1. Tyr Wiesner-Hanks December 12, 2014
nelson lab vocabulary
Tyr Wiesner-Hanks
December 12, 2014

2. Corn physiology
Corn has a male inflorescence on the top (the tassel) and multiple female inflorescences along the stem (the ears)
Female flowers can be pollinated with pollen from the same plant (selfing) or other plants (outcrossing)
Crossing is the act of making a controlled pollination

3. Selfing Selfing: pollinating an ear with pollen from the same plant A
Selfing repeatedly produces an inbred line with zero heterozygosity
Each generation of selfing reduces the heterozygosity in a line by 50% on average
Regions of the genome that are homozygous will remain homozygous, since the progeny can only inherit one possible allele from its parents
Areas that are heterozygous will slowly become homozygous, since there is a 50% chance that a progeny line will inherit the same copy of a given allele from its parent
First selfed generation is S1, second is S2, etc.
Takes about 5-7 generations to stabilize to inbred line A A S1 S1 S2 S2 S3
(inbred line)

4. Hybrids
Almost all corn planted in the US is hybrid seed
Cross two inbred lines, then plant the resultant seed
F1 = filial generation 1
F2 is generation made from selfing F1
Hybrids perform much better than either parent
Masking: Progeny are less likely to have two copies of a deleterious recessive allele (e.g. a mutation that results in loss of function)
Overdominance: heterozygote at a given allele is truly superior to either homozygote (e.g. two alleles could code for different forms of a protein that have unique functions)
F1’s are genetically uniform, but their progeny are not, due to recombination F2 A B F1 F1 F2 F2

5. Recombinant inbred lines
RILs = recombinant inbred lines
Self an F2 repeatedly
Resultant lines are inbreds (close to fully homozygous), but have mix of original chromosomes from parents F2 F2 A B F1 F1 F2 F2

6. Backcrossing
Backcrossing: Cross A to B, then cross the progeny back to B
Backcrossing repeatedly, then selfing produces a near isogenic line (NIL)
Mostly the recurrent parent (R), but a small introgression from the donor parent (D)
First backcrossed generation is called BC1, then BC2, etc.
Crossovers within the introgressed region
Self after backcrossing to make homozygous inbred line
It takes more generations of backcrossing/selfing than shown here… more like BC5S3. … D R F1 R
BC1 R
BC2
BC2
BC2S1

7. Nested Association Mapping (NAM)
Combination of recombinant inbred lines and association mapping
Take 200 diverse founders
Cross each of them to B73 (reference genome line)

8. Corn lines Temperate lines Tropical lines 282 Diversity panel
B73: The first maize line to be sequenced, reference genome for the species. Released by Iowa State in the 70s, used in many breeding programs. Also the common parent in NAM.
Tropical lines
CMLs: CIMMYT maize lines.
282 Diversity panel

9. Genes and such
Quantitative resistance: resistance to all races of the pathogen, conditioned by many genes
Quantitative trait locus (QTL): Any locus contributing to a quantitative trait
Single Nucleotide Polymorphism (SNP, “snip”)
Point in the genome where a single base varies between individuals (e.g. ATCGCT vs. ATCACT)
Most common genetic marker nowadays
Genotyping-by-sequencing (GBS)
Sequence portions of the genome, then look for SNPs within sequenced regions
Cheap, easy way to get 100k to millions of SNPs

10. GWAS Genome-wide association study (GWAS)
Looking for genetic markers that are associated with variation in a phenotype
For every locus: Test the null hypothesis that “the genotype at this locus has no effect on phenotype”
GWAS-specific lingo:
Manhattan plot: Plot the physical location of all SNPs versus the -log10(pvalue). A high –log10(p) → low p-value → highly significant predictor of phenotype
QQ plot: plot the observed p-values for all SNPs vs. the expected p-values. If you account for covariates, they should match up well for 99% of SNPs
Bonferroni correction: Divide the significant p-value cutoff by the number of hypothesis tests performed. Since we perform thousands-millions of tests, a p < 0.05 cutoff would still give us thousands of false positives.
False discovery rate (FDR)/Benjamini-Hochberg correction: another way to control false positives with many hypothesis tests. Less conservative than the Bonferroni correction.

11. Diseases we work on Foliar diseases Ear diseases
Northern leaf blight (NLB): caused by Setosphaeria turcica, grey-brown cigar-shaped lesions
Southern leaf blight (SLB)
Grey leaf spot (GLS)
Ear diseases
Fusarium ear rot: caused by Fusarium verticillioides, can lead to accumulation of fumonisin, a carcinogenic mycotoxin
Aspergillus ear rot: caused by Aspergillus flavus, can lead to accumulation of aflatoxin, a carcinogenic mycotoxin

12. Gene-for-gene qualitative resistance
Highly simplified model of R genes:
A pathogen starts to invade a plant
Plants recognize pathogen-associated molecular patterns (PAMPs) and fight the pathogen off
Pathogen releases effectors to suppress the host response
Plant’s R genes recognize effectors
R genes are named first (e.g. Ht1, Ht2, Ht3, HtN, …)
Pathogen races are then named for the R genes that do not recognize them
Ex: a race 1 pathogen does not have the AvrHt1 gene product, so it is not recognized by the Ht1 R gene
Pathogen race
(AVR/avr genes)
Host R genes
Race 0 (AvrHt1, AvrHt2)
Race 1
(avrHt1, AvrHt2)
Race 2
(AvrHt1, avrHt2
No R genes S
Ht1 R
Ht2
Ht1 & Ht2

13. NLB vocab NY001 (“New York 1”) 28A Phenotypes
An isolate of S. turcica taken locally
Race 1 (the race native to New York State; not recognized by Ht1)
Sequence coming soon
28A
An isolate of S. turcica taken by Gillian Turgeon’s Lab, selected because it tolerated genetic transformation protocols
Race 23N (not recognized by Ht2, Ht3, HtN)
The first S. turcica line sequenced.
Phenotypes
DLA (diseased leaf area): Percentage of leaf covered by lesions, estimated by eye on a weekly basis
IP (incubation period): Number of days between inoculation and first lesion.

14. Etc. Internal transcribed spacer (ITS): Flowering time
Portion of ribosomal RNA sequence that is later excised out
Often sequenced to ID fungal species
Flowering time
Measure of time to maturity
Typically days to anthesis- number of days after planting that 50% of row is shedding pollen

15. Other experimental terms
ELISA:
RNA-seq: Sequencing of the transcriptome (all the RNA present in the host) to quantify how highly each gene is expressed at certain conditions/times.
Histopathology: Stain different materials in different ways for microscopy. We use this to differentiate fungal/plant material and study pathogenesis.