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 rather than 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 at each 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 :

 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

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 and on 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).

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 a method 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.Unlike microsatellites 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.

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 a mutation 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 that are 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.

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.