Understanding Complex Traits in Maize through Structural and Functional Genomics

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Understanding Complex Traits in Maize through
Structural and Functional Genomics

• Georgia Davis

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Structural genomics

• Science related to discovery of gene order and
  organization across the genome.

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Mutation

• Changes in DNA sequence lead to
• Changes in amino acid sequence lead to
• Changes in protein or lack of protein.

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Allele

• One of two to many alternative forms of the same
  gene (eg., round allele vs. wrinkled allele).
• Alleles have different DNA sequences that cause
  the different appearances we see.

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Mendel

• Monk at the St. Thomas monastery in the Czech
  Republic.
• Performed several experiments between 1856 and
  1863 that were the basis for what we know about
  heredity today.
• Used garden peas for his research.
• Published his work in 1866.

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Mendel

• Results are remarkably accurate and some have
  said they were too good to be unbiased.
• His papers were largely ignored for more than 30
  years until other researchers appreciated its
  significance.

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Garden Pea

• Pisum sativum
• Diploid
• Differed in seed shape, seed color, flower color,
  pod shape, plant height, etc.
• Each phenotype Mendel studied was controlled by a
  single gene.

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Terms

• Wild-type is the phenotype that would normally be
  expected.
• Mutant is the phenotype that deviates from the
  norm, is unexpected but heritable.
• Notice that this definition does not imply that
  all mutants are bad in fact many beneficial
  mutations have been selected by plant breeders.

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Advantages of plants

• Can make controlled hybrids.
• Less costly and time consuming to maintain than
  animals.
• Can store their seed for long periods of time.
• One plant can produce tens to hundreds of progeny.

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Advantages of plants

• Can make inbreds in many plant species without
  severe effects that are typically seen in
  animals.
• Generation time is often much less than for
  animals.
• Fast plants (Brassica sp.)
• Arabidopsis

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Round vs. wrinkled

• The SBEI causes the round vs. wrinkled phenotype.
• SBEI starch-branching enzyme
• Wrinkled peas result from absence of the branched
  form of starch called amylopectin.
• When dried round peas shrink uniformly and
  wrinkled do not.

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Round vs. wrinkled

• The non-mutant or wild-type round allele is
  designated W.
• The mutant, wrinkled allele is designated w.
• Seeds that are Ww have half the SBEI of wild-type
  WW seeds but this is enough to make the seeds
  shrink uniformly.
• W is dominant over w.

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Round vs. wrinkled

• An extra DNA sequence is present in the wrinkled
  allele that produces a non-functional SBEI and
  blocks the starch synthesis pathway at this step
  resulting in a lack of amylopectin.

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A Molecular View
Parents
F1
F2 Progeny
WW ww Ww ¼WW ¼Ww ¼wW ¼ww
1 2 1 Genotype 3 1 Phenotype
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Xeroderma pigmentosa

• Autosomal recessive.
• UV exposure damages DNA.
• Defect in DNA damage repair.
• Risks include cancer, telangiectasia,
  disfigurement.
• Can be diagnosed before birth.
• Take total protection measures from
  sun/fluorescent light.

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Xeroderma pigmentosa
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UV damages tissue that contains molecules that
can absorb light.
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Mechanisms of UV damage

• Low penetration into tissues.
• Molecular fragmentationproteins, enzymes, and
  nucleic acids contain double bonds that can be
  ruptured by UV.
• Free radical generationmolecules of susceptible
  tissues absorb UV and eject an electron, which is
  taken up by oxygen, then termed superoxide, a
  free radical.

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Free radicals

• Are scavenged by superoxide dismutase, vitamin C,
  vitamin E, glutathione peroxidase, carotene.

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Lesion mutant in maize
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(No Transcript)
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Mutants across organisms

• Sometimes mutations in the same gene in different
  organisms have similar phenotype.
• This allows researchers to choose the organism
  with the best genetic resources to study the
  normal function of that gene.
• This also allows researchers to identify
  prospective genes for a phenotype in one species,
  based on another.

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Structural Genomics

• Genetic mapping
• Physical mapping
• In situ hybridization

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Functional Genomics

• Science related to the discovery and definition
  of the function of genes

C16
C18
C20
C22
C24
C26
Aldehydes
Alcohols
Wax Esters
RNA
Whole plant
Cellular
Biochemical
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Functional Genomics

• Trait analysis
• Gene disruption strategies
• Targeted
• Random
• DNA microarrays

• RNA profiling
• Protein chips
• Protein prediction algorithms

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Functional Genomics

• Insect Resistance
• QTL Analysis
• Biochemical Pathway Identified.
• Major QTL With Unknown Function.
• Aflatoxin Reduction
• QTL Analysis
• Major QTL With Unknown Function.
• One Biochemical Pathway Identified.

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Fall armyworm

• Present east of Rockies and South of Canada.
• Egg-adult in 4 weeks
• One female lays several hundred eggs.
• Broad host range

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Hosts of Fall Armyworm
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Southwestern Corn Borer

• Narrow host range.
• Mainly in southeastern US.

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Southwestern Corn Borer Hosts
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Germplasm
Fall armyworm damage 10 days after
infestation with 30 larvae per plant
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Lepidopteran Resistance
Beet armyworm
Corn ear worm
Fall armyworm
Southwestern corn borer
European corn borer
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Juvenile traits

• Dull epicuticular wax layer
• Fatty alcohols
• No leaf hairs
• Adventitious roots present
• No buliforme cells
• Cells are rounded

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Juvenile vs. Adult Leaves

• Leaves maintain their phase status throughout
  development.
• Number of juvenile leaves varies among inbreds.
• A number of mutants in juvenile to adult phase
  change have been identified.

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Summary of QTL Study
gl15
1
2
3
4
6
7
8
9
10
5
27
11
59
43
66
51
7
SWCB
FAW
Juvenility
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Gl15

• Apetala2-type transcription
• factor.
• Regulates long-chain wax
• ester synthesis.
• Controls epidermal juvenile
• to adult phase change.

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Functional Genomics

• Insect Resistance
• QTL Analysis
• Biochemical Pathway Identified.
• Major QTL With Unknown Function.
• Aflatoxin Reduction
• QTL Analysis
• Major QTL With Unknown Function.
• One Biochemical Pathway Identified.

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Hosts of Aspergillus flavus
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Aspergillus flavus
Infection via silk channel wounds in
kernels cracks in kernels
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Aflatoxin
Aflatoxin B1

• Potent carcinogen.
• Associated with liver cancer
• in humans.

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Health concerns
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Aflatoxin contamination

• Large environmental influence.
• Drought stress increases aflatoxin level.
• Correct genes in both fungus and host required
  for high levels of toxin formation.
• Synthesis is biochemically similar to anthocyanin
  biosyntheis in maize.

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Aflatoxin QTL Summary
D
A
A
D
Mp313E favorable allele
Va35 favorable allele
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Anthocyanin vs. aflatoxin
c1-n
a2
bz2
a1 sh2
a2 bt pr
in1
su c2
bz1
23X ? toxin
c1-p
pr
sh bz wx
c2
7X ? toxin
a1
9X ? toxin
C2I-df
r-g
c sh wx