Identifying molecular markers suitable for Frl selection in tomato breeding

Devran, Zübeyir; Kahveci, Erdem; Hong, Yiguo; Studholme, David J.; Tör, Mahmut

doi:10.1007/s00122-018-3136-0

Cited by 17 publications

(16 citation statements)

References 30 publications

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“…Finally, the gene Solyc09g011320, coding for a Serine/threonine-protein kinase, was found to be part of a gene cluster putatively involved in the tolerance to Fusarium oxysporium f.s. radicis lycopersici [39]. The role of these potential resistance genes in contrasting pathogens causing diseases will be further investigated in the parental genotypes, by applying resistance tests or molecular marker analysis.…”

Section: Genomic Characterization Of Parental Linesmentioning

confidence: 99%

Accelerating the Development of Heat Tolerant Tomato Hybrids through a Multi-Traits Evaluation of Parental Lines Combining Phenotypic and Genotypic Analysis

Olivieri

Graci

Francesca

et al. 2021

Plants

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The constitution of heat tolerant F1 hybrids is a challenge to ensure high yield and good fruit quality in the global climate. In the present work, we evaluated 15 genotypes for yield-related traits highly affected by high temperatures (HT). This phenotypic analysis allowed to identify four parental genotypes showing promising yield performances under HT conditions. Two of these genotypes also exhibited good fruit quality traits. A molecular marker analysis was carried out for six resistance genes to pathogens mostly affecting tomatoes. This analysis evidenced the presence of a maximum of three resistant alleles in parental genotypes. Exploring single nucleotide polymorphisms (SNPs) revealed by two high-throughput genotyping platforms allowed identifying additional 12 genes potentially involved in resistance to biotic stress, to be further investigated. Following these considerations, 13 F1 hybrids were constituted combining the parental genotypes and then evaluated for multiple traits under HT conditions. By estimating a hybrid index based on yield performances, desirable quality and resistance gene, we identified seven hybrids showing the best performances. The promising results obtained in the present work should be confirmed by evaluating the best hybrids selected for additional years and environments before proposing them as novel commercial hybrids that could maintain high performances under HT conditions.

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Section: Genomic Characterization Of Parental Linesmentioning

confidence: 99%

Accelerating the Development of Heat Tolerant Tomato Hybrids through a Multi-Traits Evaluation of Parental Lines Combining Phenotypic and Genotypic Analysis

Olivieri

Graci

Francesca

et al. 2021

Plants

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“…We used genomics and BSA previously to clone genes (Woods-Tör et al, 2018 ) and to generate MAS-friendly molecular markers (Devran et al, 2018 ) that are tightly linked to the gene of interest. Our experience shows that although the use of reference genomes helps the identification of variants in the region of interest, different versions of reference genome assemblies produced different results in the SNP analysis.…”

Section: Discussionmentioning

confidence: 99%

“…As previously described (Devran et al, 2018 ), we took the NGS analysis approach where the raw reads were trimmed using BBDuk (filter = 27, trimk = 27; https://sourceforge.net/projects/bbmap/ ) to remove Illumina adapters and to quality trim both ends to Q12. Subsequently, trimmed sequences from parental lines and the bulks were mapped onto the available reference cucumber genome (V2 and V3) using BBMap ( https://sourceforge.net/projects/bbmap/ ), and the alignment data were converted to the BAM format (Li et al, 2009 ).…”

Section: Methodsmentioning

confidence: 99%

“…DNA was extracted from each individual plant lines, and a gel electrophoresis was performed to determine whether high molecular weight DNAs were isolated. The resistant and susceptible bulks were generated from 20 resistant and 20 susceptible F 2 individuals, respectively, as described in earlier studies (Devran et al, 2015(Devran et al, , 2018. Genomic DNA library and sequencing have been carried out by the University of Exeter Sequencing Service after quality check of DNAs, generating 2 × 150 bp paired-end read data for each parent line and bulked (resistant and susceptible) pools with Illumina HiSeq 2500 (Illumina, Inc. San Diego, CA, USA).…”

Section: Dna Extraction and Genome Sequencingmentioning

confidence: 99%

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Genomic-Assisted Marker Development Suitable for CsCvy-1 Selection in Cucumber Breeding

Kahveci¹,

Devran

Özkaynak

et al. 2021

Front. Plant Sci.

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Cucumber is a widely grown vegetable crop plant and a host to many different plant pathogens. Cucumber vein yellowing virus (CVYV) causes economic losses on cucumber crops in Mediterranean countries and in some part of India such as West Bengal and in African countries such as Sudan. CVYV is an RNA potyvirus transmitted mechanically and by whitefly (Bemisia tabaci) in a semipersistent manner. Control of this virus is heavily dependent on the management of the insect vector and breeding virus-resistant lines. DNA markers have been used widely in conventional plant breeding programs via marker-assisted selection (MAS). However, very few resistance sources against CVYV in cucumber exist, and also the lack of tightly linked molecular markers to these sources restricts the rapid generation of resistant lines. In this work, we used genomics coupled with the bulked segregant analysis method and generated the MAS-friendly Kompetitive allele specific PCR (KASP) markers suitable for CsCvy-1 selection in cucumber breeding using a segregating F2 mapping population and commercial plant lines. Variant analysis was performed to generate single-nucleotide polymorphism (SNP)-based markers for mapping the population and genotyping the commercial lines. We fine-mapped the region by generating new markers down to 101 kb with eight genes. We provided SNP data for this interval, which could be useful for breeding programs and cloning the candidate genes.

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“…Because of its specific biochemical and molecular properties and nutritional importance, tomato is an established model to study fruit growth and development 27 . Tomato also has numerous mapped traits, developed DNA markers, abundant collections of germplasm and mutants, and an increasing number of expressed sequence tags (ESTs) 28 – 32 . There are several characteristics that make tomato an ideal model organism for both basic and applied research programs.…”

Section: Tomato a ‘Traditional’ Model Systemmentioning

confidence: 99%

High throughput sequencing unravels tomato-pathogen interactions towards a sustainable plant breeding

Campos

Félix

Patanita

et al. 2021

Horticulture Research

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Tomato (Solanum lycopersicum) is one of the most economically important vegetables throughout the world. It is one of the best studied cultivated dicotyledonous plants, often used as a model system for plant research into classical genetics, cytogenetics, molecular genetics, and molecular biology. Tomato plants are affected by different pathogens such as viruses, viroids, fungi, oomycetes, bacteria, and nematodes, that reduce yield and affect product quality. The study of tomato as a plant-pathogen system helps to accelerate the discovery and understanding of the molecular mechanisms underlying disease resistance and offers the opportunity of improving the yield and quality of their edible products. The use of functional genomics has contributed to this purpose through both traditional and recently developed techniques, that allow the identification of plant key functional genes in susceptible and resistant responses, and the understanding of the molecular basis of compatible interactions during pathogen attack. Next-generation sequencing technologies (NGS), which produce massive quantities of sequencing data, have greatly accelerated research in biological sciences and offer great opportunities to better understand the molecular networks of plant–pathogen interactions. In this review, we summarize important research that used high-throughput RNA-seq technology to obtain transcriptome changes in tomato plants in response to a wide range of pathogens such as viruses, fungi, bacteria, oomycetes, and nematodes. These findings will facilitate genetic engineering efforts to incorporate new sources of resistance in tomato for protection against pathogens and are of major importance for sustainable plant-disease management, namely the ones relying on the plant’s innate immune mechanisms in view of plant breeding.

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Identifying molecular markers suitable for Frl selection in tomato breeding

Cited by 17 publications

References 30 publications

Accelerating the Development of Heat Tolerant Tomato Hybrids through a Multi-Traits Evaluation of Parental Lines Combining Phenotypic and Genotypic Analysis

Accelerating the Development of Heat Tolerant Tomato Hybrids through a Multi-Traits Evaluation of Parental Lines Combining Phenotypic and Genotypic Analysis

Genomic-Assisted Marker Development Suitable for CsCvy-1 Selection in Cucumber Breeding

High throughput sequencing unravels tomato-pathogen interactions towards a sustainable plant breeding

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