High resolution DNA melting markers for identification of H1-linked resistance to potato cyst nematode

Although Sequence-Characterized Amplified Region (SCAR) markers linked to the potato H1 locus, which confers resistance to pathotypes Ro1 and Ro4 of the potato cyst nematode (PCN) Globodera rostochiensis , have been reported, robust markers that enable estimation of allele dosage would improve the q...

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Bibliographic Details
Published in:Molecular breeding 2018-06, Vol.38 (6), p.1-13, Article 79
Main Authors: Meiyalaghan, Sathiyamoorthy, Paget, Mark, Thompson, Shirley, Thomson, Susan, Baldwin, Samantha, Anderson, John, Genet, Russell, Lewthwaite, Stephen
Format: Article
Language:English
Subjects:
Biomedical and Life Sciences
Biotechnology
Breeding
Cultivars
Cysts
Deoxyribonucleic acid
DNA
Dosage
Gene polymorphism
Genomes
Genotyping
High resolution
Life Sciences
Loci
Markers
Melting
Molecular biology
Molecular chains
Nematodes
Nucleotides
Offspring
Pest resistance
Plant biology
Plant Genetics and Genomics
Plant Pathology
Plant Physiology
Plant Sciences
Polymorphism
Potatoes
Progeny
Scars
Single-nucleotide polymorphism
Vegetables
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Summary:Although Sequence-Characterized Amplified Region (SCAR) markers linked to the potato H1 locus, which confers resistance to pathotypes Ro1 and Ro4 of the potato cyst nematode (PCN) Globodera rostochiensis , have been reported, robust markers that enable estimation of allele dosage would improve the quality of information obtained from genotyping parental accessions (cultivars/breeding lines) and progeny populations within breeding programmes. With this in mind, we have developed single nucleotide polymorphism (SNP)-based molecular markers flanking the H1 resistance gene, using genomic re-sequence data from five elite tetraploid accessions. The published TG689 and 57R primer sequences were used in a Basic Local Alignment Search Tool (BLAST) examination of the reference potato genome, and SNPs within the vicinity of these primer regions were identified and targeted for designing probe-based High Resolution Melting (HRM) SNP assays. Evaluation of the subsequently developed HRM markers, TG689_1P and 57R_1P, against the publicly available SCAR markers, TG689 and 57R, indicated that the HRM markers enabled more reliable marker-trait association than the SCARs. Additionally, allelic dosage estimates for the H1 locus were also derived using the TG689_1P marker, providing a tool to optimise parental and progeny selections in PCN resistance breeding.
ISSN:1380-3743
1572-9788
DOI:10.1007/s11032-018-0832-z