Overview of research program Todd Vision Transcript/QTL mapping –Experimental design –Computational analysis Dissection of complex traits –Water use efficiency.

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

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

Maize RI population(184 markers, 4140 cM)

Bin Length Whole

N=976

Optimized

N=90

Random

N=90

Maximum 1.8 7.5 12.7

Expected 0.3 1.7 2.6

Selective mapping: QTLQTL 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.

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2

4

6

8

10

12

0.5 0.75 1 1.5 2

Additive effect

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cM)

selected

random

Genomic analysis of water use efficiency in rice and tomato

Jonathan Comstock and Susan McCouch, Cornell UniversityBjorn Martin and Chuck Tauer, Oklahoma State University

Todd Vision, University of North Carolina at Chapel HillGraham Farquhar, Australian National University

http://isotope.bti.cornell.edu/

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WUE AE

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Photosynthesis:

Transpiration:

Photosynthesis, transpiration, and WUE

Rice (Kasalath x Nipponbare) WUE QTL

-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

Duke Univ. John Willis

Fred Dietrich

Univ. of Washington Toby Bradshaw

CUGI Jeffery Tomkins

UNC Chapel HillTodd Vision

Michigan State Univ. Doug Schemske

Univ. of MontanaLila Fishman

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)

Isolation via pollinators and habitat in

M. 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

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)

Intrafamilial comparative maps

Livingstone et al 1999 Genetics 152:1183Gale & Devos 1998 PNAS 95:1972

Bell pepper (filled) and tomato (open) Cereal grains

Interfamilial comparative maps:genome duplication, gene loss, and gene

order rearrangement

Bancroft (2001) TIG 17, 89 after Ku et al (2000) PNAS 97, 9121

homology matrix for Arabidopsis

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

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