• Vanderzande S, Zheng P, Cai L, Barac G, Gasic K, Main D, Iezzoni A and Peace C. The cherry 6+9K SNP array: a cost-effective improvement to the cherry 6K SNP array for genetic studies. Scientific Reports 10, 7613 (2020). https://doi.org/10.1038/s41598-020-64438-x
Cherry breeding and genetic studies can benefit from genome-wide genetic marker assays. Currently, a 6K SNP array enables genome scans in cherry; however, only a third of these SNPs are informative, with low coverage in many genomic regions. Adding previously detected SNPs to this array could provide a cost-efficient upgrade with increased genomic coverage across the 670 cM/352.9 Mb cherry whole genome sequence. For sweet cherry, new SNPs wer... [more]

Publication

Li X, Singh J, Qin M, Li S, Zhang X, Zhang M, Khan A, Zhang S, Wu J. Development of an integrated 200K SNP genotyping array and application for genetic mapping, genome assembly improvement and GWAS in pear (Pyrus). Plant biotechnology journal. 2019 Jan 28.

Description

Pear (Pyrus; 2n = 34), the third most important temperate fruit crop, has great nutritional and economic value. Despite the availability of many genomic resources in pear, it is challenging to genotype novel germplasm resources and breeding progeny... [more]

Resources
Resource Titles: 
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Download SNP data
File Description File
List of the 200 481 SNP markers that were put on the array.

PBI-17-1582-s007.xlsx

The details of 2388 SNPs mapped on the 17 linkage groups PBI-17-1582-s009.xlsx 
The origin of sequencing 113 pear accessions. PBI-17-1582-s008.xlsx

 

Resources
Resource Titles: 
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Resource Blocks: 
Download SNP data
File Description File
SNP information for the initial 700K SNPs

tfGDR1035.xlsx

Genome position of 70K SNPs in Pyrus communis Bartlett DH Genome v2.0 pear_70K_genome_pos.xlsx

 

Malus x domestica primary pseudo genome v1.0

Human-Readable NameMalus x domestica primary pseudo genome v1.0
Database NameMalus_x_domestica.v1.0-primary.pseudo.fa
Database Typenucleotide
FASTA Header Formatdefault
External DatabaseJBrowse for Malus_x_domestica.v1.0-primary.pseudo.fa
RegEx/^(\S+).*/
Link-out Typejbrowse
  • Hardigan Michael A., Feldmann Mitchell J., Lorant Anne, Bird Kevin A., Famula Randi, Acharya Charlotte, Cole Glenn, Edger Patrick P., Knapp Steven J. Genome Synteny Has Been Conserved Among the Octoploid Progenitors of Cultivated Strawberry Over Millions of Years of Evolution. Front. Plant Sci., 2020 February 7; 10:1789 | https://doi.org/10.3389/fpls.2019.01789
Allo-octoploid cultivated strawberry (Fragaria × ananassa) originated through a combination of polyploid and homoploid hybridization, domestication of an interspecific hybrid lineage, and continued admixture of wild species over the last 300 years. While genes appear to flow freely between the octoploid progenitors, the genome structures and diversity of the octoploid species remain poorly understood. The complexity and absence of an octoploid g... [more]

Abstract

Allo-octoploid cultivated strawberry (Fragaria × ananassa) originated through a combination of polyploid and homoploid hybridization, domestication of an interspecific hybrid lineage, and continued admixture of wild species over the last 300 years. While genes appear to flow freely between the octoploid progenitors, the genome structures and diversity of the octoploid species remain poorly understood. The complexity and absence of an octoploid genome frustrated early efforts to study chromosome evolution, resolve subgenomic structure, and develop a single coherent linkage group nomenclature. Here, we sh... [more]

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All supplementary data files are also available in the DRYAD database (dryad.org). DOI https://doi.org/10.25338/B8R31Q
File  File Description
Affymetrix_FanaSNP_probe_info.txt  
SNPcalls.50K_genotypes.txt  
SNPcalls.850K_genotypes.txt  
Supplementary_Dataset_01.xlsx Summary of octoploid genetic maps generated by WGS sequencing, 50K SNP array, and DNA capture datasets
Supplementary_Dataset_02.xlsx 850K screening array diversity panel of octoploid strawberry cultivars and wild accessions
 
Supplementary_Dataset_03.zip Panel of 446,644 validated marker probes from the 850K SNP screening array (These consititute 850K SNP dataset in JBrowse and SNP search pages).
 
Supplementary_Dataset_04.xlsx Panel of 49,483 marker probes selected for populating the 50K SNP production array (These consititute 50K SNP dataset in JBrowse and SNP search pages) 
 
genetic_maps.xlsx.zip  

 

  • Calle Alejandro, Cai Lichun, Iezzoni Amy, Wünsch Ana. Genetic Dissection of Bloom Time in Low Chilling Sweet Cherry (Prunus avium L.) Using a Multi-Family QTL Approach. Frontiers in Plant Science. 2020. 10:1647. https://doi.org/10.3389/fpls.2019.01647
Bloom time in sweet cherry (Prunus avium L.) is a highly heritable trait that varies between genotypes and depends on the environmental conditions. Bud-break occurs after chill and heat requirements of each genotype are fulfilled, and dormancy is released. Bloom time is a critical trait for fruit production as matching cultivar adaptation to the growing area is essential for adequate fruit set. Additionally, low chilling cultivars are of interest... [more]

Rubus ulmifolius genome v1.0 scaffolds

Human-Readable NameRubus ulmifolius genome v1.0 scaffolds
Database NameRubus_ulmifolius-Burbank_thornless-genome_v1-purged_primary_contigs_HiC.fasta
Database Typenucleotide