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ARS Home » Northeast Area » Geneva, New York » Grape Genetics Research » Research » Publications at this Location » Publication #311978

Research Project: Improving Fruit Quality, Disease Resistance, and Tolerance to Abiotic Stress in Grape

Location: Grape Genetics Research

Title: Application of Genotyping-By-Sequencing for selection of locus-specific BAC clones to construct physical maps and identify candidate genes in Vitis

Author
item Lillis, Jacquelyn
item Majumdar, Raj
item Ledbetter, Craig
item Cadle-davidson, Lance

Submitted to: Annual International Plant & Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 10/31/2014
Publication Date: 1/1/2015
Publication URL: https://pag.confex.com/pag/xxiii/webprogram/Paper15550.html
Citation: Lillis, J.A., Majumdar, R., Ledbetter, C.A., Cadle Davidson, L.E. 2015. Application of Genotyping-By-Sequencing for selection of locus-specific BAC clones to construct physical maps and identify candidate genes in Vitis. Annual International Plant & Animal Genome Conference. P0876: 15550.

Interpretive Summary:

Technical Abstract: While genotyping-by-sequencing (GBS) is widely used for linkage and association mapping, its potential for physical mapping and candidate gene identification in under-characterized species has not been fully realized. Eight half-sib Vitis families (480 progeny) were genotyped using GBS and phenotyped for qualitative resistance. Initially, 581 GBS tags were identified as enriched in resistant taxa. Tag specificity was tested in a Vitis diversity panel, and 70 of 581 tags were specific to resistant taxa. A correlation matrix was constructed based on the presence of an enriched tag in orthogonal plate-row-column superpools of a BAC library to identify individual BAC clones putatively associated with the locus. Missing data, a known characteristic of GBS data, complicated deconvolution to identify BAC clones at the locus. For example, seemingly perfect deconvolution to a single plate-row-column combination could arise from two positive clones being partially genotyped. Of the 110 BAC clones selected for sequencing, 33 had seemingly perfect deconvolution, and 77 were selected with redundancy (2-8 clones from which there should be one true positive BAC). After sequencing and assembly of Illumina MiSeq paired-end reads, blast analysis indicated that 19 of the 33 (57.6%) perfect deconvolution BAC clones matched the genetically mapped locus, and 15 of the 67 (22.4%) redundant BAC clones matched the locus. The results indicate that GBS can be a rapid approach to BAC screening, but that conversion of positive GBS tags to a marker platform without missing data would improve the efficiency of BAC identification and sequencing.