Soybean Accessions Research Articles

Assessment of the Genetic Structure and Diversity of Soybean (Glycine max L.) Germplasm Using Diversity Array Technology and Single Nucleotide Polymorphism Markers.

Knowledge of the genetic structure and diversity of germplasm collections is crucial for sustainable genetic improvement through hybridization programs and rapid adaptation to changing breeding objectives. The objective of this study was to determine the genetic diversity and population structure of 281 International Institute of Tropical Agriculture (IITA) soybean accessions using diversity array technology (DArT) and single nucleotide polymorphism (SNP) markers for the efficient utilization of these accessions. From the results, the SNP and DArT markers were well distributed across the 20 soybean chromosomes. The cluster and principal component analyses revealed the genetic diversity among the 281 accessions by grouping them into two stratifications, a grouping that was also evident from the population structure analysis, which divided the 281 accessions into two distinct groups. The analysis of molecular variance revealed that 97% and 98% of the genetic variances using SNP and DArT markers, respectively, were within the population. Genetic diversity indices such as Shannon’s diversity index, diversity and unbiased diversity revealed the diversity among the different populations of the soybean accessions. The SNP and DArT markers used provided similar information on the structure, diversity and polymorphism of the accessions, which indicates the applicability of the DArT marker in genetic diversity studies. Our study provides information about the genetic structure and diversity of the IITA soybean accessions that will allow for the efficient utilization of these accessions in soybean improvement programs, especially in Africa.

<i>In vitro</i> regeneration of soybean (a review)

This is an overview of contemporary published works dedicated to the ability of soybean plants to regenerate in vitro and the techniques to achieve high regeneration rates, which is a necessary condition for the inclusion of soybean genotypes in genome editing programs. The main factors that determine the regenerative capacity of explants from various soybean accessions are considered. The greatest effect on the efficiency of regeneration is exerted by the conditions of in vitro culture initiation, type of explant, composition of the nutrient medium, shelf life of seeds, and genotypic characteristics of soybean accessions.

Efficiency of <i>in vitro</i> culture techniques applied to soybean (<i>Glycine max (L.) Merr.</i>) accessions from the VIR collection

Using a wide range of modern biotechnologies and genetic techniques to study plant germplasm accessions held by VIR makes it possible to procure valuable results, required for the development of new high-yielding cultivars adapted to adverse environmental conditions and possessing specified technological properties, particularly to identify and mark new genes and alleles useful for plant breeding. This research trend is in line with Presidential Decree No. 680 “Concerning the development of genetic technologies in the Russian Federation”. Soybean is among the key crops in agricultural production, but the use of next-generation breeding tools to obtain new soybean cultivars with desired properties is still limited. Successful application of novel methods also requires new approaches to studying soybean accessions, specifically their ability to regenerate and produce calluses for subsequent inclusion in biotechnological programs.Ten soybean accessions of various origin, contrasting in ripening schedules, were selected to study the possibility of effective introduction into in vitro culture and further assessment of their ability to produce calluses and regenerate in in vitro culture. The work included evaluating the effects of different seed sterilization techniques (one-step sterilization, using a commercial bleach, and two-step one, combining the impacts of a chlorine-containing preparation and hydrogen peroxide), types of explants (epicotyls, hypocotyls, cotyledon nodes, and cotyledon leaf segments), and phytohormone composition of nutrient medium: (1) MS + 1.13 mg/L BAP + 0.5 mg/L HA, and (2) MS +1 mg/L BAP + 0.1 mg/L IAA).The assessment results showed that the option of two-step seed sterilization was the most effective for soybean at the stage of in vitro culture initiation, while hypocotyls, epicotyls, and cotyledon nodes had the highest callus formation ability in both types of nutrient media.

Evaluation of regrowth ability of soybeans for forage utilization under two-cutting systems

Soybean (Glycine max) has the potential as forage feed because of its high protein content and low fiber. Intercropping soybean with tropical forage grasses can improve forage quality and increase yield. However, their optimum cutting interval under mixed cropping system is still unknown. This study aimed to investigate regrowth ability and performance of soybean plant under two different cutting heights in Miyazaki, Southwestern of Japan, which has a humid subtropical climate with relatively high temperature and evenly distributed precipitation throughout the year. The experimental design was randomized block design arrange in 3  2 factorial scheme (soybean cultivars  cutting treatments). Three soybean accessions (Glycine max ‘Fukuyutaka’, G. max ‘Kohamdaizu’ and G. gracilis ‘Moshidou Gong 503’) with 5 replications were cultivated under single seeding condition. Soybeans were defoliated after 50 d of cultivation under low level cutting height (LC, 7.5 cm) and high level cutting height (HC, 12 cm). ‘Fukuyutaka’ achieved 100% regrowth rate in both LC and HC. Although the regrowth rate for ‘Kohamadaizu’ was 100% in the HC, it was only 20% in LC. ‘Fukuyutaka’ was more robust and high tolerant for defoliation stress than that of ‘Kohamadaizu`. In other hand, no plants exhibited regrowth in both cutting heights for ‘Moshidou Gong 503’. For ‘Fukuyutaka’ and ‘Kohamadaizu’, the number of branching nodes with re-emergent leaves was significantly higher in the HC. In both cutting height of ‘Fukuyutaka’, plant continued elongating and exhibited vigorous growth until 2nd cutting. The cutting height levels, height of cotyledonary node and growth stage of soybean plant when harvested at the 1st cutting significantly affected the regrowth ability of soybeans. In conclusion, ‘Fukuyutaka’ showed the ability for regrowth under LC and HC. HC provided significantly higher fresh matter and dry matter weight than that LC. Further study is needed to evaluate the performance of ‘Fukuyutaka’ under intercropping cultivation with tropical forage grasses. This is the first report to establish an approach for two-cutting soybean as forage

Novel target sites for soybean yield enhancement by photosynthesis

Photosynthesis plays an important role in plant growth and development. Increasing photosynthetic rate is a main objective of improving crop productivity. Chlorophyll fluorescence is an effective method for quickly evaluating photosynthesis. In this study, four representative chlorophyll fluorescence parameters, that is, maximum quantum efficiency of photosystem II, quantum efficiency of PSII, photochemical quenching, and non-photochemical quenching, of 219 diverse soybean accessions were measured across three environments. The underlying genetic architecture was analyzed by genome-wide association study. Forty-eight SNPs were detected to associate with the four traits and explained 10.43–20.41% of the phenotypic variation. Nine candidate genes in the stable QTLs were predicted. Great differences in the expression levels of the candidate genes existed between the high photosynthetic efficiency accessions and low photosynthetic efficiency accessions. In all, we uncover 17 QTLs associated with photosynthesis-related traits and nine genes that may participate in the regulation of photosynthesis, which can provide references for revealing the genetic mechanism of photosynthesis. These QTLs and candidate genes will provide new targets for crop yield improvement through increasing photosynthesis.

Identification and molecular mapping of a major quantitative trait locus underlying branch angle in soybean.

A major quantitative trait locus (QTL) modulating soybean (Glycine max) branch angle was identified by linkage analysis using two bi-parental mapping populations with and without pedigree from wild soybean (Glycine soja). Soybean branch angle is a critical architectural trait that affects many other traits of agronomic importance associated with the plant's productivity and grain yield and is thus a vital consideration in soybean breeding. However, the genetic basis for modulating this important trait in soybean and many other crops remain unknown. Previously, we developed a recombinant inbred line (RIL) population derived from a cross between a domesticated soybean (Glycine max) variety, Williams 82, and a wild soybean (Glycine soja) accession, PI 479,752, and observed drastic variation in plant architecture including branch angle among individual RILs. In this study, one of the RILs possessing extremely wide branch angle (WBA) was crossed with an elite soybean cultivar (LD00-3309) possessing narrow branch angle (NBA) to produce an F2 population composed of 147 plants and F2-derived F3 families for inheritance analysis and QTL mapping. We found that branch angle is controlled by a major QTL located on chromosome 19, designated qGmBa1 and that WBA-derived from the wild soybean accession-is dominant over NBA. This locus was also detected as a major one underlying branch angle by QTL mapping using a subset of the soybean nested association mapping (SoyNAM) population composed of 140 RILs, which were derived from a cross between a landrace, PI 437169B, possessing WBA and an elite variety, IA3023, possessing NBA. Molecular markers located in the QTL region defined by both mapping populations can be used for marker-assisted selection of branch angle in soybean breeding.

Dissecting four correlated growth period traits using a genome-wide association study approach in soybean

Soybean [Glycine max (L.) Merr.] is a short-day, photoperiod-sensitive crop. The vegetative growth period (V), reproductive growth period (R), whole growth period (V + R) and the ratio of growth period structure (R/V) are photoperiod traits critical to adaptability and yield in soybean. To thoroughly dissect the genetic basis of these growth period traits and their correlations, a panel of 277 soybean accessions were genotyped with a single nucleotide polymorphisms (SNPs) panel and phenotyped at three field environments over three years. A genome-wide association study found 28 SNPs on fifteen chromosomes with 33 significant marker-trait associations, eleven, eight, four and ten for V, R, V + R and R/V, respectively. Two SNPs, Map-6077 and -6502, showed pleiotropy in three and two traits, respectively. Map-6077, associated with V, R, and V + R, was a synonymous SNP of the GmMFT, a member of PEBP family that has been reported to inhibit seed germination and regulate oil content. These results provide candidate SNP markers and genes for further functional experiments to advance molecular marker-assisted breeding.

Phytohormone dynamics impact fatty acid and oil accumulation during soybean seed maturation

AbstractFatty acid (FA) levels and profiles are vital for soybean oil quality, while cytokinins (CKs) and abscisic acid (ABA) are potent regulators of plant growth and development. Previous research suggested associations between FA biosynthesis and hormonal signalling networks; however, hormonal regulation of FA accumulation during soybean (Glycine max) seed maturation has never been measured. We analysed hormone and FA profiles obtained from HPLC-(ESI)-MS/MS and GC-FID screening during soybean seed maturation. A multilayered data processing approach, involving heat-maps, principal component analysis (PCA), correlation and multiregression models, suggested a strong relationship between hormone metabolism and FA/oil accumulation during seed maturation. Most strikingly, positive correlations were found between the levels of CK ribosides [transZeatin riboside (tZR), N6-isopentenyladenosine (iPR)] at the early stages of SM (R5-R6) and C18:0, C18:2 and oil content at the R8 stage. Moreover, multiple regression models revealed functional linkages between several CK derivatives and FA and oil content in mature seeds. To further test the significance of hormone regulation in FA metabolism, plants of two soybean accessions with contrasting hormone and FA profiles were sprayed with exogenous ABA and transZeatin (tZ) during the seed-filling period (R5-R6). Depending on the hormone type and concentration, these treatments distinctly modified biosynthesis of all tested FAs, except for C18:0. Most remarkably, tZ (50 nM) promoted production of C16:0, C18:1, C18:2, C18:3, and oil accumulation in maturing seeds. Overall, the results indicate impactful roles for ABA and CKs in FA accumulation during SM and represent a further step towards understanding FA biosynthesis, and potential improvements of soybean oil profiles.

Identification of genes for drought resistance and prediction of gene candidates in soybean seedlings based on linkage and association mapping

Drought is one of the primary abiotic stress factors affecting the yield, growth, and development of soybeans. In extreme cases, drought can reduce yield by more than 50%. The seedling stage is an important determinant of soybean growth: the number and vigor of seedlings will affect growth and yield at harvest. Therefore, it is important to study the drought resistance of soybean seedlings. In this study, a recombinant inbred line (RIL) population comprising 234 F6:10 lines (derived from Zhonghuang 35 × Jindou 21) and a panel of 259 soybean accessions was subjected to drought conditions to identify the effects on phenotypic traits under these conditions. Using a genetic map constructed by single nucleotide polymorphism (SNPs) markers, 18 quantitative trait loci (QTL) on 7 soybean chromosomes were identified in two environments. This included 9 QTL clusters identified in the RIL population. Fifty-three QTL were identified in 19 soybean chromosomes by genome-wide association analysis (GWAS) in the panel of accessions, including 69 significant SNPs (−log10 (P) ≥ 3.97). A combination of the two populations revealed that two SNPs (−log10 (P) ≥ 3.0) fell within two of the QTL (qPH7-4 and qPH7-6) confidence intervals. We not only re-located several previously reported drought-resistance genes in soybean and other crops but also identified several non-synonymous stress-related mutation site differences between the two parents, involving Glyma.07g093000, Glyma.07g093200, Glyma.07g094100 and Glyma.07g094200. One previously unreported new gene related to drought stress, Glyma.07g094200, was found by regional association analysis. The significant SNP CHR7-17619 (G/T) was within an exon of the Glyma.07g094200 gene. In the RIL population, the DSP value of the “T” allele of CHR7-17619 was significantly (P < 0.05) larger than the “G” allele in different environments. The results of our study lay the groundwork for cloning and molecular marker-assisted selection of drought-resistance genes in soybeans at the seedling stage.

Detection of rare nematode resistance Rhg1 haplotypes in Glycine soja and a novel Rhg1 α-SNAP.

This study pursued the hypothesis that wild plant germplasm accessions carrying alleles of interest can be identified using available single nucleotide polymorphism (SNP) genotypes for particular alleles of other (unlinked) genes that contribute to the trait of interest. The soybean cyst nematode (SCN, Heterodera glycines [HG]) resistance locus Rhg1 is widely used in farmed soybean [Glycine max (L.) Merr.]. The two known resistance-conferring haplotypes, rhg1-a and rhg1-b, typically contain three or seven to 10 tandemly duplicated Rhg1 segments, respectively. Each Rhg1 repeat carries four genes, including Glyma.18G022500, which encodes unusual isoforms of the vesicle-trafficking chaperone α-SNAP. Using SoySNP50K data for NSFRAN07 allele presence, we discovered a new Rhg1 haplotype, rhg1-ds, in six accessions of wild soybean, Glycine soja Siebold & Zucc. (0.5% of the ∼1,100 G. soja accessions in the USDA collection). The α-SNAP encoded by rhg1-ds is unique at an important site of amino acid variation and shares with the rhg1-a and rhg1-b α-SNAP proteins the traits of cytotoxicity and altered N-ethylmaleimide sensitive factor (NSF) protein interaction. Copy number assays indicate three repeats of rhg1-ds. G. soja PI 507613 and PI 507623 exhibit resistance to HG type 2.5.7 SCN populations, in part because of contributions from other loci. In a segregating F2 population, rhg1-b and rhg1-ds made statistically indistinguishable contributions to resistance to a partially virulent HG type 2.5.7 SCN population. Hence, the unusual multigene copy number variation Rhg1 haplotype was present but rare in ancestral G. soja and was present in accessions that offer multiple traits for SCN resistance breeding. The accessions were initially identified for study based on an unlinked SNP.

Identification of soybean phosphorous efficiency QTLs and genes using chlorophyll fluorescence parameters through GWAS and RNA-seq.

Soybean phosphorous efficiency QTLs were identified and candidate genes were predicted using chlorophyll fluorescence parameters through GWAS and RNA-seq. Phosphorus (P) is an essential nutrient element for crop growth and development, lack of P uptake seriously affects yield in various crops. Photosynthesis is the basis of crop production, while it is very sensitive to P deficiency. It is of great importance to study the genetic relationship between photosynthesis and P efficiency to provide genetic insight for soybean improvement. In this study, a genome-wide association study (GWAS) was performed using 292,035 SNPs and the ratios of four main chlorophyll fluorescence parameters of 219 diverse soybean accessions under P deficiency and normal P across three experiments. In total, 52 SNPs in 12 genomic regions were detected in association with the four main chlorophyll fluorescence parameters under sufficient or deficient P levels. Combined it with RNA-seq analysis, we predicted three candidate genes for the significant genomic regions. For example, the expression level of the candidate gene (Glyma.18g092900) in P deficiency tolerant accession was three times higher than that of P deficiency sensitive one under phosphorous deficiency condition. This study provides insight into genetic links between photosynthetic and phosphorous efficiency and further functional analysis will provide valuable information for understanding the underlying genetic mechanism to facilitate marker-assisted breeding in soybean.

Sensitive and Specific qPCR and Nested RT-PCR Assays for the Detection of Tobacco Streak Virus in Soybean

Tobacco streak virus (TSV) is a reemerging and understudied pathogen of soybean (Glycine max). Management of TSV is challenging due to the multiple modes of transmission, widespread susceptibility of commercial soybean, and lack of reliable diagnostic tests for the virus. Soybean plants with TSV-like, virus-like, or no symptoms were collected from commercial and research fields in seven counties in Wisconsin. Two sensitive assays were developed for the detection of TSV: a fluorescent dye-based quantitative reverse-transcription PCR (qPCR) assay and a nested reverse-transcription PCR (nRT-PCR). TSV was detected in 47 and 91% of symptomatic samples using the qPCR and nRT-PCR assays, respectively, suggesting that the nRT-PCR assay has higher sensitivity for detecting TSV. The qPCR assay’s limit of detection was determined at 10 fg and the assay was used to estimate the viral load in TSV-symptomatic samples. The titer of TSV in these samples was determined by absolute quantification and ranged from 15 fg to 0.796 ng. The two assays reported here provide diagnostic tools for the rapid and accurate detection of TSV that can aid in monitoring outbreaks, assessing management strategies, or screening soybean cultivars or accessions for resistance to the virus. [Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Structural variation of mitochondrial genomes sheds light on evolutionary history of soybeans.

The architecture and genetic diversity of mitogenome (mtDNA) are largely unknown in cultivated soybean (Glycine max), which is domesticated from the wild progenitor, Glycine soja, 5000 years ago. Here, we de novo assembled the mitogenome of the cultivar 'Williams 82' (Wm82_mtDNA) with Illumina PE300 deep sequencing data, and verified it with polymerase chain reaction (PCR) and Southern blot analyses. Wm82_mtDNA maps as two autonomous circular chromosomes (370 871-bp Chr-m1 and 62 661-bp Chr-m2). Its structure is extensively divergent from that of the mono-chromosomal mitogenome reported in the landrace 'Aiganhuang' (AGH_mtDNA). Synteny analysis showed that the structural variations (SVs) between two genomes are mainly attributed to ectopic and illegitimate recombination. Moreover, Wm82_mtDNA and AGH_mtDNA each possess six and four specific regions, which are absent in their counterparts and likely result from differential sequence-loss events. Mitogenome SV was further studied in 39 wild and 182 cultivated soybean accessions distributed world-widely with PCR/Southern analyses or a comparable in silico analysis. The results classified both wild and cultivated soybeans into five cytoplasmic groups, named as GSa-GSe and G1-G5; 'Williams 82' and 'Aiganhuang' belong to G1 and G5, respectively. Notably, except for members in GSe and G5, all accessions carry a bi-chromosomal mitogenome with a common Chr-m2. Phylogenetic analyses based on mtDNA structures and chloroplast gene sequences both inferred that G1-G3, representing >90% of cultigens, likely inherited cytoplasm from the ancestor of domestic soybean, while G4 and G5 likely inherited cytoplasm from wild soybeans carrying GSa- and GSe-like cytoplasm through interspecific hybridization, offering new insights into soybean cultivation history.

Reference Genes and Expression Analysis of Seed Desaturases Genes in Soybean Mutant Accessions.

Soybean oil is the second most-produced vegetable oil worldwide. To enhance the nutritional quality and oxidative stability of soybean oil, many soybean breeding programs are trying to increase oleic acid content and reduce linoleic and linolenic acid contents. The fatty acid profile of soybean oil is controlled by many genes, including those which code for omega-3 and omega-6 desaturases. Mutations in GmFAD2-1 and GmFAD3 genes are widely studied and their combinations can produce soybean oil with high oleic and low linoleic and linolenic content. However, few studies evaluate the effect of these mutations on gene expression. Therefore, the present study sought to identify reference genes, evaluate the expression of GmFAD2-1 and GmFAD3 seed desaturase genes in thirteen wild-type and mutated soybean accessions, and associate the expression patterns with fatty acid composition and with the GmFAD2-1 and GmFAD3 genotypes. GmCONS7 and GmUKN2 were identified as the best reference genes for combined use to normalize data. The GmFAD2-1A mutation of PI603452 accession was associated with a decrease in gene expression of GmFAD2-1A; however, downregulation may not be due to the truncated enzyme structure alone. These results suggested that there are factors other than GmFAD2-1A and GmFAD2-1B that have a considerable effect on oleic content, at least in soybeans with mutations in these two genes.

Genome-Wide Association Study to Map Genomic Regions Related to the Initiation Time of Four Growth Stage Traits in Soybean.

The time to flowering (DF), pod beginning (DPB), seed formation (DSF), and maturity initiation (DMI) in soybean (Glycine max [L.] Merr) are important characteristics of growth stage traits (GSTs) in Chinese summer-sowing soybean, and are influenced by genetic as well as environmental factors. To better understand the molecular mechanism underlying the initiation times of GSTs, we investigated four GSTs of 309 diverse soybean accessions in six different environments and Best Linear Unbiased Prediction values. Furthermore, the genome-wide association study was conducted by a Fixed and random model Circulating Probability Unification method using over 60,000 single nucleotide polymorphism (SNP) markers to identify the significant quantitative trait nucleotide (QTN) regions with phenotypic data. As a result, 212 SNPs within 102 QTN regions were associated with four GSTs. Of which, eight stable regions were repeatedly detected in least three datasets for one GST. Interestingly, half of the QTN regions overlapped with previously reported quantitative trait loci or well-known soybean growth period genes. The hotspots associated with all GSTs were concentrated on chromosome 10. E2 (Glyma10g36600), a gene with a known function in regulating flowering and maturity in soybean, is also found on this chromosome. Thus, this genomic region may account for the strong correlation among the four GSTs. All the significant SNPs in the remaining 7 QTN regions could cause the significant phenotypic variation with both the major and minor alleles. Two hundred and seventy-five genes in soybean and their homologs in Arabidopsis were screened within ± 500 kb of 7 peak SNPs in the corresponding QTN regions. Most of the genes are involved in flowering, response to auxin stimulus, or regulation of seed germination, among others. The findings reported here provide an insight for genetic improvement which will aid in breeding of soybean cultivars that can be adapted to the various summer sowing areas in China and beyond.

Genetic control and allele variation among soybean maturity groups 000 through IX

Soybean [Glycinemax (L.) Merr.] maturity determines the growing region of a given soybean variety and is a primary factor in yield and other agronomic traits. The objectives of this research were to identify the quantitative trait loci (QTL) associated with maturity groups (MGs) and determine the genetic control of soybean maturity in each MG. Using data from 16,879 soybean accessions, genome-wide association (GWA) analyses were conducted for each paired MG and across MGs 000 through IX. Genome-wide association analyses were also performed using 184 genotypes (MGs V-IX) with days to flowering (DTF) and maturity (DTM) collected in the field. A total of 58 QTL were identified to be significantly associated with MGs in individual GWAs, which included 12 reported maturity loci and two stem termination genes. Genome-wide associations across MGs 000-IX detected a total of 103 QTL and confirmed 54 QTL identified in the individual GWAs. Of significant loci identified, qMG-5.2 had effects on the highest number (9) of MGs, followed by E2, E3, Dt2, qMG-15.5, E1, qMG-13.1, qMG-7.1, and qMG-16.1, which affected five to seven MGs. A high number of genetic loci (8-25) that affected MGs 0-V were observed. Stem termination genes Dt1 and Dt2 mainly had significant allele variation in MGs II-V. Genome-wide associations for DTF, DTM, and reproductive period (RP) in the diversity panel confirmed 15 QTL, of which seven were observed in MGs V-IX. The results generated can help soybean breeders manipulate the maturity loci for genetic improvement of soybean yield.

Evaluation of genetic diversity and association mapping for seed weight and size in vegetable soybean germplasm

AbstractEdamame is a vegetable‐typesoybean [Glycine max (L.) Merr.] with large seed size, typically twice that of commodity soybean. Understanding the genetic diversity among large‐seeded germplasm as well as the genetic variation for seed size in the germplasm pool is important for edamame breeding. The objectives of this study were to analyze the genetic diversity of 343 edamame soybean accessions and 36 breeding lines, and to identify quantitative trait loci (QTLs) associated with seed weight (SW), seed volume (VOL), seed length (SL), seed breadth (SB), and seed height (SH) through genome‐wide association studies. We observed two main genetic groups among the 343 accessions and found that the breeding lines were genetically dissimilar to germplasm accessions. Through single‐ and multi‐locus models, a total of two, two, seven, one, and four SNPs were reported to be associated with SW, VOL, SL, SB, and SH located across two, two, five, one, and four chromosomes, respectively. There were three SNPs associated with SL, SB, and/or SH that were not found to be within a previously reported SL, SB, or SH QTL. The SNP ss715587475, positioned at the 24.9‐Mb position on chromosome 4, was located within the gene Glyma04g21680 which was associated with SW in Arabidopsis and may be a candidate gene for SW in edamame soybean. There were four additional SNPs positioned within genes that encode proteins that may relate to plant growth and development in soybean. Identifying and pyramiding favorable alleles for seed size and weight will enhance edamame breeding efforts.

Genome-wide association study and genomic selection for yield and related traits in soybean.

Soybean [Glycine max (L.) Merr.] is a crop of great interest worldwide. Exploring molecular approaches to increase yield genetic gain has been one of the main challenges for soybean breeders and geneticists. Agronomic traits such as maturity, plant height, and seed weight have been found to contribute to yield. In this study, a total of 250 soybean accessions were genotyped with 10,259 high-quality SNPs postulated from genotyping by sequencing (GBS) and evaluated for grain yield, maturity, plant height, and seed weight over three years. A genome-wide association study (GWAS) was performed using a Bayesian Information and Linkage Disequilibrium Iteratively Nested Keyway (BLINK) model. Genomic selection (GS) was evaluated using a ridge regression best linear unbiased predictor (rrBLUP) model. The results revealed that 20, 31, 37, and 23 SNPs were significantly associated with maturity, plant height, seed weight, and yield, respectively; Many SNPs were mapped to previously described maturity and plant height loci (E2, E4, and Dt1) and a new plant height locus was mapped to chromosome 20. Candidate genes were found in the vicinity of the two SNPs with the highest significant levels associated with yield, maturity, plant height, seed weight, respectively. A 11.5-Mb region of chromosome 10 was associated with both yield and seed weight. Overall, the accuracy of GS was dependent on the trait, year, and population structure, and high accuracy indicates that these agronomic traits can be selected in molecular breeding through GS. The SNP markers identified in this study can be used to improve yield and agronomic traits through the marker-assisted selection and GS in breeding programs.

Patterns of Genetic Variation in a Soybean Germplasm Collection as Characterized with Genotyping-by-Sequencing.

Genomic characterization is playing an increasing role in plant germplasm conservation and utilization, as it can provide higher resolution with genome-wide SNP markers than before to identify and analyze genetic variation. A genotyping-by-sequencing technique was applied to genotype 541 soybean accessions conserved at Plant Gene Resources of Canada and 30 soybean cultivars and breeding lines developed by the Ottawa soybean breeding program of Agriculture and Agri-Food Canada. The sequencing generated an average of 952,074 raw sequence reads per sample. SNP calling identified 43,891 SNPs across 20 soybean chromosomes and 69 scaffolds with variable levels of missing values. Based on 19,898 SNPs with up to 50% missing values, three distinct genetic groups were found in the assayed samples. These groups were a mixture of the samples that originated from different countries and the samples of known maturity groups. The samples that originated from Canada were clustered into all three distinct groups, but 30 Ottawa breeding lines fell into two groups only. Based on the average pairwise dissimilarity estimates, 40 samples with the most genetic distinctness were identified from three genetic groups with diverse sample origin and known maturity. Additionally, 40 samples with the highest genetic redundancy were detected and they consisted of different sample origins and maturity groups, largely from one genetic group. Moreover, some genetically duplicated samples were identified, but the overall level of genetic duplication was relatively low in the collection. These findings are useful for soybean germplasm management and utilization.

Metabolite Contents and Antioxidant Activities of Soybean (Glycine max (L.) Merrill) Seeds of Different Seed Coat Colors.

Seed coat color is one of the main agronomical traits that determine the chemical quality of soybean seeds and has been used as a parameter during cultivar development. In this study, seeds of yellow (n = 10), greenish-yellow (n = 5), and light-yellow (n = 4) soybean accessions were evaluated for their contents of total protein, total oil, total phenolic (TPC), and five prominent fatty acids including palmitic acid (PA), stearic acid (SA), oleic acid (OA), linoleic acid (LA), and linolenic acid (LLA), relative to a control cultivar, and the effect of seed coat color on each was investigated. Antioxidant activity was also evaluated using 1,1-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging activity, Trolox equivalent antioxidant capacity (TEAC), and ferric reducing antioxidant power (FRAP). The results showed significant variations of metabolite contents and antioxidant activities between the soybeans. The average TPC, DPPH-radical scavenging activity, and FRAP were each in the order of greenish-yellow > yellow > light-yellow soybeans. In contrast, light-yellow soybeans contained a high level of OA and low levels of SA, LA, and LLA, each except LA differing significantly from yellow and greenish-yellow soybeans (p < 0.05). Our findings suggest that greenish-yellow and light-yellow soybeans could be good sources of antioxidants and high-quality soybean oil, respectively.