Transcript Understanding Complex Traits in Maize through Structural

Understanding Complex Traits in
Maize through Structural and
Functional Genomics
Georgia Davis
Structural genomics
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Science related to discovery of gene order
and organization across the genome.
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
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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.
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.

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
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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
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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.
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.
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– Fast plants (Brassica sp.)
– Arabidopsis
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
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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.
Round vs. wrinkled
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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.
A Molecular View
Parents
WW
ww
F1
Ww
F2 Progeny
¼WW ¼Ww ¼wW ¼ww
1: 2 : 1 Genotype = 3: 1 Phenotype
Xeroderma pigmentosa
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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.
Xeroderma pigmentosa
UV damages tissue that contains
molecules that can absorb light.
Mechanisms of UV damage
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Low penetration into tissues.
Molecular fragmentation—proteins, enzymes,
and nucleic acids contain double bonds that
can be ruptured by UV.
Free radical generation—molecules of
susceptible tissues absorb UV and eject an
electron, which is taken up by oxygen, then
termed superoxide, a free radical.
Free radicals

Are scavenged by superoxide
dismutase, vitamin C, vitamin E,
glutathione peroxidase, carotene.
Lesion mutant in maize
Mutants across organisms
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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.
Structural Genomics
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Genetic mapping
Physical mapping
In situ hybridization
Functional Genomics
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Science related to the discovery and
definition of the function of genes
C16
C18
C20
C22
C24
Aldehydes
C26
Alcohols
Wax Esters
Whole plant
Cellular
Biochemical
RNA
Functional Genomics
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Trait analysis
Gene disruption
strategies
– Targeted
– Random
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DNA microarrays
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RNA profiling
Protein chips
Protein prediction
algorithms
Functional Genomics
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Insect Resistance
– QTL Analysis
– Biochemical Pathway Identified.
– Major QTL With Unknown Function.
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Aflatoxin Reduction
– QTL Analysis
– Major QTL With Unknown Function.
– One Biochemical Pathway Identified.
Fall armyworm
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Present east of Rockies
and South of Canada.
Egg-adult in 4 weeks
One female lays several
hundred eggs.
Broad host range
Hosts of Fall Armyworm
Southwestern Corn Borer
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Narrow host range.
Mainly in southeastern US.
Southwestern Corn Borer Hosts
Germplasm
Fall armyworm damage
10 days after infestation
with 30 larvae per plant
Lepidopteran Resistance
Fall armyworm
Corn ear worm
Beet
armyworm
Southwestern corn borer
European corn borer
Juvenile traits
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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
1
2
3
4 5
6
7 8 9 gl15
27%
43%
66%
11%
10
59%
51%
7%
SWCB
FAW
Juvenility
Gl15
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Apetala2-type transcription
factor.
 Regulates long-chain wax
ester synthesis.
 Controls epidermal juvenile
to adult phase change.
Functional Genomics

Insect Resistance
– QTL Analysis
– Biochemical Pathway Identified.
– Major QTL With Unknown Function.
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Aflatoxin Reduction
– QTL Analysis
– Major QTL With Unknown Function.
– One Biochemical Pathway Identified.
Hosts of Aspergillus flavus
Aspergillus flavus
Infection via
silk channel
wounds in kernels
cracks in kernels
Aflatoxin
Aflatoxin B1
Potent carcinogen.
Associated with liver cancer
in humans.
Health concerns
Aflatoxin contamination
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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
1L
7%
unexplained
25%
D
A
2L
8%
A
3C
7%
D
6S
8%
4L
24%
4L
21%
Mp313E favorable allele
Va35 favorable allele
Anthocyanin vs. aflatoxin
a2
a1 sh2
bz2
c1-n
bz1
a2 bt pr
in1
su c2
23X  toxin
c1-p
sh bz wx
pr
c2
7X  toxin
a1
c sh wx
r-g
C2I-df
9X  toxin