Differentially Expressed Genes Related to Isoflavone Biosynthesis in a Soybean Mutant Revealed by a Comparative Transcriptomic Analysis.

Soybean [Glycine max (L.) Merr.] isoflavones, which are secondary metabolites with various functions, are included in food, cosmetics, and medicine. However, the molecular mechanisms regulating the glycosylation and malonylation of isoflavone glycoconjugates remain unclear. In this study, we conducted an RNA-seq analysis to compare soybean genotypes with different isoflavone contents, including Danbaek and Hwanggeum (low-isoflavone cultivars) as well as DB-088 (high-isoflavone mutant). The transcriptome analysis yielded over 278 million clean reads, representing 39,156 transcripts. The analysis of differentially expressed genes (DEGs) detected 2654 up-regulated and 1805 down-regulated genes between the low- and high-isoflavone genotypes. The putative functions of these 4459 DEGs were annotated on the basis of GO and KEGG pathway enrichment analyses. These DEGs were further analyzed to compare the expression patterns of the genes involved in the biosynthesis of secondary metabolites and the genes encoding transcription factors. The examination of the relative expression levels of 70 isoflavone biosynthetic genes revealed the HID, IFS, UGT, and MAT expression levels were significantly up/down-regulated depending on the genotype and seed developmental stage. These expression patterns were confirmed by quantitative real-time PCR. Moreover, a gene co-expression analysis detected potential protein-protein interactions, suggestive of common functions. The study findings provide valuable insights into the structural genes responsible for isoflavone biosynthesis and accumulation in soybean seeds.

Transcriptome Profiling of a Soybean Mutant with Salt Tolerance Induced by Gamma-ray Irradiation.

Salt stress is a significant abiotic stress that reduces crop yield and quality globally. In this study, we utilized RNA sequencing (RNA-Seq) to identify differentially expressed genes (DEGs) in response to salt stress induced by gamma-ray irradiation in a salt-tolerant soybean mutant. The total RNA library samples were obtained from the salt-sensitive soybean cultivar Kwangan and the salt-tolerant mutant KA-1285. Samples were taken at three time points (0, 24, and 72 h) from two tissues (leaves and roots) under 200 mM NaCl. A total of 967,719,358 clean reads were generated using the Illumina NovaSeq 6000 platform, and 94.48% of these reads were mapped to 56,044 gene models of the soybean reference genome (Glycine_max_Wm82.a2.v1). The DEGs with expression values were compared at each time point within each tissue between the two soybeans. As a result, 296 DEGs were identified in the leaves, while 170 DEGs were identified in the roots. In the case of the leaves, eight DEGs were related to the phenylpropanoid biosynthesis pathway; however, in the roots, Glyma.03G171700 within GmSalt3, a major QTL associated with salt tolerance in soybean plants, was differentially expressed. Overall, these differences may explain the mechanisms through which mutants exhibit enhanced tolerance to salt stress, and they may provide a basic understanding of salt tolerance in soybean plants.

QTL mapping reveals key factors related to the isoflavone contents and agronomic traits of soybean (Glycine max).

BACKGROUND: Soybean is a valuable source of edible protein and oil, as well as secondary metabolites that can be used in food products, cosmetics, and medicines. However, because soybean isoflavone content is a quantitative trait influenced by polygenes and environmental interactions, its genetic basis remains unclear. RESULTS: This study was conducted to identify causal quantitative trait loci (QTLs) associated with soybean isoflavone contents. A mutant-based F2 population (190 individuals) was created by crossing the Korean cultivar Hwanggeum with low isoflavone contents (1,558 µg g-1) and the soybean mutant DB-088 with high isoflavone contents (6,393 µg g-1). A linkage map (3,049 cM) with an average chromosome length of 152 cM was constructed using the 180K AXIOM® SoyaSNP array. Thirteen QTLs related to agronomic traits were mapped to chromosomes 2, 3, 11, 13, 19, and 20, whereas 29 QTLs associated with isoflavone contents were mapped to chromosomes 1, 3, 8, 11, 14, 15, and 17. Notably, the qMGLI11, qMGNI11, qADZI11, and qTI11, which located Gm11_9877690 to Gm11_9955924 interval on chromosome 11, contributed to the high isoflavone contents and explained 11.9% to 20.1% of the phenotypic variation. This QTL region included four candidate genes, encoding ß-glucosidases 13, 14, 17-1, and 17-2. We observed significant differences in the expression levels of these genes at various seed developmental stages. Candidate genes within the causal QTLs were functionally characterized based on enriched GO terms and KEGG pathways, as well as the results of a co-expression network analysis. A correlation analysis indicated that certain agronomic traits (e.g., days to flowering, days to maturity, and plant height) are positively correlated with isoflavone content. CONCLUSIONS: Herein, we reported that the major QTL associated with isoflavone contents was located in the interval from Gm11_9877690 to Gm11_9955924 (78 kb) on chromosome 11. Four ß-glucosidase genes were identified that may be involved in high isoflavone contents of soybean DB-088. Thus, the mutant alleles from soybean DB-088 may be useful for marker-assisted selection in developing soybean lines with high isoflavone contents and superior agronomic traits.

New statistical selection method for pleiotropic variants associated with both quantitative and qualitative traits.

BACKGROUND: Identification of pleiotropic variants associated with multiple phenotypic traits has received increasing attention in genetic association studies. Overlapping genetic associations from multiple traits help to detect weak genetic associations missed by single-trait analyses. Many statistical methods were developed to identify pleiotropic variants with most of them being limited to quantitative traits when pleiotropic effects on both quantitative and qualitative traits have been observed. This is a statistically challenging problem because there does not exist an appropriate multivariate distribution to model both quantitative and qualitative data together. Alternatively, meta-analysis methods can be applied, which basically integrate summary statistics of individual variants associated with either a quantitative or a qualitative trait without accounting for correlations among genetic variants. RESULTS: We propose a new statistical selection method based on a unified selection score quantifying how a genetic variant, i.e., a pleiotropic variant associates with both quantitative and qualitative traits. In our extensive simulation studies where various types of pleiotropic effects on both quantitative and qualitative traits were considered, we demonstrated that the proposed method outperforms the existing meta-analysis methods in terms of true positive selection. We also applied the proposed method to a peanut dataset with 6 quantitative and 2 qualitative traits, and a cowpea dataset with 2 quantitative and 6 qualitative traits. We were able to detect some potentially pleiotropic variants missed by the existing methods in both analyses. CONCLUSIONS: The proposed method is able to locate pleiotropic variants associated with both quantitative and qualitative traits. It has been implemented into an R package 'UNISS', which can be downloaded from http://github.com/statpng/uniss.

Morpho-physiological and genetic characteristics of a salt-tolerant mutant line in soybean (Glycine max L.).

KEY MESSAGE: One major quantitative trait loci and candidate gene for salt tolerance were identified on chromosome 3 from a new soybean mutant derived from gamma-ray irradiation, which will provide a new genetic resource for improving soybean salt tolerance. Soil salinity is a worldwide problem that reduces crop yields, but the development of salt-tolerant crops can help overcome this challenge. This study was conducted with the purpose of evaluating the morpho-physiological and genetic characteristics of a new salt-tolerant mutant KA-1285 developed using gamma-ray irradiation in soybean (Glycine max L.). The morphological and physiological responses of KA-1285 were compared with salt-sensitive and salt-tolerant genotypes after treatment with 150 mM NaCl for two weeks. In addition, a major salt tolerance quantitative trait locus (QTL) was identified on chromosome 3 in this study using the Daepung X KA-1285 169 F2:3 population, and a specific deletion was identified in Glyma03g171600 (Wm82.a2.v1) near the QTL region based on re-sequencing analysis. A kompetitive allele-specific PCR (KASP) marker was developed based on the deletion of Glyma03g171600 which distinguished the wild-type and mutant alleles. Through the analysis of gene expression patterns, it was confirmed that Glyma03g171700 (Wm82.a2.v1) is a major gene that controls salt tolerance functions in Glyma03g32900 (Wm82.a1.v1). These results suggest that the gamma-ray-induced mutant KA-1285 has the potential to be employed for the development of a salt-tolerant cultivar and provide useful information for genetic research related to salt tolerance in soybeans.

A Genome-Wide Association Study of Protein, Oil, and Amino Acid Content in Wild Soybean (Glycine soja).

Soybean (Glycine max L.) is a globally important source of plant proteins, oils, and amino acids for both humans and livestock. Wild soybean (Glycine soja Sieb. and Zucc.), the ancestor of cultivated soybean, could be a useful genetic source for increasing these components in soybean crops. In this study, 96,432 single-nucleotide polymorphisms (SNPs) across 203 wild soybean accessions from the 180K Axiom® Soya SNP array were investigated using an association analysis. Protein and oil content exhibited a highly significant negative correlation, while the 17 amino acids exhibited a highly significant positive correlation with each other. A genome-wide association study (GWAS) was conducted on the protein, oil, and amino acid content using the 203 wild soybean accessions. A total of 44 significant SNPs were associated with protein, oil, and amino acid content. Glyma.11g015500 and Glyma.20g050300, which contained SNPs detected from the GWAS, were selected as novel candidate genes for the protein and oil content, respectively. In addition, Glyma.01g053200 and Glyma.03g239700 were selected as novel candidate genes for nine of the amino acids (Ala, Asp, Glu, Gly, Leu, Lys, Pro, Ser, and Thr). The identification of the SNP markers related to protein, oil, and amino acid content reported in the present study is expected to help improve the quality of selective breeding programs for soybeans.

Genetic Diversity of Korean Wild Soybean Core Collections and Genome-Wide Association Study for Days to Flowering.

The utilization of wild soybean germplasms in breeding programs increases genetic diversity, and they contain the rare alleles of traits of interest. Understanding the genetic diversity of wild germplasms is essential for determining effective strategies that can improve the economic traits of soybeans. Undesirable traits make it challenging to cultivate wild soybeans. This study aimed to construct a core subset of 1467 wild soybean accessions of the total population and analyze their genetic diversity to understand their genetic variations. Genome-wild association studies were conducted to detect the genetic loci underlying the time to flowering for a core subset collection, and they revealed the allelic variation in E genes for predicting maturity using the available resequencing data of wild soybean. Based on principal component and cluster analyses, 408 wild soybean accessions in the core collection covered the total population and were explained by 3 clusters representing the collection regions, namely, Korea, China, and Japan. Most of the wild soybean collections in this study had the E1e2E3 genotype according to association mapping and a resequencing analysis. Korean wild soybean core collections can provide helpful genetic resources to identify new flowering and maturity genes near the E gene loci and genetic materials for developing new cultivars, facilitating the introgression of genes of interest from wild soybean.

Transcriptome Analysis of Differentially Expressed Genes Associated with Salt Stress in Cowpea (Vigna unguiculata L.) during the Early Vegetative Stage.

Cowpea (Vigna unguiculata (L.), 2n = 22) is a tropical crop grown in arid and semiarid regions that is tolerant to abiotic stresses such as heat and drought. However, in these regions, salt in the soil is generally not eluted by rainwater, leading to salt stress for a variety of plant species. This study was conducted to identify genes related to salt stress using the comparative transcriptome analysis of cowpea germplasms with contrasting salt tolerance. Using the Illumina Novaseq 6000 platform, 1.1 billion high-quality short reads, with a total length of over 98.6 billion bp, were obtained from four cowpea germplasms. Of the differentially expressed genes identified for each salt tolerance type following RNA sequencing, 27 were shown to exhibit significant expression levels. These candidate genes were subsequently narrowed down using reference-sequencing analysis, and two salt stress-related genes (Vigun_02G076100 and Vigun_08G125100) with single-nucleotide polymorphism (SNP) variation were selected. Of the five SNPs identified in Vigun_02G076100, one that caused significant amino acid variation was identified, while all nucleotide variations in Vigun_08G125100 was classified as missing in the salt-resistant germplasms. The candidate genes and their variation, identified in this study provide, useful information for the development of molecular markers for cowpea breeding programs.

Quantitative Trait Loci (QTL) Analysis of Seed Protein and Oil Content in Wild Soybean (Glycine soja).

Soybean seeds consist of approximately 40% protein and 20% oil, making them one of the world's most important cultivated legumes. However, the levels of these compounds are negatively correlated with each other and regulated by quantitative trait loci (QTL) that are controlled by several genes. In this study, a total of 190 F2 and 90 BC1F2 plants derived from a cross of Daepung (Glycine max) with GWS-1887 (G. soja, a source of high protein), were used for the QTL analysis of protein and oil content. In the F2:3 populations, the average protein and oil content was 45.52% and 11.59%, respectively. A QTL associated with protein levels was detected at Gm20_29512680 on chr. 20 with a likelihood of odds (LOD) of 9.57 and an R2 of 17.2%. A QTL associated with oil levels was also detected at Gm15_3621773 on chr. 15 (LOD: 5.80; R2: 12.2%). In the BC1F2:3 populations, the average protein and oil content was 44.25% and 12.14%, respectively. A QTL associated with both protein and oil content was detected at Gm20_27578013 on chr. 20 (LOD: 3.77 and 3.06; R2 15.8% and 10.7%, respectively). The crossover to the protein content of BC1F3:4 population was identified by SNP marker Gm20_32603292. Based on these results, two genes, Glyma.20g088000 (S-adenosyl-l-methionine-dependent methyltransferases) and Glyma.20g088400 (oxidoreductase, 2-oxoglutarate-Fe(II) oxygenase family protein), in which the amino acid sequence had changed and a stop codon was generated due to an InDel in the exon region, were identified.

Genome-Wide Association Studies of Seven Root Traits in Soybean (Glycine max L.) Landraces.

Soybean [Glycine max (L.) Merr.], an important oilseed crop, is a low-cost source of protein and oil. In Southeast Asia and Africa, soybeans are widely cultivated for use as traditional food and feed and industrial purposes. Given the ongoing changes in global climate, developing crops that are resistant to climatic extremes and produce viable yields under predicted climatic conditions will be essential in the coming decades. To develop such crops, it will be necessary to gain a thorough understanding of the genetic basis of agronomic and plant root traits. As plant roots generally lie beneath the soil surface, detailed observations and phenotyping throughout plant development present several challenges, and thus the associated traits have tended to be ignored in genomics studies. In this study, we phenotyped 357 soybean landraces at the early vegetative (V2) growth stages and used a 180 K single-nucleotide polymorphism (SNP) soybean array in a genome-wide association study (GWAS) conducted to determine the phenotypic relationships among root traits, elucidate the genetic bases, and identify significant SNPs associated with root trait-controlling genomic regions/loci. A total of 112 significant SNP loci/regions were detected for seven root traits, and we identified 55 putative candidate genes considered to be the most promising. Our findings in this study indicate that a combined approach based on SNP array and GWAS analyses can be applied to unravel the genetic basis of complex root traits in soybean, and may provide an alternative high-resolution marker strategy to traditional bi-parental mapping. In addition, the identified SNPs, candidate genes, and diverse variations in the root traits of soybean landraces will serve as a valuable basis for further application in genetic studies and the breeding of climate-resilient soybeans characterized by improved root traits.

Genome wide association study to detect genetic regions related to isoflavone content in a mutant soybean population derived from radiation breeding.

Isoflavones are major secondary metabolites that are exclusively produced by legumes, including soybean. Soy isoflavones play important roles in human health as well as in the plant defense system. The isoflavone content is influenced by minor-effect quantitative trait loci, which interact with polygenetic and environmental factors. It has been difficult to clarify the regulation of isoflavone biosynthesis because of its complex heritability and the influence of external factors. Here, using a genotype-by-sequencing-based genome-wide association mapping study, 189 mutant soybean genotypes (the mutant diversity pool, MDP) were genotyped on the basis of 25,646 high-quality single nucleotide polymorphisms (SNPs) with minor allele frequency of >0.01 except for missing data. All the accessions were phenotyped by determining the contents of 12 isoflavones in the soybean seeds in two consecutive years (2020 and 2021). Then, quantitative trait nucleotides (QTNs) related to isoflavone contents were identified and validated using multi-locus GWAS models. A total of 112 and 46 QTNs related to isoflavone contents were detected by multiple MLM-based models in 2020 and 2021, respectively. Of these, 12 and 5 QTNs were related to more than two types of isoflavones in 2020 and 2021, respectively. Forty-four QTNs were detected within the 441-Kb physical interval surrounding Gm05:38940662. Of them, four QTNs (Gm05:38936166, Gm05:38936167, Gm05:38940662, and Gm05:38940717) were located at Glyma.05g206900 and Glyma.05g207000, which encode glutathione S-transferase THETA 1 (GmGSTT1), as determined from previous quantitative trait loci annotations and the literature. We detected substantial differences in the transcript levels of GmGSTT1 and two other core genes (IFS1 and IFS2) in the isoflavone biosynthetic pathway between the original cultivar and its mutant. The results of this study provide new information about the factors affecting isoflavone contents in soybean seeds and will be useful for breeding soybean lines with high and stable concentrations of isoflavones.

High-Throughput Phenotypic Characterization and Diversity Analysis of Soybean Roots (Glycine max L.).

Soybean (Glycine max L.) is a crop native to Northeast Asia, including China, Korea, and Japan, but currently cultivated all over the world. The National Agrobiodiversity Center in Korea at the Rural Development Administration (RDA) conserves approximately 26,000 accessions and conducts characterizations of its accessions, to accumulate new information. Roots are essential organs of a plant, providing mechanical support, as well as aiding water and nutrient acquisition. Currently, not much information is available in international gene banks regarding root characterization. We studied the root phenotype of 374 soybean accessions, using a high-throughput method. Eight root morphological traits (RMT) were studied and we observed that the surface area (SA), number of forks (NF), and number of tips (NT) had a positive correlation with total length (LENGTH), and that link average length (LAL) and other traits all had a negative correlation. Additionally, the correlation between seed traits (height, width, and 100-seed weight) and root traits was confirmed for the first time in this experiment. The germplasms were divided into three clusters by k-means clustering, and orthogonal projections to latent structures discriminant analysis (OPLS-DA) was used to compare clusters. The most distinctive characteristics between clusters were total lateral average length (LAD) and total lateral average length (DIAM). Cluster 3 had the highest LENGTH, SA, NF, and NF, whereas cluster 1 had the smallest LENGTH, SA, and NF. We selected the top 10 accessions for each RMT, and IT208321, IT216313, and IT216137 were nominated as the best germplasms. These accessions can be recommended to breeders as materials for breeding programs. This is a preliminary report on the characterization of the root phenotype at an international gene bank and will open up the possibility of improving the available information on accessions in gene banks worldwide.

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.

Analysis of genetic diversity and relationships of Perilla frutescens using novel EST-SSR markers derived from transcriptome between wild-type and mutant Perilla.

BACKGROUND: Perilla frutescens (Lamiaceae) is distributed in East Asia and is classified into var. frutescens and crispa. P. frutescens is multipurpose crop for human health because of a variety of secondary metabolites such as phenolic compound and essential oil. However, a lack of genetic information has hindered the development and utilization of Perilla genotypes. METHODS AND RESULTS: This study was performed to develop expressed sequence tag-simple sequence repeat (EST-SSR) markers from P. frutescens var. crispa (wild type) and Antisperill (a mutant cultivar) and used them to assess the genetic diversity of, and relationships among, 94 P. frutescens genotypes. We obtained 65 Gb of sequence data comprising 632,970 transcripts by de novo RNA-sequencing. Of the 14,780 common SSRs, 102 polymorphic EST-SSRs were selected using in silico polymerase chain reaction (PCR). Overall, successful amplification from 58 EST-SSRs markers revealed remarkable genetic diversity and relationships among 94 P. frutescens genotypes. In total, 268 alleles were identified, with an average of 4.62 alleles per locus (range 2-11 alleles/locus). The average polymorphism information content (PIC) value was 0.50 (range 0.04-0.86). In phylogenetic and population structure analyses, the genotypes formed two major groups: Group I (var. crispa) and Group II (var. frutescens). CONCLUSION: This results suggest that 58 novel EST-SSR markers derived from wild-type cultivar (var. crispa) and its mutant cultivar (Antisperill) have potential uses for population genetics and recombinant inbred line mapping analyses, which will provide comprehensive insights into the genetic diversity and relationship of P. frutescens.

Fine-mapping and candidate gene analysis for the foxglove aphid resistance gene Raso2 from wild soybean PI 366121.

KEY MESSAGE: The foxglove aphid resistance gene Raso2 from PI 366121 was fine-mapped to 77 Kb region, and one candidate gene was identified. The foxglove aphid (FA: Aulacorthum solani Kaltenbach) is an important insect pest that causes serious yield losses in soybean. The FA resistance gene Raso2 from wild soybean PI 366121 was previously mapped to a 13 cM interval on soybean chromosome 7. However, fine-mapping of Raso2 was needed to improve the effectiveness of marker-assisted selection (MAS) and to eventually clone it. The objectives of this study were to fine-map Raso2 from PI 366121 using Axiom® 180 K SoyaSNP array, to confirm the resistance and inheritance of Raso2 in a different background, and to identify candidate gene(s). The 105 F4:8 recombinant inbred lines were used to fine-map the gene and to test antibiosis and antixenosis of Raso2 to FA. These efforts resulted in the mapping of Raso2 on 1 cM interval which corresponds to 77 Kb containing eight annotated genes based on the Williams 82 reference genome assembly (Wm82.a2.v1). Interestingly, all nonsynonymous substitutions were in Glyma.07g077700 which encodes the disease resistance protein containing LRR domain and expression of the gene in PI 366121 was significantly higher than that in Williams 82. In addition, distinct SNPs within Glyma.07g077700 that can distinguish PI 366121 and diverse FA-susceptible soybeans were identified. We also confirmed that Raso2 presented the resistance to FA and the Mendelian inheritance for single dominant gene in a different background. The results of this study would provide fundamental information on MAS for development of FA-resistant cultivars as well as functional study and cloning of the candidate gene in soybean.

A Comparison of the Transcriptomes of Cowpeas in Response to Two Different Ionizing Radiations.

In this study, gene expression changes in cowpea plants irradiated by two different types of radiation: proton-beams and gamma-rays were investigated. Seeds of the Okdang cultivar were exposed to 100, 200, and 300 Gy of gamma-rays and proton-beams. In transcriptome analysis, the 32, 75, and 69 differentially expressed genes (DEGs) at each dose of gamma-ray irradiation compared with that of the control were identified. A total of eight genes were commonly up-regulated for all gamma-ray doses. However, there were no down-regulated genes. In contrast, 168, 434, and 387 DEGs were identified for each dose of proton-beam irradiation compared with that of the control. A total of 61 DEGs were commonly up-regulated for all proton-beam doses. As a result of GO and KEGG analysis, the ranks of functional categories according to the number of DEGs were not the same in both treatments and were more diverse in terms of pathways in the proton-beam treatments than gamma-ray treatments. The number of genes related to defense, photosynthesis, reactive oxygen species (ROS), plant hormones, and transcription factors (TF) that were up-/down-regulated was higher in the proton beam treatment than that in gamma ray treatment. Proton-beam treatment had a distinct mutation spectrum and gene expression pattern compared to that of gamma-ray treatment. These results provide important information on the mechanism for gene regulation in response to two ionizing radiations in cowpeas.

Identification of a Potential Gene for Elevating ω-3 Concentration and Its Efficiency for Improving the ω-6/ω-3 Ratio in Soybean.

This present study was to identify a novel candidate gene that contributes to the elevated α-linolenic acid (ALA, ω-3) concentration in PE2166 from mutagenesis of Pungsannamul. Major loci qALA5_1 and qALA5_2 were detected on chromosome 5 of soybean through quantitative trait loci mapping analyses of recombinant inbred lines. With next-generation sequencing of parental lines and Pungsannamul and recombinant analyses, a potential gene, Glyma.05g221500 (HD), controlling elevated ALA concentration was identified. HD is a homeodomain-like transcriptional regulator that may regulate the expression level of microsomal ω-3 fatty acid desaturase (FAD3) genes responsible for the conversion of linoleic acid into ALA in the fatty acid biosynthetic pathway. In addition, we hypothesized that a combination of mutant alleles, HD, and either of microsomal delta-12 fatty acid desaturase 2-1 (FAD2-1) could reduce the ω-6/ω-3 ratio. In populations where HD, FAD2-1A, and FAD2-1B genes were segregated, a combination of a hd allele from PE2166 and either of the variant FAD2-1 alleles was sufficient to reduce the ω-6/ω-3 ratio in seeds.

Detecting Genetic Mobility Using a Transposon-Based Marker System in Gamma-Ray Irradiated Soybean Mutants.

Transposable elements (TEs)-major components of eukaryotic genomes-have the ability to change location within a genome. Because of their mobility, TEs are important for genome diversification and evolution. Here, a simple rapid method, using the consensus terminal inverted repeat sequences of PONG, miniature inverted-repeat transposable element (MITE)-Tourist (M-t) and MITE-Stowaway (M-s) as target region amplification polymorphism (TE-TRAP) markers, was employed to investigate the mobility of TEs in a gamma-irradiated soybean mutant pool. Among the different TE-TRAP primer combinations, the average polymorphism level and polymorphism information content value were 57.98% and 0.14, respectively. Only the PONG sequence separated the mutant population into three major groups. The inter-mutant population variance, determined using the PONG marker (3.151 and 29%) was greater than that of the M-t (2.209 and 20%) and M-s (2.766 and 18%) markers, whereas the reverse was true for the intra-mutant population variations, with M-t and M-s values, being 15.151 (82%) and 8.895 (80%), respectively, compared with the PONG marker (7.646 and 71%). Thus, the MITE markers revealed more dynamic and active mobility levels than the PONG marker in gamma-ray irradiated soybean mutant lines. The TE-TRAP technique associated with sensitive MITEs is useful for investigating genetic diversity and TE mobilization, providing tools for mutant selection in soybean mutation breeding.

Genetic Diversity and Genome-Wide Association Study of Seed Aspect Ratio Using a High-Density SNP Array in Peanut (Arachis hypogaea L.).

Peanut (Arachis hypogaea L.) is one of the important oil crops of the world. In this study, we aimed to evaluate the genetic diversity of 384 peanut germplasms including 100 Korean germplasms and 284 core collections from the United States Department of Agriculture (USDA) using an Axiom_Arachis array with 58K single-nucleotide polymorphisms (SNPs). We evaluated the evolutionary relationships among 384 peanut germplasms using a genome-wide association study (GWAS) of seed aspect ratio data processed by ImageJ software. In total, 14,030 filtered polymorphic SNPs were identified from the peanut 58K SNP array. We identified five SNPs with significant associations to seed aspect ratio on chromosomes Aradu.A09, Aradu.A10, Araip.B08, and Araip.B09. AX-177640219 on chromosome Araip.B08 was the most significantly associated marker in GAPIT and Regularization method. Phosphoenolpyruvate carboxylase (PEPC) was found among the eleven genes within a linkage disequilibrium (LD) of the significant SNPs on Araip.B08 and could have a strong causal effect in determining seed aspect ratio. The results of the present study provide information and methods that are useful for further genetic and genomic studies as well as molecular breeding programs in peanuts.

Population Structure and Genetic Diversity in Korean Cowpea Germplasm Based on SNP Markers.

Cowpea is one of the most essential legume crops providing inexpensive dietary protein and nutrients. The aim of this study was to understand the genetic diversity and population structure of global and Korean cowpea germplasms. A total of 384 cowpea accessions from 21 countries were genotyped with the Cowpea iSelect Consortium Array containing 51,128 single-nucleotide polymorphisms (SNPs). After SNP filtering, a genetic diversity study was carried out using 35,116 SNPs within 376 cowpea accessions, including 229 Korean accessions. Based on structure and principal component analysis, a total of 376 global accessions were divided into four major populations. Accessions in group 1 were from Asia and Europe, those in groups 2 and 4 were from Korea, and those in group 3 were from West Africa. In addition, 229 Korean accessions were divided into three major populations (Q1, Jeonra province; Q2, Gangwon province; Q3, a mixture of provinces). Additionally, the neighbor-joining tree indicated similar results. Further genetic diversity analysis within the global and Korean population groups indicated low heterozygosity, a low polymorphism information content, and a high inbreeding coefficient in the Korean cowpea accessions. The population structure analysis will provide useful knowledge to support the genetic potential of the cowpea breeding program, especially in Korea.