Use of 5´-anchored primers for the enhanced recovery of specific microsatellite markers in Brassica napus L.

Varghese, James; Rudolph, Barbara; Uzunova, Maria; Ecke, Wolfgang

doi:10.1007/s001220051458

Cited by 10 publications

(5 citation statements)

References 8 publications

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“… *Previously reported markers were used from Wang et al [ 14 ], Mun et al [ 22 ], Lowe et al [ 16 ], Piquemal et al [ 17 ], Cheng et al [ 20 ], Uzunova and Ecke [ 23 ], Varghese et al [ 29 ], Cheng et al [ 20 ], Burgess et al [ 24 ], Suwabe et al [ 25 ], Kim et al [ 21 ], Choi et al [ 30 ], Batley et al [ 31 ], Long et al [ 18 ], Iniguez-Luy et al [ 32 ], Kresovich et al [ 33 ], Szewc-McFadden et al [ 34 ], Louarn et al [ 26 ], Bell and Ecker [ 35 ], Lagercrantz et al [ 36 ], Sebastian et al [ 37 ], Smith and King [ 15 ], HRI (unpublished) and Saito et al [ 38 ]. …”

Section: Resultsmentioning

confidence: 99%

“…Also included were 1,841 intron-based polymorphism (IBP) markers that were developed from B. rapa genome sequences [ 22 ]. Furthermore, 695 publically reported SSR markers were used to integrate the reference genetic map: 264 primers derived from the public domain [ 16 , 17 ], 94 primers from Wang et al [ 14 ], 71 primers designed from publicly available B. napus genome survey sequences (GSSs) [ 20 ], 45 primers isolated from B. napus [ 23 , 29 ], 41 primers from Agriculture and Agri-Food Canada [ 20 ], 35 primers obtained from Burgess et al [ 24 ], 27 primers designed from a microsatellite-enriched genomic library of B. rapa [ 25 ], 24 BAC-derived SSR primers from Kim et al [ 21 ], 21 primers developed from B. rapa by Choi et al [ 30 ], 18 primers from EST sequences of B. napus [ 31 ], 14 primers from Long et al [ 18 ], 12 primers developed by Iniguez-Luy et al [ 32 ], 11 primers originally isolated from B. napus [ 33 , 34 ], 9 database sequence-derived primers from Louarn et al [ 26 ], 4 primers isolated from an A. thaliana library [ 35 ], and one primer each from Lagercrantz et al [ 36 ], Sebastian et al [ 37 ], Smith and King [ 15 ], HRI (unpublished data) and Saito et al [ 38 ].…”

Section: Methodsmentioning

confidence: 99%

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Transcriptome sequencing of two parental lines of cabbage (Brassica oleracea L. var. capitata L.) and construction of an EST-based genetic map

et al. 2014

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BackgroundExpressed 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.ResultsTranscriptome 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.ConclusionsThis 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.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Transcriptome sequencing of two parental lines of cabbage (Brassica oleracea L. var. capitata L.) and construction of an EST-based genetic map

et al. 2014

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“…About 300 SSR sequences could not be used then for primer design due to presence of SSRs too close to an end of the sequence. We utilized some of these sequences for designing 5 ′ -anchored primers, utilizing the strategy earlier followed by Varghese et al . (2000).…”

mentioning

confidence: 99%

Development and use of anchored‐SSRs to study DNA polymorphism in bread wheat (Triticum aestivum L.)

Singh

Kumar

Bandopadhyay

et al. 2006

Molecular Ecology Notes

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In bread wheat, 21 anchored simple sequence repeat (SSR) primer pairs detecting SSR length polymorphism and 42 anchored SSR primers detecting microsatellite‐anchored fragment length polymorphisms (MFLPs) are reported. Eight bread wheat genotypes were used for detecting polymorphism. The number of alleles in SSR analysis ranged from two to six, with a mean of 2.9 alleles per SSR. The number of polymorphic bands in MFLP ranged from two to 40, with a mean of 12.74 polymorphic bands/primer combination, the SSRs with CT/GA motifs giving the highest level of polymorphism (a mean of 18.37 bands). The average value of polymorphic information content (PIC) was 0.473 for SSRs and 0.061 for MFLP.

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“…Of these, 266 markers that showed clear scorable polymorphisms between B. napus varieties were integrated into an existing B. napus genetic linkage map (Snowdon et al, 2006). Extensive efforts have been made to develop SSR markers in B. napus and its two diploid progenitors, B. rapa and B. oleracea, through genomic library screening using probes containing repeat motifs, followed by DNA sequencing (Varghese et al, 2000;Suwabe et al, 2002) . Information on Brassica microsatellites is available at http//www.brassica.info/ssrinfo.htm.…”

Section: Cabbage;mentioning

confidence: 99%

Trends in genomics and molecular marker systems for the development of some underutilized crops

2012

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The term 'underutilized' is often used to characterize the range of plant species whose potential contribution to food security, health, income generation, and environmental services has not yet been fully exploited. To harness unexploited resources, the first step is to prevent them from extinction and to conserve them inand/or ex-situ. To utilize plant species as crops, plants must be collected, conserved, evaluated, and then if necessary manipulated. In this context, significant international efforts have focused on impeding the erosion of genetic diversity. Thousands of new accessions are introduced into germplasm institutes each year. Assessment of their molecular diversity is necessary to eliminate redundant genotypes. Marker systems have been used not only for genotyping to reduce redundancy and develop a core set, but also for a wide variety of other purposes. The use of markers based on single nucleotide polymorphisms, copy number variation, and insertions/deletions, as well as genotyping by sequencing, is becoming popular for genetic mapping and analyses of quantitative trait loci. This review discusses current marker systems and genomic analyses of a number of underutilized crops.

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Use of 5´-anchored primers for the enhanced recovery of specific microsatellite markers in Brassica napus L.

Cited by 10 publications

References 8 publications

Transcriptome sequencing of two parental lines of cabbage (Brassica oleracea L. var. capitata L.) and construction of an EST-based genetic map

Transcriptome sequencing of two parental lines of cabbage (Brassica oleracea L. var. capitata L.) and construction of an EST-based genetic map

Development and use of anchored‐SSRs to study DNA polymorphism in bread wheat (Triticum aestivum L.)

Trends in genomics and molecular marker systems for the development of some underutilized crops

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