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Izzah N.K.,Seoul National University | Izzah N.K.,Indonesian Research Institute for Industrial and Beverage Crops IRIIBC | Lee J.,Seoul National University | Perumal S.,Seoul National University | And 6 more authors.
Genetic Resources and Crop Evolution | Year: 2013

Brassica oleracea L. includes various types of important vegetables that show extremely diverse phenotypes. To elucidate the genetic diversity and relationships among commercial cultivars derived by different companies throughout the world, we characterized the diversity and genetic structure of 91 commercial B. oleracea cultivars belonging to six varietal groups, including cabbage, broccoli, cauliflower, kohlrabi, kale and kai-lan. We used 69 polymorphic microsatellite markers showing a total of 359 alleles with an average number of 5.20 alleles per locus. Polymorphism information content (PIC) values ranged from 0.06 to 0.73, with an average of 0.40. Among the six varietal groups, kohlrabi cultivars exhibited the highest heterozygosity level, whereas kale cultivars showed the lowest. Based on genetic similarity values, an UPGMA clustering dendrogram and a two-dimensional scale diagram (PCoA) were generated to analyze genetic diversity. The cultivars were clearly separated into six different clusters with a tendency to cluster into varietal groups. Model-based structure analysis revealed six genetic groups, in which cabbage cultivars were divided into two subgroups that were differentiated by their head shape, whereas cauliflower and kai-lan cultivars clustered together into a single group. Furthermore, we identified 18 SSR markers showing 27 unique alleles specific to only one cultivar that can be used to discriminate 22 cultivars from the others. Our phylogenetic and population structure analysis presents new insights into the genetic structure and relationships among 91 B. oleracea cultivars and provides valuable information for breeding of B. oleracea species. In addition, we demonstrate the utility of SSR markers as a powerful tool for discriminating between the cultivars. The SSR markers described herein will also be helpful for Distinctness, Uniformity and Stability (DUS) test of new cultivars. © 2013 Springer Science+Business Media Dordrecht.

Lee J.,Seoul National University | Izzah N.K.,Seoul National University | Izzah N.K.,Indonesian Research Institute for Industrial and Beverage Crops IRIIBC | Choi B.-S.,Phyzen Genomics Institute | And 11 more authors.
DNA Research | Year: 2015

Clubroot is a devastating disease caused by Plasmodiophora brassicae and results in severe losses of yield and quality in Brassica crops. Many clubroot resistance genes and markers are available in Brassica rapa but less is known in Brassica oleracea. Here, we applied the genotyping-by-sequencing (GBS) technique to construct a high-resolution genetic map and identify clubroot resistance (CR) genes. A total of 43,821 SNPs were identified using GBS data for two parental lines, one resistant and one susceptible lines to clubroot, and 18,187 of them showed >5× coverage in the GBS data. Among those, 4,103 were credibly genotyped for all 78 F2 individual plants. These markers were clustered into nine linkage groups spanning 879.9 cM with an average interval of 1.15 cM. Quantitative trait loci (QTLs) survey based on three rounds of clubroot resistance tests using F2:3 progenies revealed two and single major QTLs for Race 2 and Race 9 of P. brassicae, respectively. The QTLs show similar locations to the previously reported CR loci for Race 4 in B. oleracea but are in different positions from any of the CR loci found in B. rapa. We utilized two reference genome sequences in this study. The high-resolution genetic map developed herein allowed us to reposition 37 and 2 misanchored scaffolds in the 02-12 and TO1000DH genome sequences, respectively. Our data also support additional positioning of two unanchored 3.3 Mb scaffolds into the 02-12 genome sequence. © 2015 The Author.

Lee J.,Seoul National University | Izzah N.K.,Seoul National University | Izzah N.K.,Indonesian Research Institute for Industrial and Beverage Crops IRIIBC | Jayakodi M.,Seoul National University | And 17 more authors.
BMC Plant Biology | Year: 2015

Black rot is a destructive bacterial disease causing large yield and quality losses in Brassica oleracea. To detect quantitative trait loci (QTL) for black rot resistance, we performed whole-genome resequencing of two cabbage parental lines and genome-wide SNP identification using the recently published B. oleracea genome sequences as reference. Results: Approximately 11.5 Gb of sequencing data was produced from each parental line. Reference genome-guided mapping and SNP calling revealed 674,521 SNPs between the two cabbage lines, with an average of one SNP per 662.5 bp. Among 167 dCAPS markers derived from candidate SNPs, 117 (70.1%) were validated as bona fide SNPs showing polymorphism between the parental lines. We then improved the resolution of a previous genetic map by adding 103 markers including 87 SNP-based dCAPS markers. The new map composed of 368 markers and covers 1467.3 cM with an average interval of 3.88 cM between adjacent markers. We evaluated black rot resistance in the mapping population in three independent inoculation tests using F2:3 progenies and identified one major QTL and three minor QTLs. Conclusion: We report successful utilization of whole-genome resequencing for large-scale SNP identification and development of molecular markers for genetic map construction. In addition, we identified novel QTLs for black rot resistance. The high-density genetic map will promote QTL analysis for other important agricultural traits and marker-assisted breeding of B. oleracea.

Izzah N.K.,Plant Genomics and Breeding Institute | Izzah N.K.,Indonesian Research Institute for Industrial and Beverage Crops IRIIBC | Lee J.,Plant Genomics and Breeding Institute | Jayakodi M.,Plant Genomics and Breeding Institute | And 5 more authors.
BMC Genomics | Year: 2014

Background: Expressed sequence tag (EST)-based markers are preferred because they reflect transcribed portions of the genome. We report the development of simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers derived from transcriptome sequences in cabbage, and their utility for map construction.Results: Transcriptome sequences were obtained from two cabbage parental lines, C1184 and C1234, which are susceptible and resistant to black rot disease, respectively, using the 454 platform. A total of 92,255 and 127,522 reads were generated and clustered into 34,688 and 40,947 unigenes, respectively. We identified 2,405 SSR motifs from the unigenes of the black rot-resistant parent C1234. Trinucleotide motifs were the most abundant (66.15%) among the repeat motifs. In addition, 1,167 SNPs were detected between the two parental lines. A total of 937 EST-based SSR and 97 SNP-based dCAPS markers were designed and used for detection of polymorphism between parents. Using an F2 population, we built a genetic map comprising 265 loci, and consisting of 98 EST-based SSRs, 21 SNP-based dCAPS, 55 IBP markers derived from B. rapa genome sequence and 91 public SSRs, distributed on nine linkage groups spanning a total of 1,331.88 cM with an average distance of 5.03 cM between adjacent loci. The parental lines used in this study are elite breeding lines with little genetic diversity; therefore, the markers that mapped in our genetic map will have broad spectrum utility.Conclusions: This genetic map provides additional genetic information to the existing B. oleracea map. Moreover, the new set of EST-based SSR and dCAPS markers developed herein is a valuable resource for genetic studies and will facilitate cabbage breeding. Additionally, this study demonstrates the usefulness of NGS transcriptomes for the development of genetic maps even with little genetic diversity in the mapping population. © 2014 Izzah et al.; licensee BioMed Central Ltd.

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