Genome mapping in salmonid fish

Transcription

1 Genome mapping in salmonid fish State of the art and perspectives Dr Karim Gharbi Kevlin/Smith Fellow in Aquatic Epidemiology and Immunogenomics

2 Milestones First microsatellite map for rainbow trout First physical map for Atlantic salmon First genetic map for coho salmon NCCCWA rainbow trout map First genetic map for rainbow trout 2 nd generation map for rainbow trout First SNP map published for Atlantic salmon 70-80s First genetic maps for Atlantic salmon First genetic map for Arctic charr INRA rainbow trout map First genetic map for brown trout Pre-genomic era SALMAP GRASP cgrasp Salmon Genome Project AquaGenome Applied Training Workshop - Stirling, 3rd December /19

3 Motivations Biomedicine Evolution Genome maps Conservation Aquaculture AquaGenome Applied Training Workshop - Stirling, 3rd December /19

4 Fact sheet Size: ~ x10 9 bp large in fish standards human genome ~ 3 x10 9 bp Chromosomes: ~ variable within species chromosome arms ~ 100 Repeat content: 20-40% highly repetitive technically challenging Evolution ancient polyploid technically challenging AquaGenome Applied Training Workshop - Stirling, 3rd December /19

5 Map units Physical distances: base pairs (kb Gb) Genetic distances: centimorgans (cm) ~ recombination frequency AquaGenome Applied Training Workshop - Stirling, 3rd December /19

6 Genetic maps ab X cd a b b a a b b a a a b b b a a b a b b a a b b a marker genotypes group order estimate distances (cm) Moen et al AquaGenome Applied Training Workshop - Stirling, 3rd December /19

7 Genetic markers Variable piece of DNA that can be used to track genetic differences among individuals Ideally highly informative, abundant, more or less evenly distributed, robust, cheap, amenable to (semi)-automated analysis May be derived from anonymous DNA (type I) or known genes (type II) SSR SNP AquaGenome Applied Training Workshop - Stirling, 3rd December /19

8 Species maps Species Reference Population Markers Type Rainbow trout Nichols et al DH (male) 1,359 AFLP, SNP, SSR Danzmann et al backcross 1,855 AFLP, SNP, SSR Guyomard et al DH (female) 903 SSR Rexroad et al outcross 1,124 SSR Atlantic salmon Danzmann et al outcross 1,671 AFLP, SNP, SSR Moen et al outcross 527 AFLP, SSR Moen et al outcross 442 SNP, SSR Brown trout Gharbi et al backcross 302 SSR Arctic charr Woram et al backcross 327 AFLP, SSR Coho salmon McClelland and Naish 2008 intercross 282 AFLP, SSR AquaGenome Applied Training Workshop - Stirling, 3rd December /19

9 Main features BT-12 Low to high density Low to medium resolution Predominantly SSR-based Large sex differences Extensive duplication Conserved between species 0.0 M01 M02 M03 M04 M05 M06 M07 M08 M09 M11 M12 M13 M14 M15 M17 M18 M20 M21 M22 M23 M24 M M01 M02 M03 M06 M07 M08 M10 M11 M12 M14 M15 M16 M17 M18 M19 M20 M21 M22 M23 M24 Gharbi et al AquaGenome Applied Training Workshop - Stirling, 3rd December /19

10 Main features Low to high density Low to medium resolution Rainbow trout Predominantly SSR-based Large sex differences Extensive duplication Conserved between species AquaGenome Applied Training Workshop - Stirling, 3rd December /19

11 Comparative maps Rainbow trout c salmon Atlantic Danzmann et al AquaGenome Applied Training Workshop - Stirling, 3rd December /19

12 QTL mapping frequency pedigree + rec cords X genetic map phenotype requency fr QTL 5 genotype A phenotype genotype B AquaGenome Applied Training Workshop - Stirling, 3rd December /19

13 Salmonid QTLs Rainbow trout growth, condition factor, temperature tolerance, spawning time, development disease resistance (viruses, parasites) smoltification Atlantic salmon growth, condition factor, maturation ti adaptive traits disease resistance (viruses, parasites) Arctic charr growth, condition factor, maturation AquaGenome Applied Training Workshop - Stirling, 3rd December /19

14 Physical maps genomic DNA fingerprinting BAC library assembly AquaGenome Applied Training Workshop - Stirling, 3rd December /19

15 Physical maps - progress Al Atlantic salmon 1 BAC library (18X, 188kb) 11.5X map published in 2005 public access via ASalBase Rainbow trout 4 BAC libraries (4.5-10X, kb) NCCCWA map (Y. Palti) due late AquaGenome Applied Training Workshop - Stirling, 3rd December /19

16 Map integration Genome Transcriptome cytogenetic map genetic map BAC libraries EST libraries SNPs Physical map SSRs AquaGenome Applied Training Workshop - Stirling, 3rd December /19

17 Technology shifts First microsatellite map for rainbow trout First physical map for Atlantic salmon First genetic map for coho salmon NCCCWA rainbow trout map First genetic map for rainbow trout 2 nd generation map for rainbow trout First SNP map published for Atlantic salmon 70-80s First genetic maps for Atlantic salmon First genetic map for Arctic charr INRA rainbow trout map First genetic map for brown trout AFLPs Microsatellites EST sequencing BAC-end sequencing SNPs SNP chips NextGen sequencing AquaGenome Applied Training Workshop - Stirling, 3rd December /19

18 Genotyping technologies Samples 100K 10K 1K 100 KASPar Sequenom Ilumina 10 Microsatellites Affymetrix K 10K 100K 500K Marker assays AquaGenome Applied Training Workshop - Stirling, 3rd December /19

19 Further resources Web links cgrasp: Salmon Genome Project: Aquaculture Genome Projects: TIGR Gene Indices: SIGENAE: g NCBI: Books Aquaculture Genome Technologies (ed Zhanjiang Liu, Blackwell Publishing) AquaGenome Applied Training Workshop - Stirling, 3rd December /19