Development of molecular markers tightly linked to Pvr4 gene in pepper using next-generation sequencing

Devran, Zübeyir; Kahveci, Erdem; Özkaynak, Ercan; Studholme, David J.; Tör, Mahmut

doi:10.1007/s11032-015-0294-5

Cited by 26 publications

(15 citation statements)

References 40 publications

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“…Bulk segregant analysis (Michelmore et al 1991) for gene mapping has been used in many different crop species as well as in microbial pathogens. Although the technique was originally used with RAPD markers, since then, it has been widely used in combination with the NGS technology (Devran et al 2015; Woods-Tör et al 2018). We utilized this advantage and sequenced the genomic DNA from resistant and susceptible bulks as well as from the parents.…”

Section: Discussionmentioning

confidence: 99%

“…DNA was extracted separately from each individual of the F 2 plant lines. The resistant and susceptible bulks were generated from twenty resistant and twenty susceptible F 2 individuals, respectively, as described (Devran et al 2015) and used for genomic sequencing. We generated 1 lane of 100 bp paired-end Illumina HiSeq 2500 sequencing data for each parent (resistant and susceptible) line and bulked (resistant and susceptible) pools.…”

Section: Methodsmentioning

confidence: 99%

“…We then randomly selected candidates to cover the 1.2 Mb region and the SNPs were converted into CAPS marker using dCAPS (http://helix.wustl.edu/dcaps/dcaps.html) (Neff et al 2002). All PCR amplifications and digestion of PCR products with relevant restriction enzymes were performed by following manufacturers’ instructions and were visualized as described (Devran et al 2015). …”

Section: Methodsmentioning

confidence: 99%

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Identifying molecular markers suitable for Frl selection in tomato breeding

et al. 2018

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Modern plant breeding heavily relies on the use of molecular markers. In recent years, next generation sequencing (NGS) emerged as a powerful technology to discover DNA sequence polymorphisms and generate molecular markers very rapidly and cost effectively, accelerating the plant breeding programmes. A single dominant locus, Frl, in tomato provides resistance to the fungal pathogen Fusarium oxysporum f. sp. radicis-lycopersici (FORL), causative agent of Fusarium crown and root rot. In this study, we describe the generation of molecular markers associated with the Frl locus. An F2 mapping population between an FORL resistant and a susceptible cultivar was generated. NGS technology was then used to sequence the genomes of a susceptible and a resistant parent as well the genomes of bulked resistant and susceptible F2 lines. We zoomed into the Frl locus and mapped the locus to a 900 kb interval on chromosome 9. Polymorphic single-nucleotide polymorphisms (SNPs) within the interval were identified and markers co-segregating with the resistant phenotype were generated. Some of these markers were tested successfully with commercial tomato varieties indicating that they can be used for marker-assisted selection in large-scale breeding programmes.Electronic supplementary materialThe online version of this article (10.1007/s00122-018-3136-0) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Identifying molecular markers suitable for Frl selection in tomato breeding

et al. 2018

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“…Multiplex genotyping assays such as GBS, RAD, and DArT have been successfully used to identify SNP markers associated with the trait of interest in understudied crops. Examples include disease resistance in lupin [23], pepper [24], cassava [25,26], and beans [27].…”

Section: Ngs-based Genotyping and Marker Analysismentioning

confidence: 99%

Perspectives on the Application of Next-generation Sequencing to the Improvement of Africa’s Staple Food Crops

Gedil¹,

Ferguson²,

Girma³

et al. 2016

Next Generation Sequencing - Advances, Applications and Challenges

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The persistent challenge of insufficient food, unbalanced nutrition, and deteriorating natural resources in the most vulnerable nations, characterized by fast population growth, calls for utilization of innovative technologies to curb constraints of crop production. Enhancing genetic gain by using a multipronged approach that combines conventional and genomic technologies for the development of stress-tolerant varieties with high yield and nutritional quality is necessary. The advent of nextgeneration sequencing (NGS) technologies holds the potential to dramatically impact the crop improvement process. NGS enables whole-genome sequencing (WGS) and re-sequencing, transcriptome sequencing, metagenomics, as well as high-throughput genotyping, which can be applied for genome selection (GS). It can also be applied to diversity analysis, genetic and epigenetic characterization of germplasm and pathogen detection, identification, and elimination. High-throughput phenotyping, integrated data management, and decision support tools form the necessary supporting environment for effective utilization of genome sequence information. It is important that these opportunities for mainstreaming innovative breeding strategies, enabled by cutting-edge "Omics" technologies, are seized in Africa; however, several constraints must be addressed before the benefit of NGS can be fully realized. African breeding programs must have access to high-throughput genotyping facilities, capacity in the application of genome selection and marker-assisted breeding must be built and supported by capacity in genomic analysis and bioinformatics. This chapter demonstrates how interventions with NGS-enabled innovative strategies can be applied to increase genetic gain with insights from the Consortium of International

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“…Moreover, 18 accessions of pepper cultivar and two semi-wild accessions were resequenced to investigate how artificial selection traces present in the pepper genome correlate with pepper breeding history [10]. Parental lines of breeding populations were also resequenced to identify the causal regions conferring resistance against the Potato virus Y [11]. The availability of NGS technology and the C. annuum reference sequence provides us with the opportunity to employ this resequencing strategy to address more specific and practical questions in genome-assisted breeding schemes to cope with BW.…”

Section: Introductionmentioning

confidence: 99%

Resequencing of Capsicum annuum parental lines (YCM334 and Taean) for the genetic analysis of bacterial wilt resistance

et al. 2016

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BackgroundBacterial wilt (BW) is a widespread plant disease that affects a broad range of dicot and monocot hosts and is particularly harmful for solanaceous plants, such as pepper, tomato, and eggplant. The pathogen responsible for BW is the soil-borne bacterium, Ralstonia solanacearum, which can adapt to diverse temperature conditions and is found in climates ranging from tropical to temperate. Resistance to BW has been detected in some pepper plant lines; however, the genomic loci and alleles that mediate this are poorly studied in this species.ResultsWe resequenced the pepper cultivars YCM344 and Taean, which are parental recombinant inbred lines (RIL) that display differential resistance phenotypes against BW, with YCM344 being highly resistant to infection with this pathogen. We identified novel single nucleotide polymorphisms (SNPs) and insertions/deletions (Indels) that are only present in both parental lines, as compared to the reference genome and further determined variations that distinguish these two cultivars from one another. We then identified potentially informative SNPs that were found in genes related to those that have been previously associated with disease resistance, such as the R genes and stress response genes. Moreover, via comparative analysis, we identified SNPs located in genomic regions that have homology to known resistance genes in the tomato genomes.ConclusionsFrom our SNP profiling in both parental lines, we could identify SNPs that are potentially responsible for BW resistance, and practically, these may be used as markers for assisted breeding schemes using these populations. We predict that our analyses will be valuable for both better understanding the YCM334/Taean-derived populations, as well as for enhancing our knowledge of critical SNPs present in the pepper genome.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-016-0931-0) contains supplementary material, which is available to authorized users.

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Development of molecular markers tightly linked to Pvr4 gene in pepper using next-generation sequencing

Cited by 26 publications

References 40 publications

Identifying molecular markers suitable for Frl selection in tomato breeding

Identifying molecular markers suitable for Frl selection in tomato breeding

Perspectives on the Application of Next-generation Sequencing to the Improvement of Africa’s Staple Food Crops

Resequencing of Capsicum annuum parental lines (YCM334 and Taean) for the genetic analysis of bacterial wilt resistance

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