Genetic characterization of group A acetylsaponin‐deficient mutants from wild soybean (Glycine soja Sieb. and Zucc.)

Group A acetylsaponins are the main causative components for bitter and astringent tastes of soybean (Glycine max). In this study, we examined the genetic nature of the absence of group A acetylsaponins in 12 Korean wild soybean (Glycine soja) accessions. In all 12 accessions, the coding region (1431‐bp) of Sg‐1 locus was identical with Sg‐1^a, which adds the xylose sugar moiety at the terminal position of the C‐22 sugar chain of SS‐A, except one nucleotide (G→A change) at +948th position. This point mutation results in change of one amino acid from tryptophan (TGG) to stop codon (TGA). We observed that the mutated Sg‐1 was controlled by a single recessive gene (sg‐1^0‐a1). This gene was mapped between BARCSOYSSR_07_1561 and BARCSOYSSR_07_1598 on soybean chromosome 7. Our study demonstrated that the mutated Sg‐1 gene in Korean wild soybeans is genetically different from those identified in Japanese soybean cultivar ‘Kinusayaka’ and wild soybean JP‐36121. We believe that the new Sg‐1 mutants can also be utilized to produce a new soybean variety without bitter and astringent properties.     

Saponin polymorphism in the Korean wild soybean (Glycine soja Sieb. and Zucc.)

Seed saponin composition of 3025 wild soybean (Glycine soja Sieb. and Zucc.) accessions collected from nine regions of Korea was analysed by thin‐layer chromatography to determine its polymorphic variation and geographical distribution and find mutants in saponin components. The saponin composition of seed hypocotyls was primarily divided into seven phenotypes, designated as Aa, Ab, AaBc, AbBc, Aa+α, AaBc+α and AbBc+α. The predominant phenotypes were AaBc (55%), Aa (33%), AaBc+α (7.5%) and Aa+α (3.3%). The frequencies of Ab, AbBc and AbBc+α were very low (0.3‐0.5%). Codominant alleles Sg‐1^a and Sg‐1^b and dominant allele Sg‐4 occupied 98.6, 1.1 and 63.3%, respectively. Alleles Sg‐3 and Sg‐5 were found to be dominant in all the analysed accessions except the mutants. Three accessions were discovered as mutants via LC‐PDA/MS/MS. The accession CWS0115 did not produce saponin Aa and Ax, CWS2133 did not produce saponin Aa and Ab and CWS5095 did not produce any group A saponins. These newly determined mutants might be utilized in producing a new soybean variety with good taste as well as in biosynthetic studies.     

Kunitz trypsin inhibitor polymorphism in the Korean wild soybean (Glycine soja Sieb. & Zucc.)

Kunitz trypsin inhibitor (KTi) in 1368 accessions of wild soybean (Glycine soja Sieb. & Zucc.), collected from three regions of Korea, was examined for allelic diversity and geographical distribution. Five electrophoretically distinguishable KTi forms were detected: three were common (Tia, Tib and Tia/Tib) and two were previously unreported (Tib^i7‐1 and Tibⁱ⁵). The Tia allele was predominant (93.49%). Alleles Tib, Tib^i7‐1 and Tibⁱ⁵ were detected with the frequencies of 3.47, 0.55 and 0.11%, respectively. The heterozygous form (Tia/Tib) was detected with the frequency of 2.26%. The nucleotide sequence of Tib^i7‐1 was identical to that of the Tib‐derived variant allele Tif, with the exception of three nucleotides: A→G at position +244, A→C at position +286 and G→C at position +601. The latter two were similar to Tia, suggesting that Tib^i7‐1 is an intermediate allele between Tia and Tib. The gene for Tibⁱ⁵ showed 100% similarity with the Japanese intermediate allele Tibⁱ⁵. This study demonstrates that Korean wild soybeans are remarkably rich source of new KTi alleles not reported before.     

Association mapping of yield-related traits and SSR markers in wild soybean (Glycine soja Sieb. and Zucc.)

Wild soybean, the progenitor of cultivated soybean, is an important gene pool for ongoing soybean breeding efforts. To identify yield-enhancing quantitative trait locus (QTL) or gene from wild soybean, 113 wild soybeans accessions were phenotyped for five yield-related traits and genotyped with 85 simple sequence repeat (SSR) markers to conduct association mapping. A total of 892 alleles were detected for the 85 SSR markers, with an average 10.49 alleles; the corresponding PIC values ranged from 0.07 to 0.92, with an average 0.73. The genetic diversity of each SSR marker ranged from 0.07 to 0.93, with an average 0.75. A total of 18 SSR markers were identified for the five traits. Two SSR markers, sct_010 and satt316, which are associated with the yield per plant were stably expressed over two years at two experimental locations. Our results suggested that association mapping can be an effective approach for identifying QTL from wild soybean.     

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.     

Identification of quantitative trait loci controlling soybean seed weight in recombinant inbred lines derived from PI 483463 (Glycine soja) × ‘Hutcheson’ (G. max)

The objective of this study was to identify quantitative trait loci (QTLs) controlling 100‐seed weight in soybean using 188 recombinant inbred lines (RIL) derived from a cross of PI 483463 and ‘Hutcheson’. The parents and RILs were grown for 4 years (2010–2013), and mature, dry seeds were used for 100‐seed weight measurement. The variance components of genotype (a), environment (e) and a × e interactions for seed weight were highly significant. The QTL analysis identified 14 QTLs explaining 3.83–12.23% of the total phenotypic variation. One of the QTLs, qSW17‐2, was found to be the stable QTL, being identified in all the environments with high phenotypic variation as compared to the other QTLs. Of the 14 QTLs, 10 QTLs showed colocalization with the seed weight QTLs identified in earlier reports, and four QTLs, qSW5‐1, qSW14‐1, qSW15‐1 and qSW15‐2, found to be the novel QTLs. A two‐dimensional genome scan revealed 11 pairs of epistatic QTLs across 11 chromosomes. The QTLs identified in this study may be useful in genetic improvement of soybean seed weight.     

The Sg-6 saponins,new components in wild soybean (Glycine soja Sieb. and Zucc.): polymorphism,geographical distribution and inheritance

Hypocotyl saponin composition of 1,198 accessions of wild soybean (Glycine soja) collected from China, Korea, Japan and Russia Far East was analyzed by thin-layer chromatography to determine polymorphic variation and geographical distribution. Eight common distinguishable saponin phenotypes were identified: Aa, Ab, AaBc, AbBc, Aa+α, Ab+α, AaBc+α and AbBc+α. The latter four +α type were new. All eight types were identified in China. Type Ab+α was absent in Korea. Types Ab+α and AbBc+α, and Aa+α and Ab+α were not identified in Japan and Russia far east, respectively. Six new triterpene saponins were detected in +α type via LC-PDA/MS/MS analyses. They were, tentatively, designated as H-αg, H-αa, I-αg, I-αa, J-αg and J-αa. These saponins were inherited together by a single dominant allele. A gene symbol Sg-6 was assigned. Hence, the new saponins were collectively named as Sg-6 saponins. The frequency of Sg-6 allele was 17.6 % in Chinese, 10.0 % in Korean and 1.0 % in Japanese wild soybean. The wild soybeans having Sg-6 saponins can be utilized in soybean breeding programs as well as in saponin biosynthesis studies in soybean.     

Genetic characterization and gene flow in different geographical-distance neighbouring natural populations of wild soybean (Glycinesoja 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.