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TAMIL NADU VETERINARY AND ANIMAL SCIENCES UNIVERSITY VETERINARY COLLEGE AND RESEARCH INSTITUTE NAMAKKAL 637 002

2 AGB 602 MOLECULAR GENETICS IN ANIMAL BREEDING -2+1

Term paper On
QUANTITATIVE TRAIT LOCI AND APPLICATIONS IN ANIMAL BREEDING

SUBMITTED TO Dr.N. MURALI, Ph.D., ASSOCIATE PROFESSOR

DEPARTMENT OF ANIMAL GENETICS AND BREEDING


NAMAKKAL.

SUBMITTED BY A. RAMACHANDRAN MVN 10001 (AGB)

DEPARTMENT OF ANIMAL GENETICS AND BREEDING VETERINARY COLLEGE AND RESEARCH INSTITUTE NAMAKKAL 637 002

2011

QUANTITATIVE TRAIT LOCI Introduction Many genes responsible for polygenic inheritance of particular characteristics are scattered around the genome. Their position is known as quantitative trait loci (QTL). It is useful to know where they are for both medical and agricultural reason. In this case of dieses susceptibility, it is useful to identify the individual genes so that their normal function can be identified and attempts made to design corrective medical treatments. In case of animal and plant breeding it would be useful to identify young individuals with favourable alleles without waiting for their expression at maturity. Those with favourable genotype could be removed earlier from selective breeding programs, while potentially high quality types could be cloned immediately (Winter et al., 2003)` 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 ). The success of quantitative genetic approaches does, however, not mean that genetic progress could not be enhanced if we could gain insight into the black box of quantitative traits. By being able to study the genetic make-up of individuals at the DNA level, molecular genetics has given us the tools to make those opportunities a reality. Molecular data is of interest for use in genetic selection because genotype information has heritability equal to 1 (assuming no genotyping errors), it can be obtained in both sexes and on all animals, it can be obtained early in life, and it may require the recording of less phenotypic information. The eventual application of molecular genetics in livestock breeding programs depends on developments in the following four key areas, which jointly culminate in the successful implementation of strategies for marker-assisted selection (MAS): i. Molecular genetics: identification and mapping of genes and genetic polymorphisms

ii. QTL detection: detection and estimation of associations of identified genes and gametes markers with economic traits iii. Genetic evaluation: integration of phenotypic and genotypic data in statistical methods to estimate breeding values of individual animals in a breeding population :: iv. Marker-assisted selection: development of breeding strategies and programs for the use of molecular genetic information in selection and mating programs. The objective of this paper is to review the potential role and integration of each of these four key areas in genetic improvement programs for livestock. ( Dekkers et al ). THE LOCATION OF GENES - MAPPING FUNCTIONS. Before genetic markers can be used to detect genes or QTLs, the relative positions of the genetic markers on the genome need to be known. Determining the relative position of markers is called "mapping" or "map development". The resulting map gives an overview of the relative locations of markers on the entire genome. We need to distinguish physical maps and linkage maps. On a physical map, distances between markers are measured in base pairs. Thus the physical map is based on biochemical knowledge of the genome. On the linkage map, the distance between markers is based on the recombination frequency between the markers. Markers are close together when there is little recombination between them, whereas markers are further apart Application of Molecular Genetics in Animal Breeding 12-9 when there is substantial recombination between them. Markers are placed on different chromosomes if they show 50% recombination. QUANTITATIVE TRAITS: DETECTION OF QTL Recall that a QTL is a gene or locus affecting a quantitative trait (Quantitative Trait Locus). Detection of linkage between a marker gene and a QTL. There are a number of similarities between the two. An important difference, however, is that the QTL genotype is not known. Thus, in contrast to markers and qualitative traits, we cannot observe the genotype for genes affecting quantitative traits. The search for QTL's in livestock has a history that goes back to the 1950's and 1960's. Genetic markers used in these studies were protein polymorphisms or blood groups. The approach followed in these studies was mostly that a number of (randomly selected) individuals from a population were typed and it was tested if genotype means differed significantly for the trait. If there was a significant effect of the marker genotype, then it was concluded that a QTL was located close to the marker gene. However, the success of these studies was limited and results were contradicting. Further, the limited number of markers that was available hampered these studies. The principle of QTL mapping is simple: trace chromosomal segments from parents to offspring and check if individuals that inherited

alternative chromosomal segments differ with respect to the quantitative trait. There are a number of different experimental designs that can be used to detect QTL: 1. 2. Crosses between (inbred) lines or breeds. Use of existing populations.

The type of design that is chosen for detecting QTL will depend upon the species and the aims of the experiment. F2-cross: What is required for this design is two (inbred) lines or breeds that differ with respect to the trait of interest. In livestock species, inbred lines, i.e. lines with an inbreeding coefficient of 1, are not available. However, lines that differ considerably for a number of interesting traits can also be used. In pigs, use has been made of crosses between the Chinese Meishan breed and commercial pig breeds. The Meishan breed is characterised by a high fertility and a high fatness. In poultry, crosses have been produced between the Red Jungle Fowl and the White Leghorn or the Sasumadorri (Japanese breed) and the White Plymouth Rock. These are crosses between unselected poultry breeds and heavily selected commercial breeds. In dairy cattle crosses have been produced between the Holstein-Friesian and Charolais breeds or between Jerseys and Holstein-Friesians. Characteristics of all these crosses are that the breeds differ considerably for one or more traits. This difference is a prerequisite, because in the F2-design, QTL will be detected that contribute to differences between breeds. Lets consider a genetic marker M and a QTL Q, and the following cross between two breeds:

Realize that in reality the QTL genotype can not be observed. To simplify things, it is assumed that the breeds are fixed for alternative marker and QTL alleles: breed 1 is fixed for marker allele M1 and QTL allele Q1 while breed 2 is fixed for marker allele M2 and QTL allele Q2. The animals from breed 1 are crossed to those of breed 2 and the resulting F1 will be genetically uniform; all animals have genotype M1M2 for the marker and Q1Q2 for the QTL, that is, they all are heterozygous for the marker and the QTL. This is important because we indicated

previously that in order to detect linkage (between a marker and the QTL) heterozygous individuals are required. Crossing the F1-individuals among each other (F1 * F1) results in an F2-population. The F1 individuals can produce four different types of gametes: M1Q1, M1Q2, M2Q1 and M2Q2. The M1Q1 and the M2Q2 gametes are the parental or non-recombinant gametes, whereas the M1Q2 and the M2Q1 gametes are the recombinant gametes. In the F2, three different marker genotypes are represented: M1M1, M1M2 and M2M2. In case there is no recombination between the marker and the QTL, i.e. the marker and the QTL are located closely together on the genome, all M1M1 individuals will have genotype Q1Q1 and all M2M2 individuals will have genotype Q2Q2. In that case, the difference in for example backfat thickness or fertility between M1M1 pigs and M2M2 pigs will reflect the difference between the Q1Q1 and Q2Q2 genotypes. In case recombination occurs between the marker and the QTL, then this contrast will be reduced because the animals with marker genotype M1M1 will also contain animals with QTL genotype Q1Q2 and Q2Q2. It can be derived that the observed difference between the M1M1 and M2M2 genotypes is equal to 2(12q)a where q is the recombination fraction between the marker and the QTL and a is the additive gene effect of the QTL on the quantitative trait. Therefore, a difference between the marker genotypes provides evidence for the presence of a QTL. Instead of looking at a single marker, in QTL mapping experiments individuals are genotyped for many markers. Based on the available marker information, the probability of being M1M1 or M2M2 is calculated for each F2 individual and at every centiMorgan. This probability is subsequently used in an analysis were the difference between M1M1 and M2M2 is tested statistically. Result of the QTL analysis for backfat thickness of a cross between Meishan boars and Dutch sows for chromosome 7 (De Koning, 2001). Arrows indicate the position of the genetic markers.

Analysis of a QTL-mapping experiment in pigs .In this experiment Meishan boars were crossed to Dutch sows. In the F2, the differences were estimated between chromosomal segments coming from the Meishan and from the Dutch pigs. This was done for each centiMorgan. For back fat thickness, this analysis resulted QTL detection in a daughter design where differences are quantified between daughters that inherited alternative marker alleles. in the profile shown in Figure 12.10. The x-axis indicates the location on pig chromosome 7 and the arrows indicate the location of the genetic markers. The y-axis shows the value of the test statistic and indicates the probability for the presence of a QTL affecting back fat thickness. If the curve passes a certain threshold then there is significant evidence for the presence of a QTL. As can be seen in Figure 12.10, there is significance evidence for QTL on chromosome 7 affecting back fat thickness and the additive effect of the QTL (a) is 2.1 mm of back fat. The difference between pigs homozygous for this QTL is therefore 4.2 mm of back fat. (De Koning, 2001). Daughter design: As an alternative to a designed experiment involving crosses between lines or breeds, existing populations can be used to map QTL. In this approach, the structure of breeding populations is used to map genes that are segregating within these populations. An experiment involving a cross between divergent populations is focussed primarily on finding QTL that explain the difference between populations, whereas an experiment within a population will reveal QTL that explain genetic variation within a population. The principle underlying the detection of QTL in an out bred population will be illustrated for a so-called daughter design, where sires have a large number of progeny and analyses are performed within half sib families. The basic idea of the design is to trace marker alleles from the sires to his offspring and to determine whether offspring that have inherited alternative marker alleles from the sire differ with respect to the quantitative trait

Identifying the gene:


In the past decade, a large number of QTL have been mapped using methods described above. However, confidence intervals for the location of QTL typically are in the order of 50 cM. The conclusions that can be drawn from the first QTL-mapping experiments are, therefore, that a chromosomal region of 50 cM contains one, or possibly more, genes affecting a quantitative trait. A region of 50 cM consist of roughly 50 million base pairs and may contain hundreds of genes. This implies that finding the actual gene responsible for the effect is not a trivial exercise, let alone finding the functional mutation. Therefore, after an initial QTL mapping study, in a

next step the region needs to be narrowed down and candidate genes need to be identified. Candidate genes can be identified by using comparative mapping. Comparative mapping refers to the use of knowledge from other species, such as the human and the mouse. Genomes of different species are very similar, which is called "conserved". In humans and mice much more information is available on the location and function of genes. This information can be transferred from one species to the other. Figure 12.12 shows the comparative map between chicken and human. If e.g. a region on chicken chromosome 1 (GGA1) is identified as carrying an important gene, then the corresponding region in the human genome can be scanned for potential candidate genes. Obviously, this approach is limited by the current knowledge about the function of genes. THE CHICKEN-HUMAN COMPARATIVE MAP.

Results from mapping studies

Although finding single genes or QTL is a tremendous task, in recent years a number of those genes have been identified. In almost all of the cases these are so-called single-gene-traits, i.e. traits that are determined by a single gene. Genes underlying quantitative traits are much more difficult to identify, because they are not only affected by multiple genes, but also by environmental factors. Table 12.2 gives an overview of single gene traits that have been identified in livestock species. These will be discussed briefly. Further, a few other genes will be briefly introduced, also some that have not yet been identified. Overview of genes affecting traits in livestock were the responsible gene and the functional mutation have been identified (Harlizius and Van der Lende, 2001)

Quantitative Trait Loci: Several genes in different livestock species have been identified. However, so far the vast majority of these genes are so called "single gene traits", i.e. traits that are determined by a single major gene and where the effect of the environment is absent or small. Recently, the research group led by Michel George in Liege has identified a gene with an effect on milk production traits, i.e. a quantitative trait. The road towards finding the gene and the effect of the gene on milk production traits will be described in the following section.

SOTFWARE USED IN QTL MAPPING & LINKAGE ANALYSIS


An Alphabetic list of Genetic Analysis Software Dendrome's QTL mapping software site Pedros's directory of biomolecular research tools POPGENE, a program for population genetics analysis DnaSP - DNA Sequence Polymorphism PLABQTL - a program for composite interval mapping of QTL

LAMARC is a package of programs for computing likelihoods for samples of data (sequences and electrophoretic polymorphisms) from populations QTL Cartographer is a package of programs that will aid in locating the genes that control quantitative traits using a molecular map of markers MQTL : Software for simplified composite QTL interval mapping in multiple environments MSIM : Software for Automated Simulation of genetic markers and QTL DISPAN, a software for the analysis of allozyme data.

Multimapper / Bayesian QTL mapping software for inbred lines (distributed as C source code) UTILIZATION OF KNOWN GENES AND QTL IN ANIMAL BREEDING Use of marker information in Dairy cattle: In dairy cattle, DNA information has been used to select against deleterious alleles such as the BLAD (Bovine Leukocyte Adhesion Deficiency) or the CVM (Complex Vertebral Malformation) mutation. Furthermore, selection has been performed for certain milk protein genotypes. Marker information on coat color has also been used, particularly in red-andwhite breeding schemes. The most likely application of marker assisted selection in dairy cattle is the screening of young bulls before they are progeny tested. Currently, bull-sires are selected based on milk yield of their daughters. The selected bulls-sires are mated to bulldams to produce the next generation of young-bulls. Quite often, multiple ovulation and embryo transfer (MOET) is applied to produce multiple sons from a single sire-dam combination. The full-sib young bulls from such a mating have identical estimated breeding values because their breeding value is estimated based on pedigree information only. Marker information would make it possible to discriminate between full brothers and select the most promising individuals to be progeny-tested. The use of marker information in pig breeding: At present, pig-breeding industry uses information from several loci or genetic markers to support selection decisions .The first test to be applied was for the Halothane-gene. The occurrence of pale, soft and exudative (PSE) meat is associated with the recessive allele at the Halothane-locus. The test allows breeders to distinguish between animals carrying alternative Halothane-alleles. There is some discussion on which allele to select for, because the recessive allele reduces meat quality (PSE), but it improves lean meat content. Some

companies adopted an approach in which the dam lines are free of the recessive allele, but the allele is still present in the sire lines. Incorporating QTL information in genetic improvement programs. Strategies for selection on QTL information: Once markers that are linked to QTL have been identified, their effects can be estimated based on the association between phenotype and genotype and used to assign a 'molecular score' to each selection candidate, which can be used to predict the genetic value of the individual and used for selection. The constitution and method of quantification of the molecular score depends on type of LD that is used and the method of marker use (see below). In addition to a molecular score, individuals can also obtain a regular estimate of the breeding value for the collective effect of all the other genes. The following three selection strategies can then be distinguished: 1) select on the molecular score alone 2) two-stage selection, with selection on molecular score, followed by selection on regular phenotype-based EBV 3) selection on an index of the molecular score and the regular EBV. Selection on molecular score alone ignores information that is available on all the other genes that affect the trait and is expected to result in the lowest response to selection, unless all genes that affect the trait are included in the molecular score. This strategy does, however, not require additional phenotypes, other than those that are needed to estimate markereffects, and can be attractive when phenotype is difficult or expensive to record (e.g. disease traits, meat quality, etc.). If both phenotypic and molecular information is available on selection candidates, index selection is expected to result in the greater response to selection than two-stage selection. The reason is similar to why two-trait selection using independent culling levels is expected to give lower multiple-trait response than index selection; twostage selection does not select individuals for which a low molecular score may be compensated by a high phenotype-based EBV. Use of molecular information to capitalize on QTL that segregate between breeds: Breed or line crosses provide the most powerful populations to identify QTL, in particular if the breeds are divergent for the main traits of interest. Such studies, however, identify QTL that segregate between rather than within breeds. Nevertheless, this information can be used for genetic improvement in a number of ways. If a large proportion of the breed difference in the trait of interest is due to a small number of genes, introgression strategies can be used. If

a larger number of genes is involved, marker-assisted selection within a synthetic line is the preferred method of improvement. The most important use of genetic markers two types 1. Marker Assisted Selection (MAS) 2. Marker Assisted Introgression (MAI). Marker Assisted Selection (MAS) Traditional selection versus MAS: For many years, man has changed the genetic make up of animals through selection without knowledge of the underlying genes. The basic assumption was that many genes affected the quantitative trait (the infinitesimal model, see Chapter 4). Thus, although the idea of genetic selection is to change allele frequencies in the population, the actual alleles are not observed. Until recently, tools to identify the genes responsible for genetic differences between individuals or populations were not available. Developments in the area of molecular biology have changed this situation and have allowed identifying genes. To understand how knowledge of genes underlying quantitative traits can be used in animal breeding, it is useful to characterize present-day animal breeding.
1. Current approaches to estimate the genetic value of an individual rely on phenotypic

observations on the individual itself and/or its relatives. For almost all traits of interest to animal breeders, differences in phenotypic observations are due to both genetic and environmental effects (P = G + E). Therefore, the phenotype of an individual gives an indication of its genetic potential. However, if environment plays an large role, then the phenotypic record is not a reliable indicator of the breeding value of an animal. The relative impact of genotype and environment on the phenotype is reflected by the heritability. A heritability close to zero reflects the situation where almost all the differences in phenotype are due to differences in the environment, whereas a heritability close to one indicates that almost all the differences in phenotype are due to differences in the genotype of individuals. Thus, based on the phenotype of an individual we can get an estimate of its breeding value. Depending on heritability of the trait, the reliability of the estimated breeding value will be larger or smaller.
2.In practice, we use not only the phenotype of the individual itself to estimate breeding

values, ut also phenotypes of its relatives. The reason is that relatives will in part carry the same alleles. Information from relatives, in particular progeny, is especially useful when heritability is low so that own phenotype does not give reliable information on the breeding value. The resemblance between breeding values of relatives is quantified by the additive

genetic relationship. The additive genetic relationship is not necessarily equal to the true resemblance between breeding values, because there is uncertainty about which alleles are transmitted to offspring (Mendelian sampling). As a result of these two factors, accurate estimation of the breeding value of an animal is possible only if heritability is high and a record on the phenotype of the individual itself is available, or when a large number of records is available on its progeny. In general, the requirement progeny records postpones the age at which the animal can be selected as a parent, and therefore limits the attainable annual genetic progress. When the genes and their effects on traits of interest are known, typing of animals at the DNA level enables estimation of breeding values independent of phenotypic observations. Marker genotypes can be obtained from blood samples that are taken as soon as the animal is born and therefore can be used to estimate an animals breeding value before the animal has a phenotypic record. Further, the noise that is introduced by environmental effects which currently makes it difficult to get a reliable estimated breeding value would be avoided, i.e. markers assisted selection does not suffer from low h2. MAS is expected to make a contribution especially for traits that are difficult to improve by traditional selection. Such traits are: Traits with low heritabilities: in that case the phenotype is a poor predictor of the breeding value e.g. fertility traits. The phenotype can be recorded in one sex only e.g. milk yield. The trait is expressed late in life e.g. longevity. The phenotype of a trait can not be recorded easily or is expensive to record e.g. disease resistance The animal needs to be sacrificed in order to record the phenotype e.g. meat quality. The reason that MAS is expected to make a contribution to selection for these traits is that MAS makes it possible to estimate breeding values independent of phenotypic observations. For the traits mentioned above, phenotypic observations cannot be obtained in time, are difficult to obtain or are not very informative. For traits where traditional selection has been applied very successfully e.g. growth in broilers, MAS is not likely to have a big impact. Most traits of economic importance are quantitative traits controlled by a fairly large number of genes. Some genes, however, especially those of large effect, might be detected and localized in gene mapping studies. Once localized, information on the genotype of the QTL itself or the genotypes of linked markers can be used to aid selection. It is very unlikely that all genes affecting a trait will ever be detected and therefore unidentified genes affecting the

trait will remain. Those unidentified genes are called "polygenes". The total genetic variation is thus decomposed in a polygenic part and a part explained by QTL. Information on QTL therefore adds to the accuracy of the estimated breeding value, and selection will be based on both phenotypic and marker information.

Marker-assisted introgression
The aim of an introgression program is to introduce one or more favorable genes (target genes) from a breed that is inferior for other performance characteristics (the donor breed) into a high performance line that lacks the target genes (the recipient breed). This is done through an initial F1 cross followed by multiple backcrosses to the recipient breed and one or more generations of intercrossing The aim of the backcross generations is to maintain the target gene(s) while ecovering the background genome of the recipient breed. The purpose of the intcrcrosses is to fix the line for the target gene(s). The effectiveness of introgression schemes is limited by the ability to identify backcross or intercross individuals that carry the target gene(s) and by the ability to identify backcross individuals that have a high proportion of the recipient genome, in particular in the region(s) around the target gene(s). The latter affects the number of backcross generations required to recover the recipient genome. Molecular genetics can enhance the effectiveness of both phases of an introgression program. Effectiveness of the backcrossing phase can be increased in two ways: 1. by identifying carriers of the target gene(s) (foreground selection), 2. by enhancing recovery of the donor genetic background (background selection). Effectiveness of the intercrossing phase can also be enhanced through foreground selection on the target gene(s). Foreground selection relies on population-wide LD in the crossbred population between the target gene(s) and linked markers. Ideally, the target gene can be identified directly through a genetic test or even based on phenotype (e.g. the naked neck gene), in which case the LD will be complete. If linked markers must be used, the effectiveness of foreground selection depends on the number of target genes and on the confidence interval for the position of those genes. The latter determines the size of the genomic region that must be introgressed. Both factors have a large impact on the number of individuals that is required to find individuals that are carriers for all target genes during the backcrossing phase and homozygous during the intercrossing phase. For the introgression of multiple target genes, gene pyramiding strategies can be used during the backcrossing phase to reduce the number of individuals required .Alternatively, the requirement that selected backcross individuals

must be heterozygous for all target genes could be relaxed. Although this will result in a decline in the frequency of the target genes in the backcross population, it may still be large enough to enable subsequent selection for these genes during the intercross phase. (Hospital and Charcosset 1997). MAIN PROBLEMS RELATED TO THE USE OF MOLECULAR GENETICS IN THE IMPROVEMENT 1.Direct use of a discovered QTL effect for selection across families is not possible. 2. By the time the information about the inferred genotypes is known, frequently the animals involved in the study are not available as candidates for selection, because they will be too old. 3. Advantage from within-family selection for a QTL bracketed by markers over BLUP or phenotypic selection alone is frequently low and the methodology to exploit this information for selection is complex and relatively inefficient. 4. There are statistical estimation errors, causing both false positive and false negative effects, particularly when the effect of the QTL is small. 5. There is a lack of consistency of the effect of the same QTL between studies, caused by QTL by genetic background (epistasis) of QTL by environment interactions. 6. The net economic effect of the QTL may be lower than the effect on single traits, because unfavourable effects on other traits. 7. Selection using QTL is more complex than phenotypic selection alone. QTL information (whether the information on the QTL is direct or indirect), adds to the list of traits used as selection criteria. Issues such as reduction of selection intensities and relative emphasis given to each trait, make optimal selection more difficult, with a need for adequate relative weights for the QTL, and the polygenic portions of the genetic variation for each trait at each generation (year). 8. Short-term gains due to MAS may be at the expense of medium to long-term polygenic responses for important traits.

CONCLUSION In livestock, knowledge of effects of specific genes and gene combinations on important traits could lead to their enhanced control to create new, more useful populations. The use of specific gene information is not a panacea, but could help to increase rates of genetic improvement, and open opportunities for using additive and non-additive genetic effects of

domestic species, provided wise improvement goals are used and this new technology is optimally used together with the so called traditional' or conventional' methods based on phenotypic and genealogical information. Detecting genes related to disease and their expression in humans from studies on the genome, could lead to the development of therapies and the development of drugs for specific individuals, and enhanced early diagnosis of individuals with high-risk genotypes, allowing for preventive or remedial actions, even gene therapy. In animals, this knowledge could lead, in addition, to select against defective genes. The limited reports that are available in plants primarily focus on the introgression of known genes or QTL regions and few results of a similar nature are available for Plant and mouse studies on the introgression of QTL regions show that foreground selection based on markers was effective in moving the targeted region into the recipient genome. However, the improvement in performance of the recipient breed was generally less than expected based on the initial QTL effect estimates . Apart from false positives or overestimation of effects in the initial population, reasons suggested for the lower response include presence of epistatic interactions among QTL and between QTL and the genetic background, and genotype by environment interactions. Similar factors could reduce the realized gain from MAS in synthetic or purebred populations. Given the uncertainties about the sustainability of marker effects, it appears prudent to use molecular genetic information in a manner that does not prevent progress toward the overall breeding goal that can be achieved through conventional selection. A crucial concept in this regard is to apply MAS in selection space that is not or under-utilized by conventional selection . A prime example is pre-selection on the basis of markers among members of a full-sib family for further testing, prior to availability of individual or progeny records. In such situations conventional selection has no basis for selection because EBV are derived from pedigree information, which is the same for all members of a full-sib family. Family members can, however, differ for the markers they inherited, which then provides a basis for selection, instead of having to make a random choice. An important decision for the application of MAS is which QTL or markers should be used in selection. QTL mapping studies typically apply very stringent thresholds based on genome-wide testing to reduce the rate of false positives. Reference 1. 1.Winter P.C ,G.I.Hickey and H.l Flectcher, 2003. Quantitative inheritance. Chapter in : Instant notes genetics. Second edition. Viva Books Private Limited. Page no. 168-169.

2. Dekkers, J.C.M., Hospital, F. 2002. The use of molecular genetics in improvement of agricultural populations. Nature Reviews: Genetics 3: 22-32. 3. de Koning, D. J., L. L. Janss, A. P. Rattink, P. A. van Oers, B. J. De Vries, M. A. Groenen, J. J. van der Poel, P. N. de Groot, E. W. Brascamp, and J. A. van Arendonk. 1999. Detection of quantitative trait loci for backfat thickness and intramuscular fat content in pigs. Genetics 152:16791690. . 4. Harlizius, B. and T. van der Lende. 2001. Contribution of genomics to unravel the physiological background of Physiol. Ses. GPh3, 1-12 5. Hospital, F., Charcosset, A., 1997. Marker-assisted introgression of quantitative trait loci. Genetics 147, 1469-1485. economically important traits in livestock. Proceedings of 52 Nd Annual Meeting of the EAAP. Budapest. Genet. Anim.