Development and preliminary evaluation of a 90 K Axiom® SNP array for the allo-octoploid cultivated strawberry Fragaria x ananassa

被引：151

作者：

Bassil, Nahla V. ^{[1
]}

Davis, Thomas M. ^{[2
]}

Zhang, Hailong ^{[2
]}

Ficklin, Stephen ^{[3
]}

Mittmann, Mike ^{[4
]}

Webster, Teresa ^{[4
]}

Mahoney, Lise ^{[2
]}

Wood, David ^{[2
]}

Alperin, Elisabeth S. ^{[1
]}

Rosyara, Umesh R. ^{[5
]}

Putten, Herma Koehorst-vanc ^{[6
]}

Monfort, Amparo ^{[7
]}

Sargent, Daniel J. ^{[8
]}

Amaya, Iraida ^{[9
]}

Denoyes, Beatrice ^{[10
]}

Bianco, Luca ^{[8
]}

van Dijk, Thijs ^{[6
]}

Pirani, Ali ^{[4
]}

Iezzoni, Amy ^{[5
]}

Main, Dorrie ^{[3
]}

Peace, Cameron ^{[3
]}

Yang, Yilong ^{[2
]}

Whitaker, Vance ^{[11
]}

Verma, Sujeet ^{[11
]}

Bellon, Laurent ^{[12
]}

Brew, Fiona ^{[12
]}

Herrera, Raul ^{[13
]}

de Weg, Eric van ^{[6
]}

机构：

[1] USDA ARS, NCGR, Corvallis, OR 97331 USA

[2] Univ New Hampshire, Durham, NH 03824 USA

[3] Washington State Univ, Pullman, WA 99164 USA

[4] Affymetrix, Santa Clara, CA USA

[5] Michigan State Univ, E Lansing, MI 48824 USA

[6] Wageningen UR Plant Breeding, Wageningen, Netherlands

[7] CSIC IRTA UAB UB, IRTA Ctr Res Agr Genom, Barcelona, Spain

[8] Fdn Edmund Mach, Res & Innovat Ctr, I-38010 San Michele All Adige, TN, Italy

[9] IFAPA Ctr Churriana, Malaga, Spain

[10] INRA, UMR BFP, Bordeaux, France

[11] Univ Florida, GCREC, Wimauma, FL USA

[12] Affymetrix UK Ltd, Wooburn Green, High Wycombe, England

[13] Univ Talca, Inst Ciencias Biol, Talca, Chile

来源：

BMC GENOMICS | 2015年 / 16卷

基金：

美国食品与农业研究所;

关键词：

Fragaria; Genotyping array; Plant breeding; Polyploidy; Strawberry; Single nucleotide polymorphism; Reduced ploidy; SINGLE-NUCLEOTIDE POLYMORPHISMS; LINKAGE MAP; GENOME; SEQUENCE; WHEAT; GENE; IDENTIFICATION; REARRANGEMENTS; DUPLICATION; EVOLUTION;

D O I：

10.1186/s12864-015-1310-1

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

Background: A high-throughput genotyping platform is needed to enable marker-assisted breeding in the allo-octoploid cultivated strawberry Fragaria x 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 (R) Axiom (R) 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' x '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.

引用

页数：30

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