Statistical Genomics & Bioinformatics

Linkage map construction in blackcurrant using genotyping by sequencing data

Genetic linkage maps are a vital tool for locating genes responsible for important traits such as yield or disease resistance in plants and animals, and modern genotyping technologies are leading to increasingly dense maps. Genotyping by sequencing is a recent approach that enables large numbers of single nucleotide polymorphism sites (SNPs) to be detected and is suitable for the analysis of crops such as blackcurrant that do not have a sequenced genome. Each segregating SNP has two alleles, and the data are obtained as read counts of each allele in two parents and their F1 offspring. Graphical exploration led to a method based on functional regression to identify the genotypes for each individual. After construction of the linkage map, further SNPs with unusual segregation patterns were detected and were mapped as quantitative traits using the allele count data. This identified that some of these unusual patterns were likely to be due to the presence of a third allele (a null allele) with a zero read count at a SNP, which was allowed for in subsequent analyses. Taken as a whole, the method gave a high-quality linkage map with up to 200 SNPs on each linkage group and more approximate locations for many SNPs of lower quality. This is an important tool towards identifying candidate genes for key economic traits.

plotted diagram for SNP site countsPlotting read counts for a SNP site shows that the parents (circles) have both alleles (are of genotype AB). Their offspring (crosses) show three classes AA, AB and BB in a 1:2:1 ratio.

Further details from:
Christine Hackett and Katharine Preedy

Article date 2015

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