Sung-Taeg Kang

Development, validation and genetic analysis of a large soybean SNP genotyping array

Cultivated soybean (Glycine max) suffers from a narrow germplasm relative to other crop species, probably because of under-use of wild soybean (Glycine soja) as a breeding resource. Use of a single nucleotide polymorphism (SNP) genotyping array is a promising method for dissecting cultivated and wild germplasms to identify important adaptive genes through high-density genetic mapping and genome-wide association studies. Here we describe a large soybean SNP array for use in diversity analyses, linkage mapping and genome-wide association analyses. More than four million high-quality SNPs identified from high-depth genome re-sequencing of 16 soybean accessions and low-depth genome re-sequencing of 31 soybean accessions were used to select 180,961 SNPs for creation of the Axiom(®) SoyaSNP array. Validation analysis for a set of 222 diverse soybean lines showed that 170,223 markers were of good quality for genotyping. Phylogenetic and allele frequency analyses of the validation set data indicated that accessions showing an intermediate morphology between cultivated and wild soybeans collected in Korea were natural hybrids. More than 90 unanchored scaffolds in the current soybean reference sequence were assigned to chromosomes using this array. Finally, dense average spacing and preferential distribution of the SNPs in gene-rich chromosomal regions suggest that this array may be suitable for genome-wide association studies of soybean germplasm. Taken together, these results suggest that use of this array may be a powerful method for soybean genetic analyses relating to many aspects of soybean breeding.

Novel major quantitative trait loci regulating the content of isoflavone in soybean seeds

Despite their medicinal, pharmaceutical, and nutritional importance of isoflavones, the genetic basis controlling the amounts of isoflavones in soybean seeds is still not well understood. The main obstacle is the great variability in the content of isoflavone in seeds harvested from different environments. In this study, quantitative trait loci (QTL) for the content of different isoflavones including daidzein, genistein, and glycitein were investigated in a population of recombinant inbred lines derived from the cross of “Hwangkeum” (Glycine max) by “IT182932” (Glycine soja). Seeds analyzed were harvested in three different experimental environments. QTL analyses for isoflavone content were conducted by composite interval mapping across a genomewide genetic map. Two major QTL were mapped to soybean chromosomes 5 and 8, which were designated QDZGT1 and QDZGT2, respectively. Both loci have not been previously reported in other isoflavone sources. The results from this study will be useful in cloning genes that can control the contents of isoflavones in soybean and for the development of soybean lines containing a high or low isoflavone content.

Quantitative trait loci associated with oligosaccharide and sucrose contents in soybean (Glycine max L.)

Oligosaccharides and sucrose are very important nutritional components in soybean seeds. However, little information is available about their inheritance. We used molecular markers to identify the genomic regions significantly associated with the quantitative trait locus (QTL) that controls oligosaccharide and sucrose contents in segregating F2:10 Rl lines. Two related, but independent, QTLs were identified for oligosaccharides — near marker satt546 on linkage group (LG) D1b+W and satt278 on LG L. Four others, for sucrose content, were located at LG B1 (satt197), D1b+W (satt546), and L (satt523 and satt278). Finally, we found two common QTLs, on LG D1b+W and L, that are associated with both oligosaccharides and sucrose.

Detection of novel QTLs for foxglove aphid resistance in soybean

Key messageTheRaso2, novel QTL for Korea biotype foxglove aphid resistance in soybean from PI 366121 was identified on chromosome 7 using GoldenGate SNP microarray.AbstractFoxglove aphid, Aulacorthum solani (Kaltenbach), is a hemipteran insect that infects a wide variety of plants worldwide and causes serious yield losses in crops. The objective of this study was to identify the putative QTL for foxglove aphid resistance in wild soybean, PI 366121, (Glycine soja Sieb. and Zucc.). One hundred and forty-one F4-derived F8 recombinant inbred lines developed from a cross of susceptible Williams 82 and PI 366121 were used. The phenotyping of antibiosis and antixenosis resistance was done through choice and no-choice tests with total plant damage and primary infestation leaf damage; a genome-wide molecular linkage map was constructed with 504 single-nucleotide polymorphism markers utilizing a GoldenGate assay. Using inclusive composite interval mapping analysis for foxglove aphid resistance, one major candidate QTL on chromosome 7 and three minor QTL regions on chromosomes 3, 6 and 18 were identified. The major QTL on chromosome 7 showed both antixenosis and antibiosis resistance responses. However, the minor QTLs showed only antixenosis resistance response. The major QTL mapped to a different chromosome than the previously identified foxglove aphid resistance QTL, Raso1, from the cultivar Adams. Also, the responses to the Korea biotype foxglove aphid were different for Raso1, and the gene from PI 366121 against the Korea biotype foxglove aphid was different. Thus, the foxglove aphid resistance gene from PI 366121 was determined to be an independent gene from Raso1 and was designated as Raso2. This result could be useful in breeding for new foxglove aphid-resistant soybean cultivars.

GenoCore: A simple and fast algorithm for core subset selection from large genotype datasets

Selecting core subsets from plant genotype datasets is important for enhancing cost-effectiveness and to shorten the time required for analyses of genome-wide association studies (GWAS), and genomics-assisted breeding of crop species, etc. Recently, a large number of genetic markers (>100,000 single nucleotide polymorphisms) have been identified from high-density single nucleotide polymorphism (SNP) arrays and next-generation sequencing (NGS) data. However, there is no software available for picking out the efficient and consistent core subset from such a huge dataset. It is necessary to develop software that can extract genetically important samples in a population with coherence. We here present a new program, GenoCore, which can find quickly and efficiently the core subset representing the entire population. We introduce simple measures of coverage and diversity scores, which reflect genotype errors and genetic variations, and can help to select a sample rapidly and accurately for crop genotype dataset. Comparison of our method to other core collection software using example datasets are performed to validate the performance according to genetic distance, diversity, coverage, required system resources, and the number of selected samples. GenoCore selects the smallest, most consistent, and most representative core collection from all samples, using less memory with more efficient scores, and shows greater genetic coverage compared to the other software tested. GenoCore was written in R language, and can be accessed online with an example dataset and test results at https://github.com/lovemun/Genocore.

Transcriptomic Profiling of Soybean in Response to High-Intensity UV-B Irradiation Reveals Stress Defense Signaling

The depletion of the ozone layer in the stratosphere has led to a dramatic spike in ultraviolet B (UV-B) intensity and increased UV-B light levels. The direct absorption of high-intensity UV-B induces complex abiotic stresses in plants, including excessive light exposure, heat, and dehydration. However, UV-B stress signaling mechanisms in plants including soybean (Glycine max [L.]) remain poorly understood. Here, we surveyed the overall transcriptional responses of two soybean genotypes, UV-B-sensitive Cheongja 3 and UV-B-resistant Buseok, to continuous UV-B irradiation for 0 (control), 0.5, and 6 h using RNA-seq analysis. Homology analysis using UV-B-related genes from Arabidopsis thaliana revealed differentially expressed genes (DEGs) likely involved in UV-B stress responses. Functional classification of the DEGs showed that the categories of immune response, stress defense signaling, and reactive oxygen species (ROS) metabolism were over-represented. UV-B-resistant Buseok utilized phosphatidic acid-dependent signaling pathways (based on subsequent reactions of phospholipase C and diacylglycerol kinase) rather than phospholipase D in response to UV-B exposure at high fluence rates, and genes involved in its downstream pathways, such as ABA signaling, mitogen-activated protein kinase cascades, and ROS overproduction, were upregulated in this genotype. In addition, the DEGs for TIR-NBS-LRR and heat shock proteins are positively activated. These results suggest that defense mechanisms against UV-B stress at high fluence rates are separate from the photomorphogenic responses utilized by plants to adapt to low-level UV light. Our study provides valuable information for deep understanding of UV-B stress defense mechanisms and for the development of resistant soybean genotypes that survive under high-intensity UV-B stress.

Genetic analysis of new short petiole gene in soybean

The short petiole trait is valuable for the development of plant ideotype with high yield. Soybean breeding line, SS98206SP, showed extremely short petioles in greenhouse and field. In this study, the short petiole of two mutant lines, SS98206SP and D76-1609, were investigated to determine the genetic segregations. These two mutants were crossed with each other and with two normal petiole genotypes. Genetic analysis indicated that the short petioles in D76-1609 and SS98206SP were controlled by a single recessive gene, respectively. The short petiole gene in SS98206SP was non-allelic with lps, conferring short petiole in D76-1609. Two recessive genes showed complementary relationship having short petioles with recessive homozygote (LPS1-lps?lps?, lps1lps1LPS?-, lps1lps1lps?lps?). Our data indicated that the short petioles in SS98206SP were controlled by a single recessive gene designated as lps3.

Identification of Quantitative Trait Loci (QTLs) Associated with Oil and Protein Contents in Soybean (Glycine max L.)

Soybean oil and protein contents are very important as a nutritional component of food. The seed composition as oil and protein are polygenic traits. In this study, the KeunolkongIksan10 populations were evaluated with SSR markers to identify QTLs related to oil and protein contents. Three related independent QTLs near the marker satt100 on LG C2, satt546 on LG D1b＋W and satt418 on LG L were identified oil contents. The three independent QTLs near the marker satt556 on LG B2, satt414 on LG J and satt238 on LC L were identified of protein contents. In the results of this study, common QTLs on LG L was associated with seed oil and protein contents. In the result of this study, it is believed that the seed composition material as oil and protein contents were mainly controlled by environmental stresses and they are seed size on genotypes.

Differences in the metabolic profiles and antioxidant activities of wild and cultivated black soybeans evaluated by correlation analysis

Wild soybeans are considered a potential resource for soybean domestication and an important source of genetic diversity for soybean crop improvement. Understanding metabolite-caused bioactivity differences between cultivated and wild soybeans is essential for designing a soybean with enhanced nutritional traits. In this study, the non-targeted metabolic profiling of 26 soybean varieties, 15 wild black soybeans (WBS) and 11 cultivated black soybeans (CBS), using liquid chromatography-mass spectrometry (LC-MS) in combination with multivariate analysis revealed significant differences in 25 differential metabolites. Among these, the soyasaponins Ab and Bb were found to be characteristic metabolites expressed more substantially in CBS than in WBS. Three different antioxidant assays and correlation analysis identified major and minor antioxidants that contributed to WBS having an antioxidant activity 4- to 8-fold stronger than that of CBS. Epicatechin, procyanidin B2, and cyanidin-3-O-glucoside were identified by both association analysis and the online LC-ABTS radical scavenging assay as being major antioxidants.

Fiber-Optic Localized Surface Plasmon Resonance sensor combined with micro fluidic channel

This paper proposes Fiber-Optic Localized Surface Plasmon Resonance (FO LSPR) sensor combined with micro fluidic channel, which enables the continuous supply of fluid for bio-reaction. The proposed method can prevent the degradation of the sensing characteristics due to the change of measurement condition. The feasibility of the FO LSPR sensor with micro fluidic channel is proved by Computational Fluid Dynamics simulation (CFD). Also, the proposed method has been evidenced by measuring the output intensity of the FO LSPR sensor at various refractive index solutions. Finally, Prostate Specific Antigen (PSA) immunoassay was measured to verify the possibility of the fabricated sensor system as a biosensor.