The 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.
[Note: this dataset has been superseded by version 2: https://doi.org/10.15482/USDA.ADC/1522673 ] This collection contains supplementary data for the manuscript "Legacy genetics of Arachis cardenasii in the peanut crop shows profound benefits of international seed exchange," which describes the impact of alleles from a wild relative of peanut, Arachis cardenasii, through analysis of those alleles across cultivars and breeding lines across many countries. The initial challenging cross, between tetraploid cultivated peanut (Arachis hypogaea) and the diploid species A. cardenasii, was carried out in the late 1960s. Subsequent work produce a tetraploid line that contained introgressed regions from A. cardenasii. Those chromosomal regions, several containing important resistance genes, were used in numerous breeding lines. The genetic legacy from A. cardenasii is documented in the files in this collection. The information includes genotyping data across peanut cultivars and breeding lines, generated through both genotyping arrays ("SNP chips") and whole-genome sequencing. Information in this collection also includes data related to impact of A. cardenasii on disease- and pest resistance in modern peanut varieties.
[Note: This version supersedes version 1: https://doi.org/10.15482/USDA.ADC/1520889 Changes in version 2: A new Dataset was added - DataSet1-CardAlleles-iii.xlsx Datasets were renamed and renumbered in accordance to article revisions, and some changes made (see below for details): SupplementaryData1-Worldwide-genotypes-ii.xlsx => DataSet3-Worldwide-genotypes-ii.xlsx (Data with very minor changes, including the removal of three of 710 markers) SupplementaryData2-Lineages-FieldData-ii.xlsx => DataSet4-Lineages-FieldData-iv.xlsx (this file underwent minor revisions, with some extra comments added) SupplementaryData3-Fingerprints.tar => DataSet5-Fingerprints.tar (Data unchanged) SupplementaryData4-Austp183.xlsx => DataSet6-Austp183.xlsx (Data unchanged) SupplementaryData5-introgression.tar => DataSet2-WGSIntrogression.tar (A Dataset more stringently filtered with more control genotypes was used, cutting the number of markers from 2,566,180 to 2,337,866. More genotype output files were added, including controls. A genome-ordered list of A. cardenasii GKP 10017 diagnostic bases was added (Acard-diag_bases.txt.gzip).] Description This collection contains supplementary data for the manuscript "Legacy genetics of Arachis cardenasii in the peanut crop shows profound benefits of international seed exchange," which describes the impact of alleles from a wild relative of peanut, Arachis cardenasii, through analysis of those alleles across cultivars and breeding lines across many countries. The initial challenging cross, between tetraploid cultivated peanut (Arachis hypogaea) and the diploid species A. cardenasii, was carried out in the late 1960s. Subsequent work produce a tetraploid line that contained introgressed regions from A. cardenasii. Those chromosomal regions, several containing important resistance genes, were used in numerous breeding lines. The genetic legacy from A. cardenasii is documented in the files in this collection. The information includes genotyping data across peanut cultivars and breeding lines, generated through both genotyping arrays ("SNP chips") and whole-genome sequencing. Information in this collection also includes data related to impact of A. cardenasii on disease- and pest resistance in modern peanut varieties.
The GSOR website describes the GSOR germplasm collection; provides information on how to donate to the collection and how to request from the collection.
Recent USDA/ARS patented technologies on crop production and protection that are available for licensing are described, including summary, contact, benefits, and applications. Updated June 2018.