Amaranth (Amaranthus sp. L.) is an important group of plants that includes grain, vegetable, and ornamental types. Centers of diversity for Amaranths are Central and South America, India, and South East Asia, with secondary centers of diversity in West and East Africa. The present study was performed to determine the genetic diversity and population structure of 75 amaranth accessions: 65 from South America and 10 from South Asia as controls using 14 SSR markers. Ninety-nine alleles were detected at an average of seven alleles per SSR locus. Model-based structure analysis revealed the presence of two subpopulations and 3 admixtures, which was consistent with clustering based on the genetic distance. The average major allele frequency and polymorphic information content (PIC) were 0.42 and 0.39, respectively. According to the model-based structure analysis based on genetic distance, 75 accessions (96%) were classified into two clusters, and only three accessions (4%) were admixtures. Cluster 1 had a higher allele number and PIC values than Cluster 2. Model-based structure analysis revealed the presence of two subpopulations and three admixtures in the 75 accessions. The results of this study provide effective information for future germplasm conservation and improvement programs in Amaranthus.

Rice (Oryza sativa) is an excellent model monocot with a known genome sequence for studying developmental seeds. In the study, the seeds of 10th day after flowering (DAF) were conducted RNA-Seq of the variety Shindongjin and Sugary mutant using RNA-seq technique. Approximately 202 and 214 million high-quality paired-end reads (101-bp in size) were generated in Shindongjin and Sugary mutant, respectively. Comprehensive analysis on the transcript levels of genes which encode starch-synthesis enzymes is fundamental for the assessment of the function of each enzyme and the regulatory mechanism of starch biosynthesis in seeds. Quantitative real-time PCR was also used to validate the expression profiles of 28 rice genes encoding six classes of enzymes, viz., ADPglucose pyrophosphorylase (AGPase), starch synthase, starch branching enzyme, starch debranching enzyme, starch phosphorylase, and disproportionating enzyme at different developmental grain- filling stages (DAF 1-14) between Shindongjin and Sugary mutant. The results showed that the expression of most of starch synthesis genes were up-regulated except the cytosolic AGPase small subunit2b (AGPS2b), which sharply decreased at grain-filling stages in Sugary mutant. These results will expand our understanding of the complex molecular and cellular events in rice grain-filling stages and provide a fundamental understanding of future studies on developmental endosperm in rice and other cereal crops.

Somatic embryogenesis is a process where a plant or embryo is derived from a single somatic cell or group of somatic cells. Application of this process include: clonal propagation of genetically uniform plant material; elimination of viruses; provision if source tissue for genetic transformation; generation of whole plants from single cells called protoplasts; development of synthetic seed technology. In this study tissue culture was carried out for mass propagation of cassava using somatic embryogenesis. For tissue culture set up, we used cassava variety (“Rayong5”, “Rayong7”, “Rayong9”, “Rayong11”) developed in Rayong Field Crop Research Center(RYFCRC). In induction of callus step, the callus formed from each cassava variety. “Rayong 7“ showed the highest induction rate of 95%, while induction rate of other varies were ranged from 50% to 85%. In the case of weight of callus ”Rayong5“ has the highest weight. Results in the present study would be useful in mass propagation of cassava by somatic embryogenesis.

Direct seeding of rice is increasingly being practiced in both rainfed and irrigated areas because of labor shortage for transplanting and opportunities for crop intensification. However, slow seed germination and delayed seedling establishment will become a major problem for rice production in flood-prone lowland areas as sowing method shifts from transplanting to direct seeding. Identification of anoxia-induced ethylene response factors is suggestive because genes belonging to this gene family play a crucial role in rice tolerance to submergence. In this study, genetic structure variability of three AG related genes, Sub1 (Sub1A, Sub1B, Sub1C), Sub2 (OsGAPPH) and Ramy3D were examined by using whole-genome resequencing data of 84 accessions of rice core set. Some new SNPs and InDels found in exon part of anaerobic germination related genes in the present study would be useful in developing markers to identify the submergence resistant varieties in the future molecular breeding.

Rice blast disease caused by the fungal pathogen Magnaporthe oryzae is one of the most destructive rice diseases worldwide. Resistance to rice blast pathogen mostly shows a quantitative trait controlled by several genes. A total of 13 major blast resistance (R) genes were reported in a number of Korean rice varieties using molecular markers. The Pi-ta gene, which locates near to the centromere of chromosome 12, was haplotyping using 1790 accessions including cultivated and wild varieties in previous research. However, the genetic variations of other R genes in rice still not clear. Three R genes, Pi9, Pia, and Pib on chromosome 6, 11 and 2 respectively, were resequenced among 84 accessions of rice core set. Different types of halotype among the 84 accessions were detected. Some new SNPs and InDels found in exon part of R genes were expected to result into amino acid changes following analysis of the genetic code variations, and the germplam in this rice core set which are resistance to blast were explored. We are expecting to develop the new functional markers and incorporate of resistance genes into existing rice cultivars and finally these apply outcomes in breeding rice resistance to blast diseases.

Preharvest sprouting (PHS) not only causes reduction of grain yield, but also affects the quality of grains, resulting into significant economic losses. PHS is governed by multiple genes. Little is known about the large genetic variation of preharvest sprouting in rice. In the present study, genetic variations of four PHS genes, OsVP1, Osaba1, Alpha-amylase3D and OsGA20ox1 were studied by using whole-genome resequencing data of 84 accessions of rice core set. A total of haplotype groups; 27, 29, 6 and 14, for OsVP1, Osaba1, Alpha-amylase3D and OsGA20ox1, respectively, were detected among the 84 accessions. Some new SNPs and InDels were found in exon part of PHS related genes were expected to result in amino acid changes following analysis of the genetic code variations, and the germplasm or varieties which are resistant to preharvest sprouting were explored. Based on this step, phenotyping for PHS is ongoing, and the association mapping of PHS will be conducted by using SNPs resulted from the haplotyping data. The present results will be ultimately useful to the molecular breeding for the development of PHS resistant rice cultivars.

AGenome-wide association studies (GWAS) have proven a useful technique for identifying genetic loci responsible for natural variation in rice. With the fast developed next-generation sequencing technology, it is possible for people to carry out GWAS by phenotyping different traits. However, how to make full use of huge data, abandon unnecessary data, and solve the problem of data application effectively seems still an obstacle for many researchers. Taking the case of whole-genome resequencing of Korean authentic rice core set, here we present a general technological path of GWAS including: 1) a schematic view of sequencing-based GWAS in rice; 2) a user-friendly and interactive web application for GWAS in rice by the aid of experience from Arabidopsis; 3) Haplotype and association analysis of candidate genes in a certain mechanism pathway, giving 10 starch synthesis genes as example; and 4) functional validation by Trans- and Mata-Omics analysis.

Amaranths (Amaranthus sp.) are cosmopolitan and include grain, vegetable, ornamental and weed types. Forteen simple sequence repeat (SSR) markers were used to analyze the genetic diversity of 59 accessions of cultivated amaranth from Asian countries. A total of 63 alleles were detected with an average of 4.5 per locus. The averaged values of gene diversity and polymorphism information content (PIC) were 0.35 and 0.33, respectively. Alleles per locus in accessions from South Asia was 4.35, whereas 2.93 and 3.79 alleles per locus were found in Nepal and India, respectively. The mean gene diversity in Central Asia and East Asia was 0.36 and 0.28, respectively, whereas the mean PIC values were 0.27 and 0.22, respectively. The genetic diversity and PIC of the India amaranths were higher than that of other Asian countries. The model-based structure analysis revealed the presence of three subpopulations, which was basically consistent with clustering based on genetic distance. An AMOVA analysis showed that the between-population component of genetic variance was less than 56.16% in contrast to 43.84% for the within-population component. The overall FST value was 0.56, reflecting genetic differentiation within Asian amaranths. These findings could be used for designing effective breeding programs aimed at broadening the genetic bases of commercially grown varieties.

Aroma development in rice has been reported due to the lack of function of betaine aldehyde dehydrogenase gene (badh2) on rice chromosome 8. A lot of functional markers have been designed based on the InDels, such as 7bp deletion in exon 2, 803bp deletion in exon 4 and 5, 8bp deletion in exon 7, and 3bp insertion in exon 13. Although there were a lot of functional SNPs, other InDels have not been detected by a PCR-based marker. Here we developed a simple, co-dominant, functional cleaved amplified polymorphic sequence (CAPS) marker for fragrance trait based on 1bp insertion in exon 14. The developed marker showed a high efficiency in discriminating that special aromatic rice variety, and displayed perfect co-segregation with the trait of fragrance in the F2 population. This new marker developed in the present study would be useful in molecular breeding of fragrant rice varieties.

Vitamin E and phytosterols are both valuable nutrients that act as antioxidants in human bodies. Understanding the genetic basis of these traits is necessary for the improvement of nutritional quality by breeding. In this study, 119 rice accessions of diverse origin were genotyped using 232 SSR markers to identify marker–trait associations with Vitamin E and phytosterols in rice. Analysis of population structure revealed four subgroups in the population. Linkage disequilibrium (LD) patterns and distributions are of fundamental importance for genome-wide mapping associations. The mean r2 value for all intra-chromosomal loci pairs was 0.3361. LD between linked markers decreased with distance. Marker–trait associations were investigated using the unified mixed-model approach, considering both population structure (Q) and kinship (K). In total, 81 marker–trait associations were identified using 232 different SSR markers covering 12 chromosomes. The results suggest that association mapping in rice is a viable alternative to quantitative trait loci mapping. The results from this association mapping study will be the basis for improving rice nutritional quality.

This study was set up to get plants from anther culture of Chrysanthemum (Dendranthema grandiflorum) gardenmum cultivar “Yes Morning’ and potmum cultivar “Peace Pink” for breeding program. The induction of callus was quick and high on MS basal medium supplemented with 1.0 mg/L of 2,4-D + 2.0 mg/L of 6-BA + 4% W/V sucrose. Induction potential was slightly increased by addition of 250 mg/L Casein hydrolysate to the induction medium. Calluses were allowed to differentiate on MS basal medium + 2.0 mg/L of BA + 0.1 mg/L of NAA + 3%W/V sucrose. The rate of callus formation differed little between the cultivars. A pretreatment of anthers at 4℃ for 48h enhanced both the induction and differentiation ratio. Multiple shoots were initiated from most of the calluses and were shifted to MS basal medium + 0.1 mg/L of NAA + 3%W/V sucrose for rooting. Regenerated plantlets were acclimatized and transferred to the soil. Some of the regenerated plants showed slow growth with little morphological difference.

Rice(Oryza sativa L.) feeds more than 50% of the world’s population and is one of the most important crops in the world. To evaluate the variation between different rice classfications, genetic diversity amoung a diverse set of rice collection including 59 breedlines, 23 landraces, 18 weedy rices and 35 introductions were analysed using 134 SSR markers located on the 12 chromosomes. In total, 1269 alleles were identified with an average of 9.47 per locus. Of the 1269 alleles, 460 (36.2%) were common, with a frequency of 0.05–0.5; 741 (58.4%) were rare (frequency < 0.05) and 68 (5.4%) were abundant (frequency > 0.5). A relatively high Polymophism information content (PIC) value was detected in landraces with smaller number of accessions than that of breedlines. Model-based structure analysis revealed the presence of six subpopulations, which was essentially consistent with the clustering based on genetic distance. One hundred and eight accessions (80.0%) showed a clear relation to each cluster based on their inferred ancestry value (>70%), while the remaining 27 accessions (15.4%) of which nine from landraces and fifteen from introductions were categorized as admixtures. Landrace and introductions distributed to almost all the six subpopulations whereas most of breedlines distributed to two distinct subpopulations. In conculusion, landraces in the present study showed critical importance in preservation of genetic diversity and rice breeding programs.

The purpose of this study was to develop the best mushroom cultivation conditions and the combination of mushroom culture media in order for mushroom producers and consumers. To reach this target, we first investigated the genetic relationship and developed suitable conditions of mycelial growth in Hypsizygus marmoreus strains. One superior strain of H. marmoreus was selected from 124 strains using bag culture. One hundred and twenty four strains were genetically classified into four main groups using two Universal Rice primers, URP2R and URP17R. The studies on the effects of different temperature (17, 21, 25, 29, 33℃) showed that 25℃ is the best temperature for mycelial growth for almost all strains while at 33℃ most of mycelium stop growth. Finally, ten strains were selected according to the groups identified by their temperature requirements. The length of mycelial growth in PDA, MCM, GPYM, MEA and MYP were longer than those in Czapek Dox. The selected ten strains of H. marmoreus showed heavier dry weight of mycelia at pH 3.0∼7.0 than any other pH. Although it was not show distinct requirement of carbon and nitrogen sources for vegetative growth according to strains, mainly the mycelial growth of the ten selected strains were observed at media including xylan and yeast extract, peptone, tryptone, respectively. Moreover, higher C/N ratio was observed in higher dry weight of mycelia.

Panax ginseng C.A. Meyer, commonly known as Korean or Asian ginseng, is a perennial herb which is native to Korea and China. Its roots are highly prized for several medicinal properties. Therefore, Ginseng has been a top-ranked subject of many fields of scientific research worldwide. However, very limited number of research work has been published on species authentication using DNA marker system. In this study, 22 simple sequence repeat (SSR) markers were used to analyze the genetic diversity and population structure of 167 ginseng cultivars from 11 regions and 10 breed varieties. A total number of 111 alleles were detected, with an average of 5.05 per locus. The average expected heterozygosity and polymorphism information content (PIC) for SSR locus were 0.35 and 0.30, respectively. The model-based structure analysis revealed that 66.5% of all cultivars could be grouped into three populations with inferred value (allele shared >70%) membership. More than 33% of tested cultivars derived from two ancestries, which was basically consistent with clustering based on genetic distance. Almost all of the cultivars shared the ancestry with S1 and S2 except 1 China Jilin and 3 USA cultivars. The result indicated that most of Korean ginsengs are closely interrelated between the two ancestors but USA ginsengs are totally different from Asian cultivars.

The plant family chrysanthemum is known for its medicinal, ornamental, and economic purposes. Owing to its economic and biological significance to the difficult identification based on morphological characters, it is useful to develop DNA barcodes. DNA sequence data enable not only the inference of phylogenetic relationships but also provide an efficient method for species-level identifications under terms DNA barcoding or DNA taxonomy. The purpose of this study is to evaluate the utility of DNA barcoding in discriminating Chrysanthemum species. Four cpDNA regions (matK, rpoC, rpoB, trnH-psbA) and one nuclear (ITS) marker have sequenced from 28 specimens of 11 species from 4 genera of Chrysanthemum which were collected from 5 provinces in Korea. Comparisons of within and between species levels of sequence divergence showed that genetic variation between species exceeds variation within species.

Allele mining in starch synthesis-related genes (SSRGs) has facilitated the discovery of desired natural sequence variations for eating quality in rice. This study investigated the sequence variations from 10 SSRGs, and further evaluated their relationship with the amylose content (AC) and rapid viscosity analysis profiles in a global collection of rice accessions by association mapping (AM). In total, 83 sequence variations were found in 10 sequenced amplicons, including 73 single nucleotide polymorphisms (SNPs), eight insertion-deletions (InDels) and two polymorphic simple sequence repeats (SSRs). Four subpopulations were identified by population structure analysis based on 170 genome-wide SSR genotypes. AM revealed 11 significant associations between three phenotypic indices and three sequence variations. One SNP with a g/c transversion at the 63rd nucleotide downstream of the OsBEIIb gene termination codon on rice chromosome 2 was significantly associated with multiple trait indices in both the general linear and mixed linear models (GLM and MLM), including the final viscosity (p < 0.001, R2 = 23.87%) in both 2009 and 2010, and AC (p < 0.01, R2 = 11.25%) and trough viscosity (p < 0.01, R2 = 20.43) in 2010. This study provides a new perspective of allele mining for breeding strategies based on marker-assisted selection.

In this study, we examined the variation of 30 phenolic compounds in the mungbean (Vigna radiata (L.) Wilczek) germplasms. Recent studies showed that the potential health benefits from the antioxidnant activity of the phenolic compounds. The average concentration of phenolic compounds among the 70 mungbean germplasms was 2424.9 μg g-1. Among the mungbean germplasms, 25 kinds of mungbean germplasms were higher than others. Specially, 69 (IT 182280) (3836.63 ㎍ g-1) and 63 (IT 180525) (3491.51 ㎍ g-1) revealed highest levels of the total phenolic compounds. On the other hand, 27 (IT 154078) (1624 ㎍ g-1) was revealed lowest concentration of the total phenolic compounds. Among the individual phenolic compounds, rutin (avg. 1776.09 ㎍ g-1) showed highest concentrations, pyrogallol (144.31 ㎍ g-1), gentisic acid (119.19 ㎍ g-1) and chlorogenic acid (78.24 ㎍ g-1) were relatively higher than other phenolic compounds. The germplasm of 69 (IT 182280) had the highest rutin (3156.87 ㎍ g-1) concentraion. While, the biochanin A (avg. 2.02 ㎍ g-1) and formonetin (avg. 2.61 ㎍ g-1) had the lowest levels among the mungbean germplasms. This study indicateded that determination of the functional substances in mungbean germplasms and it is more valuable for the future crop cultivation and food industries.

For the development of SSR marker system in Vicia villosa Roth, an enriched library was constructed by using a modified biotin-streptavidin capture method and the selected clones were sequenced with GS-FLX(454). Of 37,794 sequenced reads, we found that 8,474 reads (22.4%) were redundant, leaving 29,320 unique ones (77.6%). Among the unique clones, 17,174 reads (58.6%) were having microsatellite repeating motifs. Sequence analysis of all SSR-containing reads revealed a predominance of the di-nucleotide SSRs (62.5%). The tri-nucleotide and the tetra-nucleotide SSRs were 5.7% and 22.5%, respectively. As the di-nucleotide type, the AG/GA class of repeat motif was most frequently identified (55.0% of the total di-nucleotide SSRs), followed by the CT/TC class (19.5%), and the TA/AT class (12.1%). Among the tri-nucleotide SSRs, the AGT/GTA/TAG class of repeat motifs was predominant (22.2%), followed by the ACT/CTA/TAC class (17.8%). Among the tetra-nucleotide SSRs, the CTTT/TTTC/TTCT/TCTT class of repeat motifs was predominant (31.2%), followed by the AAAG/AAGA/AGAA/ GAAA class (19.9%). Finally, we designed 779 primer pairs from the flanking sequences of SSR containing reads. We are undertaking the analysis of polymorphisms using the diverse collected accessions of Vicia villosa Roth now. This newly developed SSR marker set shall provide a very useful tool for implementing molecular diversity assessment and population structure studies of Vicia villosa Roth onward.