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HORT6033 Genetic Techniques in Plant Breeding (Fall 2014)
(The course will be called Molecular Plant Breeding)
(Instructor: Ainong Shi)
Class estimate questions (Date: 08/25/2014)
Student name:
Please answer below questions as you know! If you don’t know, just answer: don’t know! Thanks!
1. What is called for the below procedure? Answer:
(Below fig from https://www.neb.com/)
2. What type of marker for below figure? Answer:
(Below image from http://www.cdfd.org.in/)
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3. Below is a type of molecular marker. What is called? Answer:
(http://learn.genetics.utah.edu/content/pharma/snips/)
4. Suppose:
Pea has two flower colors: purple and white, controlled by a major gene ‘T1’ and the purple is
dominant. Parent 1 is purple flower (T1T1) and Parent 2 white flower (t1t1).
Questions:
(1) If we make a cross between the two parents, what is the color in F1?
Color=
(2) If the F1 self-pollinated, what is the expected ratio between purple to white color plants in
the F2 population?
Purple : white =
(3) If F1 is backcrossed to Parent 1, what is the expected ratio between purple to white color
plants in BC1F1(P1) population?
Purple : white =
(4) If F1 is backcrossed to Parent 2, what is the expected ratio between purple to white color
plants in BC1F1(P2) population?
Purple : white =
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5. Below is a phylogenetic tree among 44 spinach genotypes:
Santorini
Cherokee
Polar_Bear
Bordeavx
Menoroa
Nordic_IV
Avenger
Cheetah
Falcon
Tarpy
Eagle
NSL92513
NSL65915
NSL81329
Polka
NSL68263
NSL81328
NSL37031
NSL42771
NSL40592
NSL68264
NSL92009
NSL184378
Bossanova
NSL32678
NSL184379
Bison
Regal
Bolero
Bloomsdale_Long_Standing
NSL32629
Cypress
Crocodile
NSL31384
Sardinia
Space
Denali
Coho
Greyhand
Tyee
NSL186328
Lazio
Unipack277
NSL184380
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Questions:
(1) What tools (software) can create above genetic diversity tree? Answer:
(2) See the bottom spinach line NSL184380, which spinach line is the closest one according the
genetic diversity? Answer:
(3) From the top two lines, which one, Santorini or Cherokee is closer to NSL184380 (bottom)?
Answer:
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6. What tools (software) can be used to create a genetic map like below? Just give one!
(http://www.funpecrp.com.br/gmr/year2007/vol3-6/gmr0340_full_text.html)
Answer:
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7. Below are two figures of QTL mapping. What kinds of tools (software) can be used to create
these maps? Answer:
From the two figures, which SNPs are best ones which can be used in marker-assisted selection?
Answer:
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8. Below figure is part of the procedure to develop SNP markers for Sw-5 gene of Tomato spotted
wilt virus (TSWV) resistance. What tools (software) can be used to design PCR primers? Just give
one!
Answer:
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9. Which software can create below figure? Answer:
What is this software doing? Answer:
(http://archive.gramene.org/diversity/tools.html)
10. The Sw-5 gene of tomato spotted wilt virus resistance has two alleles, Sw-5 and sw-5, where Sw5 is the resistance allele and sw-5 is the susceptible allele. We have identified and validated that
the SNP marker Sw5-snp2 is an allele-specific marker for the Sw-5 gene, which was developed
from the Sw-5 gene sequence. The SNP Sw5-snp2 has two genotypes [AA] and [GG]. Ten tomato
cultivars have been genotyped and phenotyped as below table, please fill in the below table
which gene, Sw-5 or sw-5 for each cultivar!
Tomato cultivar
Sw5snp2
TWSV
Talladega
Sophya
BHN-444
LA3667
Anahu (LA0655)
LA0656
LA1802
Royal Red
(LA2088)
Mobox
(LA2821)
Motella (LA2823)
AA
AA
AA
AA
GG
GG
GG
GG
GG
GG
R
R
R
R
S
S
S
S
S
S
Please fill which gene (Sw-5 or
sw-5) for each cultivar
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11. Suppose plant height phenotypic variation (VP) equals to 100, genetic values (VG) to 75, and
additive genetic values (VA) to 50.
Questions:
(1) What is the broad-sense heritability (HG2) of the plant height?
Answer: HG2 =
(2) What is the narrow-sense heritability (hA2) of the plant height?
Answer: hA2 =
12. Suppose a bean segregating population with the mean of 60 cM tall of the plant height and its
narrow-sense heritability (hA2) is 50%, if we select 100 plants averaged 70 cM,
Question:
What is the expected genetic gain (∆G) for selection of taller plant height?
Answer: ∆G=
13. Suppose: A SNP marker M1 [A/C] is linked to the pea color gene ‘T1’ with the recombination
rate r. In the above 1-(4) BC1F1(P2) population, the genotypes and phenotypes and their count
are below.
Questions:
(1) Write the Chi-square (χ2) formula using above count for testing M1 and T1 as a single allele:
Answer: χ2 (M1) =
Answer: χ2 (T1) =
(2) What is the recombination rate r between M1 and T1?
Answer: r =
14. If there are 100 individuals and the recombination rate r between M1 and T1 is 0.1 in above
BC1F1(P2) population, what are the expected count for the four genotypes?
ACT1t1 =
CCt1t1 =
ACt1t1 =
CCT1t1 =