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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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Genomic basis for biologically effective ploidy reduction. A. Site-specific ploidy reduction in one or more subgenomes is a proportional consequence of site-specific deletion within the alternate subgenomes. Site-specific ploidy may be reduced from the octoploid (8x) to the hexaploid (6x), tetraploid (4x), or diploid (2x) levels. B. Alignment of Illumina short reads to the ‘Hawaii 4’ v1.1 reference genome reveals a ~1.5 kb region of localized read depth reduction, indicative of ploidy reduction, in octoploid F. ×ananassa ‘Winter Dawn’, corresponding to the site of a ~1.5 kb deletion in diploid F. iinumae relative to the F. vesca diploid reference genome. The deletion is absent in diploid F. mandshurica, a close relative of F. vesca. Visualized in Integrated Genome Viewer (IGV, Broad Institute).
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Fig15: Genomic basis for biologically effective ploidy reduction. A. Site-specific ploidy reduction in one or more subgenomes is a proportional consequence of site-specific deletion within the alternate subgenomes. Site-specific ploidy may be reduced from the octoploid (8x) to the hexaploid (6x), tetraploid (4x), or diploid (2x) levels. B. Alignment of Illumina short reads to the ‘Hawaii 4’ v1.1 reference genome reveals a ~1.5 kb region of localized read depth reduction, indicative of ploidy reduction, in octoploid F. ×ananassa ‘Winter Dawn’, corresponding to the site of a ~1.5 kb deletion in diploid F. iinumae relative to the F. vesca diploid reference genome. The deletion is absent in diploid F. mandshurica, a close relative of F. vesca. Visualized in Integrated Genome Viewer (IGV, Broad Institute).

Mentions: In addition to “technical ploidy reduction”, our outcome benefitted from “biological” ploidy reduction, which derived from the fortuitous existence of localized regions of effectively reduced ploidy in an otherwise octoploid genomic context, with the ploidy reduction assumed to be the result of large or small scale insertions and deletions among subgenomes (Figure 15).Figure 15


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)

Genomic basis for biologically effective ploidy reduction. A. Site-specific ploidy reduction in one or more subgenomes is a proportional consequence of site-specific deletion within the alternate subgenomes. Site-specific ploidy may be reduced from the octoploid (8x) to the hexaploid (6x), tetraploid (4x), or diploid (2x) levels. B. Alignment of Illumina short reads to the ‘Hawaii 4’ v1.1 reference genome reveals a ~1.5 kb region of localized read depth reduction, indicative of ploidy reduction, in octoploid F. ×ananassa ‘Winter Dawn’, corresponding to the site of a ~1.5 kb deletion in diploid F. iinumae relative to the F. vesca diploid reference genome. The deletion is absent in diploid F. mandshurica, a close relative of F. vesca. Visualized in Integrated Genome Viewer (IGV, Broad Institute).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig15: Genomic basis for biologically effective ploidy reduction. A. Site-specific ploidy reduction in one or more subgenomes is a proportional consequence of site-specific deletion within the alternate subgenomes. Site-specific ploidy may be reduced from the octoploid (8x) to the hexaploid (6x), tetraploid (4x), or diploid (2x) levels. B. Alignment of Illumina short reads to the ‘Hawaii 4’ v1.1 reference genome reveals a ~1.5 kb region of localized read depth reduction, indicative of ploidy reduction, in octoploid F. ×ananassa ‘Winter Dawn’, corresponding to the site of a ~1.5 kb deletion in diploid F. iinumae relative to the F. vesca diploid reference genome. The deletion is absent in diploid F. mandshurica, a close relative of F. vesca. Visualized in Integrated Genome Viewer (IGV, Broad Institute).
Mentions: In addition to “technical ploidy reduction”, our outcome benefitted from “biological” ploidy reduction, which derived from the fortuitous existence of localized regions of effectively reduced ploidy in an otherwise octoploid genomic context, with the ploidy reduction assumed to be the result of large or small scale insertions and deletions among subgenomes (Figure 15).Figure 15

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