QTL Application

8/6/2019 QTL Application

1/6

QUANTITATIVE TRAIT LOCI AND THEIR APPLICATION IN ANIMAL BREEDING

The explosive growth in genomics research has driven life science industries to

develop alternative information and analysis platforms that allow livestock improvement

programs considering different pathways to genetic analysis. One such possibility consist of

identifying the QTL contributing to the genetic variance of the production traits of interest in

the relevant populations. Most quantitative traits in farm animals are controlled by many

hundreds og genes, each with a small effect. The polygenic nature of variation means that the

trait value is affected by segregating allelic variants at numerous loci, scattered throughout

the genome and by environmental factors. These features make it impossible to identify or

track individual polygene in heredity. It is customary to refer to traits exhibiting polygenic

quantitative genetic variations as Quantitative Traits and to the polygenic loci responsible

for genetic variation in quantitative traits as Quantitative Trait Loci or QTL.

NEED FOR QTL STUDIES

Molecular genetics analyses of quantitative traits lead to the identification of broadly

two types of genetic markers ( causal mutations ) and indirect markers ( non functional

genetic markers that are linked to QTL ).Causal mutations are hard to find for quantities traits

and few examples are available. A gene with a large effect such as the halothane gene is very

much the exception. Nevertheless much research is now under way to identify possible genes

with useful effects on performance. The function of most of the genes so far detected is

unknown. By contrast indirect markers are abundant across the genome and their linkages

with QTLs have been established by evidence of empirical association of genotype with trait

phenotype. This form the basis for selection of individuals based on genetic marker ratherthan phenotype, a process known as marker assisted selection ( MAS ).

BASIC PRINCIPLE AND ADVANTAGES OF QTL MAPPING

A non observable gene ( Q ) with a quantitative effect on a trait is assumed to be

syntenic with a molecular marker ( M ) at a physical distance that precludes independent

assortment of QTL and marker alleles at meiosis.Use of MAS depends on Correlation of

molecular genotype with genetic value for the trait .MARKER ASSISTED SELECTION

( MAS ),thus,aims to substitute selection at the DNA level , for selection on the basis of

phenotype .Ideally , MAS is based on DNA-level screen for the specific sequence variant ateach QTL that is associated with a favourable effect on the trait value.MAS is thus

advantageous since it enables selection early in life,equally in both sexes,and without

requiring costly trait evaluation.This will increase the intensity of selection and decrease the

generation interval.MAS unaffected by micro-environmental variation,this will increase the

accuracy of selection.

The main benefit of MAS would be in traits such as meat quality or disease

resistance , which are difficult or expensive to measure in the live animals,or in reproduction

which occurs late in life or in one sex only.There are however a number of problems :


2/6

DNA testing is still relatively expensive in relation to the small benefits of most markers on

performance.

There is no further benefit after the marker has been made homozygous.

Marker effects are often inconsistent between lines and even families.

Due to the high number of candidates and traits, there is a statistically high chance of false

positive markers.A lready the number of markers reported would explain more than 100% of

the genetic variation for some traits.

Selection on markers causes a loss of selection on other traits.

Markers may have unknown harmful as well as beneficial effects.There may therefore be

good reasons why selection has not fixed apparently favourable QTLs at 100 % in these

populations.

BIASES IN QUANTITATIVE TRAIT LOCI ANALYSIS

Typically , quantitative trait loci ( QTL ) are located by measuring associations

between Mendelian markers and the trait of interest in a mapping population ( for

example ,an F2 from a cross between selected lines.However , several factors make it

difficult to estimate the True numbers and effects of loci that influence a quantitative trait.

Closely linked QTL with opposite effects tend to be missed , as there are few ecombinants

that could reveal their presence.

There is a lower limit for the size of a QTL that can be detected,Which will very according

to the size of the experiment and the properties of the trait; real QTL with effects below this

limit are nearly always undetected.

Closely linked QTL with effects in the same direction tend to give the appearance of a single

QTL of larger effect.Indeed , simulation studies have shown that under the infinitesimal

model,the chance coupling of linked factors can lead to the appearance pf large-effect.The

effect can be exacerbated if recombination rates vary,or if the actual loci tend to be clustered

( for example , in a multi-gene family ).

Unless samples are large (>500,for example),the effects of statistically significant QTL are

substantially overestimated.

APPROSCHES FOR QTL IDENTIFICATION:

Indirect markers linked to QTL are the most widely reported and there are broadly

two approaches used to identify such markers ( Anderson et al.2001).First is the directed

search using candidate gene in unstructured populations and the second involves genome

wide searches in specialized populations ( F2 cross or backcross ).Candidate gene markers

are polymorphism within a functional gene and are often tightly linked to the QTL .Genome

wide scan for indirect markers identify simultaneous segregation of a genetic markers and the


3/6

Qtl across families due to their tight linkage within 10-20 cm that precludes their separation

due to meiotic crossing over.

Structured populations are required for QTL association studies.Traditional breeding

schemes in farm animals involve mating of selected sires with a large number of dams to

produce large half sib families .In large sib families from hetero zygote sires and / or dams

the segregation of both sets of parental alleles can be determined.The performance data is

analyzed using analyses of variance ( ANOVA ) in which trait means of alternate groups of

sib ( according to the parental marker allele inherited ) are compared within (sire) family.The

sume of squares associated with marker genetype is calculated for each family and these are

aggregated across families so that evidence for segregation of a QTL can be evaluated .This

approach provides the basis for the family designs which have been utilized by animal

breeders for the detection of marker-QTL associations.Three family designs have emerged in

animal breeding programmes:

1.HALF SIB DESIGN

2.FULL SIB DESIGN

3.GRAND-DAUGHTER DESIGN AND IS PRESENTED IN

Half sib and granddaughter are commonly used in farm animals while full sib design

ids used in species with large litter size pig.In granddaughter design the pedigree consists of

a number of bulles,each with many sons by different dams.The genotypes of a son for a

quantitative trait is assessed using trait data collected from large number of his daughters

( grand daughters of the original sires ).Markers data are collected on the original bulls andon their sons , but not on any females in the pedigree.The design allows QTLs , Which were

heterozygous in the originals bulls to be detected.

Another design for QTL detection is the selective genotyping that requires the

genotyping of only a sub-samble of the available individuals determined by truncating the

distribution of phenotypes within each family.Only a small proporation ( 1-10 %) of

individuals with the most extreme phenotypes in both tails of the progeny distribution are

genotyped .Marker allele frequencies between the two opposing tails of the phenotypic

distribution are than compared.If there is no QTL linked to the marker,marker allele gene

frequencies in both tails should be similar.However ,if a QTL is linked to the marker ,the

divergent selection should result in considerable marker allele frequency can easily be

adopted to our buffalo breeding populations.

QTL data can be applied to develop marker assisted selection ( MAS ) ,which aims to

substitute selection at the DNA level,for selection on the basis of phenotype.Operationally

there are distinct steps,which can make increasing contribution to MAS .These steps include

the following:

1.Identification of chromosomal regions containing the QTL s of interest ( 10-20 cm ).

2.Specification of QTL location within these regions ( 5 cm).


4/6

3.Identification of markers in tight linkage to the QTL ( 1-2 cm ).

4.identification of potential Candidate Genes in the narrow region.

5.Identification of the specific gene associated with the trait variation.

6.Identification of the functional site at the gene.

MARKER ASSISTED INTROGRESSION

As an alternative to selection within a line , a marker can be used to introduce QTL

from one line into another by marker -assisted introgression.Suppose for example that a

single gene for prolificacy is to be introduced from Meishan into Landrace. An F1 cross of

the two is then backcrossed to Landrace over several generations ,gradually increasing the

prpporation of Landrace while selecting for the desirable gene.In the absence of a DNA test,this is the method by which Cotswold introduced the dominant white coat colour gene from

the large white into its White Duroc line.Only genes with large effects on the trait are

preferred for gene introgression programmes ( Gama et al.1992 ).

NEW TYPES OF MARKERS

The main disadvantage of existing markers is their high cost and low accuracy.The

majority are random segments of DNA of the form CACACA ( microsatellites) that show

genetic variation in the number of repeats.The inaccuracy stems from the weakness of the

linkage in predicting the presence of the QTL.Either closer markers are needed or ideally amethod of detecting the QTL directly.Several new options are now appearing.

AFLPs Amplified fragment polymorphisms can be generated by enzymes which cut the

chromosomes only at specific sequences .The presence of different genes results in DNA

fragments of different length,which can be correlated with performance traits.Patented by

KeyGene NV in the Netherlands and applied in plants ,this has the advantage of producing a

set of markers specific to noe line.It also overcomes any patents on published markers.

SNPs Single nucleotide polymorphisms are changes in a single specific coading unit of the

genetic code.They are easy to detect and usually occur within the functional gene.Unlikemicrosatellites SNP tests can be automated on DNA microarray chips.

ESTs Expressed sequence tags allow genes to be detected when they are switched on.This

would allow selection for animals expressing rapid early growth ,earlier puberty,or perhaps

for immune response.ESTs will provide the key to how genes are organised and controlled.

As the number of mapped genes increases ,AFLPs are likely to provide alternative markers

for QTLs or hot spots that are already known.Microarray technology already allows 30000

SNP DNA tests to be conducted on a single chip the size of a microscope slide,to be both

powerful and cheap.


5/6

STATUS OF IMPORTANT QTL IDENTIFICATION IN FARM ANIMALS AND QTL

CLONING

QTL identification has been exceptionally fecund in recent years when several QTLs

and markers have been identified in ruminants of economic importance .This list is growing

very fast.Some examples are given below:

These impressive results indicate that a anew epoch has begun in research in animal

genetics.Numerous programmes are underway to achieve the next steps .i.e.the cloning of

these new genes.

QTL CLONING:

All the tools necessary to atten this goal already exist and already the first successful

positional cloning experiment has been achieved in cattle,with the identification of the gene

responsible for the double muscling phenotype (Grobet et al 1977).The discovery of amutation causing an analogous phenotype in the mouse (MC Pherron et al 1977) made it

possible to identify the homologous human gene.Mutation analysis of the normal and mutant

animals revealed a detection of 11 bases systematically found in carrier animals (Grobet et al

1977).clearly ,this success was made possible in cattle .i.e.dense genetic maps,cosmid and

YAC libraries and comparative genomic analysis of man,mouse and cattle.

Though map based cloning has been used successfully to isolate mutant alleles

imparting discrete phenotypes governed by single or major genes,however ,QTLs continue to

be refractory to cloning ,for several reasons.Individual QTLs exert a relatively small effect on

phenotype,which can be observed by the effects of other genes or by non-gebetic factors thatare difficult to control.Breeding approaches can be used to create populations segregating for

individual QTLs ,but are time and labour intensive.

Identification of new genes affecting quantitative traits are rapidly increasing and lot

of theoretical and experimental results of QTL detection has accumulated .However the

initial enthusiasm generated for the potential genetic gains by molecular genetic applications

have been hampered by evidence of limitation of precision of estimates of QTL effects with

the present mood of cautious optimism( Young 2000).Unless genetic markers capture most

of the genetic variation for the trait,selection should be bassed on a combination of marker

and conventional phenotypic data.Further advances in molecular technology ,associated

reproductive and health technologes and genome programmes will soon create wealth of

information that can be exploited for the genetic improvement of farm animals.

While we consider the major contributions in QTL analysis from technical and

statistical perspectives ,it must be emphasized that technology is only as useful as the extent

to which it finds applications .In the regard ,the trend that is detected in literature is not

entirely satisfying.The hung numbers of puplications in the area of QTL detection by number

of QTLs identified and actually utilized in animal improvement programmes .The reasons for

this are many ,and include the cost of implementation of mapping experiments in livestock

species.


6/6

Meantime,it is important to realise that modern selective breeding programs have

been successful,cheap and safe,and that for present there is little pressure to its position in

relation to the new technologies and the public.

Documents

QTL Application