Submitted to: Molecular Genetics and Genomics
Publication Type: Peer reviewed journal
Publication Acceptance Date: 12/11/2003
Publication Date: 3/16/2004
Citation: Simko, I., Haynes, K.G., Ewing, E.E., Costanzo, S., Christ, B.J., Jones, R.W. 2004. Mapping genes for resistance to Verticillium albo-atrum in tetraploid and diploid potato populations using haplotype association tests and genetic linkage analysis. Molecular Genetics and Genomics. 271:522-531 Interpretive Summary: Verticillium wilt is a serious soil-borne disease in potatoes which results in early plant senescence and reduced tuber yields. The purpose of this study was to determine whether genetic differences could be found in potato varieties which would help to explain why some are more resistant than others. We studied one location on potato chromosomes of 30 varieties, a location called the StVe1 locus, which had previously been shown to be involved in resistance. Our purpose was to see how this locus differed in different varieties. We found that we could group all 30 varieties in one of three groups, which shows that they are not widely divergent. This also means that the resistance from the StVel locus probably came from only a few ancestors. This will help breeders and molecular geneticists to understand this resistance better and perhaps improve it.
Technical Abstract: StVe1 - a putative QTL for resistance against Verticillium dahliae, was previously mapped to potato chromosome 9. To develop allele specific, SNP-based markers within the locus, the StVe1 fragment from a set of 30 North American potato cultivars was analyzed. Due to the polyploid heterozygous nature of cultivated potato, all PCR products were cloned prior to sequencing. The frequency of SNPs, extent of linkage disequilibrium (LD), and haplotype diversity in the StVe1 DNA fragment was investigated. The StVe1 nucleotide diversity was high (1 variation per 15bp), as a result of an abundance of both synonymous and non-synonymous substitutions. Three distinct and highly diverse haplotypes can be distinguished at the StVe1 locus, which were detected in 97%, 33%, and 13% of the cultivars analyzed. The small number of haplotypes observed suggests that the genetic base of cultivated potato in North America is built upon a small group of progenitor genotypes. Data from the StVe1 DNA fragment show that over short distances of about 800bp SNP loci comprising the haplotypes are in LD with each other. Detected base variations were validated on the tetraploid level with cycle sequencing or haplotype-specific PCR amplification, and will be used for association mapping in larger populations. Results from the present work suggest that SNP-based markers can be used to develop a genome-wide molecular map of potato.