Por favor, use este identificador para citar o enlazar a este item:
http://hdl.handle.net/10261/248413
COMPARTIR / EXPORTAR:
SHARE CORE BASE | |
Visualizar otros formatos: MARC | Dublin Core | RDF | ORE | MODS | METS | DIDL | DATACITE | |
Título: | Development and preliminary evaluation of a 90 K Axiom® SNP array for the allo-octoploid cultivated strawberry Fragaria × ananassa |
Autor: | Bassil, Nahla; Davis, T. M.; Zhang, Hailong; Ficklin, Stephen; Mittmann, Mike; Webster, Teresa; Mahoney, Lise; Wood, David; Alperin, Elisabeth S.; Rosyara, Umesh R.; Koehorst-van Putten, Herma J. J.; Monfort, Amparo CSIC ORCID CVN; Sargent, Daniel J.; Amaya, Iraida; Denoyes, Béatrice; Bianco, Luca; Dijk, Thijs van; Pirani, Ali; Iezzoni, Amy; Main, Dorrie; Peace, Cameron; Yang, Yilong; Whitaker, Vance M.; Verma, Sujeet; Bellon, Laurent; Brew, Fiona; Herrera, Raul; Weg, Eric van de | Fecha de publicación: | 2015 | Editor: | BioMed Central | Citación: | BMC Genomics 16: 155 (2015) | Resumen: | [Background]: A high-throughput genotyping platform is needed to enable marker-assisted breeding in the allo-octoploid cultivated strawberry Fragaria × ananassa. Short-read sequences from one diploid and 19 octoploid accessions were aligned to the diploid Fragaria vesca ‘Hawaii 4’ reference genome to identify single nucleotide polymorphisms (SNPs) and indels for incorporation into a 90 K Affymetrix® Axiom® array. We report the development and preliminary evaluation of this array. [Results]: About 36 million sequence variants were identified in a 19 member, octoploid germplasm panel. Strategies and filtering pipelines were developed to identify and incorporate markers of several types: di-allelic SNPs (66.6%), multi-allelic SNPs (1.8%), indels (10.1%), and ploidy-reducing “haploSNPs” (11.7%). The remaining SNPs included those discovered in the diploid progenitor F. iinumae (3.9%), and speculative “codon-based” SNPs (5.9%). In genotyping 306 octoploid accessions, SNPs were assigned to six classes with Affymetrix’s “SNPolisher” R package. The highest quality classes, PolyHigh Resolution (PHR), No Minor Homozygote (NMH), and Off-Target Variant (OTV) comprised 25%, 38%, and 1% of array markers, respectively. These markers were suitable for genetic studies as demonstrated in the full-sib family ‘Holiday’ × ‘Korona’ with the generation of a genetic linkage map consisting of 6,594 PHR SNPs evenly distributed across 28 chromosomes with an average density of approximately one marker per 0.5 cM, thus exceeding our goal of one marker per cM. [Conclusions]: The Affymetrix IStraw90 Axiom array is the first high-throughput genotyping platform for cultivated strawberry and is commercially available to the worldwide scientific community. The array’s high success rate is likely driven by the presence of naturally occurring variation in ploidy level within the nominally octoploid genome, and by effectiveness of the employed array design and ploidy-reducing strategies. This array enables genetic analyses including generation of high-density linkage maps, identification of quantitative trait loci for economically important traits, and genome-wide association studies, thus providing a basis for marker-assisted breeding in this high value crop. |
Descripción: | This is Scientific Contribution Number 2565 from the New Hampshire Agricultural Experiment Station. | Versión del editor: | https://doi.org/10.1186/s12864-015-1310-1 | URI: | http://hdl.handle.net/10261/248413 | DOI: | 10.1186/s12864-015-1310-1 | E-ISSN: | 1471-2164 |
Aparece en las colecciones: | (CRAG) Artículos |
Ficheros en este ítem:
Fichero | Descripción | Tamaño | Formato | |
---|---|---|---|---|
deveanana.pdf | 3,83 MB | Adobe PDF | Visualizar/Abrir |
CORE Recommender
PubMed Central
Citations
84
checked on 25-abr-2024
SCOPUSTM
Citations
140
checked on 23-abr-2024
WEB OF SCIENCETM
Citations
142
checked on 22-feb-2024
Page view(s)
41
checked on 29-abr-2024
Download(s)
54
checked on 29-abr-2024