Marker assisted selection for genetic improvement of animal populations when a single QTL is marked

SummaryA Monte Carlo simulation study to evaluate the benefits of marker assisted selection (MAS) in small populations with one marked bi-allelic quantitative trait locus (QTL) is described. In the base generation, linkage phase equilibrium between the markers, QTL and polygenes was assumed and frequencies of 0·5 for the two QTL alleles were used. Six discrete generations of selection for a single character measured on both sexes followed. An additive genetic model was used with the QTL positioned midway between two highly polymorphic markers. Schemes were simulated with a distance of 10 cM between the QTL and either of the two markers and with the QTL explaining 1/8 of the total genetic variance in the base generation. Values of 0·5, 0·25 or 0·1 were assumed for the heritability. Eight males and 16, 32 or 64 females were selected each generation with each dam producing four sons and four daughters as candidates for the next generation. Animals were evaluated with a conventional BLUP animal model or with a model using marker information. MAS resulted in substantially higher QTL responses (4–54%), especially with low heritabilities, than conventional BLUP but lower polygenic responses (up to 4%) so that the overall effect on the total genetic response, although in the majority of cases favourable, was relatively small. With QTLs of larger size (explaining 25% of the genetic variance) comparable results were found. When the distance between the QTL and the markers was reduced to 2 cM, genetic responses were increased very slightly with a heritability of 0·5 whereas with a heritability of 0·1 responses were increased by up to 10%, compared with conventional BLUP. Results emphasize that MAS should be most useful for lowly heritable traits and that once QTLs for such traits have been identified the search for closely linked polymorphic markers should be intensified.

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Genetic variation in a line of mice selected to its limit for high body weight

Animal Science ◽

10.1017/s0003356100022856 ◽

1974 ◽

Vol 19 (3) ◽

pp. 273-289 ◽

Cited By ~ 5

Author(s):

W. K. Al-Murrani ◽

R. C. Roberts

Keyword(s):

Body Weight ◽

Genetic Variance ◽

Genetic Model ◽

Random Mating ◽

Inbred Lines ◽

High Body Weight ◽

High Body ◽

Lower Body Weight ◽

Recessive Genes ◽

Selection For

SUMMARYA line of mice, at its limit to selection for high body weight did not decline in performance over 11 generations of random mating, neither did it respond when selection was renewed. The experiment tested a method of improving body weight by a scheme which had earlier increased litter size under similar circumstances. The scheme was to derive partially inbred lines from the plateaued line, to select during inbreeding and, finally, to cross the best inbreds. Body weight was not increased, but the study allowed further examination of the residual genetic variance in the line.During inbreeding, the inbred lines became clearly differentiated in body weight, proving that loci controlling body weight had not become fixed. There was also a significant response to selection for a lower body weight during inbreeding. The pattern of results suggested the segregation of recessive genes, detrimental to high body weight but which selection had become inefficient at removing. A genetic model compatible with the results accommodated several such recessives, perhaps as many as 10, each with an effect of about two-thirds of a standard deviation (or some equivalent combination of gene number and effect), and at frequencies of around 0·2. Nevertheless, the total improvement in body weight to be gained by their elimination was only half a gram, or less than 2 %. Thus, substantial genetic effects can occur at individual loci despite trivially low heritabilities and negligible potential gains.

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A classical setting for associations between markers and loci affecting quantitative traits

Genetics Research ◽

10.1017/s0016672399004231 ◽

1999 ◽

Vol 74 (3) ◽

pp. 271-277 ◽

Cited By ~ 25

Author(s):

DAHLIA M. NIELSEN ◽

B. S. WEIR

Keyword(s):

Genetic Marker ◽

Quantitative Trait ◽

Quantitative Traits ◽

Genetic Variance ◽

Genetic Model ◽

Marker Locus ◽

Multiple Alleles ◽

Classical Setting ◽

Tests Of Association ◽

Trait Locus

We examine the relationships between a genetic marker and a locus affecting a quantitative trait by decomposing the genetic effects of the marker locus into additive and dominance effects under a classical genetic model. We discuss the structure of the associations between the marker and the trait locus, paying attention to non-random union of gametes, multiple alleles at the marker and trait loci, and non-additivity of allelic effects at the trait locus. We consider that this greater-than-usual level of generality leads to additional insights, in a way reminiscent of Cockerham's decomposition of genetic variance into five terms: three terms in addition to the usual additive and dominance terms. Using our framework, we examine several common tests of association between a marker and a trait.

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Marker-assisted selection in an outbred poultry breeding nucleus

Animal Science ◽

10.1017/s1357729800014442 ◽

1996 ◽

Vol 62 (1) ◽

pp. 171-180 ◽

Cited By ~ 14

Author(s):

S. van der Beck ◽

J. A. M. van Arendonk

Keyword(s):

Genetic Variance ◽

Genetic Model ◽

Phenotypic Variance ◽

Family Selection ◽

Poultry Breeding ◽

Cumulative Response ◽

Trait Locus ◽

Final Selection ◽

Selection Of ◽

Variance Explained

AbstractThe value of using a marker for a quantitative trait locus (QTL) affecting a sex-limited trait in an outbred poultry breeding nucleus was studied. Marker and QTL were in linkage equilibrium in the base population. The recombination rate between marker and QTL was 0-05. A closed nucleus with 9000 chickens per generation was deterministically simulated. The genetic model contained polygenes and a QTL linked to a marker. Genetic effects explained proportionately 0·3 of the phenotypic variance before selection. Under selection, polygenic variance reached an equilibrium and QTL variance decreased continuously over time. Cocks were selected in two steps. First the best cocks of each full-sib family were selected (within-family selection) while final selection took place after information on fiill-sibs was available. Hens were selected after they had completed production. The effect of using marker information in estimating breeding values was studied in an ongoing breeding programme. Transmission of marker alleles was always traceable. Cumulative response over five generations increased proportionately by 0·06 to 0·13 if a marker linked to a QTL that explained 0·2 of the genetic variance was used. Cumulative response increased up to 0·28 if the QTL explained 0-8 of the genetic variance. Additional response due to the use of a marker increased with increasing intensity of within-family selection of cocks, increased with increasing variance explained by the QTL and was higher if within-family selection of cocks was carried out after rather than before their sibs had complete records.

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A Population Genetics Model of Marker-Assisted Selection

Genetics ◽

10.1093/genetics/146.3.1173 ◽

1997 ◽

Vol 146 (3) ◽

pp. 1173-1183

Author(s):

Z W Luo ◽

R Thompson ◽

J A Woolliams

Keyword(s):

Linkage Disequilibrium ◽

Marker Assisted Selection ◽

Genetic Variance ◽

Additive Genetic Variance ◽

Phenotypic Selection ◽

Genetic Response ◽

Factors Affecting ◽

Short And Long Term ◽

Trait Locus ◽

Rate Of Dissipation

A deterministic two-loci model was developed to predict genetic response to marker-assisted selection (MAS) in one generation and in multiple generations. Formulas were derived to relate linkage disequilibrium in a population to the proportion of additive genetic variance used by MAS, and in turn to an extra improvement in genetic response over phenotypic selection. Predictions of the response were compared to those predicted by using an infinite-loci model and the factors affecting efficiency of MAS were examined. Theoretical analyses of the present study revealed the nonlinearity between the selection intensity and genetic response in MAS. In addition to the heritability of the trait and the proportion of the marker-associated genetic variance, the frequencies of the selectively favorable alleles at the two loci, one marker and one quantitative trait locus, were found to play an important role in determining both the short- and long-term efficiencies of MAS. The evolution of linkage disequilibrium and thus the genetic response over several generations were predicted theoretically and examined by simulation. MAS dissipated the disequilibrium more quickly than drift alone. In some cases studied, the rate of dissipation was as large as that to be expected in the circumstance where the true recombination fraction was increased by three times and selection was absent.

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Marker assisted selection for confirming F1 plants for tidal tolerant rice variety development

Amazonian Journal of Plant Research ◽

10.26545/ajpr.2020.b00075x ◽

2020 ◽

Vol 4 (3) ◽

pp. 668-678

Author(s):

Mithun Saha ◽

Md. Niuz Morshed Khan ◽

Sujan Kumar Kundu ◽

Md. Monirul Islam ◽

Sabina Yasmin ◽

...

Keyword(s):

Marker Assisted Selection ◽

Rice Variety ◽

Selection For

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SELECTION FOR BLOOD PRESSURE LEVELS IN MICE

Genetics ◽

10.1093/genetics/76.3.537 ◽

1974 ◽

Vol 76 (3) ◽

pp. 537-549

Author(s):

Gunther Schlager

Keyword(s):

Blood Pressure ◽

Systolic Blood Pressure ◽

Genetic Variance ◽

Additive Genetic Variance ◽

Population Bottleneck ◽

Control Line ◽

Selected Lines ◽

High Line ◽

Selection For ◽

Random Control

ABSTRACT Response to two-way selection for systolic blood pressure was immediate and continuous for about eight generations. In the twelfth generation, the High males differed from the Low males by 38 mmHG; the females differed by 39 mmHg. There was little overlap between the two lines and they were statistically significant from each other and from the Random control line. There appeared to be no more additive genetic variance in the eleventh and twelfth generations. Causes for the cessation of response are explored. This is probably due to a combination of natural selection acting to reduce litter sizes in the Low line, a higher incidence of sudden deaths in the High line, and loss of favorable alleles as both selection lines went through a population bottleneck in the ninth generation.—In the eleventh generation, the selected lines were used to produce F1, F2, and backcross generations. A genetic analysis yielded significant additive and dominance components in the inheritance of systolic blood pressure.

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