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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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IntegratedPHR-SNP linkage map of allo-octoploid strawberry using the ‘Holiday’ × ‘Korona’ family (n = 75). A total of 6,593 markers were placed on this map. Linkage groups are named according to Van Dijk et al. [38]. Large gaps mostly coincide with homozygous regions as revealed by SSR-haplotype profiles [38]).
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Fig11: IntegratedPHR-SNP linkage map of allo-octoploid strawberry using the ‘Holiday’ × ‘Korona’ family (n = 75). A total of 6,593 markers were placed on this map. Linkage groups are named according to Van Dijk et al. [38]. Large gaps mostly coincide with homozygous regions as revealed by SSR-haplotype profiles [38]).

Mentions: Removing the data from the four above-mentioned offspring and another 102 SNPs that were easily identified as causing major problems in mapping gave 6,594 mapped PHR SNPs (Additional file 10), which resulted in a genetic map of 2,050 cM, accounting for 82% of the initial 8,084 PHR SNP that were polymorphic in HK. The genetic length of the individual linkage groups varied greatly (Figure 11). The mapped SNPs showed an uneven distribution across the subgenomes as most markers were from subgenome A, followed by B (Figure 11, Table 5). Overall, subgenomes C and D had the least number of markers, except in LG6C & 6D (Table 5). This general pattern was in accordance with commonalities in the approaches for subgenome assignment and that for designing SNPs, as both used F. vesca genomic sequences as a reference. Subgenomes A to D were distinguished by decreasing similarity to the F. vesca genomic sequences as revealed by decreasing amplification efficiency of F. vesca-based SSR markers [38]. Design of the array SNP markers included a step of aligning re-sequencing data to the published F. vesca genome sequence. Consequently, subgenomes C and D were expected to have the largest sequence divergence to F. vesca based on SSR data, and were thus expected to have a lower proportion of their re-sequenced fragments aligned to the reference genome sequence, which would lead to reduced representation of corresponding SNP markers.Figure 11


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)

IntegratedPHR-SNP linkage map of allo-octoploid strawberry using the ‘Holiday’ × ‘Korona’ family (n = 75). A total of 6,593 markers were placed on this map. Linkage groups are named according to Van Dijk et al. [38]. Large gaps mostly coincide with homozygous regions as revealed by SSR-haplotype profiles [38]).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig11: IntegratedPHR-SNP linkage map of allo-octoploid strawberry using the ‘Holiday’ × ‘Korona’ family (n = 75). A total of 6,593 markers were placed on this map. Linkage groups are named according to Van Dijk et al. [38]. Large gaps mostly coincide with homozygous regions as revealed by SSR-haplotype profiles [38]).
Mentions: Removing the data from the four above-mentioned offspring and another 102 SNPs that were easily identified as causing major problems in mapping gave 6,594 mapped PHR SNPs (Additional file 10), which resulted in a genetic map of 2,050 cM, accounting for 82% of the initial 8,084 PHR SNP that were polymorphic in HK. The genetic length of the individual linkage groups varied greatly (Figure 11). The mapped SNPs showed an uneven distribution across the subgenomes as most markers were from subgenome A, followed by B (Figure 11, Table 5). Overall, subgenomes C and D had the least number of markers, except in LG6C & 6D (Table 5). This general pattern was in accordance with commonalities in the approaches for subgenome assignment and that for designing SNPs, as both used F. vesca genomic sequences as a reference. Subgenomes A to D were distinguished by decreasing similarity to the F. vesca genomic sequences as revealed by decreasing amplification efficiency of F. vesca-based SSR markers [38]. Design of the array SNP markers included a step of aligning re-sequencing data to the published F. vesca genome sequence. Consequently, subgenomes C and D were expected to have the largest sequence divergence to F. vesca based on SSR data, and were thus expected to have a lower proportion of their re-sequenced fragments aligned to the reference genome sequence, which would lead to reduced representation of corresponding SNP markers.Figure 11

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