01af196a37b7ea2a38f2684ee81ff471 pmc_9866729.pdf 362dd997edf343b9918d673f1e055976ab67c493 pmc_9866729.pdf 940acc8de8cf562f084f56a1e093dfa174b72efe586004b18b971feb3560bb17 pmc_9866729.pdf Title: Development and Evaluation of an AxiomTM 60K SNP Array for Almond (Prunus dulcis) Subject: A high-density single nucleotide polymorphism (SNP) array is essential to enable faster progress in plant breeding for new cultivar development. In this regard, we have developed an Axiom 60K almond SNP array by resequencing 81 almond accessions. For the validation of the array, a set of 210 accessions were genotyped and 82.8% of the SNPs were classified in the best recommended SNPs. The rate of missing data was between 0.4% and 2.7% for the almond accessions and less than 15.5% for the few peach and wild accessions, suggesting that this array can be used for peach and interspecific peach almond genetic studies. The values of the two SNPs linked to the RMja (nematode resistance) and SK (bitterness) genes were consistent. We also genotyped 49 hybrids from an almond F2 progeny and could build a genetic map with a set of 1159 SNPs. Error rates, less than 1%, were evaluated by comparing replicates and by detection of departures from Mendelian inheritance in the F2 progeny. This almond array is commercially available and should be a cost-effective genotyping tool useful in the search for new genes and quantitative traits loci (QTL) involved in the control of agronomic traits. Keywords: Prunus dulcis; Prunus persica; SNP; Axiom array; genotyping Author: Henri Duval, Eva Coindre, Sebastian E. Ramos-Onsins, Konstantinos G. Alexiou, Maria J. Rubio-Cabetas, Pedro J. Martínez-García, Michelle Wirthensohn, Amit Dhingra, Anna Samarina and Pere Arús Creator: LaTeX with hyperref Producer: pdfTeX-1.40.21 CreationDate: Wed Jan 11 11:21:56 2023 CET ModDate: Wed Jan 11 11:31:22 2023 CET Tagged: no UserProperties: no Suspects: no Form: none JavaScript: no Pages: 12 Encrypted: no Page size: 595.276 x 841.89 pts (A4) Page rot: 0 File size: 1632900 bytes Optimized: no PDF version: 1.7 name type encoding emb sub uni object ID ------------------------------------ ----------------- ---------------- --- --- --- --------- LPYGPS+VnURWPalladioL-Bold Type 1 Custom yes yes no 10 0 OCHYOC+VnURWPalladioL Type 1 Custom yes yes no 15 0 ZSHPUF+URWPalladioL-Bold Type 1 Custom yes yes no 19 0 EOGGUQ+URWPalladioL-Roma Type 1 Custom yes yes no 24 0 RXZLUB+URWPalladioL-Ital Type 1 Custom yes yes no 28 0 GAFJBD+URWPalladioL-BoldItal Type 1 Custom yes yes no 32 0 VBAQIR+CMSY10 Type 1 Builtin yes yes no 36 0 VTLKDP+TimesNewRomanPS-BoldItalicMT Type 1C WinAnsi yes yes no 55 0 EOGGPH+PalatinoLinotype,Bold TrueType WinAnsi yes yes no 95 0 EOGGPJ+PalatinoLinotype TrueType WinAnsi yes yes no 98 0 EOGGPL+PalatinoLinotype,Italic TrueType WinAnsi yes yes no 101 0 EOGGPH+PalatinoLinotype,Bold TrueType WinAnsi yes yes no 113 0 EOGGPJ+PalatinoLinotype TrueType WinAnsi yes yes no 116 0 EOGGPL+PalatinoLinotype,Italic TrueType WinAnsi yes yes no 119 0 EOGGPH+PalatinoLinotype,Bold TrueType WinAnsi yes yes no 158 0 EOGGPJ+PalatinoLinotype TrueType WinAnsi yes yes no 161 0 EOGGPL+PalatinoLinotype,Italic TrueType WinAnsi yes yes no 164 0 MKHHVF+EURB10 Type 1 Builtin yes yes no 185 0 EOGGPH+PalatinoLinotype,Bold TrueType WinAnsi yes yes no 202 0 EOGGPJ+PalatinoLinotype TrueType WinAnsi yes yes no 205 0 EOGGPL+PalatinoLinotype,Italic TrueType WinAnsi yes yes no 208 0 OVNEXW+EURM10 Type 1 Builtin yes yes no 215 0 Jhove (Rel. 1.22.1, 2019-04-17) Date: 2023-10-19 02:23:29 CEST RepresentationInformation: pmc_9866729.pdf ReportingModule: PDF-hul, Rel. 1.12.1 (2019-04-17) LastModified: 2023-01-26 02:11:26 CET Size: 1632900 Format: PDF Version: 1.7 Status: Well-Formed and valid SignatureMatches: PDF-hul MIMEtype: application/pdf PDFMetadata: Objects: 400 FreeObjects: 1 IncrementalUpdates: 0 DocumentCatalog: PageLayout: SinglePage PageMode: UseNone Outlines: Item: Title: Introduction Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@262b2c86 Item: Title: Results Discussion Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@371a67ec Children: Item: Title: Array Design Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@5ed828d Children: Item: Title: SNPs Array Selection Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@50d0686 Item: Title: Distribution of Array SNPs Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@7a3d45bd Item: Title: Validation of the Axiom 60K Almond Array Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@1e7c7811 Children: Item: Title: Validation of the Array on the Diversity Panel Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@77ec78b9 Item: Title: Validation of the Three Additional SNPs Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@1a3869f4 Item: Title: Validation of the Array with a F2 Progeny Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@a38d7a3 Item: Title: Evaluation of the Error Rates in Different Analyses Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@77f99a05 Children: Item: Title: Comparison of “Texas” Genotyping with the “Texas” Reference Genome Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@63440df3 Item: Title: Comparison of Array Data from Three Replicates of the “Ferrastar” Variety Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@3aeaafa6 Item: Title: Comparison between Expected and Observed Homozygote F2 Data Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@76a3e297 Item: Title: Materials and Methods Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@4d3167f4 Children: Item: Title: Plant Material Resequenced Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@ed9d034 Item: Title: SNP Calling and Selection of SNPs for Array Development Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@6121c9d6 Item: Title: Plant Material for the 60K SNP Array Validation Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@87f383f Item: Title: Genotyping and SNP Analysis Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@4eb7f003 Item: Title: Conclusions Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@eafc191 Item: Title: References Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@612fc6eb Info: Title: Development and Evaluation of an AxiomTM 60K SNP Array for Almond (Prunus dulcis) Author: Henri Duval, Eva Coindre, Sebastian E. Ramos-Onsins, Konstantinos G. Alexiou, Maria J. Rubio-Cabetas, Pedro J. Martínez-García, Michelle Wirthensohn, Amit Dhingra, Anna Samarina and Pere Arús Subject: A high-density single nucleotide polymorphism (SNP) array is essential to enable faster progress in plant breeding for new cultivar development. In this regard, we have developed an Axiom 60K almond SNP array by resequencing 81 almond accessions. For the validation of the array, a set of 210 accessions were genotyped and 82.8% of the SNPs were classified in the best recommended SNPs. The rate of missing data was between 0.4% and 2.7% for the almond accessions and less than 15.5% for the few peach and wild accessions, suggesting that this array can be used for peach and interspecific peach almond genetic studies. The values of the two SNPs linked to the RMja (nematode resistance) and SK (bitterness) genes were consistent. We also genotyped 49 hybrids from an almond F2 progeny and could build a genetic map with a set of 1159 SNPs. Error rates, less than 1%, were evaluated by comparing replicates and by detection of departures from Mendelian inheritance in the F2 progeny. This almond array is commercially available and should be a cost-effective genotyping tool useful in the search for new genes and quantitative traits loci (QTL) involved in the control of agronomic traits. 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