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Title: Fast and robust generation of high-resolution genetic maps in grapevine interspecific hybrid half-sib families using the HetMappS pipeline and R/qtl

item BARBA, PAOLA - Cornell University
item HYMA, KATIE - Cornell University
item WANG, MINGHUI - Cornell University
item Londo, Jason
item ACHARYA, CHARLOTTE - Cornell University
item MITCHELL, SHARON - Cornell University
item SUN, QI - Cornell University
item REISCH, BRUCE - Cornell University
item Cadle-Davidson, Lance

Submitted to: Annual International Plant & Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 11/15/2014
Publication Date: 1/1/2015
Citation: Barba, P., Hyma, K., Wang, M., Londo, J.P., Acharya, C., Mitchell, S., Sun, Q., Reisch, B., Cadle Davidson, L.E. 2015. Fast and robust generation of high-resolution genetic maps in grapevine interspecific hybrid half-sib families using the HetMappS pipeline and R/qtl. Annual International Plant & Animal Genome Conference, San Diego, CA.

Interpretive Summary:

Technical Abstract: Genotyping-by-sequencing (GBS) provides an opportunity for fast and inexpensive generation of unbiased SNPs. However, due to its low coverage, GBS SNPs have a higher proportion of missing data and genotyping error associated with heterozygote undercalling than traditional genotyping platforms. These features can make genetic mapping with GBS markers a challenging task, particularly in highly heterozygous species and even more so since current mapping software struggles to analyze markers sets larger than 3,000 simultaneously. We applied HetMappS synteny and de novo pipelines to 384-plex GBS SNPs from four half-sib grapevine interspecific hybrid families to generate high-resolution genetic maps. Starting from more than 300,000 SNPs obtained from the TASSEL-GBS pipeline, pseudo-testcross markers were identified, grouped and phased to generate parental linkage maps with between 1000 and 5000 markers each. After map curation with R/qtl genetic distances were similar to previously published SSR maps, and the new maps showed good coverage across the physical distance of the reference genome. Moreover, parental maps derived from different half-sib crosses with both the synteny and de novo pipelines showed a high degree of correspondence, for example with conserved areas of low recombination frequency indicative of centromeric regions. These maps were used to locate the flower sex locus, supporting previous genetic analysis, and suggested chromosome location assignments for scaffolds from random chromosomes of the 12X.0 reference genome. Relative to more commonly used SSR markers, this approach provides a major advance in map resolution at a fraction of the time and cost typically needed for SSR map construction.