Publication datasets

This page provide easy access to the datasets that are mentioned to be available from GDR in publications. Data are integrated in GDR and there are various ways to access them.

Links to publication pages where data can be accessed and additional links to search/browse pages to access data are available below.

 
tfGDR accession number Publication Access Data
tfGDR1052

Kenta Shirasawa, Akihiro Itai, Sachiko Isobe. Genome sequencing and analysis of two early-flowering cherry (Cerasus × kanzakura) varieties, ‘Kawazu-zakura’ and ‘Atami-zakura’. bioRxiv 2021.09.08.459382; doi: https://doi.org/10.1101/2021.09.08.459382

Paper under peer review

 ATM_KWZ_KENTA_JP_16Sept21.zip
N/A Howard, N.P., Peace, C., Silverstein, K.A.T. et al. The use of shared haplotype length information for pedigree reconstruction in asexually propagated outbreeding crops, demonstrated for apple and sweet cherry. Hortic Res 8, 202 (2021). https://doi.org/10.1038/s41438-021-00637-5

Search SNP Genotype Data

Genotype data
tfGDR1051 Longji Wang, Ting Lei, Guoming Han, Junyang Yue, Xueru Zhang, Qi Yang, Haixiang Ruan, Chunyang Gu, Qiang Zhang, Niuniu Zhang, Tao Qian, Liping Gao, Yunsheng Wang. The chromosome-scale reference genome of Rubus chingii Hu provides insight into the biosynthesis pathway of hydrolyzable tannins. Plant J. 2021 Jun 26. Genome page
tfGDR1050 Howard NP, Troggio M, Durel CE, Muranty H, Denancé C, Bianco L, Tillman J, and Weg E. Integration of Infinium and Axiom SNP array data in the outcrossing species Malus × domestica and causes for seemingly incompatible calls. BMC Genomics 22, 246 (2021).  SNP genotype data
tfGDR1049

whole genome assembly data of three apricot genomes

Wang et al. 2021 submitted for publication
tfGDR1046 Alejandro Calle, Manuel J. Serradilla, Ana Wünsch, QTL mapping of phenolic compounds and fruit colour in sweet cherry using a 6+9K SNP array genetic map. Scientia Horticulturae 2021; 280: 109900 pub
N/A

D’Amico-Willman K.M., Niederhuth C., Willman M.R., Gradziel T.M., Ouma W.Z., Meulia T., Fresnedo-Ramírez J. 2020. DNA methylation status is associated with divergent exhibition of non-infectious bud failure, an age-related disorder, in twin almonds (Prunus dulcis [Mill.] D.A.Webb). to be submitted.

 

Funding sources: The Ohio State University CFAES-SEEDS program grant 2019-125, the Almond Board of California Grant HORT35, the Translational Plant Sciences Graduate Fellowship, the Cancer Center Support Grant (CCSG) P30CA016058, the AFRI-EWD Predoctoral Fellowship 2019-67011-29558 from the USDA National Institute of Food and Agriculture, and the Ohio Supercomputer Center.

Nonpareil_v1.tar.gz (whole genome data of the almond cultivar ‘Nonpareil’)

  • Prunus_dulcis_cv_Nonpareil_Chlorplast_ver1.fasta: plastid genomic sequence 
  • Prunus_dulcis_cv_Nonpareil _ver1.fasta: nuclear genomic sequence of the gene space
  • Prunus_dulcis_cv_Nonpareil_ver1.gff: gff file with the gene annotation of the nuclear genomic sequence
  • Md5_AlmondGenomeFiles.txt: checksum file to verify the integrity of the three previous files.
tfGDR1045 Michael Wisniewski, Timothy Artlip, Jia Liu, Jing Ma, Erik Burchard, John Norelli, and Christopher Dardick. Fox Hunting in Wild Apples: Searching for Novel Genes in Malus sieversii. International journal of molecular sciences. 2020 Dec 14; 21(24). 

About 3000 apple-FOX Arabidopsis library sequences from Malus sieversii

Available for BLAST

pub
tfGDR1044 The chromosome-level draft genome of a diploid
plum (Prunus salicina),  submitted to Gigascience by Liu et al.

Access all the data from the genome page.
tfGDR1043 Calle, A., Balas, F., Cai, L. Iezzoni, A., López-Corrales, M., Serradilla, MJ., Wünsch, A. Fruit size and firmness QTL alleles of breeding interest identified in a sweet cherry ‘Ambrunés’ × ‘Sweetheart’ population. Molecular Breeding 40, 86 (2020). https://doi.org/10.1007/s11032-020-01165-1 pub
tfGDR1042 Montanari S, Postman J, Bassil NV, Neale DB. Reconstruction of the Largest Pedigree Network for Pear Cultivars and Evaluation of the Genetic Diversity of the USDA-ARS National Pyrus Collection.. G3 (Bethesda, Md.). 2020 Jul 16.

pub

Access data in Genotype Search

genotype data with pear Axiom 70K SNP array

 (file 1, file 2, file 3, file 4)

 
tfGDR1041 Calle, A., Wünsch, A. Multiple-population QTL mapping of maturity and fruit-quality traits reveals LG4 region as a breeding target in sweet cherry (Prunus avium L.). Horticulture Research 7, 127 (2020). https://doi.org/10.1038/s41438-020-00349-2 pub
N/A Stijn Vanderzande, Ping Zheng, Lichun Cai, Barac Goran, Ksenija Gasic, Dorrie Main, Amy Iezzoni, Cameron Peace. The cherry 6+9K SNP array: a cost-effective improvement to the cherry 6K SNP array for genetic studies. Scientific Reports 10, 7613 (2020).

Vanderzande_2020_Supplementary_Table_S1.xlsx

Vanderzande_2020_Supplementary_Table_S2.xlsx

Vanderzande_2020_Supplementary_Table_S3.xlsx

 

pub
tfGDR1040 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

pub

 

 
tfGDR1039 Cockerton HM, Li B, Vickerstaff RJ, Eyre CA, Sargent DJ, Armitage AD, Marina-Montes C, Garcia-Cruz A, Passey AJ, Simpson DW, Harrison RJ. Identifying Verticillium dahliae Resistance in Strawberry Through Disease Screening of Multiple Populations and Image Based Phenotyping. Frontiers in plant science. 2019; 10:924.

pub

 

SNP genotype data for mapping population available in the pub page above
N/A
  • Vanderzande S, Hias N, Edge-Garza D, Costes E, Davey M, Keulemans J. (2016) Sylleptic branching in winter headed trees in apple (Malus x domestica): genetic effects and relationships with other tree architectural characteristics. Tree Genetics & Genomes 12: 87
  • Vanderzande S, Micheletti D, Troggio M, Davey M, Keulemans J. (2017) Genetic diversity, population structure and linkage disequilibrium of elite and local apple accessions from Belgium using the IRSC array. Tree Genetics & Genomes 13: 125
 Phenotypic_and_Genotypic_data_Stijn_Vanderzande
tfGDR1038 Vanderzande S, Howard NP, Cai L, Da Silva Linge C, Antanaviciute L, Bink MCAM, Kruisselbrink JW, Bassil N, Gasic K, Iezzoni A, van de Weg E, Peace C. High-quality, genome-wide SNP genotypic data for pedigreed germplasm of the diploid outbreeding species apple, peach, and sweet cherry through a common workflow. PLOS ONE 14(6): e0210928. https://doi.org/10.1371/journal.pone.0210928

pub

SNP and haplotype genotype data: apple, peach and sweet cherry

Access genotype data in Genotype Search

Access haplotype data in Haplotype Search

iSCAN data: apple, sweet cherry
tfGDR1037 Cai L, Quero-García J, Barreneche T, Dirlewanger E, Saski C, Iezzoni A. A fruit firmness QTL identified on linkage group 4 in sweet cherry (Prunus avium L.) is associated with domesticated and bred germplasm. Scientific reports. 2019 Mar 21; 9(1):5008.
tfGDR1036 da Silva Linge C, Antanaviciute L, Abdelghafar A, Arús P, Bassi D, Rossini L, Ficklin S, Gasic K. High-density multi-population consensus genetic linkage map for peach. PloS one. 2018; 13(11):e0207724.

pub
tfGDR1035 Montanari S, Bianco L, Allen BJ, Martínez-García PJ, Bassil NV, Postman J, Knäbel M, Kitson B, Deng CH, Chagné D, Crepeau MW, Langley CH, Evans K, Dhingra A, Troggio M, Neale DB. Development of a highly efficient Axiom™ 70 K SNP array for Pyrus and evaluation for high-density mapping and germplasm characterization. BMC genomics. 2019 May 02; 20(1):331.
N/A High-density linkage maps constructed in sweet cherry (Prunus avium L.) using cross- and self-pollination populations reveal chromosomal homozygosity in inbred families and non-syntenic regions with the peach genome pub
tfGDR1034 Mapping X-disease Phytoplasma Resistance" in Prunus virginiana. accepted to Frontiers in Plant Science pub 
tfGDR1033 Identification of bloom date QTLs and haplotype analysis in tetraploid sour cherry (Prunus cerasus) pub | haplotype data
N/A Serra O, Giné-Bordonaba J, Eduardo I, Bonany J, Echeverria G, Larrigaudière C, Arús P. Genetic analysis of the slow-melting flesh character in peach.Tree Genetics & Genomes (2017) 13: 77. genotype/phenotype data
tfGDR1032 Biscarini and Nazzicari et al. Genome-enabled predictions for fruit weight and quality from repeated records in European peach progenies. BMC genomics. 2017. 18(1):432. genotype/phenotype data
tfGDR1031 Mora et al. Integrated QTL detection for key breeding traits in multiple peach progenies. BMC genomics. 2017. 18(1):404. genotype/phenotype data
tfGDR1030 Marchese A, Giovannini D, Leone A, Mafrica R, Palasciano M, Cantini C, Di Vaio C, De Salvador FR, Giacalone G, Caruso T, Marra FP. S-genotype identification, genetic diversity and structure analysis of Italian sweet cherry germplasm. Tree Genetics & Genomes (2017) 13: 93. pub | project
tfGDR1029 Mgbechi-Ezeri J, Porter L, Johnson KB, Oraguzie N. Assessment of sweet cherry (Prunus avium L.) genotypes for response to bacterial canker disease. Euphytica. 2017; 213:145. pub
N/A Martínez-García PJ, Parfitt DE, Ogundiwin EA, Fass J, Chan HM, Ahmad R, Lurie S, Dandekar A, Gradziel TM, Crisosto CH. Tree genetics & genomes. 2013; 9(1):19-36. pub | map data (POP_DG, POP_DF, concensus), SNP info
N/A Urrestarazu J, Denancé C, Ravon E, Guyader A, Guisnel R, Feugey L, Poncet C, Lateur M, Houben P, Ordidge M et al. BMC plant biology. 2016 Jun 08; 16(1):130. pub | genotype data 
tfGDR1028 Barać G, Ognjanov V, Obreht Vidaković D, Dorić D, Ljubojević M, Dulić J, Miodragović M, Gašić K (2107) Genetic diversity and population structure of European ground cherry (Prunus fruticosa Pall.) using SSR markers. Scientia Horticulturae pub | project | genotype data
tfGDR1027 Pagliarani G., Dapena E. , Miñarro M. , Denancé C. , Lespinasse Y. , Rat-Morris E. , Troggio M. , Durel C.E. , Tartarini S. Fine mapping of the rosy apple aphid resistance locus Dp-fl on Linkage Group 8 of the apple cultivar ‘Florina’. Tree Genetics & Genomes 2016, 12:56 pub
tfGDR1025 José Luis Zeballos, Walid Abidi , Rosa Giménez, Antonio J. Monforte, María Ángeles Moreno, Yolanda Gogorcena. Mapping QTLs associated with fruit quality traits in peach [Prunus persica (L.) Batsch] using SNP maps. Tree Genetics & Genomes June 2016, 12:37 pub
tfGDR1023 Mahoney et al. A high density linkage map of the ancestral diploid strawberry, F. iinumae, using SNP markers from the IStraw90 Array and GBS. The Plant Genome 2016 9(2) pub
tfGDR1021 Ben Sadok et al. Apple fruit texture QTLs: year and cold storage effects on sensory and instrumental traits. Tree Genetics & Genomes 2015 11:119 pub
tfGDR1020 Tsuruta and Mukai. Hybrid seedling inviability locus (HIs1 ) mapped on linkage group 4 of the Japanese flowering cherry, Cerasus  x yedoensis 'Somei-yoshino'. Tree Genetics & Genomes 2015 11:88 pub
tfGDR1019 Castède et al. Mapping of Candidate Genes Involved in Bud Dormancy and Flowering Time in Sweet Cherry (Prunus avium). PloS one. 2015; 10(11):e0143250. pub
tfGDR1018 Montanari et al. Genetic mapping of Cacopsylla pyri resistance in an interspecific pear (Pyrus spp.) population. Tree Genetics & Genomes 2015 11:74 pub
tfGDR1017 Gao et al. Genetic diversity of Malus cultivars and wild relatives in the Chinese National Repository of Apple Germplasm Resources. Tree Genetics & Genomes 2015 11:106 pub | genotype search (dataset name: Gao_Chinese_National_Repository_Apple_2015)
tfGDR1016 Leforestier et al. Genomic basis of the differences between cider and dessert apple varieties. Evolutionary applications. 2015 Aug; 8(7):650-61.

pub | genotype search (dataset name: Dessert_and_cider_core_collections_8k_SNP)
tfGDR1015 Nuñez-Lillo et al. Identification of candidate genes associated with mealiness and maturity date in peach [Prunus persica (L.) Batsch] using QTL analysis and deep sequencing. Tree Genetics & Genomes 2015, 11:86 pub
tfGDR1014 Guajardo et al. Construction of high density sweet cherry (Prunus avium L.) linkage maps using microsatellite markers and SNPs detected by genotyping-by-sequencing (GBS). PLoS ONE 2015. pub
tfGDR1013 Micheletti et al. Whole-Genome Analysis of Diversity and SNP-Major Gene Association in Peach Germplasm. PloS one. 2015; 10(9):e0136803. pub | project | peach SNP genotype data
tfGDR1012 Genetic analysis of the flowering date and number of petals in rose tfGDR1012(will be integrated to GDR when more marker data is received)
tfGDR1010 Donoso et al. High-density mapping suggests cytoplasmic male sterility with two restorer genes in almond × peach progenies. Horticulture Research 2015 2: 15016 pub
tfGDR1008 Kawamura et al. Inheritance of garden rose architecture and its association with flowering behaviour. Tree Genetics & Genomes 2015, 11:22 pub
N/A Bai Y, Dougherty L, Xu K. Towards an improved apple reference transcriptome using RNA-seq. Molecular genetics and genomics : MGG. 2014 Feb 16. project page
N/A Cachi and Wünsch. Characterization of self-compatibility in sweet cherry varieties by crossing experiments and molecular genetic analysis. Tree Genetics & Genomes 2014 10(5):1205-1212 pub | genotype search (dataset name: Wunsch_Sweet_Cherry_Self-compatibility_2014)
N/A Duval et al. High-resolution mapping of the RMia gene for resistance to root-knot nematodes in peach. Tree genetics & genomes. 2014; 10(2):297-306. pub
N/A Clark et al. A consensus ‘Honeycrisp’ apple (Malus × domestica) genetic linkage map from three full-sib progeny populations. Tree genetics & genomes. 2014; 10(3):627-639. pub
tfGDR1005 Torres-Hernández et al. Genetic variability in Malacomeles denticulata (Rosaceae) from central Mexico revealed with SSR markers. Genetic resources and crop evolution. 2013; 60(7):2191-2200. pub | genotype search (dataset name: Núñez-Colín_Malacomeles_SSR_2013)
tfGDR1004 Zhebentyayeva et al. Dissection of chilling requirement and bloom date QTLs in peach using a whole genome sequencing of sibling trees from an F mapping population. Tree Genetics & Genomes 2014 10(1)35 pub
tfGDR1003 Frett et al. Mapping quantitative trait loci associated with blush in peach [Prunus persica (L.) Batsch]. Tree Genetics & Genomes 2014 April, 10(2):367-381. pub
tfGDR1001 Yang et al. Mapping quantitative trait loci associated with resistance to bacterial spot (Xanthomonas arboricola pv. pruni) in peach. Tree Genetics & Genomes 2013 9:573-586 pub