Selective genotyping for determination of linkage between a marker locus and a quantitative trait locus

Summary“Selective genotyping” is the term used when the determination of linkage between marker loci and quantitative trait loci (QTL) affecting some particular trait is carried out by genotyping only individuals from the high and low phenotypic tails of the entire sample population. Selective genotyping can markedly decrease the number of individuals genotyped for a given power at the expense of an increase in the number of individuals phenotyped. The optimum proportion of individuals genotyped from the point of view of minimizing costs for a given experimental power depends strongly on the cost of completely genotyping an individual for all of the markers included in the experiment (including the costs of obtaining a DNA sample) relative to the cost of rearing and trait evaluation of an individual. However, in single trait studies, it will almost never be useful to genotype more than the upper and lower 25% of a population. It is shown that the observed difference in quantitative trait values associated with alternative marker genotypes in the selected population can be much greater than the actual gene effect at the quantitative trait locus when the entire population is considered. An expression and a figure is provided for converting observed differences under selective genotyping to actual gene effects.

[1]  U. Pieper,et al.  Effects of marked chromosome sections on milk performance in cattle , 1985, Theoretical and Applied Genetics.

[2]  M. Soller,et al.  The Efficiency of Experimental Designs for the Detection of Linkage between a Marker Locus and a Locus Affecting a Quantitative Trait in Segregating Populations , 1978 .

[3]  R. Elston,et al.  A general model for the genetic analysis of pedigree data. , 1971, Human heredity.

[4]  K. Sax,et al.  The Association of Size Differences with Seed-Coat Pattern and Pigmentation in PHASEOLUS VULGARIS. , 1923, Genetics.

[5]  R. Fernando,et al.  Associations between genetic markers and growth and carcass traits in a paternal half-sib family of Angus cattle. , 1990, Journal of animal science.

[6]  J. Jensen.  Estimation of recombination parameters between a quantitative trait locus (QTL) and two marker gene loci , 1989, Theoretical and Applied Genetics.

[7]  H. Grüneberg,et al.  Introduction to quantitative genetics , 1960 .

[8]  S. Simpson.  Detection of linkage between quantitative trait loci and restriction fragment length polymorphisms using inbred lines , 1989, Theoretical and Applied Genetics.

[9]  S. Tanksley,et al.  Use of naturally-occurring enzyme variation to detect and map genes controlling quantitative traits in an interspecific backcross of tomato , 1982, Heredity.

[10]  T. Helentjaris,et al.  Molecular marker-facilitated investigations of quantitative trait loci in maize. II. Factors influencing yield and its component traits , 1987 .

[11]  A. Robertson,et al.  The Association between Blood Groups and Several Production Characteristics in Three Danish Cattle Breeds , 1961 .

[12]  S. Knapp,et al.  Using molecular markers to estimate quantitative trait locus parameters: power and genetic variances for unreplicated and replicated progeny. , 1990, Genetics.

[13]  Eric S. Lander,et al.  Resolution of quantitative traits into Mendelian factors by using a complete linkage map of restriction fragment length polymorphisms , 1988, Nature.

[14]  A. Kahler,et al.  Associations between quantitative traits and enzyme loci in the F2 population of a maize hybrid , 1986, Theoretical and Applied Genetics.

[15]  T. Brody,et al.  On the power of experimental designs for the detection of linkage between marker loci and quantitative loci in crosses between inbred lines , 2004, Theoretical and Applied Genetics.

[16]  J. Wendel,et al.  Molecular-marker-facilitated investigations of quantitative-trait loci in maize. I. Numbers, genomic distribution and types of gene action. , 1987, Genetics.

[17]  Weller Ji.  Maximum likelihood techniques for the mapping and analysis of quantitative trait loci with the aid of genetic markers. , 1986 .

[18]  G. Haenlein,et al.  Associations of bovine blood and milk polymorphisms with lactation traits: Guernseys. , 1987, Journal of dairy science.

[19]  M. Soller,et al.  Optimum spacing of genetic markers for determining linkage between marker loci and quantitative trait loci , 1994, Theoretical and Applied Genetics.

[20]  J. Beckmann,et al.  Marker-based mapping of quantitative trait loci using replicated progenies , 1990, Theoretical and Applied Genetics.

[21]  J. Beckmann,et al.  Genetic polymorphism in varietal identification and genetic improvement , 1983, Theoretical and Applied Genetics.

[22]  S. N. Gaunt,et al.  Associations of bovine blood and milk polymorphisms with lactation traits: Holsteins. , 1987, Journal of dairy science.

[23]  H. Geldermann.  Investigations on inheritance of quantitative characters in animals by gene markers I. Methods , 2004, Theoretical and Applied Genetics.

[24]  E. Lander,et al.  Mapping mendelian factors underlying quantitative traits using RFLP linkage maps. , 1989, Genetics.

[25]  A. Hill.  Quantitative linkage: a statistical procedure for its detection and estimation , 1975, Annals of human genetics.

[26]  M. Soller,et al.  Linkage analysis of quantitative traits in an interspecific cross of tomato (lycopersicon esculentum x lycopersicon pimpinellifolium) by means of genetic markers. , 1988, Genetics.

[27]  J. Weller,et al.  Mapping and analysis of quantitative trait loci in Lycopersicon (tomato) with the aid of genetic markers using approximate maximum likelihood methods , 1987, Heredity.

[28]  J. Beckmann,et al.  Trait-based analyses for the detection of linkage between marker loci and quantitative trait loci in crosses between inbred lines , 1987, Theoretical and Applied Genetics.