QTL Mapping Part 1

Summary

This lecture explores the application of linkage disequilibrium in QTL analysis, using monkey flowers as a case study. It discusses two flower types adapted for bee and hummingbird pollination and how QTL mapping can determine the number and location of genes influencing these traits. The research aims to understand the genetic changes behind the diversification of flower types and if they resulted from a few large mutations or many small ones.

Takeaways

• 🌺 The lecture discusses the application of linkage disequilibrium in QTL (Quantitative Trait Locus) analysis using monkey flowers as a case study.
• 🐝 Different floral types in the genus Mimulus have evolved to attract specific pollinators, such as bees and hummingbirds, which is reflected in their physical characteristics.
• 🧬 QTL analysis is a method used to identify the number of genes influencing a trait, their location in the genome, and their effect on the phenotype.
• 🔍 The candidate Locus method is used to further investigate the genes found through QTL mapping to understand their protein products and their impact on the phenotype.
• 🌱 Practical applications of QTL mapping include genetic engineering of crops and predicting disease risk based on multiple genes.
• 🧬 The researchers aimed to understand the genetic changes that led to the diversification of flower types in monkey flowers, specifically the evolution of traits adapted for different pollinators.
• 🧐 The study explores whether the observed diversification resulted from a few large genetic changes or many small changes accumulating over time.
• 📊 QTL mapping involves identifying marker loci throughout the genome to locate QTLs that are in linkage disequilibrium with the markers.
• 🔬 The process of QTL mapping involves creating F1 and F2 generations to observe the distribution of traits and identify correlations between marker genotypes and phenotypes.
• 🌼 The research uses the F2 generation to measure phenotypes and look for statistical correlations with marker genotypes to determine the genetic basis of floral traits.

Q & A

What is the main topic of the lecture?

The lecture focuses on the concept of linkage disequilibrium and its application in QTL (Quantitative Trait Locus) analysis, using a case study of two species of monkey flowers in the genus Mimulus.

What are the two types of floral phenotypes discussed in the genus Mimulus?

The two types of floral phenotypes are those adapted to attract bees (bee-pollinated flower types) and those adapted to attract hummingbirds (hummingbird-pollinated flower types).

How do bee-pollinated flowers differ from hummingbird-pollinated flowers?

Bee-pollinated flowers tend to be purple or pink, have large petals for landing pads, and a broad short passageway to the nectar. Hummingbird-pollinated flowers are usually red, have long narrow entrances, and lack landing pads since hummingbirds hover.

What is a quantitative trait locus (QTL)?

A QTL is a gene that influences a quantitative trait, which is a trait influenced by multiple genes at different loci. QTLs contribute to the continuous variation in phenotypes observed in traits like flower morphology.

What is the purpose of QTL mapping?

QTL mapping is used to determine how many QTLs are involved in producing a trait, their location in the genome, and to understand what their protein products do and how they affect the phenotype.

What is the candidate locus method and how does it relate to QTL mapping?

The candidate locus method is used after QTL mapping to focus on particular loci in the genome where QTLs exist. It involves sequencing the gene, producing the protein, and studying its effect on the phenotype.

What are the practical applications of QTL mapping and the candidate locus method?

These techniques are used in genetic engineering, particularly for crop plants to identify and manipulate genes for desired traits, and in predicting disease risk by understanding the genes involved in diseases.

What evolutionary question were the researchers trying to answer with their study on monkey flowers?

The researchers were investigating whether the diversification of flower types in monkey flowers was the result of a small number of large changes or a large number of small changes in the genetic makeup.

What is the significance of the phylogeny in understanding the evolution of flower types in Mimulus?

The phylogeny helps to infer the likely phenotype of the common ancestor of the two species and suggests that the hummingbird-pollinated phenotype may have evolved twice independently in the genus.

How do researchers use QTL analysis to answer evolutionary questions?

By identifying the QTLs responsible for differences in floral phenotypes and examining whether these are due to a few large-effect mutations or many small-effect mutations, researchers can gain insights into the evolutionary processes at work.

What is the role of marker loci in QTL mapping?

Marker loci are scattered randomly in the genome and are used to identify QTLs that are in linkage disequilibrium with them. They provide a known genotype and location that can be correlated with the phenotype to locate QTLs.

Outlines

00:00

🌺 Introduction to QTL Analysis in Monkey Flowers

The lecture begins by introducing the concept of QTL (Quantitative Trait Locus) analysis within the context of studying evolution at multiple levels. The focus is on the application of linkage disequilibrium to analyze quantitative traits, which are influenced by multiple genes. The lecture uses a case study of two species of monkey flowers in the genus Mimulus to illustrate this method. These flowers exhibit a wide range of floral types, categorized into two main types: bee-pollinated flowers with large petals and broad passageways, and hummingbird-pollinated flowers with red coloration and long, narrow entrances. The goal is to understand how many genes are involved in these traits, their locations in the genome, and their functions. The lecture also touches on practical applications of QTL analysis, such as genetic engineering in crops and disease risk prediction.

05:01

🧬 QTL Mapping and Evolutionary Questions

This section delves into the methodology of QTL mapping, starting with the identification of marker loci scattered throughout the genome. The importance of these markers is to identify the alleles and genotypes of individuals in the study. The lecture explains the concept of linkage disequilibrium, where the presence of a marker allele is correlated with a particular QTL allele more often than by chance, indicating their proximity on the chromosome. The researchers aimed to answer evolutionary questions about the diversification of flower types, specifically whether this was due to a few large mutations or many small ones. They used QTL analysis to determine if a small number of QTLs with large effects or a large number of QTLs with small effects were responsible for the differences in floral phenotypes between bee- and hummingbird-pollinated flowers.

10:03

🌼 Crossbreeding and Phenotypic Variation

The third paragraph describes the experimental crossbreeding of the two monkey flower species to create an F1 generation of heterozygotes at all QTLs and marker loci. This generation is then used to produce an F2 generation, which can be either homozygous or heterozygous at each QTL and marker locus. This results in a continuous distribution of traits, as different combinations of alleles produce varying aspects of the floral phenotype. The F2 generation is the focus for measuring phenotypes and looking for statistical correlations between the genotype at the marker locus and the flower's phenotype. This process helps to identify the QTLs responsible for the differences in floral traits between the species and to understand the genetic basis of these traits.

Keywords

💡Evolution

Evolution refers to the process by which species of organisms change over time through genetic variation and natural selection. In the video, evolution is discussed in the context of how different species of monkey flowers have evolved different flower types to attract specific pollinators, illustrating the concept of adaptation through evolutionary processes.

💡Linkage Disequilibrium

Linkage Disequilibrium is a phenomenon in genetics where certain alleles are found together more often than would be expected by chance. It is important in the video because it is a key concept in QTL analysis, helping to identify the proximity of QTLs to known genetic markers, which is crucial for understanding the genetic basis of phenotypic traits.

💡QTL Analysis

QTL Analysis stands for Quantitative Trait Locus analysis, a method used to identify genes associated with quantitative traits. The video uses QTL analysis as a case study to explore the genetic basis of different floral types in monkey flowers, aiming to understand the genetic changes that led to the diversification of these traits.

💡Quantitative Traits

Quantitative Traits are characteristics that vary along a continuum and are influenced by multiple genes. In the script, floral traits such as flower color and shape are described as quantitative traits, which are the focus of the QTL analysis in the study of monkey flowers.

💡Genetic Markers

Genetic Markers are specific locations on DNA that can be easily identified and used to track the inheritance of particular genes. The video mentions genetic markers as tools in QTL mapping to identify the chromosomal location of QTLs by looking for linkage disequilibrium with these markers.

💡Phylogeny

Phylogeny is the evolutionary history and relationships among individuals or groups of organisms. In the video, the phylogeny of monkey flowers is discussed to understand the ancestral state and the evolutionary changes that led to the current diversity of flower types.

💡Adaptation

Adaptation in biology refers to the process by which an organism becomes better suited to its environment. The video discusses how different flower types in monkey flowers are adaptations to attract specific pollinators, such as bees or hummingbirds.

💡Protein Products

Protein Products are the functional molecules encoded by genes that perform various tasks within an organism. The video mentions the importance of identifying the protein products of QTLs to understand how they influence phenotypic traits, which is part of the candidate locus method.

💡Genetic Engineering

Genetic Engineering is the direct manipulation of an organism's genes using biotechnology. The video script mentions genetic engineering as a practical application of QTL analysis, particularly in the context of crop improvement to enhance desired traits.

💡Disease Risk Prediction

Disease Risk Prediction involves identifying genetic factors that contribute to the likelihood of developing certain diseases. The video highlights how QTL analysis can be used to predict disease risk by understanding the genetic basis of complex traits influenced by multiple genes.

💡F2 Generation

The F2 Generation refers to the second filial generation in genetic crosses, resulting from the mating of F1 hybrids. In the video, the F2 generation of monkey flowers is crucial for QTL analysis because it displays a wide range of phenotypes, allowing researchers to correlate genotypes at marker loci with specific floral traits.

Highlights

Introduction to the concept of linkage disequilibrium and its key role in quantitative trait locus (QTL) analysis.

Case study focused on two species of monkey flowers in the genus *Mimulus*, which have different pollination strategies (bee vs. hummingbird).

Differences between bee-pollinated and hummingbird-pollinated flower phenotypes, with bee-pollinated flowers tending to be purple or pink with large landing pads, and hummingbird-pollinated flowers being red and narrow.

QTL analysis helps identify how many genes influence quantitative traits and where in the genome they are located.

QTL mapping provides insights into genetic contributions to traits, but a candidate locus method is needed to identify the function of specific genes involved.

Application of QTL mapping in fields like genetic engineering and disease risk prediction, showcasing its broader practical implications.

Researchers aimed to understand the genetic changes that led to diversification between *Mimulus* species, focusing on whether these changes were caused by large mutations or numerous small mutations.

QTL mapping can reveal whether phenotypic differences result from a few QTLs with large effects or many QTLs with small effects.

The study's evolutionary significance: examining whether evolutionary changes act as small incremental 'tinkering' or larger, more significant changes.

Marker loci are randomly scattered throughout the genome and used to identify nearby QTLs through linkage disequilibrium.

A strong statistical correlation between marker genotypes and phenotypes indicates linkage disequilibrium between the marker and QTL, providing insights into their physical proximity on chromosomes.

Researchers experimentally crossbred *Mimulus* species to study the genetic differences in flower phenotypes, specifically targeting QTLs and marker loci.

The F1 generation, which was heterozygous for all QTLs and markers, was crossed to produce an F2 generation, where continuous variation in traits was observed.

QTL mapping in the F2 generation allowed researchers to correlate specific genetic markers with observable flower traits, revealing how many QTLs contribute to differences in phenotype.

QTL analysis combined with candidate locus methods can help pinpoint which proteins affect phenotype and the nature of their influence, offering broader insights into trait evolution.

Transcripts

in this web lecture we're going to wrap

up our discussion of evolution at

multiple loai by examining one of the

most important applications of the

concept of linkage disequilibrium and

that is qtl analysis or quantitative

trait Locus analysis and we're going to

illustrate this method using a case

study from some research that was done

on two species of monkey flowers in the

genus mimulus so the genus mimus

includes flowers with a very wide range

of floral types that generally come into

a couple of categories some of them like

this m louisi that you see with a pink

flower are classic flower types that are

adapted to attract bees as pollinators

bees see much better in the purple

pinkish part of the light spectrum they

don't see the color red very well so

these flowers tend to be purple purple

or pink and bees also need a place to

land when they're going and Gathering

nectar so they tend to have large pedals

that serve as landing pads close to the

nectaries and there's usually just a

very broad short passageway to get into

the flow to get at the nectar so this is

a classic B pollinated flow

phenotype the other type of flower that

you see in this genus is a classic

morphology that's associated with

hummingbird pollinators so hummingbirds

see much better in the red part of the

spectrum they're attracted to things

that are red so these flowers tend to be

red they tend to have very long narrow

entrances to the nectaries that are

perfect for hummingbird tongues they

lack these landing pads because

hummingbirds hover they don't need to

land to be able to collect the nectar so

we've got two very classic flower types

but before we go into the detail details

of This research let's think a little

bit about qtl analysis itself and what

are quantitative trait Loi we've talked

a lot about quantitative traits remember

these are traits that are influenced by

a number of genes at different loai and

the more genes that are involved the

more you tend to see this normal

distribution of phenotypes a continuous

variation in phenotype and each gene

that contributes to one of these

quantitative traits is called a

quantitative trait Locus or a qtl so

it's one of those genes that has some

influence along with a bunch of other

genes on a quantitative trait so one of

the things we might want to know about

one of these quantitative traits is how

many of these Loi are involved in

producing this trait how many have an

influence and where in the genome are

they located both of these questions we

can answer by using this qtl mapping

technique but more importantly we want

to know something about what these genes

actually do so what are their protein

products and how do those protein

products affect the phenotype what kind

of influence does each protein product

have in order to get at that question we

need to use a separate method called a

candidate Locus method where once you

find the neighborhood in the genome

where the qtl exists by using your qtl

mapping then you can f focus in on

particular loai in that area and

sequence the gene produce the protein

and be able to study that so the qtl

mapping is basically just going to

answer these questions about how many

and where and there are many many

practical applications for these two

techniques combined one of which is uh

genetic engineering uh particularly of

the food supply so if we want to know

something about the traits we're

interested in for crop plants for examp

for example we want to be able to

identify how many of these genes where

are they what do they do and how can we

fiddle with them to make them produce

the traits that we like even more how

can we crossbreed to maximize these

traits another one is prediction of

disease risk so many diseases are

affected by multiple genes and we really

would like to know how many of those

genes where they are what they do to be

able to figure out how much risk a

person has for having one of these

disorders but the application that these

researchers looking at monkey flowers

had was was more evolutionary let's take

a look at the philogyny for this genus

to understand what this question is so

our two species here M cardinalis and M

louisi you can see by the philogyny are

sister taxa and so one thing we would

want to know is what was the phenotype

of this common ancestor of the two

looking at this philogyny of the whole

clade we we can see that it was probably

a b pollinator phenotype why because the

next outgroup out is a b pollinator

flower type and also the most basil

group in the entire lineage is also a b

pollinator type flower so we see one CLA

that's entirely hummingbird pollinated

flowers and then this one isolated

lineage that is also a hummingbird

phenotype so most parsimonious solution

is that the hummingbird type phenotype

evolved twice independently one giving

rise to this whole clay and one giving

rise to this one single species that

arose from a common ancestor that was of

this B pollinated flower type so what

the researchers wanted to know was what

were the genetic changes that occurred

that caused this

diversification and specifically they're

interested in an issue that I asked you

to consider when you read the chapter on

adaptation this idea of mutations of

large effect versus many mutations with

small effect accumulating to produce

diversification between species so they

wanted to know was this diversification

the result of a small number of large

changes or a very large number of small

changes to produce this so this is a big

evolutionary question I also asked you

in that prep assignment on the

adaptation chapter to think about this

idea aidea of evolution working as a

tinker making lots of little small

changes to something that is already in

existence versus Evolution working as an

inventor creating something entirely new

all at once so this is what they wanted

to get at so how can we use qtl analysis

to answer that question well when you

find the quantitative traits that cause

these differences between the flowers

you can look to see if it is a small

number of qtls and then using the

candidate Locus techniques you can find

out if those are proteins that have a

large effect on the phenotype or small

effect you can also tell if you have a

large number of qtls that contribute to

those differences and each of them have

a small effect so that is the question

that they were trying to answer with

this

research so let's take a look at how

this is done first let's take a look at

the general approach of Q mapping the

first thing you need to do is to find

what we call Marker loai so these are

going to be scattered randomly in the

genome and for a good marker Locus you

need to be able to identify what the

alals are and you need to be able to

figure out what the genotype is for all

the individuals that you're looking at

so markers are usually alisy Loi that

can be easily genotyped using simple

molecular techniques so these are going

to be the

the LOI where you know what the genotype

is in each individual you know where

those marker Loi are located so this is

this is one of the known in this

research you need enough of these

markers so that you can be reasonably

sure that one of them is going to be

close to one of your qtls so you want to

make sure that each qtl has a marker

nearby that's going to identify it so at

the very minimum you need to have one on

every chromosome best case scenario is

that you have markers pretty densely

throughout the genome to be able to

clearly identify as many of these qtls

as you possibly can if a marker is in

linkage disequilibrium with a

qtl then you know that one marker Al

will be found with a particular qtl Al

more often than expected by chance

that's a definition of linkage

disequilibrium right so remember that

it's a QT L that actually influences the

phenotype so the qtl is the unknown you

don't know where it is you don't know

what its genotype is you can measure the

phenotype and you can measure the

genotype of the

marker so it's the qtls that influence

the phenotype but the qtl's are are

unknown the markers have no effect on

the phenotype they're just randomly

chosen Loi where you can easily figure

out what the alos are but the Gen type

is known and the location is known so

you can use these two known you can

measure the phenotype you can figure out

the genotype at the marker Locus and if

there's a statistical correlation

between the phenotype which remember is

caused by the qtl and the genotype at

the marker the only explanation is that

it's in linkage disequilibrium with the

qtl and that means that it's likely to

be close to it on the chromosome make

sure you understand why this is true if

you don't make sure you go back and

review that part of uh where we

discussed in class why the position on

the chromosome is important for linkage

disequilibrium so you can think of these

markers as being kind of like the gas

gauge in your car when you run out of

gas your car doesn't stop moving because

your gas gauge went to zero right the

gas gauge is just an indicator of what's

going on in the gas tank your car

stopped moving because there's no gas in

the tank so you can think think of the

marker genotype as being the gas gauge

it's got to be a reliable indicator of

what's going on in there otherwise it's

completely useless to you the actual

level of gas in the tank you can think

of as being like the qtl that's what's

actually causing the effect the

phenotype in this case would be whether

the car is moving or not it's the actual

qtl that's causing the phenotype it's

the actual level of gas in the car

that's responsible for whether the car

is moving or not

so let's take a look at how they did

this so in terms of the qtls that cause

this difference in Floral phenotype

between the bee pollinator phenotype and

the hummingbird pollinator phenotype at

all the qal that are responsible for

those traits each species is going to be

homozygous for whatever the AL is that

causes the trait to be like the bee

pollinated flower or like the

hummingbird pollinated flower so you've

got two Al types that are all homozygous

so these two flowers are never found

hybridizing in the wild they almost

never ever produce Offspring together

they never cross but they can be very

easily crossed experimentally so by just

hand pollinating them you can easily

cross these two and they have fertile

offspring and so you can take all of

these flowers that are homozygous at all

of the qtls and breed them together they

also used marker alals that were

entirely homozygous for one Al in one of

these types and homozygous for a

different Al in the um cardinalis

flowers so we have not only qtls that

are all homozygous but we also have

Marco alal that are all homozygous and

hom homozygous for different alals in

the two

species so we take all these parental

homozygotes and breed them to get an F1

generation that's composed entirely of

heterozygotes at all the qtls and also

all of the marker loai we can then

crossbreed these F1 heterozygotes to

produce an F2

generation and the F2 Generation can be

homozygous for either alil or

heterozygous at each qtl at each marker

Locus and this is where you get that

continuous distribution of traits

because you've got this SCP rambling of

heterozygotes and homozygotes at

different loai producing different parts

of that floral

phenotype this is the generation on

which you're going to actually measure

these phenotypes and look for the

statistical correlation between the

genotype at the marker and the phenotype

of the flower for different floral

characteristics let's look a little more

in depth at how this works