SNP-based codominant markers for a recessive gene conferring resistance to corky root rot (<i>Rhizomonas suberifaciens</i>) in lettuce (<i>Lactuca sativa</i>)

Moreno-Vázquez, Santiago; Ochoa, O.; Faber, Nanne; Chao, Shiaoman; Jacobs, Jeanne M. E.; Maisonneuve, Brigitte; Kesseli, Rick; Michelmore, Richard W.

doi:10.1139/g03-073

Cited by 25 publications

(17 citation statements)

References 31 publications

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“…The Gro1 -specific marker was not correlated with the resistance phenotype, while H1 -specific marker was indicative of resistance in only four cultivars [46]. A similar example can be shown for lettuce, where markers most tightly linked to the cor resistance gene were the least useful for diagnostic when tested in a large collection of cultivars [47]. There are several other examples of markers tightly linked to resistance genes, but whose use present problems in material different from the original in which they were identified [48].…”

Section: Discussionmentioning

confidence: 97%

Association mapping and marker-assisted selection of the lettuce dieback resistance gene Tvr1

et al. 2009

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BackgroundLettuce (Lactuca saliva L.) is susceptible to dieback, a soilborne disease caused by two viruses from the family Tombusviridae. Susceptibility to dieback is widespread in romaine and leaf-type lettuce, while modern iceberg cultivars are resistant to this disease. Resistance in iceberg cultivars is conferred by Tvr1 - a single, dominant gene that provides durable resistance. This study describes fine mapping of the resistance gene, analysis of nucleotide polymorphism and linkage disequilibrium in the Tvr1 region, and development of molecular markers for marker-assisted selection.ResultsA combination of classical linkage mapping and association mapping allowed us to pinpoint the location of the Tvr1 resistance gene on chromosomal linkage group 2. Nine molecular markers, based on expressed sequence tags (EST), were closely linked to Tvr1 in the mapping population, developed from crosses between resistant (Salinas and Salinas 88) and susceptible (Valmaine) cultivars. Sequencing of these markers from a set of 68 cultivars revealed a relatively high level of nucleotide polymorphism (θ = 6.7 × 10-3) and extensive linkage disequilibrium (r2 = 0.124 at 8 cM) in this region. However, the extent of linkage disequilibrium was affected by population structure and the values were substantially larger when the analysis was performed only for romaine (r2 = 0.247) and crisphead (r2 = 0.345) accessions. The association mapping approach revealed that one of the nine markers (Cntg10192) in the Tvr1 region matched exactly with resistant and susceptible phenotypes when tested on a set of 200 L. sativa accessions from all horticultural types of lettuce. The marker-trait association was also confirmed on two accessions of Lactuca serriola - a wild relative of cultivated lettuce. The combination of three single-nucleotide polymorphisms (SNPs) at the Cntg10192 marker identified four haplotypes. Three of the haplotypes were associated with resistance and one of them was always associated with susceptibility to the disease.ConclusionWe have successfully applied high-resolution DNA melting (HRM) analysis to distinguish all four haplotypes of the Cntg10192 marker in a single analysis. Marker-assisted selection for dieback resistance with HRM is now an integral part of our breeding program that is focused on the development of improved lettuce cultivars.

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Section: Discussionmentioning

confidence: 97%

Association mapping and marker-assisted selection of the lettuce dieback resistance gene Tvr1

et al. 2009

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“…This is a simple, low cost, and highly reproducible marker system which can be developed on the basis of single or a few nucleotide changes. It has been applied in, e.g., Arabidopsis (Drenkard et al 2000), soybean (Jeong and Maroof 2004;Kim et al 2005;Yuan et al 2007), apple (Gao et al 2005), maize (Shin et al 2006), rice (Hayashi et al 2004(Hayashi et al , 2006 and lettuce (Moreno-Vázquez et al 2003). For each SNP locus, two allele-specific forward (or reverse) primers (each matching one of the SNPvariants at the 3 0 -end) and two normal reverse (or forward) primers with matching melting temperatures were designed (Fig.…”

Section: Snp Detectionmentioning

confidence: 99%

Development of SNP markers and haplotype analysis of the candidate gene for rhg1, which confers resistance to soybean cyst nematode in soybean

Zhang

Smulders³

et al. 2009

Mol Breeding

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Soybean cyst nematode (SCN; Heterodera glycines Ichinohe) is one of the most destructive pests in the cultivation of soybean (Glycine max (L.) Merr.) worldwide. Markers based on the SCN resistance gene will enable efficient marker-assisted selection (MAS). We sequenced the candidate gene rhg1 in six resistant and two susceptible soybean genotypes and identified 37 SNPs (single nucleotide polymorphisms) among the sequences, of which 11 were in the coding region. Seven of these 11 SNPs led to changes in the amino acid sequence of the gene. The amino acid sequence we obtained differs from the previously published one by a stretch of 26-27 amino acids. Six codominant allele-specific SNP markers based on agarose gel detection were developed and tested in 70 genotypes, among which occurred only nine different haplotypes. Two neutrality tests (Tajima's D and Fu and Li's F) were significant for the six SNP loci in the 70 genotypes, which is consistent with intensive directional selection. A strong LD pattern was detected among five SNPs except 2868T [ C. Two SNPs (689C [ A and 757C [ T) formed one haplotype (689C-757C) that was perfectly associated with SCN resistance. The new allele-specific PCR markers located in the alleged sequence of the rhg1 candidate gene, combined with the microsatellite marker BACR-Satt309, will significantly improve the efficiency of MAS during the development of SCNresistant cultivars.Keywords Haplotype Á SCN Á SNP marker Á Soybean Abbreviations ACASAgarose gel-based co-dominant allelespecific ADAS Agarose gel-based dominant allele-specific LD Linkage disequilibrium LRR Leucine-rich repeats MAS Marker-assisted breeding QTNs Quantitative trait nucleotide

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“…Previously, we detected a 186 bp insertion (Ls268, GenBank AY207405.1 and AY207406.1) in lettuce that we used to design a codominant marker (SC268) for the recessive resistance gene cor (Moreno-Va´zquez et al, 2003). This fragment was present in most resistant genotypes (represented by the cultivar Green Lake) and absent in most susceptible genotypes (represented by the cultivar Diana).…”

Section: Resultsmentioning

confidence: 99%

“…The DNA extraction procedure, primer sequences, PCR conditions, cloning and other molecular procedures were described in Moreno-Va´zquez et al (2003).…”

Section: Methodsmentioning

confidence: 99%

hATpin, a Family of MITE-like hAT Mobile Elements Conserved in Diverse Plant Species that Forms Highly Stable Secondary Structures

Moreno-Vázquez

Ning

2005

Plant Mol Biol

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We identified a 178 bp mobile DNA element in lettuce with characteristic CGAGC/GCTCG repeats in the subterminal regions. This element has terminal inverted repeats and 8-bp target site duplications typical of the hAT superfamily of class II mobile elements, but its small size and potential to form a single-stranded stable hairpin-like secondary structure suggest that it is related to MITE elements. In silico searches for related elements identified 252 plant sequences with 8-bp target site duplications and sequence similarity in their terminal and subterminal regions. Some of these sequences were predicted to encode transposases and may be autonomous elements; these constituted a separate clade within the phylogram of hAT transposases. We demonstrate that the CGAGC/GCTCG pentamer maximizes the hairpin stability compared to any other pentamer with the same C + G content, and the secondary structures of these elements are more stable than for most MITEs. We named these elements collectively as hATpin elements because of the hAT similarity and their hairpin structures. The nearly complete rice genome sequence and the highly advanced genome annotation allowed us to localize most rice elements and to deduce insertion preferences. hATpin elements are distributed on all chromosomes, but with significant bias for chromosomes 1 and 10 and in regions of moderate gene density. This family of class II mobile elements is found primarily in monocot species, but is also present in dicot species.

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SNP-based codominant markers for a recessive gene conferring resistance to corky root rot (Rhizomonas suberifaciens) in lettuce (Lactuca sativa)

Cited by 25 publications

References 31 publications

Association mapping and marker-assisted selection of the lettuce dieback resistance gene Tvr1

Association mapping and marker-assisted selection of the lettuce dieback resistance gene Tvr1

Development of SNP markers and haplotype analysis of the candidate gene for rhg1, which confers resistance to soybean cyst nematode in soybean

hATpin, a Family of MITE-like hAT Mobile Elements Conserved in Diverse Plant Species that Forms Highly Stable Secondary Structures

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