Fall 2014
HORT6033
Molecular
Plant Breeding
INSTRUCTOR: AINONG SHI
HORT6033 web site: http://comp.uark.edu/~ashi/MB
Fall 2014 HORT6033
Molecular Plant Breeding
Lecture 6 (09/10/2014)
I. Mendel genetics
II.Example
III.Research Project
IV.Homework
V.Questions
Mendel Genetics
• Genetics is the study of genes.
• Inheritance is how traits, or
characteristics, are passed on from
generation to generation.
• Chromosomes are made up of genes,
which are made up of DNA
• Arrangement of nucleotides in DNA
• DNA  RNA  Proteins
• Genetic material (genes,chromosomes,
DNA) is found inside the nucleus of a
cell.
Biology Junction
Gene – a unit of heredity; a section of DNA
sequence encoding a single protein
Genome – the entire set of genes in an organism
Alleles – two genes that occupy the same
position on homologous chromosomes and that
cover the same trait (like ‘flavors’ of a trait), such
as Sw-5 and sw-5 of tomato spotted wilt virus
resistance.
Locus – a fixed location on a strand of DNA
where a gene or one of its alleles is located.
Genotype – the genetic makeup of an organisms,
Such as Sw5Sw5
Phenotype – the physical appearance
of an organism (Genotype + environment)
Such as Tomato spotted wilt virus resistace
Monohybrid cross: a genetic cross involving a
single pair of genes (one trait); parents differ by a
single trait.
P = Parental generation
F1 = First filial generation; offspring from a
genetic cross.
F2 = Second filial generation of a genetic cross
Homozygous – having identical genes (one
from each parent) for a particular
characteristic such as Sw-5Sw-5
Heterozygous – having two different genes for
a particular characteristic, such as Sw-5sw-5.
Dominant – the allele of a gene that masks or
suppresses the expression of an alternate
allele; the trait appears in the heterozygous
condition.
Recessive – an allele that is masked by a
dominant allele; does not appear in the
heterozygous condition, only in homozygous.
Flower color
For example, flower color:
P = purple (dominant)
p = white (recessive)
If you cross a homozygous Purple (PP) with a
homozygous white (pp):
PP

Pp
pp
ALL PURPLE (Pp)
Cross the F1 generation:
Pp
P
p

Pp
P
p
PP
Pp
Pp
pp
Genotypes:
1 PP
2 Pp
1 pp
Phenotypes:
3 Purple
1 White
1. 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=
(1) If the F1 self-pollinated, what is the expected ratio between purple to
white color plants in the F2 population?
Purple : white =
(1) If F1 is backcrossed to Parent 1, what is the expected ratio between
purple to white color plants in BC1F1(P1) population?
Purple : white =
(1) If F1 is backcrossed to Parent 2, what is the expected ratio between
purple to white color plants in BC1F1(P2) population?
Purple : white =
Public Talk for Mendel Genetics
http://www.slideshare.net/mazz4/genetics-a-d29687785?next_slideshow=1
Two Gene Model
P1 (AABB) x P2 (aabb)  F1 (AaBa)
F2
AABB x aabb
male
AB
(1-r)/2
ab
(1-r)/2
Ab
r/2
aB
r/2
AB
(1-r)/2
AABB
(1-r)(1-r)/4
AaBb
(1-r)(1-r)/4
AABb
r(1-r)/4
AaBB
r(1-r)/4
ab
(1-r)/2
AaBb
(1-r)(1-r)/4
aabb
(1-r)(1-r)/4
Aabb
r(1-r)/4
aaBb
r(1-r)/4
Ab
r/2
AABb
r(1-r)/4
Aabb
r(1-r)/4
AAbb
r*r/4
AaBb
r*r/4
aB
r/2
AaBB
r(1-r)/4
aaBb
r(1-r)/4
AaBb
r*r/4
aaBB
r*r /4
Female
When r=0.5, two genes independent, i.e. two genes are located at different chromosomes;
When r=0, two genes are located at same locus, i.e. same gene or no crossover
Genotypes and their frequencies postulated for the two allele A and B with
a recombination frequency (r) in F2 and F2:3 population derived from a
cross P1(AAbb) x P2 (aaBB).
Male
F2
AAbb x aaBB†
Ab
(1-r)/2
aB
(1-r)/2
Female
AB
r/2
ab
r/2
Ab
(1-r)/2
AAbb
(1-r)(1-r)/4
R‡
AaBb
(1-r)(1-r)/4
Seg=R
aB
(1-r)/2
AaBb
(1-r)(1-r)/4
Seg=R
aaBB
(1-r)(1-r)/4
R
AB
r/2
AABb
r(1-r)/4
R
AaBB
r(1-r)/4
R
AABb
r(1-r)/4
R
AaBB
r(1-r)/4
R
AABB
r*r/4
R
Aabb
r(1-r)/4
Seg
aaBb
r(1-r)/4
Seg‡
AaBb
r*r/4
Seg=R
ab
r/2
Aabb
r(1-r)/4
Seg
aaBb
r(1-r)/4
Seg
AaBb
r*r/4
Seg=R§
aabb
r*r /4
S‡
† A,
presence of Rsv1 allele; B, presence of Rsv1-y allele; a, presence of rsv1 allele; b, presence of rsv1-y allele.
‡ R, resistant; S, susceptible; Seg, segregating for resistant and susceptible.
§ Since it is extremely difficult to distinguish F
2:3 lines that are segregating for two closely genes (AaBb) from F2:3 lines
that are homogenous resistant due to limitation of population, lines with AaBb are grouped with All R class marked
Seg=R in the table.
LINKED
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 =
Research Project Available in UAF Vegetable Breeding program
I. Dandelion
1. EST-SSR discovery and validation in dandelion
2. EST-SNP discovery and validation in dandelion
II. Spinach
Association analysis and SNP markers for leaf traits in spinach
Association analysis and SNP markers for mineral components in spinach
SNP discovery and genetic diversity in spinach
SSR discovery and genetic diversity in spinach
Slowing-booting and QTL mapping in spinach
QTL mapping and SNP marker identification for downy mildew resistance in spinach
Develop a SNP set for spinach variety determination
III. Chicory and Endive
EST-SSR discovery and validation in chicory and endive
EST-SNP discovery and validation in chicory and endive
SNP discovery and genetic diversity in chicory
SNP discovery and genetic diversity in endive
Develop a SNP set for chicory and endive variety determination
Research Project Available in UAF Vegetable Breeding program
IV. Cowpea
1. EST-SSR discovery and validation in cowpea and genetic diversity
2. EST-SNP discovery and validation in cowpea and genetic diversity
3. SNP discovery from genotyping by sequencing in cowpea
4. Genetic diversity analysis for world-wide cowpea germplasm
5. Association analysis of low phosphorus efficiency in cowpea
6. Association analysis of aphid tolerance in cowpea
7. Association analysis of cowpea bacterial blight in cowpea
8. Association analysis for morphological traits in cowpea
9. Association analysis of salt tolerance in cowpea
10. Association analysis of cowpea mosaic virus in cowpea
11. Association analysis of iron deficiency chlorosis in cowpea
12. Association analysis of seed size in cowpea
13. Association analysis of maturity in cowpea
14. Association analysis of seed ANTIOXIDNT content in cowpea
15. Association analysis of seed protein content in cowpea
16. Develop a SNP set for cowpea variety determination