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Overview of research program Todd Vision

Overview of research program Todd Vision. Transcript/QTL mapping Experimental design Computational analysis Dissection of complex traits Water use efficiency (tomato & rice) Speciation and species differences (Mimulus) Comparative genomics Analysis software Database efforts.

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Overview of research program Todd Vision

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  1. Overview of research programTodd Vision • Transcript/QTL mapping • Experimental design • Computational analysis • Dissection of complex traits • Water use efficiency (tomato & rice) • Speciation and species differences (Mimulus) • Comparative genomics • Analysis software • Database efforts

  2. Transcript/QTL mapping • Goal: optimize resolution in a linkage map • Strategy: • Genotype a larger population than needed, but only for a set of framework markers • Select a reduced sample having complementary crossovers • Outcome: • Fewer cosegregating transcript markers • QTL located with more precision • Genotyping/phenotyping reduced, controlled • MapPop software • http://www.bio.unc.edu/faculty/vision/lab/mappop

  3. Maize RI population(184 markers, 4140 cM)

  4. Selective mapping: QTL QTL mapping resolution (width of 95% confidence interval in cM) for selected versus random samples with QTL of varying additive effect size. Simulations performed for five QTL on a map of 1000 cM in selected samples of 100 (out of a base population of 500) versus random samples of 100.

  5. Genomic analysis of water use efficiency in rice and tomato Jonathan Comstock and Susan McCouch, Cornell University Bjorn Martin and Chuck Tauer, Oklahoma State University Todd Vision, University of North Carolina at Chapel Hill Graham Farquhar, Australian National University http://isotope.bti.cornell.edu/

  6. Photosynthesis, transpiration, and WUE Photosynthesis: Transpiration:

  7. Rice (Kasalath x Nipponbare) WUE QTL

  8. What are the loci underlying speciation and species differentiation?- What is the origin of the incompatible alleles?- What evolutionary forces have shaped them? the genus Mimulus

  9. Univ. of Washington Toby Bradshaw Michigan State Univ. Doug Schemske Duke Univ. John Willis Fred Dietrich CUGI Jeffery Tomkins Univ. of Montana Lila Fishman UNC Chapel Hill Todd Vision

  10. Hybrid sterility inM. guttatus vs. nasutus • Minor QTL • Differences in floral morphology • Major QTL • a pair of epistatically interacting nuclear loci that cause complete pollen sterility in 1/8 of the hybrid F2 offspring • A cytonuclear incompatibility system causes complete male sterility in 1/4 of offspring carrying the M. guttatus cytoplasm M. nasutus growing in a mixed clump with M. guttatus in Shirley Creek, Calaveras Co, California. The red lines indicate M. nasutus flowers (photo: Mark MacNair)

  11. Isolation via pollinators and habitat inM. lewisii vs. cardinalis • Two major QTL underlying differences in pollination syndrome have been mapped • Introgression of the anthocyanin QTL (yup) from M. cardinalis into M. lewisii reduces bee visitation by 80%. • Allelic substitution from M. lewisii into M. cardinalis at the major nectar QTL (NEC1) reduces hummingbird visitation by 50%. lewisii F1 cardinalis F2

  12. From QTL to gene in Mimulus • Tools for positional cloning (or, making a model species out of a schlep species) • Nearly isogenic lines (to Mendelize QTL) • Expressed sequence tags (cDNA sequences) • Polymorphic markers (SSR, SNP) • Comparative maps (e.g. to tomato & Arabidopsis) • Large-insert clones (BAC libraries) • Transformation technology (to test candidate clones)

  13. Intrafamilial comparative maps Bell pepper (filled) and tomato (open) Cereal grains Gale & Devos 1998 PNAS 95:1972 Livingstone et al 1999 Genetics 152:1183

  14. Interfamilial comparative maps:genome duplication, gene loss, and gene order rearrangement Bancroft (2001) TIG 17, 89 after Ku et al (2000) PNAS 97, 9121

  15. homology matrix for Arabidopsis

  16. Comparative genomics:Analysis software • FISH: Fast Identification of Segmental Homology • http://www.bio.unc.edu/faculty/vision/lab/FISH • Identification • Dynamic programming provides speed and optimality guarantee • Can be generalized to multiple alignments • Statistical assessment • Null model of duplication and transposition • Closed-form equation for calculating p-values (i.e. no permutation testing) • eAssembler: Reconstruction of ancestral genomes for remote comparative mapping

  17. Summary • Transcript/QTL mapping • Selective mapping • MapPop • Dissection of complex traits • Water use efficiency (tomato & rice) • Speciation and species differences (Mimulus) • Comparative genomics • FISH, eAssembler • Phytome

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