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Overview of research program Todd Vision

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1 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

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

3 Maize RI population (184 markers, 4140 cM)
Bin Length Whole N=976 Optimized N=90 Random Maximum 1.8 7.5 12.7 Expected 0.3 1.7 2.6

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

6 Photosynthesis, transpiration, and WUE

7 Rice (Kasalath x Nipponbare) WUE QTL

8 What are the loci underlying speciation and species differentiation
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 in M. 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 in M. lewisii vs. cardinalis
lewisii F1 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%. 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 Comparative map in its simplest form is a mapping from position to position in two or more genomes Uses 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 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

18 Summary Transcript/QTL mapping Dissection of complex traits
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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