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Raveendar,,Sebastin,Chung,,Jong-Wook,Lee,,Gi-An,Lee,,Jung-Ro,Lee,,Kyung-Jun,Shin,,Myoung-Jae,Cho,,Yang-Hee,Ma,,Kyung-Ho Korean Society of Breeding Science 2016 Plant Breeding and Biotechnology Vol.4 No.3
Raveendar,,Sebastin,Lee,,Jung-Ro,Park,,Jae-Wan,Lee,,Gi-An,Jeon,,Young-Ah,Lee,,Won-Hee,Cho,,Gyu-Taek,Ma,,Kyung-Ho,Lee,,Sok-Young,Chung,,Jong-Wook Korean Society of Breeding Science 2015 Plant Breeding and Biotechnology Vol.3 No.2
Raveendar,,Sebastin,Jeon,,Young-Ah,Lee,,Jung-Ro,Lee,,Gi-An,Lee,,Kyung,Jun,Cho,,Gyu-Taek,Ma,,Kyung-Ho,Lee,,Sok-Young,Chung,,Jong-Wook Korean Society of Breeding Science 2015 Plant Breeding and Biotechnology Vol.3 No.2
Raveendar,,Sebastin,Lee,,Jung-Ro,Park,,Jae-Wan,Lee,,Gi-An,Jeon,,Young-Ah,Lee,,Yun,Jeong,Cho,,Gyu-Taek,Ma,,Kyung-Ho,Lee,,Sok-Young,Chung,,Jong-Wook Korean Society of Breeding Science 2015 Plant Breeding and Biotechnology Vol.3 No.1
Raveendar,,Sebastin,Lee,,Jung-Ro,Shim,,Donghwan,Lee,,Gi-An,Jeon,,Young-Ah,Cho,,Gyu-Taek,Ma,,Kyung-Ho,Lee,,Sok-Young,Sung,,Gi-Ho,Chung,,Jong-Wook Cambridge University Press 2017 Plant genetic resources Vol.15 No.4
<B>Abstract</B><P>The genus <I>Vicia</I> L., one of the earliest domesticated plant genera, is a member of the legume tribe <I>Fabeae</I> of the subfamily <I>Papilionoideae</I> (<I>Fabaceae</I>). 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, <I>matK</I>, <I>rbcL</I> and <I>psbA-trnH</I>) were evaluated on 110 samples that represented 34 taxonomically best-known species in the <I>Vicia</I> genus. Topologies of the phylogenetic trees based on an individual locus were similar. Individual locus-based analyses could not discriminate closely related <I>Vicia</I> species. We proposed a concatenated data approach to increase the resolving power of ITS2. The DNA barcodes <I>matK</I>, <I>psbA-trnH</I> and <I>rbcL</I> were used as an additional tool for phylogenetic analysis. Among the four barcodes, three-barcode combinations that included <I>psbA-trnH</I> with any two of the other barcodes (ITS2, <I>matK</I> or <I>rbcL</I>) provided the best discrimination among <I>Vicia</I> 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 <I>Vicia</I> accessions, 17 of the 34 known <I>Vicia</I> species could be identified with varying levels of confidence. From our analyses, the combined barcoding markers are useful in the early diagnosis of targeted <I>Vicia</I> species and can provide essential baseline data for conservation strategies, as well as guidance in assembling germplasm collections.</P>
Raveendar,,Sebastin,Lee,,Kyung,Jun,Shin,,Myoung-Jae,Cho,,Gyu-Taek,Lee,,Jung-Ro,Ma,,Kyung-Ho,Lee,,Gi-An,Chung,,Jong-Wook Korean Society of Breeding Science 2017 Plant Breeding and Biotechnology Vol.5 No.4
( Sebastin Raveendar ), ( Jong-wook Chung ), ( Gi-an Lee ), ( Jung-ro Lee ), ( Kyung-jun Lee ), ( Myoung-jae Shin ), ( Yang-hee Cho ), ( Kyung-ho Ma ) 한국육종학회 2016 Plant Breeding and Biotechnology Vol.4 No.3
Tomato (Solanum lycopersicum L.) is one of the most economically important plants in the family Solanaceae. Understanding its genetic diversity of accessions is vital for additional collection of tomato germplasms. The objective of this study was to determine the genetic diversity and population structure of 355 tomato accessions from Asia using 18 simple-sequence repeats (SSRs). A total of 176 alleles were detected at an average of ten alleles per SSR locus. The average major allele frequency and polymorphic information content were 0.69 and 0.39, respectively. Model-based structure analysis revealed two subpopulations (88%), including admixtures (11%) in the 355 Asian tomato accessions, consistent with clustering results based on genetic distance. The overall FST value was 0.135, indicating a moderate differentiation between the inferred subpopulations. Analysis of molecular variance showed that the genetic variance among geographical groups was less than 6%, in contrast to 86% of genetic variance among individuals. The results from this study will provide important information for future germplasm conservation and improvement programs for tomato.
( Sebastin Raveendar ), ( Jung Ro Lee ), ( Jae Wan Park ), ( Gi An Lee ), ( Young Ah Jeon ), ( Yun Jeong Lee ), ( Gyu Taek Cho ), ( Kyung Ho Ma ), ( Sok Young Lee ), ( Jong Wook Chung ) 한국육종학회 2015 Plant Breeding and Biotechnology Vol.3 No.1
We investigated the species discriminatory efficiency of the proposed plant barcoding loci ITS2 and matK in Vicia species. In 2011, China Plant BOL Group proposed the addition of nuclear ITS2 to matK be accepted as a 2-locus DNA barcode to classify plant species. The matK region was chosen as a DNA barcode because of its effective species discriminating power, high quality sequence recovery, and easy experimental analysis. Integration of matK sequences into Vicia phylogeny could improve phylogenetic reconstruction of this species. To assess the ability of barcoding loci to resolve Vicia species, we sampled 36 of the taxonomically best known groups in the genus. Topologies of the phylogenetic trees based on ITS2 and matK analyses were similar but a few accessions were placed into distant phylogenetic groups. Neither ITS2 nor matK analyses alone could discriminate some closely related Vicia species. Thus, we have proposed a concatenated data approach to increase the resolving power of ITS2 and used matK as an additional tool for phylogenetic analysis in Vicia because characterization of the nucleotide sequences of the matK region was easier to recover and more cost-effective than those of the ITS region.
Chloroplast DNA sequences are a versatile tool for species identification and phylogenetic reconstruction of land plants. Different chloroplast loci have been utilized for phylogenetic classification of plant species. However, there is no evidence for a short sequence that can distinguish all plant species from each other. Molecular markers derived from the complete chloroplast genome can provide effective tools for species identification and phylogenetic resolution. Thus, the complete chloroplast genome sequence of Korean landrace “Subicho” pepper (Capsicum annuum var. annuum) has been determined here. The total length of the chloroplast genome is 156,878 bp, with 37.7% overall GC content. A pair of IRs (inverted repeats) of 25,801 bp was separated by a small single copy (SSC) region of 17,929 bp and a large single copy (LSC) region of 87,347 bp. The chloroplast genome harbors 132 known genes, including 87 protein-coding genes, 8 ribosomal RNA genes, and 37 tRNA genes. A total of seven of these genes are duplicated in the inverted repeat regions, nine genes and six tRNA genes contain one intron, while two genes and a ycf have two introns. Analysis revealed 144 simple sequence repeat (SSR) loci and 96 variants, mostly located in the non-coding regions. The types and abundances of repeat units in Capsicum species were relatively conserved and these loci will be useful for developing molecular markers.
The wild species are considered as primary and secondary genepools for the world's most important food crops. Here, we sequenced the complete chloroplast (cp) genome sequence of an American wild licorice, Glycyrrhiza lepidota for the first time to investigate their phylogenetic relationship among inverted-repeat-lacking clade (IRLC) legumes. The total length of the chloroplast genome is 127,939 bp, with 34.2% overall GC content. The chloroplast genome harbors 110 known genes, including 76 protein-coding genes, four ribosomal RNA genes, and 30 tRNA genes. Similar to other closely related plastomes, rpl22 and rps16 are absent. A total of 464 cp microsatellites (cpSSRs) were analyzed in the G. lepidota. The majority of the SSRs in this cp genome are penta-nucleotides (61.6%). Locally collinear blocks (LCBs) identified between the Glycyrrhiza glabra and G. lepidota cp genomes were showed that they were well conserved with respect to gene organization and order. Moreover, the phylogenetic analysis indicates that G. lepidota is closely related to its confamilial counterparts than to the other taxa of the IRLC legumes.