Potato Genome Project Structural Genomics 2.Functional Genomics

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Presentation transcript:

Potato Genome Project Structural Genomics 2.Functional Genomics Generation of a comprehensive genomic resource of Solanaceae resistance (R) gene sequences of wild potato, tomato and pepper genomes (the SOLAR database) 2.Functional Genomics Generation of a comprehensive functional genomic resource composed of expression profiles of significant points in growth, development and response to abiotic and biotic stresses, and a set of functionally defined genes identified through virus-induced gene silencing to be involved in host response to pathogens 3.Outreach A training program for high school and college students to teach applications of bioinformatics and data mining for marker development for potato breeding for crop improvement

Synteny between Solanaceae Genomes 1 2 3 4 5 6 7 8 9 10 11 12 The Solanaceae share highly conserved genomes Chromosome number and organization Genome sequence Sequence and function of gene location and resistance hotspot location Potato 1 2 3 4 5 6 7 8 9 10 11 12 Pepper 1 2 3 4 5 6 7 8 9 10 11 12 Tomato Resistance hotspots

Chromosome 5 Resistance Region Potato R1, phyt3, Pi1,Nb, Rx2, Gpa, Grp GP21 GP179 Tomato Bs4 GP21 GP179

S. demissum is an allo-hexaploid Chromosome #5 5A 5B 5C R1, phyt3, Pi1,Nb, Rx2, Gpa, Grp

S.demissum Chromosome 5 Resistance Region R1, phyt3, Pi1, Nb, Rx2, Gpa, Grp Chromosome #5 GP21 132D05 GP179 132D05 GP179 8~12 BACs per genome ~0.5Mb per genome R1 GP179 SPUD237 132D05S GP21 A B C Haplotype Sd_Bs4 R1 Sd_Prf

S.demissum Chromosome 11 Resistance Region Potato I phyt3 L, cmv1, phyt3 I2 Tomato Pepper RMcl, Ry, Na, Sen1, R3a, R3b, R5, R6, R7, R8, R9, R10, phyt7

S. demissum is hexaploid Chromosome #11 11A 11B 11C RMcl, Ry, Na, Sen1, N R3a, R3b, R5, R6, R7, R8, R9, R10, phyt7

S.demissum Chromosome 11 Resistance Region RMcl, Ry, Na, Sen1, Chromosome #11 193I9R 56F6R 39E18F A Haplotype B

S.demissum Chromosome 11 Resistance Region R3a, R3b, R5, R6, R7, R8, R9, R10, phyt7 Chromosome #11 381T 373T 51S 11~16 BACs 1.5Mb 381T 373T 381T TG105 373T A Haplotype B C

S.demissum Chromosome 11 Resistance Region R3a, R3b, R5, R6, R7, R8, R9, R10, phyt7 Chromosome #11 381T 373T 51S 12~16 BACs ~1.5Mb 373T 51S GP185 373T 51S A Haplotype B C

Distance tree for all I2/R3 homologues from the MLB locus 6 5 1 100 100 4 100 100 100 100 3 0.1 substitution/site 2 GP185 region GP250 region