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Genomics
Quantitative traits
Lecture 13
By Ms. Shumaila Azam
Quantitative Traits
•
Mendel worked with traits that were all discrete, either/or traits: yellow
or green, round or wrinkled, etc. Different alleles gave clearly
distinguishable phenotypes.
•
However, many traits don’t fall into discrete categories: height, for
example, or yield of corn per acre. These are “quantitative traits”.
•
The manipulation of quantitative traits has allowed major increases in
crop yield during the past 80 years. This is an important part of why
today famine is rare. Until very recently, crop improvement through
quantitative genetics was the most profitable aspect of genetics.
•
Early in the history of genetics is was argued that quantitative traits
worked through a genetic system quite different from Mendelian
genetics. This idea has been disproved, and the theory of quantitative
genetics is based on Mendelian principles.
Quantitative Traits
• Quantitative traits refer to phenotypes
(characteristics) that vary in degree and
can be attributed to polygenic effects,
i.e., product of two or more genes, and
their environment.
Types of Quantitative Trait
1. continuous trait: can take on
any value: height, for
example.
2. countable (meristic) can
take on integer values only:
number of bristles, for
example.
3. threshold trait: has an
underlying quantitative
distribution, but the trait
only appears only if a
threshold is crossed.
Quantitative Traits are Caused by
Mendelian Genes
• In 1909 Herman Nilsson-Ehle from Sweden did a
series of experiments with kernel color in wheat.
• Wheat is a hexaploid, the result of 3 different species
producing a stable hybrid. There are thus 3 similar
but slightly different genomes contained in the wheat
genome, called A, B, and D.
• Each genome has a single gene that affects kernel
color, and each of these loci has a red allele and a
white allele. We will call the red alleles A, B, and D,
and the white alleles a, b, and d.
• Inheritance of these alleles is partially dominant, or
“additive”. The amount of red pigment in the kernel
is proportional to the number of red alleles present,
from 0 to 6.
Wheat Kernel Color
•
•
•
The cross: AA BB DD x aa bb dd. Red x white.
F1: Aa Bb Dd phenotype: pink, intermediate between the parents.
Now self these.
F2: alleles follow a binomial distribution:
–
–
–
–
–
–
–
•
•
1/64 have all 6 red alleles = red
6/64 have 5 red + 1 white = light red
10/64 have 4 red + 2 white = dark pink
15/64 have 3 red + 3 white = pink
10/64 have 2 red + 4 white = light pink
6/64 have 1 red + 5 white = very pale pink
1/64 have all 6 white = white
Add a bit of environmental variation and human inability to distinguish
similar shades: you get a quantitative distribution.
This demonstrates that a simple Mendelian system: 3 genes, 2 alleles
each, partial dominance--can lead to a quantitative trait.
More Wheat Kernel Color
Multifactorial Traits
• Multifactorial traits are determined by multiple
genetic and environmental factors acting together
• Multifactorial = complex traits = quantitative traits
• Most traits that vary in the population, including
common human diseases with the genetic
component, are complex traits
• Genetic architecture of a complex trait = specific
effects and combined interactions of all genetic and
environmental factors
8
Quantitative Inheritance
• Quantitative traits = phenotypes differ in quantity
rather than type (such as height)
• In a genetically heterogeneous population, genotypes
are formed by segregation and recombination
• Variation in genotype can be eliminated by studying
inbred lines = homozygous for most genes, or F1
progeny of inbred lines = uniformly heterozygous
• Complete elimination of environmental variation is
impossible
9
Quantitative trait Locus
• A quantitative trait locus (QTL) is a region of DNA that is
associated with a particular phenotypic trait.
• These QTLs are often found on different chromosomes.
• Knowing the number of QTLs that explains variation in the
phenotypic trait tells us about the genetic architecture of a trait.
• QTLs underlie continuous traits (those traits that vary
continuously, e.g. height) as opposed to discrete traits (traits that
have two or several character values, e.g. red hair in humans, a
recessive trait, or smooth vs. wrinkled peas used by Mendel in
his experiments).
• Generally a single phenotypic trait is usually determined by
many genes. Consequently, many QTLs are associated with a
single trait.
• Quantitative trait loci (QTLs) are stretches
of DNA containing or linked to the genes that
underlie a quantitative trait.
• Mapping regions of the genome that contain
genes involved in specifying a quantitative
trait is done using molecular tags
– AFLP
– SNPs etc.
Uses
• It may tell us that plant height is controlled by
many genes of small effect, or by a few genes
of large effect.
• Another use of QTLs is to identify candidate
genes underlying a trait.
– Once a region of DNA is identified as contributing
to a phenotype, it can be sequenced.
– The DNA sequence of any genes in this region can
then be compared to a database of DNA for genes
whose function is already known.
• Classical QTL analyses are combined
with gene expression profiling i.e. by
DNA microarrays.
– describe cis- and trans-controlling elements
for the expression of often diseaseassociated genes.