Gyu-Taek Cho

Development and Molecular Characterization of 55 Novel Polymorphic cDNA-SSR Markers in Faba Bean (Vicia faba L.) Using 454 Pyrosequencing

Faba bean (Vicia faba L.) is a major food source and fodder legume, popularly known for its high content of seed-protein. Its role is critical in crop rotation, and for fixing nitrogen effectively. Polymorphic simple sequence repeat markers from transcript sequences (cDNA; simple sequence repeat [SSR]) were developed for faba bean (Vicia faba). We found that 1,729 SSR loci from 81,333 individual sequence reads and 240 primer pairs were designed and synthesized. In total, 55 primer pairs were found to be polymorphic and scorable consistently when screened in 32 accessions. The number of alleles ranged from 2 to 15, frequency of major alleles per locus varied from 0.17 to 0.91, the genotypes number ranged from 2 to 17, observed and expected heterozycosity values ranged from 0.00 to 0.44 and 0.17 to 0.89 and overall PIC values ranged from 0.16 to 0.88 respectively. These markers will be a useful tool for assessing the genetic diversity, understanding the population structure, and breeding patterns of faba bean.

Development of 65 Novel Polymorphic cDNA-SSR Markers in Common Vetch (Vicia sativa subsp. sativa) Using Next Generation Sequencing

Vetch (Vicia sativa L.) is one of the most important annual forage legumes in the World due to its multiple uses (i.e., hay, grain, silage and green manure) and high nutritional value. However, detrimental cyanoalanine toxins in its plant parts including seeds and its vulnerability to hard winter conditions are currently reducing the agronomic values of vetch varieties. Moreover, the existence in the public domain of very few genomic resources, especially molecular markers, has further hampered breeding efforts. Polymorphic simple sequence repeat markers from transcript sequences (cDNA; simple sequence repeat [SSR]) were developed for Vicia sativa subsp. sativa. We found 3,811 SSR loci from 31,504 individual sequence reads, and 300 primer pairs were designed and synthesized. In total, 65 primer pairs were found to be consistently scorable when 32 accessions were tested. The numbers of alleles ranged from 2 to 19, frequency of major alleles per locus were 0.27–0.87, the genotype number was 2–19, the overall polymorphism information content (PIC) values were 0.20–0.86, and the observed and expected heterozygosity values were 0.00–0.41 and 0.264–0.852, respectively. These markers provide a useful tool for assessing genetic diversity, population structure, and positional cloning, facilitating vetch breeding programs.

Assessment of genetic diversity and population structure in mungbean

This study was carried out to assess the genetic diversity and to analyze the population genetic structure for a total of 692 mungbean accessions preserved at National Agrobiodiversity Center (NAC) of the Rural Development Administration (RDA), Korea. Mungbean accessions were collected from 27 countries in nine different geographic regions, and were genotyped using 15 microsatellite markers, which were developed in our previous study. A total of 66 alleles were detected among 692 accessions at all the loci with an average of 4.4 alleles per locus. All the microsatellite loci were found to be polymorphic. The expected heterozygosity (HE) and polymorphism information content (PIC) ranged from 0.081 to 0.588 (mean = 0.345) and from 0.080 to 0.544 (mean = 0.295), respectively. Of the 66 alleles, 17 (25.8%) were common (frequency range between 0.05 and 0.5), 15 (22.7%) were abundant (frequency range > 0.5), and 34 (51.5%) were rare (frequency range < 0.05). Locus GB-VR-7 provided the highest number of rare alleles(eight), followed by GB-VR-91(six) and GB-VR-113(four). Country-wide comparative study on genetic diversity showed that accessions from the USA possessed the highest genetic diversity (PIC) followed by Nepal, Iran, and Afghanistan. And region-wide showed that accessions from Europe possessed the highest average genetic diversity, followed by accessions from the USA, South Asia, West Asia, and Oceania. Twenty-seven countries were grouped into seven clades by phylogenetic relationship analysis, but clustering pattern did not strictly follow their geographical origin because of extensive germplasm exchange between/among countries and regions. As a result of a model-based analysis (STRUCTURE) of microsatellite data, two distinct genetic groups were identified which shared more than 75% membership with one of the two genetic groups. However the genetic group pattern did not reflect their geographical origin. The Duncan’s Multiple Range Test among these two genetic groups and an admixed group, with a mean of 16 phenotypic traits, showed significant difference in 12 quantitative and qualitative traits on the basis of ANOVA. These 15 newly developed SSR markers proved to be useful as DNA markers to detect genetic variation in mungbean germplasm for reasonable management and crossbreeding purposes.

Cross-Amplification of Vicia sativa subsp. sativa Microsatellites across 22 Other Vicia Species

The temperate and herbaceous genus Vicia L. is a member of the legume tribe Fabeae of the subfamily Papilionoideae. The genus Vicia comprises 166 annual or perennial species distributed mainly in Europe, Asia, and North America, but also extending to the temperate regions of South America and tropical Africa. The use of simple sequence repeat (SSR) markers for Vicia species has not been investigated as extensively as for other crop species. In this study, we assessed the potential for cross-species amplification of cDNA microsatellite markers developed from common vetch (Vicia sativa subsp. sativa). For cross-species amplification of the SSRs, amplification was carried out with genomic DNA isolated from two to eight accessions of 22 different Vicia species. For individual species or subspecies, the transferability rates ranged from 33% for V. ervilia to 82% for V. sativa subsp. nigra with an average rate of 52.0%. Because the rate of successful SSR marker amplification generally correlates with genetic distance, these SSR markers are potentially useful for analyzing genetic relationships between or within Vicia species.

Transcriptome Analysis of Two Vicia sativa Subspecies: Mining Molecular Markers to Enhance Genomic Resources for Vetch Improvement

The vetch (Vicia sativa) is one of the most important annual forage legumes globally due to its multiple uses and high nutritional content. Despite these agronomical benefits, many drawbacks, including cyano-alanine toxin, has reduced the agronomic value of vetch varieties. Here, we used 454 technology to sequence the two V. sativa subspecies (ssp. sativa and ssp. nigra) to enrich functional information and genetic marker resources for the vetch research community. A total of 86,532 and 47,103 reads produced 35,202 and 18,808 unigenes with average lengths of 735 and 601 bp for V. sativa sativa and V. sativa nigra, respectively. Gene Ontology annotations and the cluster of orthologous gene classes were used to annotate the function of the Vicia transcriptomes. The Vicia transcriptome sequences were then mined for simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers. About 13% and 3% of the Vicia unigenes contained the putative SSR and SNP sequences, respectively. Among those SSRs, 100 were chosen for the validation and the polymorphism test using the Vicia germplasm set. Thus, our approach takes advantage of the utility of transcriptomic data to expedite a vetch breeding program.

The Complete Chloroplast Genome of Capsicum frutescens (Solanaceae)

Premise of the study: We report the complete sequence of the chloroplast genome of Capsicum frutescens (Solanaceae), a species of chili pepper. Methods and Results: Using an Illumina platform, we sequenced the chloroplast genome of C. frutescens. The total length of the genome is 156,817 bp, and the overall GC content is 37.7%. A pair of 25,792-bp inverted repeats is separated by small (17,853 bp) and large (87,380 bp) single-copy regions. The C. frutescens chloroplast genome encodes 132 unique genes, including 87 protein-coding genes, 37 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. Of these, seven genes are duplicated in the inverted repeats and 12 genes contain one or two introns. Comparative analysis with the reference chloroplast genome revealed 125 simple sequence repeat motifs and 34 variants, mostly located in the noncoding regions. Conclusions: The complete chloroplast genome sequence of C. frutescens reported here is a valuable genetic resource for Capsicum species.

Agricultural Status in Kazakhstan Republic and Korean Strategies for Agriculture Technical Cooperation with Kazakhstan

The purpose of this paper was to introduce agricultural status of the Tajikistan republic for whom are interested in agriculture of Tajikistan. Tajikistan is situated in the south-east of Central Asia and shares borders with Afghanistan, China, Kyrgyzstan, and Uzbekistan. The total land area of the Republic is 143.1 thousands km and 93 percent of the territory is mountain, and nearly half of the country area is located at 3,000 masl and above. Agriculture accounts for approximately 21.4% of GDP in 2011, and approximately 74% of the population resides in rural areas, and 49.8% of the work force is engaged in agricultural production in 2009. Because of a little amount of precipitation, almost all of arable land(702 thousands ha, 94.6%) should be irrigated. Important crops in Tajikistan are wheat, cotton, barley, corn, potato, onion, rice, and tomato. Because of low crop productivity Tajikistan imports many agricultural products including wheat, wheat flour, and potato. The livestock industry occupied 21.7% of total agricultural product and important livestock are cattle, sheep, goat, rabbit and chicken. There are about 5,000 plant species in Tajikistan, including 650 endemic species and Tajikistan is homeland for fifty plant species including dwarf wheat, sesame, melon, radish, garlic, apple, pear, grape, and berries, etc. The total amount of conserved samples ex situ is 5317, out of which 981 are local varieties and landraces, and 1775 are breeding materials. At present, though there is no agriculture technical cooperative project between Korea and Tajikistan, it will be needed to develop cooperative projects in various field of agriculture in the near future. Plant genetic resources can be a good example of cooperative projects on the basis of mutual profit.

The complete chloroplast genome sequence of wild oat, Avena sterilis L. (Poaceae) and its phylogeny

Abstract Wild oat, Avena sterilis L. is a stout broad-leaved annual grass resembling cultivated oats in general appearance. In this study, we sequenced the complete chloroplast (cp) genome sequence of A. sterilis for the first time to investigate their phylogenetic relationship in the family Poaceae. The complete cp genome sequence is 135,887 bp in length with 38.5% overall GC content and exhibits a typical quadripartite structure comprising one pair of inverted repeats (21,603 bp) separated by a small single-copy region (12,575 bp) and a large single-copy region (80,106). The cp genome encodes 111 unique genes, 76 of which are protein-coding genes, four rRNA genes, 30 tRNA genes, and 18 duplicated genes in the inverted repeat region. The phylogenetic analysis indicated A. sterilis closely clustered with the cultivated oat, A. sativa L.

The complete chloroplast genome sequences of little millet (Panicum sumatrense Roth ex Roem. and Schult.) (Poaceae)

Abstract Little millet, Panicum sumatrense Roth ex Roem. & Schult., is an important cultivated species under the tribe Paniceae, sub-family Panicoideae and family Poaceae. In this study, for the first time we sequenced the complete chloroplast (cp) genome of P. sumatrense to investigate their phylogenetic relationship in the family Poaceae. The complete cp genome sequence of P. sumatrense is 139,384 bp in length with 38.6% overall GC content and exhibits a typical quadripartite structure comprising one pair of inverted repeats (22,723 bp) separated by a small single-copy region (12,583 bp) and a large single-copy region (81,355 bp). The P. sumatrense cp genome encodes 125 unique genes, which include 91 protein-coding genes, 4 rRNA genes, 30 tRNA genes, and 20 genes were duplicated in the inverted repeat region. This newly determined cp genome (P. sumatrense) could be valuable information for the breeding programs of this cereal crops in the family Poaceae.

Comparative efficacy of four candidate DNA barcode regions for identification of Vicia species

The genus Vicia L., one of the earliest domesticated plant genera, is a member of the legume tribe Fabeae of the subfamily Papilionoideae ( Fabaceae ). The taxonomic history of this genus is extensive and controversial, which has hindered the development of taxonomic procedures and made it difficult to identify and share these economically important crop resources. Species identification through DNA barcoding is a valuable taxonomic classification tool. In this study, four DNA barcodes (ITS2, matK , rbcL and psbA-trnH ) were evaluated on 110 samples that represented 34 taxonomically best-known species in the Vicia genus. Topologies of the phylogenetic trees based on an individual locus were similar. Individual locus-based analyses could not discriminate closely related Vicia species. We proposed a concatenated data approach to increase the resolving power of ITS2. The DNA barcodes matK , psbA-trnH and rbcL were used as an additional tool for phylogenetic analysis. Among the four barcodes, three-barcode combinations that included psbA-trnH with any two of the other barcodes (ITS2, matK or rbcL ) provided the best discrimination among Vicia species. Species discrimination was assessed with bootstrap values and considered successful only when all the conspecific individuals formed a single clade. Through sequencing of these barcodes from additional Vicia accessions, 17 of the 34 known Vicia species could be identified with varying levels of confidence. From our analyses, the combined barcoding markers are useful in the early diagnosis of targeted Vicia species and can provide essential baseline data for conservation strategies, as well as guidance in assembling germplasm collections.