Overview of research program Todd Vision

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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

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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

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Maize RI population(184 markers, 4140 cM)
Bin Length Whole N976 Optimized N90 Random N90
Maximum 1.8 7.5 12.7
Expected 0.3 1.7 2.6
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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.
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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/
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Photosynthesis, transpiration, and WUE
Photosynthesis Transpiration
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Rice (Kasalath x Nipponbare) WUE QTL
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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
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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
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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)
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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
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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)

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Intrafamilial comparative maps
Bell pepper (filled) and tomato (open)
Cereal grains
Gale Devos 1998 PNAS 951972
Livingstone et al 1999 Genetics 1521183
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Interfamilial comparative mapsgenome
duplication, gene loss, and gene order
rearrangement
Bancroft (2001) TIG 17, 89 after Ku et al (2000)
PNAS 97, 9121
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homology matrix for Arabidopsis
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Comparative genomicsAnalysis 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

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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