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Genetic Response from Marker Assisted Selection in an Outbred Population for Differing Marker Bracket Sizes and with Two Identified Quantitative Trait Loci
Richard Spelmana and Henk Bovenhuisaa Department of Animal Breeding, Wageningen Institute of Animal Sciences, Wageningen Agricultural University, 6700 AH, Wageningen, The Netherlands
Corresponding author: Richard Spelman, Department of Animal Science, Massey University Private Bag 11222, Palmerston North, New Zealand, r.j.spelman{at}massey.ac.nz (E-mail).
Communicating editor: B. S. WEIR
| ABSTRACT |
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Effect of flanking quantitative trait loci (QTL)-marker bracket size on genetic response to marker assisted selection in an outbred population was studied by simulation of a nucleus breeding scheme. In addition, genetic response with marker assisted selection (MAS) from two quantitative trait loci on the same and different chromosome(s) was investigated. QTL that explained either 5% or 10% of phenotypic variance were simulated. A polygenic component was simulated in addition to the quantitative trait loci. In total, 35% of the phenotypic variance was due to genetic factors. The trait was measured on females only. Having smaller marker brackets flanking the QTL increased the genetic response from MAS selection. This was due to the greater ability to trace the QTL transmission from one generation to the next with the smaller flanking QTL-marker bracket, which increased the accuracy of estimation of the QTL allelic effects. Greater negative covariance between effects at both QTL was observed when two QTL were located on the same chromosome compared to different chromosomes. Genetic response with MAS was greater when the QTL were on the same chromosome in the early generations and greater when they were on different chromosomes in the later generations of MAS.
QUANTITATIVE trait loci (QTL) are being detected in many species using many different experimental designs. In outbred livestock populations, half-sib experimental designs (![]()
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Theoretical evaluation of MAS in breeding schemes has been undertaken starting with the work of ![]()
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Molecular geneticists are continually developing and applying different methods in trying to get closer to the QTL of interest (![]()
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Genome scans have identified multiple QTL that affect the same trait (e.g., ![]()
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The objective of this study is to quantify the effect of differing sizes of flanking QTL-marker brackets on genetic response from MAS. In addition, genetic response from two QTL on the same and different chromosome(s) is investigated. Furthermore for the two QTL situation, genetic responses are investigated for two QTL of the same size, and also one large QTL and one small QTL.
| MATERIALS AND METHODS |
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Simulation model:
A stochastic simulation modeling a closed nucleus breeding scheme with discrete generations (each animal present as parent for only one generation) was developed. The initial generation of animals (termed base population) were unselected, unrelated and non-inbred. Each generation had 1024 animals with equal numbers of males and females. A single trait was simulated with base population heritability of 0.35, where heritability is the additive genetic variance divided by the phenotypic variance. The additive genetic variance was divided between unmarked additive polygenic variation (which will be referred to as polygenic variance) and variation due to the marked chromosomal region(s) (which will be referred to as QTL). Phenotypic records were recorded on females only. The highest ranking 12.5% of males and 50% of females for estimated genetic merit were selected as parents of the next generation. As phenotypes were only available on females, male genetic merit was estimated from pedigree information (e.g., sire, dam, and full- and half-sib information) and female genetic merit from own performance and pedigree information. Selection of males and females was undertaken after the single phenotypic record for females was available. Each sire was mated to four females (avoiding half-sib and closer matings) and each mating resulted in four offspring (two male and two female). Each female was mated to one sire only.
QTL alleles for the unselected base population were drawn from the distribution N(0, 1/2VQTL), where VQTL is the variance explained by the QTL. Two QTL variances were used in this study: 5% and 10% of phenotypic variance. The additive genetic variance (polygenic variance plus QTL variance) was 35% throughout the study. The number of QTL alleles in the base population was twice the number of parents selected from this generation. The large number of alleles represents the situation where the assumed QTL effect is actually due to a cluster of closely linked QTL.
A polygenic effect for each animal in the base population was sampled from the distribution N(0, Va), where Va is the polygenic variance. In subsequent generations, the polygenic component was sampled from the distribution N{1/2as + 1/2ad , 1/2[1 - 1/2(Fs + Fd)]Va}, where s and d denote sire and dam, a is the true polygenic value, and F is the inbreeding coefficient that was calculated using the algorithm presented by ![]()
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Marker alleles were simulated for all animals in the base population. It was assumed that the linkage map had six markers that bracketed the postulated QTL position (Figure 1). For the individuals in the base population, marker genotypes were simulated for each of the marker loci assuming five alleles with equal frequency. ![]()
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The required number of sires (64) and dams (256) were simulated for the base population and mated to produce the first generation. Three generations of selection were undertaken without using marker genotypes in the estimation of an animal's genetic merit. Polygenic variance decreases while selection is undertaken because of induced negative covariance between polygenes (![]()
Breeding value estimation:
Breeding value estimation (estimation of genetic merit) of polygenic and marker linked effects for MAS was undertaken using the model described by ![]()
Mixed model equations (![]()
=
, and G-1 = inverse of the matrix that describes the relationship between the QTL alleles,
=
This model is an extension of the methods of ![]()
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In brief, the computational method for marked-QTL considers that in the base population, the number of QTL alleles is equal to twice the number of base animals. In the next generation, the transmission of the parental QTL alleles is followed by inference on the marker haplotype. When transmission of marker haplotype can be followed, the Q matrix links the progeny's phenotype to the transmitted parental QTL allelic effect. When it is uncertain which QTL allele was transmitted, a new QTL allelic effect is formed in the evaluation procedure. The progeny's phenotype is linked via the Q matrix to the new QTL allelic effect and the new QTL allelic effect is linked to its parents through the G matrix i.e., the expectation of the new QTL allelic effect is equal to the mean of the parental QTL allelic effects.
The evaluation model does not assume that the exact location of the QTL within a marker bracket is known, but postulates that it is within the marker bracket. Probability statements are either that QTL transmission can be followed by inference on the marker haplotype, or it cannot. Thus probability statements, other than 0 or 1, are not made about transmission based on recombination events between flanking markers (double recombination) and postulated position relative to single markers (for further description of model see ![]()
If the origin of the marker allele could not be established at the closest flanking markers around the postulated QTL, based on parental and offspring marker genotypes, then the next informative marker in the haplotype was used. If allele origin could not be determined for at least one side of the marker haplotype, QTL transmission could not be determined according to the rules of ![]()
From generation -3, conventional mixed model equations (marker information not used) (![]()
Estimates on polygenic and QTL effects were obtained using iteration of the data (![]()
Differing flanking marker-QTL size:
The size of the interval between the two flanking QTL-markers was varied to determine the genetic benefit for MAS of localizing a QTL to a small chromosomal area. The four distances studied were 15 cM, 10 cM, 5 cM, and 2 cM. Distance to markers outside the flanking QTL-markers was kept constant in all simulations at 5 cM (Figure 1). One hundred and sixty replicates were simulated for both MAS and the control for each scenario investigated.
Two QTL:
Two QTL were simulated either on the same or on different chromosomes. The number of alleles simulated for each QTL was twice the number of base parents. The variances due to QTL were either the same size or one accounted for 75% of the QTL variance and the other 25%. The combined variance of the two QTL was either 5% or 10% of the phenotypic variance, i.e., the same levels as used for the one QTL models. When the two QTL were placed on the same chromosome the distance between the two QTL was 30 cM. Thirty centimorgans was chosen as this distance is the approximate level of resolution that one can identify two separate QTL in current livestock QTL experiments (![]()
The control for the two QTL scenarios was conventional selection on the genetic model of polygenic variance and variance at two QTL. One hundred and sixty replicates were simulated for both MAS and the control for each scenario investigated.
| RESULTS |
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Genetic gain with base model:
The rate of genetic gain for the breeding scheme modeled for a trait of 35% heritability, which consisted solely of polygenic variance, was close to 0.3
P per generation. Equilibrium response with this model was reached after three to four generations of conventional BLUP selection, confirming that three generations of conventional breeding was sufficient to mimic the introduction of MAS into an ongoing breeding scheme.
Flanking QTL-marker size:
The smaller the flanking QTL-marker bracket the greater the cumulative superiority of MAS over the control (Table 1 and Table 2). The 5-cM bracket had, on average, 90% and 85% of the genetic superiority of MAS (over the control), which was achieved with the 2-cM bracket for the 5% and 10% QTL, respectively. The 10-cM bracket achieved an average genetic response of some 80% relative to that of the 2-cM bracket for both sized QTL (results not shown). For the 5% QTL and 15-cM bracket, the MAS superiority was quite variable, relative to the 2-cM bracket (Table 1) and lower than that of the 10% QTL (Table 1 and Table 2). The relative superiority of the 5% QTL for the 15-cM bracket is similar to that of the 20-cM bracket for the 10% QTL (results not shown).
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The difference in relative response of the 15-cM bracket to the 2-cM bracket between the 5% and 10% QTL, after generation one, may reflect that the value of phenotypes is a curvilinear function, i.e., the first phenotypes per QTL allelic effect have a larger effect on accuracy than the additional ones. The number of phenotypes needed per QTL allelic effect to get a certain accuracy will be larger for the 5% QTL than the 10% QTL, since the 5% QTL explains less of the phenotypic variance. Thus, for the 5% QTL, the 15-cM flanking QTL-marker bracket may move the accuracy of QTL estimation off the plateau-like level of the curvilinear slope. However, for the 10% QTL, the reduction in number of phenotypes per allelic effect when going from a 10-cM bracket to a 15-cM bracket may only reduce accuracy a little. This was observed with the reduction in QTL accuracy decreasing more for the 5% QTL than the 10% QTL when going from a 10-cM to a 15-cM bracket (not shown).
The source of the extra genetic gain with the smaller marker brackets was from extra gain made at the QTL when moving from a 15-cM bracket to a 5-cM bracket for the 5% and 10% QTL (Table 1 and Table 2). Moving from a 5-cM to a 2-cM bracket, for the 10% QTL, the increase in overall genetic gain was from extra QTL response in the first two generations. In the next three generations the extra gain was from both QTL and polygenic and in the last two generations it came from a reduction in polygenic loss (Table 2). For the 5% QTL the extra genetic gain from going from a 5-cM bracket to a 2-cM bracket came from primarily an increase in QTL response with polygenic loss staying stable (Table 1).
Ability to follow transmission of QTL: The ability to unambiguously follow QTL transmission from parent to offspring based on marker haplotype decreased over generations (Table 3). The size of the flanking QTL-marker bracket affected the ability to follow QTL transmission in the first four to five generations of MAS but after seven generations there were only minor differences (Table 3). Reduction in ability to follow QTL transmission was greater for the 10% QTL compared to the 5% QTL due to greater QTL selection pressure and therefore faster fixation (results not shown).
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Correlation of estimated and true QTL effects: The smaller the flanking QTL-marker bracket the higher the correlation between estimated and true QTL effects for the 5% QTL (Table 4). This was also observed for the 10% QTL where the correlation between estimated effects and true effects was higher than that for the 5% QTL (results not presented). The correlation increased in the first three to four generations of MAS as more information (phenotypes) accumulated for the estimation of QTL allelic effects. In the last three to four generations of MAS, the correlation decreased as the ability to follow QTL transmission decreased and, therefore, new QTL allelic effects were formed in the evaluation method. The new allelic effects were allocated the average of the parental effects that resulted in lower accuracy.
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For the 10% QTL, the BLUP evaluation method was slightly biased in the later generations and genetic gain at the QTL was overestimated. This is probably due to the decrease in QTL variation through changes in allele frequencies, which violates the assumptions of the model. ![]()
Two QTL:
For the two QTL that together explained 10% of the phenotypic variance, the genetic response was similar regardless of the relative size of the two QTL (Table 5). In the early generations of MAS, the genetic response with MAS was greater when the two QTL were located on the same chromosome than when they were on different chromosomes. In the later generations, the rate of genetic gain when the two QTL were on the same chromosome was less than when they were on different chromosomes. Comparing the two QTL that had a cumulative variance of 10% to one 10% QTL, the genetic superiority over no MAS was nearly the same for the first five generations. In the last two generations, the two QTL model had greater superiority over the control compared to the one QTL model. This was due to there being more QTL variance for the two QTL genetic model in the later generations compared to the single 10% QTL.
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For the 5% QTL, the relative size of the two QTL had an effect on the percentage superiority of MAS over the control (Table 5). Having two QTL that were unequal in size resulted in lower percentage superiority in the later generations than that achieved with QTL of equal size. The lower response for the unequal QTL size for the 5% QTL was due to the size of the smaller QTL explaining only 1.25% of the phenotypic variance. MAS with a single QTL of this size (1.25%) was not superior to that without MAS (results not shown) as the accuracy of the QTL allelic effects was low for the breeding scheme structure simulated.
When the two QTL were positioned on the same chromosome, the level of negative covariance between the two QTL was greater than when the QTL were on different chromosomes (Figure 2). The negative covariance increased in the generations previous to the introduction of MAS. With the introduction of MAS, the level of negative covariance between the QTL increased and the negative covariance remained at a higher level when the two QTL were on the same chromosome. When one QTL comprised 75% of the QTL variance and the other 25%, the level of negative covariance was less than that observed for two QTL of equal size (not shown). The level of negative covariance between the polygenic component and the QTL component was not affected by the relative location of the two QTL nor relative size (not shown). The same trends were observed for two QTL that had a cumulative variance of 5%.
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When the two QTL were of unequal size (75% and 25%), greater selection response was made at the larger QTL, as was expected. The level of contribution to the QTL variance from the two QTL changed over the generations. For the 10% QTL, the QTL variance in generation four was comprised of 66% from the larger QTL and 34% from the smaller, and by generation seven it was 50:50. For the 5% QTL, the QTL variance in generation seven was comprised of 60% from the larger QTL and 40% from the smaller QTL. In comparison, the level of variance contributed in the control was some 70:30 after seven generations for both sized QTL.
| DISCUSSION AND CONCLUSIONS |
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Negative covariance between two QTL was maintained at a higher level when the two QTL were on the same chromosome in contrast to being on different chromosomes. This is to be expected as the decay of negative covariance is slowed by linkage (![]()
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The accuracy of allelic effect estimates was reasonably high at the start of MAS (Table 4). This was because of marker genotypes being present on all five generations prior to the start of MAS. When MAS started with fewer previous generations of marker genotypes and phenotypes the genetic response to MAS was reduced (![]()
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The greater accuracy in estimation of QTL effects with the smaller flanking brackets resulted in greater gain at the QTL when reducing bracket size from 15 cM to 10 cM and subsequently to 5 cM as would be expected. However, the greater polygenic response, or equivalently, the reduction in polygenic loss when reducing the bracket from 5 cM to 2 cM for the 10% QTL, was not expected. In the last two generations the greater response from the smaller bracket was solely from the polygenic component. The polygenic response may be due to the QTL allele being more accurately estimated in the 2-cM bracket situation and, therefore, the adjustment of phenotype in estimation of polygenic value is more correct. In the last two generations, when one QTL may be predominant, the same QTL allele may be selected for both bracket sizes but it is selected in animals with better polygenic value for the 2-cM bracket situation.
The genetic evaluation system used in this study (![]()
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In the MA-BLUP method that was used in this study, a shortcoming was when the two QTL effects for a parent were the same and QTL transmission from the marker haplotype could not be followed. In this situation, a new QTL effect was formed in MA-BLUP for the offspring. An improvement would be to identify via the evaluation method if two QTL effects were presumed to be the same in a parent and offspring of this parent get allocated this QTL effect in the Q matrix regardless of the marker haplotype information. This may have improved the accuracy of estimation of QTL effects in later generations.
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| ACKNOWLEDGMENTS |
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The authors acknowledge the helpful comments of JOHAN VAN ARENDONK in the preparation of this manuscript. R. J. SPELMAN thanks Livestock Improvement Corporation for financial support.
Manuscript received July 14, 1997; Accepted for publication November 24, 1997.
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