Two CAPS markers predict Verticillium wilt resistance in wild Solanum species

Uribe, Pedro; Jansky, Shelley; Halterman, Dennis

doi:10.1007/s11032-013-9965-2

Cited by 28 publications

(25 citation statements)

References 33 publications

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“…Examples of those showing associations are cacao (Theobroma cacao L.; Whitkus et al, 1998), breadfruit [Artocarpus altilis (Parkinson) Fosberg; Zerega et al, 2004], wild potato species (Solanum verrucosum Schltdl. For example, studies analyzing multiple species of cultivated and wild relatives of potato have investigated the relationship between disease and pest resistance with geography and taxonomy and have failed to find associations ( Jansky et al, 2006( Jansky et al, , 2008Spooner et al, 2009;Cai et al, 2011;Chung et al, 2011;Khiutti et al, 2012;Uribe et al, 2013;Limantseva et al, 2014;Pérez et al, 2014). However, a number of studies show no relationship between geographic origin and traits of interest.…”

Section: Comparison Of Representative and Custom Methods Of Generatinmentioning

confidence: 99%

Comparison of Representative and Custom Methods of Generating Core Subsets of a Carrot Germplasm Collection

et al. 2019

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Crop breeding programs are interested in using genetic resources but have difficulty identifying useful accessions from germplasm collections. To efficiently use the diversity present in large germplasm collections, breeders often identify a subset of accessions that represent the larger collection. Methods to identify these subsets, which are called core collections, do not consistently capture functional diversity, and breeders would benefit from methods that help create custom core collections using existing data from variety trials or breeding programs. Making use of high‐density genomic data and existing phenotypic data from a collection of 433 domesticated carrot (Daucus carota L.) accessions, we tested whether it is possible to develop custom subsets of accessions for specific breeding purposes. We found that for this collection, representative strategies were effective in developing core collections that capture the diversity of the collection, but they were no better than random sampling, likely because the collection itself is not strongly subdivided. Custom strategies generated subsets that differed from the total collection with altered genetic, geographic, and phenotypic compositions. When used as training populations for genomic prediction of the other accessions in the collection, however, these custom cores did not produce a substantial improvement over traditional core collections. Increasing the size of the core did improve prediction accuracy, suggesting that it is possible to improve the usefulness of core collections by identifying custom subsets that are large enough to represent the functional genetic diversity present in the collection.

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Section: Comparison Of Representative and Custom Methods Of Generatinmentioning

confidence: 99%

Comparison of Representative and Custom Methods of Generating Core Subsets of a Carrot Germplasm Collection

et al. 2019

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“…The QTL on chromosome 9, which accounted for 17% of the explained variance, included the locus for the Ve2 , Verticillium wilt resistance gene (Kawchuk et al, 2001). The genetic map location of the Ve2 gene was confirmed using a CAPS marker (Uribe et al, 2014; Fig. 2).…”

Section: Resultsmentioning

confidence: 93%

“…Wild Solanum species were found to be sources of Verticillium resistance and have been introgressed to S. tuberosum in potato breeding programs (Concibido et al, 1994; Corsini and Pavek, 1996; Corsini et al, 1988; Jansky and Rouse, 2000; Jansky et al, 2004; Lynch et al, 1997; Simko et al, 2004c). Development of markers to predict resistance to Verticillium wilt has involved PCR of the region conserved between Ve1 and Ve2 to clone orthologous Ve genes from several resistant wild Solanum species (Bae et al, 2008; Uribe et al, 2014). The cloned genes from the wild species were found to have high sequence identity with Ve2 .…”

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confidence: 99%

Verticillium dahliaeDisease Resistance and the Regulatory Pathway for Maturity and Tuberization in Potato

et al. 2018

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Verticillium dahliae Kleb. is a pathogenic fungus causing wilting, chlorosis, and early dying in potato (Solanum tuberosum L.). Genetic mapping of resistance to V. dahliae was done using a diploid population of potato. The major quantitative trait locus (QTL) for Verticillium resistance was found on chromosome 5. The StCDF1 gene, controlling earliness of maturity and tuberization, was mapped within the interval. Another QTL on chromosome 9 co-localized with the Ve2 Verticillium wilt resistance gene marker. Epistasis analysis indicated that the loci on chromosomes 5 and 9 had a highly significant interaction, and that StCDF1 functioned downstream of Ve2. The StCDF1 alleles were sequenced and found to encode StCDF1.1 and StCDF1.3. Interaction between the Ve2 resistance allele and the StCDF1.3 was demonstrated, but not for StCDF1.1. Genome-wide expression QTL (eQTL) analysis was performed and genes with eQTL at the StCDF1 and Ve2 loci were both found to have similar functions involving the chloroplast, including photosynthesis, which declines in both maturity and Verticillium wilt. Among the gene ontology (GO) terms that were specific to genes with eQTL at the Ve2, but not the StCDF1 locus, were those associated with fungal defense. These results suggest that Ve2 controls fungal defense and reduces early dying in Verticillium wilt through affecting genetic pathway controlling tuberization timing. V erticillium wilt is caused by fungal colonization of the vascular system in plants (Johnson and Dung, 2010;Pegg and Brady, 2002) and is primarily a problem in temperate regions with decreased incidence in the tropics. Verticillium dahliae is the species with the greatest economic impact as a result of its broad

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“…The difficulty of resistance screening, coupled with the information that Ve orthologs in potato map to chromosome 9 (same location as Ve1 and Ve2 in tomato), has led to the search for molecular markers linked to VW resistance. More recently, two CAPS markers were identified in potato hybrids from wild and cultivated parents (Bae et al, 2008;Uribe et al, 2014). More recently, two CAPS markers were identified in potato hybrids from wild and cultivated parents (Bae et al, 2008;Uribe et al, 2014).…”

Section: Discussionmentioning

confidence: 99%

“…More recently, two CAPS markers were identified in potato hybrids from wild and cultivated parents (Bae et al, 2008;Uribe et al, 2014). Sequence information of Ve2 was gathered from selected VW resistant and susceptible wild potato species and used to develop separate CAPS markers associated with resistance (Uribe et al, 2014). Additional markers were investigated in an attempt to increase their usefulness on a wider array of germplasm.…”

Section: Discussionmentioning

confidence: 99%

Structural Variation within the Potato Ve Gene Locus and Correlation with Molecular Marker Analysis

Meier

Halterman

2016

Crop Science

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Plant breeders rely on molecular markers to guide the selection of traits that are difficult to phenotype or that show wide variation in field trials as they seek to uncover the intricate relationship between an organism's genotype and resulting phenotype. Specificity of molecular markers in wild potato (Solanum spp.) and other less‐adapted germplasm is complicated by the existence of homologous gene clusters. This study examines the consistency and effectiveness of two previously published cleaved amplified polymorphic sequence (CAPS) markers that have been shown to predict Verticillium wilt (VW) resistance. The genome of resistant diploid potato clone C287 was resequenced, and examination of the Ve locus indicated only two homologous regions when compared with the three found in the reference potato genome DM1‐3. The prevalence of each homologous region was examined within a panel of 83 diverse wild potato species. Both structural and genetic sequence variation is predicted to complicate the use of molecular markers developed within specific genetic backgrounds. This study demonstrates that primers designed in the noncoding flanking regions of gene homologs increases specificity and avoids off‐target binding. It is suggested that markers be developed by using more specific primers in these regions coupled with conserved primers within the gene's coding sequence.

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Two CAPS markers predict Verticillium wilt resistance in wild Solanum species

Cited by 28 publications

References 33 publications

Comparison of Representative and Custom Methods of Generating Core Subsets of a Carrot Germplasm Collection

Comparison of Representative and Custom Methods of Generating Core Subsets of a Carrot Germplasm Collection

Verticillium dahliaeDisease Resistance and the Regulatory Pathway for Maturity and Tuberization in Potato

Structural Variation within the Potato Ve Gene Locus and Correlation with Molecular Marker Analysis

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