybean population, and 1 cultivated soybean variety population were studied using 20 nuclear microsatellite markers (SSRs). We found based on microsatellite polymorphisms that the mixed populations were characterized by higher mean heterozygosity (H o = 0.029) and outcrossing rate (t m = 6.35 %), and lower fixation index (F is = 0.891), and the semi-wild plants had distinctly higher heterozygosity (H o = 0.081) than that of the wild plants (H o = 0.007). The occurrence of semi-wild plants influenced population genetic structure but not geographical population differentiation. These mixed populations exhibited strong ecogeographical differentiation, which suggests that their original populations were colonized over a long phytogeographical history. The introgression occurred through pollen gene flow from the soybean fields into wild populations and created the semi-wild plants, with significant genetic differentiation from the typical wild ones. Introgressive genes could become established by two possible modes in wild soybean populations by both self-segregation and/or intrapopulation secondary hybridization. The latter deserves attention because of the possibility of rapid transgene escape.

Phylogenetic relationships, interspecific hybridization and origin of some rare characters of wild soybean in the subgenus Glycine soja in China

The Glycine subgenus Soja includes two species, cultivated soybean [(Glycine max (L.) Merr.)] and the progenitor wild soybean (G. soja). However, a morphologically intermediate form, the semi-wild soybean (G. gracilis), exists between the two species, and its taxonomic position is under debate. In this study, we evaluated phylogenetic relationships and occurrence events within the subgenus Soja based on genetic variation of SSR loci using a set of accessions comprising wild soybeans (≤3.0 g 100-seed weight), semi-wild soybeans (>3.0 g) and soybean landraces (≥4.0 g). The results showed that semi-wild soybean accessions collected in natural fields should be treated as a variant of G. soja and not of G. max, and were genetically differentiated from the soybean landraces, even large-seeded semi-wild soybean accessions (6.01–9.0 g) with seed weights overlapping with or exceeding those of soybean landraces. Evolutionary bottleneck analysis indicated that semi-wild soybean is not a transitional form in the domestication of cultivated soybeans from wild soybean. G. soja contained two genetically differentiated forms, small-seeded type (typical, plus 2.01–2.50 g) and a large-seeded type (2.51–3.0 g). Genetically, the large-seeded wild soybean was closer to the semi-wild soybean, although in morphology it resembled the typical wild soybean. Ancestry analysis confirmed that cultivated soybean genes have introgressed into modern wild soybean populations. The green cotyledon character and other rare characters such as white flower, grey pubescence, no-seed bloom, and coloured seed-coats (brown, green, and yellow) in wild soybean were shown to be involved in introgression from cultivated soybeans.

Natural introgression from cultivated soybean (Glycine max) into wild soybean (Glycine soja) with the implications for origin of populations of semi-wild type and for biosafety of wild species in China

Introgression from soybean cultivars to its wild progenitor species is an interesting antidromic recombination in natural ecosystem with many consequences, including the alteration of genetic diversity, the origin of semi-wild soybean, and implication for biosafety of the wild progenitor species with future release of the genetically modified varieties. Although such interspecific introgression is not suspected to be ubiquitous in the sympatric regions of wild and cultivated soybeans, the documentations published based on some molecular experimental analyses on the introgression have been little substantiated by the occurring process morphologically and remain deficient for unquestionable evidence, owing to the lack of actual insight into the population dynamics. Here, we found the phenomenon of gene escape and presented the evidence for occurrence of introgression from soybeans into the wild species and for how originates about the semi-wild type soybean based on morphological investigation of population dynamics. Our results suggest that more attention should be paid to the escape of genetically modified genotypes to safeguard the biosafety of wild soybean gene pool, if GM soybeans are released in China, the place of origin of cultivated soybeans.

Endosperm Size Diversity in Domesticated, Wild, and Semiwild Soybean

ABSTRACTPast literature documents that domesticated soybean, Glycine max (L.) Merr., has trivial to almost nonexistent galactomannan‐containing endosperm in mature dormant seeds. Current preliminary observations confirm limited endosperm for many domesticated soybean accessions, but show that many others have markedly larger endosperm, as do all wild (G. soja Sieb. & Zucc.) and semiwild (G. gracilis Skvortz.) accessions. A trend toward small endosperm seems to have taken place during soybean domestication, which may be explained by some undesirable effects of galactomannans on monogastric animals. The broad diversity of genetic resources for endosperm size and associated galactomannans in available domesticated, wild, and semiwild accessions suggests use of soybean as a model plant for exploring differences, including water relations, between endospermic and nonendospermic legume seeds. It also suggests their use for breeding domesticated soybean with even smaller amounts of galactomannans for use in animal feeds, large amounts of galactomannans for commercial use, or genetic manipulation of the endosperm for other uses.

Phenotypic diversity of the big seed type subcollection of wild soybean (Glycine soja Sieb. et Zucc.) in China

Wild soybean (Glycine soja), the progenitor of soybeans, has become an important germplasm source for soybean breeding. The Chinese G. soja germplasm collection includes two subcollections, one typical wild soybean (G. soja) and the other ‘big seed type’ (semi-wild soybean, G. gracilis). In order to understand the nature of this big seed type subcollection, a considerable number of 1,185 accessions were investigated focusing on phenotypes, compositional structure and genetic diversity of this subcollection. The results showed that there were 617 combined morphotypes formed by six major morphological traits. The morphotype number and diversity gradually decreased among four sections from small to large 100-seed weight sizes. The big seed subcollection accumulated distinctly high frequencies for white flower, grey pubescence, seed non-bloom and four seed coat colours (green, yellow, brown and black), differing from the typical G. soja. Between the two subcollections, only the compositional structures of leaf shapes were almost in agreement. A rare strip-shaped leaf only appeared in typical G. soja and small-seeded grade (100-seed wt) of the big seed type. Seed non-bloom trait showed that the increased frequencies were concomitant with the augmenting of 100-seed weight. The data suggested that white flower accumulated rapidly in the big seed type, followed by seed non-bloom, while the slowest rate of accumulation was grey pubecence, and that the ‘large-seeded type (2.51–3 g 100-seed wt)’ of typical G. soja and the ‘smallest-seeded type (3.01–3.5 g 100-seed wt)’ of the big seed type could have a closer genetic relationship. The morphotype number and genetic diversity showed reduced values with increased 100-seed weights. The geographical distribution of genetic diversity indicated two tendencies: decreased from north to south and also from east to west. Our results suggested that Northeast China was the first centre of morphological diversity for the big seed type, and the North was the secondary centre in China.

Characterization of root architecture in an applied core collection for phosphorus efficiency of soybean germplasm

In the present study, we constructed an “applied core collection” for phosphorus (P) efficiency of soybean germplasm using a GIS-assisted approach. Systematic characterization and comparative analysis of root architecture were conducted to evaluate the relationship between root architecture and P efficiency and its possible evolutionary pattern. Our results found that: i) root architecture was closely related to P efficiency in soybean. Shallow root architecture had better spatial configuration in the P-rich cultivated soil layer hence higher P efficiency and soybean yield; ii) there was a possible co-evolutionary pattern among shoot type, root architecture and P efficiency. The bush cultivated soybean had a shallow root architecture and high P efficiency, the climbing wild soybean had a deep root architecture and low P efficiency, while the root architecture and P efficiency of semi-wild soybean were intermediate between cultivated and wild soybean; iii) P availability regulated root architecture. Soybean roots became shallower with P addition to the topsoil, indicating that the co-evolutionary relationship between root architecture and P efficiency might be attributed to the long-term effects of topsoil fertilization. Our results could provide important theoretical basis for improving soybean root traits and P efficiency.

Genetic Variation and Relationships among Cultivated, Wild, and Semiwild Soybean

Some annual Glycine accessions are intermediate between the standard phenotypes of Glycine max (L.) Merr. and Glycine soja Sieb. & Zucc. and have been labeled semiwild. Few studies have examined both the genetic and phenotypic relationships among G. soja, G. max, and semiwild‐types by combining morphological traits and DNA markers. The objectives of this research were to quantify genetic variation within G. soja, G. max, and semiwild accessions; to investigate the relationships among the G. soja, G. max, and semiwild accessions; and to examine the relationships among phenotypes on the basis of morphological traits and genotypes on the basis of DNA markers. Ninety‐two semiwild, G. soja, and G. max accessions from the USDA Soybean Germplasm Collection were evaluated for 20 phenotypic traits and with 137 RAPD markers. Mahalanobis distances and a Jaccard genetic similarity matrix were calculated for phenotypic traits and DNA data, respectively. Nonhierarchical and hierarchical clustering as well as multidimensional scaling (MDS) were used to evaluate relationships among semiwild, G. soja, and G. max accessions. Principal component analysis was applied to identify the morphological traits that were most significant in separating the three groups. For the accessions examined, unique RAPD markers were found for each taxonomic type. Three clusters defined by either phenotypic or DNA data are highly consistent and strongly corresponded to G. soja, G. max, and semiwild classifications. On the basis of the analysis of RAPD data, G. soja accessions have the greatest genetic diversity and semiwild accessions the least. Glycine max and semiwild accessions are more closely related to each other than to G. soja accessions. These data will be useful in helping to define a core collection of annual Glycine

Genetic Variation and Relationships among Cultivated, Wild, and Semiwild Soybean

Some annual Glycine accessions are intermediate between the standard phenotypes of Glycine max (L.) Merr. and Glycine soja Sieb. & Zucc. and have been labeled semiwild. Few studies have examined both the genetic and phenotypic relationships among G. soja, G. max, and semiwild-types by combining morphological traits and DNA markers. The objectives of this research were to quantify genetic variation within G. soja, G. max, and semiwild accessions; to investigate the relationships among the G. soja, G. max, and semiwild accessions; and to examine the relationships among phenotypes on the basis of morphological traits and genotypes on the basis of DNA markers. Ninety-two semiwild, G. soja, and G. max accessions from the USDA Soybean Germplasm Collection were evaluated for 20 phenotypic traits and with 137 RAPD markers. Mahalanobis distances and a Jaccard genetic similarity matrix were calculated for phenotypic traits and DNA data, respectively. Nonhierarchical and hierarchical clustering as well as multidimensional scaling (MDS) were used to evaluate relationships among semiwild, G. soja, and G. max accessions. Principal component analysis was applied to identify the morphological traits that were most significant in separating the three groups. For the accessions examined, unique RAPD markers were found for each taxonomic type. Three clusters defined by either phenotypic or DNA data are highly consistent and strongly corresponded to G. soja, G. max, and semiwild classifications. On the basis of the analysis of RAPD data, G. soja accessions have the greatest genetic diversity and semiwild accessions the least. Glycine max and semiwild accessions are more closely related to each other than to G. soja accessions. These data will be useful in helping to define a core collection of annual Glycine

Construction of a soybean linkage map using an F2 hybrid population from a cultivated variety and a semi-wild soybean

Construction of a soybean linkage map using an F2 hybrid population from a cultivated variety and a semi-wild soybean

Maturation and germination of somatic embryos as affected by sucrose and plant growth regulators in soybeans Glycine gracilis Skvortz and Glycine max (L.) Merr.

The effects of sucrose on maturation and of plant growth regulators on germination of soybean somatic embryos were investigated for the purpose of developing an efficient culture method for plant recovery. Somatic embryos produced on medium with a low sucrose concentration (5 gl-1), less than 1 mm in length, 0.6 mg in fresh weight, and green in color, were grown for 2 weeks on MS medium containing 5 gl-1 or 30 gl-1 sucrose and then for another 5 weeks on MS medium containing 5–90 gl-1 sucrose. The highest increase in fresh weight of somatic embryos was obtained in the treatment of transferring from 30 gl-1 sucrose (2 weeks) to 60 gl-1 (5 weeks). With the increase in fresh weight, the somatic embryos gradually changed color from green to yellow, and finally to white, when they stopped growth. Soybean seed storage proteins (β-conglycinin and glycinin) were accumulated in somatic embryos under tissue specific and stage specific control analogous to that in zygotic embryos. Exogenous gibberellic acid was effective in promoting precocious germination of premature soybean somatic embryos, but was not necessary for the germination of mature somatic embryos. The efficiency of somatic embryo germination was as high as 77% from semi-wild soybean and 60–64% from cultivated soybeans, showing that the plant regeneration system developed in this study was efficient and practical.