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

Bassil NV, Davis TM, Zhang H, Ficklin S, Mittmann M, Webster T, Mahoney L, Wood D, Alperin ES, Rosyara UR, Koehorst-Vanc Putten H, Monfort A, Sargent DJ, Amaya I, Denoyes B, Bianco L, van Dijk T, Pirani A, Iezzoni A, Main D, Peace C, Yang Y, Whitaker V, Verma S, Bellon L, Brew F, Herrera R, van de Weg E - BMC Genomics (2015)

Bottom Line: 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 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.

View Article: PubMed Central - PubMed

Affiliation: USDA-ARS, NCGR, Corvallis, OR, USA. nahla.bassil@ars.usda.gov.

ABSTRACT

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.

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Related in: MedlinePlus

Distribution of minor allele frequency (MAF ≥ 0.1 in green, ≥ 0.35 in blue) of SNPs across seven LGs. MAF is shown according to physical location on the F. vesca ‘Hawaii 4’ v1.0 reference genome in 65 diverse strawberry accessions.
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Fig14: Distribution of minor allele frequency (MAF ≥ 0.1 in green, ≥ 0.35 in blue) of SNPs across seven LGs. MAF is shown according to physical location on the F. vesca ‘Hawaii 4’ v1.0 reference genome in 65 diverse strawberry accessions.

Mentions: SNP polymorphism as present in wider germplasm was estimated based on MAF in the 12,609 PHR SNPs obtained after filtering across the 65 diverse cultivar accessions (Diversity set, Additional file 1). MAF ranged from 0 to 0.50 with 0 indicating monomorphism and 0.50 indicating the presence of both alleles at equal frequency. Approximately 91% (11,518) of the SNPs were polymorphic as indicated by a MAF ≥0.10. These polymorphic SNPs (MAF ≥0.10), and a highly polymorphic fraction of SNPs with MAF ≥0.35 (4,097 SNPs or 32.5% of the total), were well distributed across the seven pseudochromosomes of the F. vesca ‘Hawaii 4’ v. 1.1 reference genome according to physical location (Figure 14). The largest SNP gap was 642 Kbp in length and observed on linkage group 4 (Figure 14). Nine (0.07%) SNPs were monomorphic, while 1,082 SNPs (7.1%) exhibited low polymorphism with an observed MAF <0.10 in the evaluated germplasm.Figure 14


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

Bassil NV, Davis TM, Zhang H, Ficklin S, Mittmann M, Webster T, Mahoney L, Wood D, Alperin ES, Rosyara UR, Koehorst-Vanc Putten H, Monfort A, Sargent DJ, Amaya I, Denoyes B, Bianco L, van Dijk T, Pirani A, Iezzoni A, Main D, Peace C, Yang Y, Whitaker V, Verma S, Bellon L, Brew F, Herrera R, van de Weg E - BMC Genomics (2015)

Distribution of minor allele frequency (MAF ≥ 0.1 in green, ≥ 0.35 in blue) of SNPs across seven LGs. MAF is shown according to physical location on the F. vesca ‘Hawaii 4’ v1.0 reference genome in 65 diverse strawberry accessions.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4374422&req=5

Fig14: Distribution of minor allele frequency (MAF ≥ 0.1 in green, ≥ 0.35 in blue) of SNPs across seven LGs. MAF is shown according to physical location on the F. vesca ‘Hawaii 4’ v1.0 reference genome in 65 diverse strawberry accessions.
Mentions: SNP polymorphism as present in wider germplasm was estimated based on MAF in the 12,609 PHR SNPs obtained after filtering across the 65 diverse cultivar accessions (Diversity set, Additional file 1). MAF ranged from 0 to 0.50 with 0 indicating monomorphism and 0.50 indicating the presence of both alleles at equal frequency. Approximately 91% (11,518) of the SNPs were polymorphic as indicated by a MAF ≥0.10. These polymorphic SNPs (MAF ≥0.10), and a highly polymorphic fraction of SNPs with MAF ≥0.35 (4,097 SNPs or 32.5% of the total), were well distributed across the seven pseudochromosomes of the F. vesca ‘Hawaii 4’ v. 1.1 reference genome according to physical location (Figure 14). The largest SNP gap was 642 Kbp in length and observed on linkage group 4 (Figure 14). Nine (0.07%) SNPs were monomorphic, while 1,082 SNPs (7.1%) exhibited low polymorphism with an observed MAF <0.10 in the evaluated germplasm.Figure 14

Bottom Line: 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 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.

View Article: PubMed Central - PubMed

Affiliation: USDA-ARS, NCGR, Corvallis, OR, USA. nahla.bassil@ars.usda.gov.

ABSTRACT

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.

Show MeSH
Related in: MedlinePlus