Homework # 2
Due January 21
Alleles at the Blp locus in barley determine if the mature inflorescence (the “head”) is black or
white. See http://barleyworld.org/oregonwolfe/images for pictures of the Oregon Wolfe Barley
(OWB) populations.

For this assignment, choose the n = 82 Hordeum bulbosum-derived doubled haploid
(DH) population – the “OWB Hb Phenotypes” hyperlink. These doubled haploids are
not numbered consecutively, but there are 82 of them. They were all derived from the
cross of the Dom x the Rec parent.

Plan ahead and take a few minutes to become familiar with viewing these images and
manipulating the slide show.

To complete this assignment you will need to classify the head color of each doubled
haploid as “black” or “white”. Most heads will be easy to classify in this qualitative
fashion, but a few are challenging. For the purposes of this assignment, there is no
right or wrong answer for these ambiguous heads – you just need to set objective
criteria for deciding what is black and what is white. An example is OWBHb 39.
Overall, the head looks white but some parts appear to be black. You decide what to
classify it as. Personally, I’d say white. Later in the course you’ll learn ways to assess
data quality based on haplotypes. Or you may treat these difficult-to-score-heads as
missing data and not include them in your analysis.
1. Fill in the Excel scoring sheet with the doubled haloid numbers and head colors.
Examples are provided for the first 4 doubled haploids and the two parents. Note the
challenging-to-score doubled haploid progeny on your score sheet and briefly state why
you decided they are black (or white), or indicate that you are treating them as missing
data.
2. Draw (or use Excel to make) a frequency distribution showing the number of BlpBlp
(black-headed) and blpblp (white-headed) doubled haploid progeny. Some heads may
appear to be intermediate in color. For this homework, however, every head has to be
described as black or white. In your histogram, be sure to indicate the phenotype of each
of the parents.
3. Which term best describes this frequency distribution?
a. Qualitative (Discontinuous)
b. Quantitative (Continuous)
4. How many loci do you hypothesize are responsible for determining head color in this
population?
5. Calculate a chi square to test your hypothesis regarding the number of loci that determine
head color in this population – fill in the following table. Note: Parents are NOT used for
calculating the chi square test.
Phenotype
# Observed (O)
# Expected (E)
Totals
82
82
O-E
(O-E)2/E
6. Calculated X2 = _______ ; df = _______ ; probability = _______
7. Do you accept or reject your hypothesis?
8. How many alleles are segregating at the Blp locus in this population (the parents are
completely homozygous)?
9. Briefly describe what you think is going on with the “challenging” heads. In other
words, what makes them difficult to classify.
10. Do you think that “challenging-to-score” phenotypes are unique to the Oregon Wolfe
Barley? Briefly defend your answer.