1. Genes, traits, and morphs

2. Genotype Phenotype (trait) https://www.ncbi.nlm.nih.gov/nuccore

3. From gene to phenotype DNA Covered barley: Lemma and palea adhere
to seed
RNA
Other genes
Pathways
Environmental
signals
Protein

4. The 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).

5. The locus, a gene and alleles
Allelic state
Phenotype
Covered
Naked N N
Homozygous dominant
Covered is dominant to naked
The dominant allele is functional
The recessive allele is due to loss of function N n
Heterozygous n n
Homozygous recessive

6. DNA Five carbon sugar – deoxyribose Phosphate group One of four bases
Purines
Five carbon sugar – deoxyribose
Phosphate group
One of four bases
Pyrmidines

7. Nucleotide + Nucleotide + Nucleotide + ……
DNA: Polymerization
Nucleotide + Nucleotide + Nucleotide + ……

8. Transcription
mRNA (substitute u for t)
DNA
join(1..83, )

9. Translation
mRNA (substitute u for t)
Protein

10. Plant Gene Structure

11. From protein to phenotype
Covered barley:
Lemma and palea adhere
to seed
Other genes
Pathways
Environment signals
Protein

12. ERF 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 Functions and Application of the AP2/ERF Transcription Factor Family in Crop Improvement.

13. The 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.
Other genes (lipid biosynthesis)
Environmental signals
Protein

14. Monomorphism
Genetically the same, generation after generation (unless……)
Phenotypically the same, generation after generation (unless……)

15. Monomorphism to …........polymorphism
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

16. Phenotypic polymorphisms
Due to mutations
Naked Eye Polymorphism
(NEP)

17. Genotypic polymorphisms
Due to mutations
Addition, subtraction, or substitution of DNA sequence

18. Polymorphisms Genotypic
Types
Insertion/ Deletion (InDel)
Single nucleotide substitution (SNP)
(17kb) Or

19. Polymorphisms Genotypic
Wild type
Effect on phenotype
Causal
Mutant
(17kb)

20. Polymorphisms Genotypic
Wild type
Effect on phenotype
Neutral
Mutant

21. The source of polymorphisms
Mutation
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

22. The source of polymorphisms and the beginning of deliciousness…
Mutation
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

23. The source of polymorphisms
Mutation
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

24. The source of polymorphisms
Mutation
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

25. The source of polymorphisms
Mutation
The source of polymorphisms
Caused by errors in
DNA replication

26. The source of polymorphisms
Mutation
The source of polymorphisms
Caused by errors in
DNA repair in response to
errors during replication
DNA damage by mutagens

27. Mutations 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*** bp deletion, alignment

28. Mutations result from heritable changes in DNA sequence
May affect transcription, translation, and phenotype
Single nucleotide substitutions can have different consequences on phenotype
Silent
*** CTG GGA GAT TAT GGC TTT AAG***
*** CTG GGA GAT TAT GGC TTC AAG*** alignment
Leu Gly Asp Tyr Gly Phe Lys
Leu Gly Asp Tyr Gly Phe Lys translation
Missense
*** CTG GGA GAT TAT GGC TAT AAG*** alignment
Leu Gly Asp Tyr Gly Tyr Lys translation
Nonsense
*** CTG GGA GAT TAG GGC TTT AAG*** alignment
Leu Gly Asp Tyr Gly Phe Lys
Leu Gly Asp STOP translation

29. Mutations result from heritable changes in DNA sequence
May affect transcription, translation, and phenotype

30. Targeted mutations result from heritable changes in DNA sequence
May affect transcription, or translation, phenotype (target), or phenotypes (non-target)

31. The source of polymorphisms
Mutation
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

32. Mutation CRISPR Clustered regularly interspaced palindromic repeats
The tools
Target sequence
Cas enzymes (CRISPR-associated nucleases;
(e.g. Cas9)
gRNA (Guide RNA)

33. Mutation 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

34. Genes, traits, and morphs