Fruitbreedomics, Angers (F) 28.03.11   The apple genome sequence:  summary, updates and developments WP6: Development of m...
SNP genotyping at FEM-IASMA <ul><li>2,084 SNPs derived from a preliminary (5x) Golden D. genome assembly </li></ul><ul><li...
SNP transferability 8 genes 119 M. domestica cvs. T SNP  = 14.8% T SNP  (MAF >0.1) =  30.2%  <ul><li>209 selected and mapp...
LD in apple <ul><li>235 SNPs from 6 regions (on 5 chrom) on 304 cultivars. </li></ul><ul><li>LD (r 2 ) decays below 0.2 at...
Genetic structure in  Malus 27 SSRs on 150 accessions M. domestica M. sieversii M. sylvestris Displayed only diploids Clus...
Approach / Methodology <ul><li>Beadexpress </li></ul><ul><ul><li>Goldengate techn. (96 to 384) </li></ul></ul><ul><li>iSca...
Objectives <ul><li>D6.1 low density apple genotyping (384 SNPs) </li></ul><ul><ul><li>384 SNPs array available (4 th  mont...
Interactions planned with other WPs <ul><li>Task T6.1 Development of low-density chip (384 SNPs) </li></ul><ul><ul><li>WP4...
Partners involved <ul><li>Task T6.1 FEM (I) </li></ul><ul><ul><li>INRA Angers (F) </li></ul></ul><ul><li>Task T6.2 FEM (I)...
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FruitBreedomics KOM 29 03-2011 8 WP6 presentation

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  • 1) The crude estimated of SNP transferability = the heterozygous state of a SNP from one cultivar to another, within M. domestica, was Tsnp = 14.8%, derived from crude amplicon re-sequencing. However, a simple selection for SNP with MAF &gt; 0.1 enabled to obtain Tsnp = 30.2% 2) a similar results was obtained based on a set of 209 SNPs Golden D SNPs selected also to be polymorphich across apple EST databases. In this case Tsnp = 40.9% etc.
  • FruitBreedomics KOM 29 03-2011 8 WP6 presentation

    1. 1. Fruitbreedomics, Angers (F) 28.03.11 The apple genome sequence: summary, updates and developments WP6: Development of marker/gene arrays for high-throughput genotyping Riccardo Velasco, FEM-IASMA (I)
    2. 2. SNP genotyping at FEM-IASMA <ul><li>2,084 SNPs derived from a preliminary (5x) Golden D. genome assembly </li></ul><ul><li>1,632 combined in 34 SNPlex sets of 48 SNP markers each </li></ul><ul><li>4 SNPlex sets at once (192 markers) on 184 individuals (using 2 x 384 well plates) </li></ul><ul><li>Ca. 36,000 genotypes per day </li></ul>SNP mining in the Golden D genome sequence Coding regions of Golden Delicious = 1/227 bp 1/52 a whole genome estimate, a genic region estimate is less polymorphic Freedom Evo LiHa with Tecan 96 multi-channel pipetting head (TeMO) Platform
    3. 3. SNP transferability 8 genes 119 M. domestica cvs. T SNP = 14.8% T SNP (MAF >0.1) = 30.2% <ul><li>209 selected and mapped SNPs </li></ul><ul><li>185 accessions </li></ul><ul><li>123 M. domestica cvs </li></ul>40.9% 25.1% 7.2% Micheletti et al 2011 Genetic diversity of the genus Malus… TGG in press 1) 2) T SNP T SNP
    4. 4. LD in apple <ul><li>235 SNPs from 6 regions (on 5 chrom) on 304 cultivars. </li></ul><ul><li>LD (r 2 ) decays below 0.2 at approx. 50 kb . Therefore, to carry out genome wide association, a reasonable estimation is at least one informative SNP every 10 kb (>= 75,000 SNPs or, similarly, 1-2 SNP per gene ). </li></ul><ul><li>however </li></ul><ul><li>A 50k SNP chip can probably work in many situations if germplasm collections are not too diverse </li></ul>Micheletti, Salvi et al, in preparation.
    5. 5. Genetic structure in Malus 27 SSRs on 150 accessions M. domestica M. sieversii M. sylvestris Displayed only diploids Cluster analysis by DICE/UPGMA STRUCTURE (K =2-8) Micheletti, Salvi et al, in preparation. 2 3 4 5 6 7 8 K = Old cultivars M. sieversii M. sylvestris Modern cultivars
    6. 6. Approach / Methodology <ul><li>Beadexpress </li></ul><ul><ul><li>Goldengate techn. (96 to 384) </li></ul></ul><ul><li>iScan genotyper </li></ul><ul><ul><li>Goldengate techn. (1,536) </li></ul></ul><ul><ul><li>Infinium techn. (3k to 200k) </li></ul></ul><ul><li>HiScan genotyper/sequencer </li></ul><ul><ul><li>Infinium techn. (up to 200k) </li></ul></ul><ul><ul><li>Sequencing (50 to 200 Gb) </li></ul></ul>
    7. 7. Objectives <ul><li>D6.1 low density apple genotyping (384 SNPs) </li></ul><ul><ul><li>384 SNPs array available (4 th month) </li></ul></ul><ul><li>D6.2/D6.3 medium density arrays (3-9K SNPs) </li></ul><ul><ul><li>SNP list based on apple resequencing projects (12 th month) </li></ul></ul><ul><ul><li>Medium density apple 3-9K SNPs array (12 th month) </li></ul></ul><ul><ul><li>Medium density peach 3-9K SNPs array (12 th month) </li></ul></ul><ul><li>D6.4 high density apple genotyping (50K(?) SNPs) </li></ul><ul><ul><li>Final LD extension analysis in apple (18 th month) </li></ul></ul><ul><ul><li>First draft of high density apple array (18 th month) </li></ul></ul><ul><ul><li>First draft of high density peach array (18 th month) </li></ul></ul><ul><ul><li>GWA genotyping array (based on LD extension) (24 th month) </li></ul></ul><ul><li>D6.5 protocols for MAB </li></ul><ul><ul><li>Final update for MAB protocols (36 th month) </li></ul></ul>
    8. 8. Interactions planned with other WPs <ul><li>Task T6.1 Development of low-density chip (384 SNPs) </li></ul><ul><ul><li>WP4 for apple germplasm survey </li></ul></ul><ul><li>Task T6.2 Development of medium chip (3-9K SNPs) </li></ul><ul><ul><li>WP3 for characterization of genotypes </li></ul></ul><ul><li>Task T6.3 development of high density chip (50 to 200K SNPs, depending on LD) </li></ul><ul><ul><li>WP4 for GWA of core collections </li></ul></ul><ul><li>Task T6.4 New marker techology for MAB </li></ul><ul><ul><li>WP1 implementation of MAB protocols </li></ul></ul><ul><ul><li>WP2 preparation of pre-breeding material </li></ul></ul>
    9. 9. Partners involved <ul><li>Task T6.1 FEM (I) </li></ul><ul><ul><li>INRA Angers (F) </li></ul></ul><ul><li>Task T6.2 FEM (I) </li></ul><ul><ul><li>PFR New Zealand (NZ) </li></ul></ul><ul><ul><li>WSU Washington State University (USA) </li></ul></ul><ul><li>Task T6.3 FEM (I) </li></ul><ul><ul><li>INRA Angers (F) </li></ul></ul><ul><ul><li>WSU Washington State University (USA) </li></ul></ul><ul><ul><li>IRTA Barcellona (E) </li></ul></ul><ul><ul><li>PFR New Zealand (NZ) </li></ul></ul><ul><li>Task T6.4 FEM (I) </li></ul><ul><ul><li>INRA Angers (F) </li></ul></ul><ul><ul><li>EVD Waedensville (CH) </li></ul></ul>

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