Plant Science

SNP mapping in blackcurrant

Genetic mapping studies in crop species are well-established, but are often limited by a shortage of molecular markers. To address this, a large-scale discovery process has been undertaken at JHI to develop many single nucleotide polymorphism (SNP) markers by comparison of DNA of the two parents of the SCRI 9328 blackcurrant mapping population using the second generation sequencing technology 454 pyrosequencing. From the SNPs detected, a subset of 384 high-quality SNPs was used to develop an assay using the Illumina BeadXpress platform. Illumina data consists of two intensity values (X,Y) for each SNP, measuring the intensities of the fluorescent dyes associated with the two alleles of the SNP. After normalisation, the intensities are transformed to a combined SNP intensity, R = (X+Y), and an intensity ratio, theta = (2/p)*arctan(Y/X). Since the SNPs have been developed from their parents, plants from the mapping population should comprise at least two of the three possible genotypes AA, AB or BB at each SNP. Hence we expected the BeadStudio software to be able to separate the genotypes and hence classify the individuals according to the theta score for each SNP.

We found that 184 of the SNPs segregated clearly and so could be mapped by linkage analysis, but the remainder were classified as non-segregating by BeadStudio software. To explore these further, BioSS analysed the theta scores for each non-segregating SNP as quantitative traits on the assumption that they consisted of genetic information plus measurement error, using QTL analysis based on the map of segregating SNPs and additional SSR markers. A further 52 SNPs showed a single location on the genome explaining more than 50% of the variance of the theta scores. A similar analysis was conducted for a second blackcurrant mapping population, MP7. The two maps agreed well in their marker placing, whether the SNP was placed by linkage analysis or QTL mapping methods, allowing further research to be based on a larger number of markers.

linkage groups portrayal Linkage group 1 of the SCRI9328 and MP7 populations, with horizontal bars showing the positions of mapped SNPs and diagonal bars indicating those which are shared between the populations. Vertical bars are confidence intervals for SNP locations when mapped as QTLs, showing the positions of shared QTLs (A,B), QTLs in SCRI9328 and markers in MP7 (C), QTLs in MP7 and markers in SCRI9328 (D) and QTLs in SCRI9328 only (E to I).

Further details from: Christine Hackett

Article date 2011

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