Genotype wwwpnasorg cgi doi 101073 pnas0711034105 Phenotype trait https wwwncbinlmnihgovnuccore DNA R NA Protein Covered barley Lemma and palea adhere ID: 930269
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Slide1
Genes, traits, and morphs
Slide2Genotype
www.pnas.org
#
cgi
#
doi
#
10.1073
#pnas.0711034105
Phenotype (trait)
https://
www.ncbi.nlm.nih.gov/nuccore
Slide3DNA
R
NA
Protein
Covered barley:
Lemma and
palea
adhere
t
o seed
Other genes
Pathways
Environmental
signals
From gene to phenotype
Slide4The locus, a gene,
and alleles
The
nud
locus:
Location
of the
nud
gene
,
on
barley chromosome
7H.
Alleles at this locus include
Nud
and
nud
.
The
Nud
allele is functional and the naturally-occurring
nud
allele is due to loss of function (a 17 kb deletion of DNA, including the
nud
gene).
7H
7H
Slide5Homozygous dominant
Heterozygous
Homozygous recessive
N
N
N
n
n
n
Phenotype
Covered
Covered
Naked
Allelic state
The locus,
a gene
and alleles
Covered is dominant to naked
The dominant allele is functional
The recessive allele is due to loss of function
Slide6http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/N/Nucleotides.html
DNA
Five carbon sugar – deoxyribose
Phosphate group
One of four bases
Purines
Pyrmidines
Slide7http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/N/Nucleotides.html
Nucleotide + Nucleotide + Nucleotide + ……
DNA: Polymerization
Slide8mRNA (substitute u for t)
Transcription
DNA
join(1..83,284..884)
Slide9mRNA (substitute u for t)
Translation
Protein
Slide10Plant Gene Structure
Slide11Protein
Covered barley:
Lemma and
palea
adhere
t
o seed
Other genes
Pathways
Environment signals
From protein to phenotype
Slide12ERF Transcription Factor
Transcription factors
General: Required for transcription.
Regulatory: Bind to specific DNA sequences and regulate
the expression of those sequences (genes).
Can activate or repress.
ERF = Ethylene responsive factor
Xu et al. 2011.
Functions and Application of the AP2/ERF Transcription Factor Family in Crop
Improvement.
http
://
onlinelibrary.wiley.com/doi/10.1111/j.1744-7909.2011.01062.x/full#f1
Slide13The
Nud ERF transcription factor
Regulates an unknown gene (genes) involved in a pathway leading to synthesis of
a lipid gum that causes the lemma and palea
to adhere to the seed.
Protein
Other genes (lipid biosynthesis)
Environmental signals
Slide14Monomorphism
Genetically the same, generation after generation (unless……)
Phenotypically the same, generation
after
generation (unless……)
Slide15Mono
morphism to
…........polymorph
ism
Genetically the same, generation after generation,
until a change in sequence
Phenotypically the same, generation
after generation,
until a change in sequence leads to a change in the trait
Slide16Phenotypic polymorphisms
Due to mutations
Naked Eye Polymorphism
(NEP)
Slide17Genotypic polymorphisms
Due to mutations
Addition, subtraction, or substitution of DNA sequence
Slide18Polymorphisms
Genotypic
Types
Insertion/ Deletion (
InDel
)
Single nucleotide substitution (SNP)
-------------------------------------------------------------- (17kb)
Or
Slide19Polymorphisms
Genotypic
Effect
on phenotype
Causal
Wild type
Mutant
-------------------------------------------------------------------------------------------------- (17kb)
Slide20Polymorphisms
Genotypic
Effect
on phenotype
Neutral
Wild type
Mutant
Slide21Mutation
The source of polymorphisms
Naturally occurring
Random
Rare
Usually
deleterious
The source of genetic variation
Caused by errors in
DNA replication
DNA repair
Naturally occurring color variant in hops.
Shaun Townsend, OSU
Slide22Mutation
The source of polymorphisms and the beginning of deliciousness
…
Naturally occurring
Random
Rare
Usually
deleterious
The source of genetic variation
Caused by errors in
DNA replication
DNA repair
Delicious
Red Delicious
Fuji
Slide23Mutation
The source of polymorphisms
Induced
Ionizing radiation (e.g. gamma rays)
Random BUT can target specific types of changes (e.g. deletions)
Rare BUT can manipulate frequency
Usually
deleterious
A potential source
of genetic variation
Caused by errors in
DNA replication
DNA repair
Gamma ray induced sexual variant
in hops.
Shaun
Townsend, OSU
Slide24Mutation
The source of polymorphisms
Induced
Chemicals
(e.g. ethyl
methanesulfonate
(EMS
))
Random BUT can target specific types of changes, e.g. G:C to A:T
Rare BUT can manipulate frequency (e.g. dosage)
Usually
deleterious
A potential source
of genetic variation
Caused by errors in
DNA replication
DNA repair
Slide25Mutation
The source of polymorphisms
Caused
by errors in
DNA
replication
https://
evolution.berkeley.edu
/
evolibrary/article/evo_20
Slide26Mutation
The source of polymorphisms
Caused
by errors in
DNA repair
in response to
errors during replication
DNA damage by mutagens
https://
www.ncbi.nlm.nih.gov
/books/NBK21114/#A8425
Slide27Mutations result from heritable changes
in
DNA sequence
May affect transcription, translation, and phenotype
An insertion/deletion event can produce a frameshift
*** CTG GGA GAT TAT GGC TTT AAG
*** CTG GGA TAA G codon alignment
Leu
Gly
Asp Tyr
Gly
Phe
Lys
Leu
Gly
STOP G translation
*** CTGGGAGATTATGGCTTTAAG***
*** CTGGGA - - - - - - - - - - -TAAG*** 11
bp deletion, alignment
Slide28Silent
*** CTG GGA GAT TAT GGC TT
T
AAG***
*** CTG GGA GAT TAT GGC TT
C
AAG*** alignment
Leu
Gly Asp Tyr Gly Phe
Lys
Leu
Gly
Asp Tyr
Gly
Phe
Lys translation
Missense
*** CTG GGA GAT TAT GGC TT
T AAG****** CTG GGA GAT TAT GGC TAT AAG*** alignmentLeu Gly Asp Tyr
Gly Phe LysLeu Gly Asp Tyr Gly Tyr Lys translation
Nonsense
*** CTG GGA GAT TAT GGC TT
T
AAG****** CTG GGA GAT TAG GGC TTT AAG*** alignmentLeu Gly Asp Tyr Gly Phe LysLeu Gly Asp STOP translation
Mutations result from heritable changes in DNA sequence
May affect transcription, translation, and phenotype
Single nucleotide substitutions can have different consequences on phenotype
Slide29Mutations result from heritable changes in DNA sequence
May affect transcription, translation, and phenotype
https://
ghr.nlm.nih.gov
/primer/
mutationsanddisorders
/
possiblemutations
Slide30Targeted
mutations result from heritable changes in DNA sequence
May affect transcription,
or translation,
phenotype (target), or phenotypes (non-target)
Slide31Mutation
The source of polymorphisms
CRISPR-Cas
gene editing
Target specific DNA sequences
“Knock out”
Change in function due to addition/deletion/change in sequence
A powerful source
of genetic
variation
Slide32Mutation
CRISPR
Clustered regularly interspaced palindromic repeats
The tools
Target sequence
Cas
enzymes (CRISPR-associated nucleases;
(
e.g. Cas9)
gRNA (Guide RNA)
https://
www.ncbi.nlm.nih.gov
/
pubmed
/27252719
Slide33Mutation
CRISPR
A powerful source
of genetic
variation
Parthenocarpic
(seedless) tomato
Parthenocarpy
– production of seedless fruits without fertilization
Auxin-mediated
Targeted genes associated with auxin signaling
High mutation rate
No off-target mutations
https://www.nature.com/articles/s41598-017-00501-
4
Slide34Genes, traits, and morphs