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Data from: Construction of a High-Density American Cranberry (Vaccinium macrocarpon Ait.) Composite Map Using Genotyping-by-Sequencing for Multi-pedigree Linkage Mapping
dataset
posted on 2024-02-13, 13:25 authored by Brandon Schlautman, Giovanny Covarrubias-Pazaran, Luis Diaz-Garcia, Massimo Iorizzo, James J. Polashock, Edward Grygleski, Nicholi Vorsa, Juan ZalapaThe American cranberry (Vaccinium macrocarpon Ait.) is a recently domesticated, economically important, fruit crop with limited molecular resources. New genetic resources could accelerate genetic gain in cranberry through characterization of its genomic structure and by enabling molecular-assisted breeding strategies. To increase the availability of cranberry genomic resources, genotyping-by-sequencing (GBS) was used to discover and genotype thousands of single nucleotide polymorphisms (SNPs) within three interrelated cranberry full-sib populations. Additional simple sequence repeat (SSR) loci were added to the SNP datasets and used to construct bin maps for the parents of the populations, which were then merged to create the first high-density cranberry composite map containing 6073 markers (5437 SNPs and 636 SSRs) on 12 linkage groups (LGs) spanning 1124 cM. Interestingly, higher rates of recombination were observed in maternal than paternal gametes. The large number of markers in common (mean of 57.3) and the high degree of observed collinearity (mean Pair-wise Spearman rank correlations >0.99) between the LGs of the parental maps demonstrates the utility of GBS in cranberry for identifying polymorphic SNP loci that are transferable between pedigrees and populations in future trait-association studies. Furthermore, the high-density of markers anchored within the component maps allowed identification of segregation distortion regions, placement of centromeres on each of the 12 LGs, and anchoring of genomic scaffolds. Collectively, the results represent an important contribution to the current understanding of cranberry genomic structure and to the availability of molecular tools for future genetic research and breeding efforts in cranberry.
Resources in this dataset:
Resource Title: Journal article with supplementary data files.
File Name: Web Page, url: https://academic.oup.com/g3journal/article/7/4/1177/6031795#supplementary-data
Funding
USDA: 2008-51180-04878
USDA-NIFA: 2013-67013-21107
USDA-ARS: 3655-21220-001-00
National Science Foundation: DBI-1228280
USDA-NIFA: Hatch project 1008691
History
Data contact name
Zalapa, JuanData contact email
jezalapa@wisc.eduPublisher
G3: Genes, Genomes, GeneticsTemporal Extent Start Date
2017-01-01Theme
- Not specified
Geographic Coverage
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Topic Category
- biota
National Agricultural Library Thesaurus terms
Vaccinium macrocarpon; genotyping by sequencing; chromosome mapping; genetic improvement; cranberries; genomics; breeding; genotype; single nucleotide polymorphism; microsatellite repeats; loci; data collection; parents; linkage groups; germ cells; pedigree; segregation distortion; centromeresOMB Bureau Code
- 005:18 - Agricultural Research Service
OMB Program Code
- 005:040 - National Research
Primary article PubAg Handle
Pending citation
- No
Public Access Level
- Public
