Senna tora (L.) Roxb. belongs to Leguminosae and its seeds are usually roasted and boiled in water to produce tea in Korea. Also the plants are well known for the treatment of Hypertension, Hepatitis, Constipation and Conjunctivitis. This study was conducted to investigate the morphological characteristics and pollen germination rates of Senna tora with the aim of genetic mapping of this species. First, we investigated morphological characteristics of domestic and international genotypes containing 51 lines in Korea and 2 lines in China. No significant differences in growth characteristics were observed among 53 genotypes. However, ST-9 line which was collected in Pyung-chang showed high growth rate at the early stage. The flower of Senna tora consists of 5 petals, 10 surgeries (7 main surgeries, 3 small surgeries), 1 pistil, and 5 sepals. After bud emergence, each petal was white in 1-2 days, turn into ivory in a week, then yellow in 8-9 days and finally bloomed in 9-10 days. Although the average flowering times of the plants were July 24, ST9 flowered in July 12. In addition, the flowers of ST9 differed from the flowers of the other genotypes. Flower of ST9 joined together with one another. Therefore, ST9 showing high growth rate at the early stage and unique flowering characteristics was selected to as the paternal line for genetic mapping study. Second, we investigated pollen germination rates for each stage of flower development. Pollen started to germinate at the yellow bud stage and pollen germination rate was highest in the bloomed flower stage. This results show that self-fertilization hardly occurs when the flower is ivory bud stage, and there is no need to use young bud flowers for artificial crossing. This work is intended to serve as the basis for the breeding of new varieties in Senna tora.

The depletion of stratospheric ozone has resulted in increased amount of ultraviolet-B radiation (UV-B: 280-320 nm) reaching the Earth’s surface and could cause significant biological effect in plants. In this study, putative quantitative trait loci (QTL), which is responsible to UV-B resistance in soybean, was identified using recently developed high-density 180K Axiom SoyaSNP genotyping array. A population of 115 recombinant inbred lines (RILs) derived from a cross between susceptible Keunolkong and resistant Iksan 10 was analyzed. A total 8,970 polymorphic SNP markers were used to construct linkage map. The both parents and RILs were grown with supplemental UV-B radiation in a greenhouse condition. Three categories of UV-B induced morphological damage, degree of leaf chlorosis, leaf shape change, and total plant damage were evaluated. Using composite interval mapping analysis, one major QTL associated with all of the phenotypic traits was detected on 7.7cM of soybean chromosome 7 with 22 of LOD score accounting for about 60% of phenotypic variance. Also, the allele from Iksan 10 were responsible for the UV-B resistance. Thus, the UV-B resistance QTL on chromosome 7 from Iksan 10 was designated to qUVBR1, corresponding to 30kb on the Williams 82 genome assembly (Glyma2.0) including 7 candidate genes. This result could be useful in breeding for new foxglove aphid resistant soybean cultivars. In addition, these results provided useful information not only for marker-assisted selection for UV-B resistance soybean, but also for the future identification of putative candidate genes, responsible for UV-B resistance in soybean.

Soybean is an important worldwide crop of dietary protein and oil resources for human foods and animal feeds. However, soybean breeding and improvement has been experienced challenges by a narrow germplasms. SNP genotyping array is regarded as a promising tool for dissecting wild and cultivated germplasms to find important genes by high-density genetic mapping and genome-wide association studies (GWAS). Here, we present the establishment of a large soyaSNP array and its use for diversity analysis and high density linkage mapping. More than 4 million high-quality SNPs identified from 16 high-depth and 31 low-depth soybean genome resequencing data were used to select 180,961 SNPs for the Axiom® SoyaSNP array. Our validation analysis for a set of 222 diverse soybean lines showed that a total of 171,161 markers were good quality for genotyping. Of the converted SNPs, 82.6% SNPs had a marker spacing of less than 9 kb and 17.4% SNPs greater than 9 kb, thereby suggesting that our array is likely suitable for GWAS of soybean germplasms. In the GWAS for seed protein content in the wild soybean germplasms with the size of 1,135 accessions, 22 loci on 12 chromosomes showed significant association (-logP>4). The highest associated peaks were shown at the 28 Mbp region on Gm05 (-logP=5.89), at 45 Mbp on Gm03 (-logP=5.32), and at 2.8 Mbp on Gm17 (-logP=5.00). Of the 22 associations, 8 corresponded with the location of previously reported seed protein QTLs and 14 regions is thought to be new QTLs for seed protein content in wild soybean. This array is being used to construct high-density genetic maps in two recombinant inbred lines and nested-association mapping populations with 30 combinations used Daepung cultivar as hub-parents, with an objective to confirm large structural variations of chromosomes using the ultra-high-density maps.

An important worldwide plant source of dietary protein and oil, modern breeding and improvement of soybean is suffered from a narrow cultivated germplasm relative to other crop species likely because of underuse of wild soybeans as breeding resources. SNP genotyping array is regarded as a promising tool for dissecting wild and cultivated germplasms to find important adaptive genes by high-density genetic mapping and genome-wide association studies (GWAS). Here, we present the establishment of a large soybean SNP array and its use for diversity analysis and high density linkage mapping. More than 4 million high-quality SNPs identified from 16 high-depth and 31 low-depth soybean genome resequencing data were used to select 180,961 SNPs for the AxiomÒ SoyaSNP array. Our validation analysis for a set of 222 diverse soybean lines showed that a total of 171,161markers were of good quality for genotyping. Of the converted SNPs, 82.6% 82.6% SNPs had a marker spacing of less than 9 kb and 17.4% SNPs greater than 9 kb with the 297 inter-SNP spacings of >100 kb and with 812 kb of the largest spacing, thereby suggesting that our array is likely suitable for GWAS of soybean germplasm. This array is being used to construct high-density genetic map in populations generated from intermatings of two cultivated and two wild soybeans, with an objective to confirm large structural variations of chromosomes using the ultra-high-density maps

Mungbean (Vigna radiata) is a fast-growing, warm-season legume crop that is primarily cultivated in developing countries of Asia. We constructed a draft genome sequence of mungbean to facilitate genome research into the subgenus Ceratotropis and to enable a better understanding of the evolution of leguminous species. The draft genome sequence covers 80% of the estimated genome, of which 50.1% consists of repetitive sequences. In total, 22,427 high confidence protein-coding genes were predicted. Based on the de novo assembly of additional wild mungbean species, the divergence of what was eventually domesticated and the sampled wild mungbean species appears to have predated domestication. Moreover, the de novo assembly of a tetraploid Vigna species (Vigna reflexo-pilosa var. glabra) provided genomic evidence of a recent allopolyploid event. To further study speciation, we compared de novo RNA-seq assemblies of 22 accessions of 18 Vigna species and protein sets of Glycine max and Cajanus cajan. The species tree was constructed by a Bayesian Markov chain Monte Carlo method using highly confident orthologs shared by all 24 accessions. The present assembly of V. radiata var. radiata will facilitate genome research and accelerate molecular breeding of the subgenus Ceratotropis.

This study was carried out to determine the effects of different harvesting stage on nutritive value and the quality of ensiled kenaf after fermentation among six kenaf cultivars. Six kenaf cultivars including two different maturity groups, mid-late maturing (Auxu, Jangdae and Jinju) and early-maturing (Baekma, Jeokbong and C14), were planted on May 14, 2013. Four harvesting times were made at intervals of 20 days from 15 July to 16 September, 2013. In all cultivars, the CP (crude protein) contents were decreased by a delayed harvest; the CP contents of kenaf silage were ranged from 92 to 184 g kg-1. Interestingly, there were no significant difference of NDF (neutral detergent fiber) and ADF (acid detergent fiber) content between the cultivars, however NDF and ADF content of kenaf silage were significantly increased by a late harvest. The silages of all cultivars displayed a low pH ranges less than 4.0, which is sufficient for stable storage. The lactic acid contents in Auxu were from 2.57 to 3.21%, which is higher than other cultivars. The harvesting stages did not affect to the concentrations of butyric acid and acetic acid in all cultivars. These results indicate that the harvesting stage is more important for the quality of kenaf silage than cultivar differences. And kenaf silage could be also used as fodder for ruminants.

KAS360-22 종자에 1998년 250 Gy의 감마선을 조사하였다. 그 후대에서 미이라병에 저항성을 가지는 계통을 선발･육성하여, ‘원율’로 명명하고 2009년에 최종적으로 품종보호권을 출원 신청하여 2012년 등록 완료하였다. 원품종 KAS360-22의 종피색이 노란색인데 반하여 신품종 ‘원율’은 갈색을 나타냈다. 100립중은 재래종 KAS360-22이 17.2 g, ‘원율’은 27.5 g으로 종자무게는 증가하였으며, ‘일품검정콩’(27.4g)과는 별다른 차이를 보이지 않았다. 신품종 ‘원율’의 10a 당 수량은 미이라병 발병 조건에서 233.3 kg으로 재래종 KAS360-22 (24.9 kg)에 비교하여 10.6배 가량 높았고, 대조구 ‘일품검정콩’(121.4 kg)에 비교하여도 1.9배 가량 높아 밥밑용 콩으로 안정적인 수량 확보가 가능할 것으로 사료된다.

Copy number variations (CNVs) are considered major sources of genetic variation, and CNVs may influence phenotypic variation and gene expression. To detect CNVs, rice seeds were exposed with 100～400 Gy of gamma-ray (GA, 60Co), cosmic-ray (CR) by Russia ISS, and 30 and 40 Gy of ion beam (IB, 220 Mev carbon ion). After the exposed rice seeds were cultured in 1/2 MS medium for 14 days, they were used for array-based Comparative genomic hybridization (CGH) analysis using Agilent’s RICE CGH array. As a results, the highest number of CNVs (Gain 808 and Loss 24,080) were detected in the CR treatment, whereas GA100 (100 Gy of GA) was identified the least CNVs. Compared individual chromosome, the chromosome 8 and 11 were identified the highest CNVs, the chromosome 3 had the least CNVs. Most of identified CNVs existed in the range of 10～500kb. In particular, the same CNV locations among different types of ionizing radiation were observed in chromosome 12, and these CNVs contained the commonly 5 amplified genes, containing retrotransposon protein, NADH-ubiquinone oxidoreductase chain 3, heavy metal transport/detoxification protein domain containing protein, and 2 unknown proteins. Other studies were reported that Ty1 (Long Terminal Repeat-retrotransposon family 1) transcription and retrotransposition were induced by different environmental stresses such as ionizing radiation, UV-light exposure, DNA damage and nutrient starvation in Saccharomyces cerevisiae. Our results also show that retrotransposon protein (LOC_Os12g34016) was specifically amplified by different types of ionizing radiation.

VitE (tocotrienols and tocopherols) are micronutrients with antioxidant properties synthesized by photosynthetic bacteria and plants that play important roles in animal and human nutrition. A new mutant line, T1001-1, was isolated from in vitro mutagenized population by ionizing radiation and shown to have increased VitE contents. The total VitE content was 26% increased in the T1001-1 mutant seeds compare with cv. Dongan (wild-type). In addition, we showed that the mutant confers retarded seedling growth during the early seedling growth stage in rice. To study the molecular mechanism of VitE biosynthesis, we used the rice microarray to identify genes that are upor down-regulated in T1001-1 mutant. In addition, we identified differentially regulated pathway using MapMan analysis, which provides deep insight into changes in transcript and metabolites. Our results enhanced the transcription of genes involved in starch and lipid metabolism in T1001-1 mutant. To identify the molecular mechanisms of the events involving transcription factors in tocopherol accumulation, we compared the expression patterns of transcription factors. The AP2-EREBP, WRKY, C2H2 transcription factor were up-regulated, whereas the MYB family was down-regulated in T1001-1 mutant. Our results demonstrate change of important transcript in high level of VitE accumulating rice mutant.

To determine the expression levels of genes related to the salt stress response in rice, gene expression profiles were investigated through microarray analysis using the rice mutant line Till-II-877. There were no significant changes in physiological response under salt stress of the mutant increased less than that in the WT. The intensity of gene expression was analyzed and compared between the wild type and mutant lines using a microarray. Among the most significantly affected pathways, α-linolenic acid metabolism and linoleic acid metabolism (in lipid metabolism), fructose and mannose metabolism and glycolysis-gluconeogenesis (in carbohydrate metabolism), cysteine and methionine metabolism (in amino acid metabolism), and carbon fixation (in the energy metabolism of photosynthetic organisms) showed changes in gene expression levels under salt stress. These results further our understanding of the effects of salt stress in rice and may aid in the development of salt-tolerant rice cultivars.

Soluble sugar content in soybean seed is an important quality attribute for soyfood and feed. Usually, soluble sugars comprise 6 to 17% of total dry wt. in mature soybean seeds. In this study, 414 soybean mutant lines induced by gamma-ray were screened by colormetric assay, FACE (Fluorophore-assisted carbohydrate electrophoresis), and GC-MS to identify the change of soluble sugar contents. Among 414 soybean mutant lines, 12 mutant lines derived from three different soybean cultivars (Hwanggum, Paldal, and Bangsa) showed higher level of soluble sugar content compared to their original cultivars. However, 5 mutant lines derived from soybean landrace KAS 636-15 showed lower level in the colormetric assay. In FACE, 17 soybean mutant lines selected by colormetric assay also showed different band intensity compared with their original cultivars. However, there were no different soluble sugar patterns between soybean original cultivars and mutant lines. Finally, the variations of soluble sugar content in 17 soybean mutant lines were confirmed by using GC-MS. These mutant lines will be used for genetic study to find mutations of genes related soluble sugar biosynthesis.

Ionizing radiation is known to cause chromosomal alterations such as inversions and deletions and affects gene expression within the plant genome. To monitor the genome-wide transcriptome changes by ionizing radiation, we used rice Affimetrix GeneChip microarray to identify genes that are up- or down regulated by gamma-ray (200 Gy, 60Co source), cosmic-ray and ion beam (40 Gy, 220 MeV carbon ion). The overall expression patterns between gamma-ray and ion beam were similar but cosmic-ray was regulated differently. Combined results from all 3 radiations identified 27 up-regulated genes and 188 down regulated genes. These results mean the induction of similar mechanism changes in treatments of gamma ray and ion beam. However the different expression in treatment of cosmic-ray might be due to the other environmental conditions. Among the commonly up- or down- regulated genes, we chose highly up- or down- regulated several genes and confirmed its regulation in response to ionizing radiation exposure by RT-PCR analysis. Moreover, we showed that specific co-expression networks of candidate radio marker genes by ARACNE algorithm. Our results present profiles of gene expression related to different ionizing radiation and marker gene to predict sensitivity to ionizing radiation, such as GS (glutelin subunit) and FBX322.

A dietary deficiency of tryptophan can cause pellagra and lead to low levels of serotonin that is associated with depression, aggression, anxiety and overeating in humans. Thus, enhancement of tryptophan content in rice has great potential benefit for human and animal diets. In this study, a total of 1,350 rice mutant population was used to identify single nucleotide polymorphisms (SNPs) in Oryza sativa anthranilate synthase alpha1(OASA1) gene that was associated with negative feedback in tryptophan biosynthesis. For high-throughput TILLING analysis, 5 fluorescence-labeled primer sets were designed to cover exon regions of OASA1 locus and PCR amplifications were analyzed using ABI3130xl DNA sequencer. Through the screening of 1,350 mutant lines, nine mutant lines produced one or two cleaved fragments in the PCR products of OASA1 locus. The full sequencing of nine mutant lines revealed that total 31 SNPs were located in the regions of OASA1. In particular, three mutant lines contained SNPs in coding regions that resulted in an amino acid change. The tryptophan contents of the three mutant lines were 2.2- to 2.3-fold higher than the wild type. These high-tryptophan mutant lines will be used rice breeding programs and contribute directly to enhancing human nutrition.

Kenaf (Hibiscus cannabinus) is an annual herbaceous plant of the family Malvaceae that has been planted in Africa for more than 4000 years and used as source of fiber, energy and feed stock. Also, kenaf seeds are good source for edible oil used for first class cooking oil and margarine production. The seeds can be used for lubrication, soap, paint and varnishes. This study was carried out to evaluate fatty acids variation among sixteen kenaf germplasm and gamma-ray induced mutants derived from Jinju and Auxu. Linoleic, oleic, and palmitic acid were the predominant fatty acids in all kenaf seed oils. The sixteen accessions showed a wide range of fatty acid compositions, spanning from 28.94 to 43.36% saturated, 56.64 to 71.05% total unsaturated, 15.52 to 46.85% monounsaturated, and 13.56 to 48.97% polyunsaturated fatty acids. The mutant lines derived from Jinju, significantly surpassed parental mean for all the palmitic and oleic acid. Also, the mutant lines derived from Auxu showed broad ranges of variation in oleic and linoleic acid and narrow ranges of variation in stearic and palmitic acid. The relative amount of monounsaturated fatty acids (MUFA) were increased at all the gamma-ray induced mutants. These results will provide a valuable information to assist parental selection of kenaf breeding.

The protein in soybean seeds accounts for approximately 40% of the dry seed weight. Two major storage proteins, 7S and 11S, constitute 70-80% of the total storage proteins in the seeds. In this study, the variation of total soluble protein extracts from 1152 soybean landraces that have been collected from South Korea were studied using high-throughput screening method with HT Protein Express Labchip (Caliper Life Sciences, Inc.). Seven distinct protein band patterns - four protein sub-units of 11S and three sub-units of 7S, were taken into account and their presence or absence were analyzed. Among the 1152 landraces, 525 genotypes were identified as lacking lipoxygenase, 255 lacking α1 subunit, 680 lacking α subunit, 169 lacking β subunit, 140 lacking acidic, 114 lacking Kunitz Trypsin Inhibitor (KTi) and 199 lacking basic protein patterns. The high-throughput protein analysis is helpful in screening a large number of populations with less time and minimum labor. The selected genotypes with low amounts or lacking of anti-nutritional factors such as trypsin inhibitor, lipoxygenase and α subunit would be used for future breeding purpose of quality improvement in soybean protein.

Scientific studies have shown that essential fatty acidintake can have a dramatic impact on human health. Soybean [Glycine max(L.) Merr.] oil from current commercial cultivars typically containsaround 8%linolenic acid (18:3) known as omega-3 fatty acid. Omega-3 fatty acid plays an important role to prevent cardiovascular disease and cancer. Relatively high 18:3 content in seed oil is a trait of the wild soybean (Glycine soja Sieb. and Zucc.) ancestor of modern soybean cultivars. Wild soybean is native to Korean peninsula and recently thousands of wild soybeans collected by soybean researchers in Korea. The objective of this study were to determine the linolenic acid content for wild soybean collection and to determine the stability of linolenic acid content derived from wild soybean over environments. Fatty acid profile for 1,806 wild soybean accessions collected from South Korea was determined by GC. The range of linolenic acid was 7.3 to 23.7% with an average 15.6%. We developed a recombinant inbred population from a cross PI483463 (wild soybean with 15% 18:3) and Hutcheson (cultivar with 8% 18:3). Three RILs, RIL156, RIL159 and RIL166, with high linolenic acid content (over 14%), parents and Williams 82 as checks were grown in nine environments over 2008-2011. Results showed that the content of linolenic acid for the PI483463, Hutcheson, and Williams 82 ranged from 14.8 to 17.1, 8.5 to 9.7, and 6.9 to 8.4 % and averaged 15.4, 9.2 and 8.0%, respectively. However selected RILs 156, 159, and 166 ranged from 10.7 to 15.7, 14 to 15.8, and 14.8 to 15.8, and averaged 13.9, 14.9, and 15.2, respectively. Among the tested accessions, RIL166 was the most stable with the lowest range and CV, and had a relatively lower stability coefficient value than other genotypes. Genes related to high linolenic acid from wild soybean may be useful in developing higher linolenic acid soybean genotypes and would broaden the use of soybean in food applications to improve human nutrition and health.

Hypernodulation soybean mutant, SS2-2, is characterized with greater nodulation and nitrogen fixing ability in the root nodule than its wild type, Shinpaldalkong 2. The present study was performed to identify a genetic locus conferring hypernodulation in soybean mutant SS2-2 and to determine whether the gene controlling the hypernodulation of SS2-2 is allelic to that controlling the supernodulation of nts382 mutant. Hybridization studies between SS2-2 and Taekwangkong revealed that the recessive gene was responsible for the hypernodulation character in soybean mutant SS2-2. Allelism was also tested by crossing supernodulating mutant nts382 and hypernodulating mutant SS2-2 that both hypernodulation and supernodulation genes were likely controlled by an identical locus. Molecular marker mapping of hypernodulation gene in SS2-2 using SSR markers confirmed that the gene conferring hypernodulation was located at the same loci with the gene conferring supernodulation. It is interesting to note that the same gene controlled the super- and hyper-nodulation characters, although SS2-2 and nts 382 exhibited differences in the amount of nodulation in the root system. Further genetic studies should be needed to clarify the genetic regulation of super- and hyper-nodulation in soybean.

Two different types of molecular markers, simple sequence repeat (SSR) and single nucleotide polymorphism (SNP), were used to measure genetic diversity among five Korean, eight Thai, and three wild soybeans. For SSR analysis, a total of 20 markers were surveyed to detect polymorphisms. For SNP analysis, four primers were designed from consensus sequence regions on disease resistance protein homolog genes, and used to amplify the genomic region. The PCR products were sequenced. A number of polymorphic SSR and SNP bands were scored on all genotypes and their genetic similarity was measured. Clustering analysis was performed independently on both types of markers. Clustering based on SSR markers separated the genotypes into three main groups originated from Korea, Thailand, and wild soybeans. On the other hand, two main groups were classified using SNP analysis. It seemed that SSR was more informative than SNP in this study. This may be due to the fact that SNP was surveyed on the smaller genomic region than SSR. Grouping based on the combined data of both markers revealed similar results to that of SNP rather than that of SSR. This might be due to the fact that more loci from SNP were considered to measure genetic relatedness than those from the SSR.

This study was performed to evaluate the growth and nodulation characters of hypernodulating soy-bean mutant, SS2-2, and to know the growth and yield performance of the mutant in infertile soil. Soil fertility was adjusted by mixing the different ratios of soil components including clay, river sand, and horticultural bed, which resulted in fertile and infertile soil. Dry weight, nitrogen concentration, and leaf nitrate reductase of each plant were measured around V6 stage (47 days after planting) and around R3 stage (82 days after planting). There were significant effects of soil fertility and soybean genotype on the total dry weights including root, nodule, stem, leaf, and pod dry weight at V6 and R3 stages. Total dry weight of hypernodulating mutant, SS2-2, was clearly less than that of its wild type, Sinpaldalkong 2. However, nodule development on the roots of SS2-2 was much greater than that of Sinpaldalkong 2, regardless of soil fertility. Though SS2-2 was smaller in plant size than Sinpaldalkong 2, genotypic difference in total nitrogen content was not significant at both V6 and R3 stages because SS2-2 fixed more nitrogen biologically than its wild type in the root nodule. The SS2-2 mutant showed lower plant yield in both infertile and fertile soil. The SS2-2 contained more crude seed protein than Sinpaldalkong 2, and was characterized with reduced top and root growth.