Selective genotyping of one or both phenotypic extremes of a population can be used to detect linkage between markers and quantitative trait loci (QTL) in situations in which full-population genotyping is too costly or not feasible, or where the objective is to rapidly screen large numbers of potential donors for useful alleles with large effects. Data may be subjected to ‘trait-based’ analysis, in which marker allele frequencies are compared between classes of progeny defined based on trait values, or to ‘marker-based’ analysis, in which trait means are compared between progeny classes defined based on marker genotypes. Here, bidirectional and unidirectional selective genotyping were simulated, using population sizes and selection intensities relevant to cereal breeding. Control of Type I error was usually adequate with marker-based analysis of variance or trait-based testing using the normal approximation of the binomial distribution. Bidirectional selective genotyping was more powerful than unidirectional. Trait-based analysis and marker-based analysis of variance were about equally powerful. With genotyping of the best 30 out of 500 lines (6%), a QTL explaining 15% of the phenotypic variance could be detected with a power of 0.8 when tests were conducted at a marker 10 cM from the QTL. With bidirectional selective genotyping, QTL with smaller effects and (or) QTL farther from the nearest marker could be detected. Similar QTL detection approaches were applied to data from a population of 436 recombinant inbred rice lines segregating for a large-effect QTL affecting grain yield under drought stress. That QTL was reliably detected by genotyping as few as 20 selected lines (4.5%). In experimental populations, selective genotyping can reduce costs of QTL detection, allowing larger numbers of potential donors to be screened for useful alleles with effects across different backgrounds. In plant breeding programs, selective genotyping can make it possible to detect QTL using even a limited number of progeny that have been retained after selection.
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Bernier J, Kumar A, Ramaiah V, Spaner D, Atlin G (2007) A large-effect QTL for grain yield under reproductive-stage drought stress in upland rice. Crop Sci 47:507–518
Darvasi A, Soller M (1992) Selective genotyping for determination of linkage between a marker locus and a quantitative trait locus. Theor Appl Genet 85:353–359
Darvasi A, Soller M (1994) Selective DNA pooling for determination of linkage between a molecular marker and a quantitative trait locus. Genetics 138:1365–1373
Falconer DS (1989) Introduction to quantitative genetics, 3rd edn. Longman, New York
Foolad MR, Zhang LP, Lin GY (2001) Identification and validation of QTLs for salt tolerance during vegetative growth in tomato by selective genotyping. Genome 44:444–454
Gallais A, Moreau L, Charcosset A (2007) Detection of marker-QTL association by studying change in marker frequencies with selection. Theor Appl Genet 114:669–681
Holland JB, Nyquist WE, Cervantes-Martinez CT (2003) Estimating and interpreting heritability for plant breeding: an update. Plant Breed Rev 22:9–111
Kosambi DD (1944) The estimation of map distances from recombination values. Ann Eugen 12:172–175
Lander ES, Botstein D (1989) Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121:185–199
Lebowitz RJ, Soller M, Beckmann JS (1987) Trait-based analysese for the detection of linkage between marker loci and quantitative trait loci in crosses between inbred lines. Theor Appl Genet 73:556–562
Lee C (2005) Selection bias in quantitative trait loci mapping. J Hered 96:363–367
Lin JZ, Ritland K (1996) The effects of selective genotyping on estimates of proportion of recombination between linked quantitative trait loci. Theor Appl Genet 93:1261–1266
Liu HB (1998) Statistical genomics: linkage, mapping, and QTL analysis. CRC Press, New York, pp 493–517
Lyttle TW (1991) Segregation distorters. Ann Rev Genet 25:511–557
Mather KN, Jinks JL (1982) Biometrical genetics: the study of continuous variation, 3rd edn. Chapman and Hall, New York, pp 135–175
Ronin YI, Korol AB, Weller JI (1998) Selective genotyping to detect quantitative trait loci affecting multiple traits: interval mapping analysis. Theor Appl Genet 97:1169–1178
SAS Institute (2003) Release 9.1. SAS Institute, Inc, Cary
Steel RGD, Torrie JH, Dickey DA (1997) Principles and procedures of statistics: a biometrical approach, 3rd edn. McGraw Hill Inc, New York
Tanksley SD, Nelson JC (1996) Advanced backcross QTL analysis: a method for the simultaneous discovery and transfer of valuable QTLs from unadapted germplasm into elite breeding lines. Theor Appl Genet 92:191–203
Tenesa A, Visscher PM, Carothers AD, Knott SA (2005) Mapping quantitative trait loci using linkage disequilibrium: marker- versus trait-based methods. Beh Genet 35:219–228
Wan J, Yamaguchi Y, Kato H, Ikehashi H (1996) Two new loci for hybrid stability in cultivated rice (Oryza sativa L.). Theor Appl Genet 92:183–190
Xu S, Vogl C (2000) Maximum likelihood analysis of quantitative trait loci under selective genotyping. Heredity 84:525–537
Xu Y, Wang J, Crouch J (2008) Selective genotyping and pooled DNA analysis: an innovative use of an old concept. In: Recognizing past achievement, meeting future needs. Proceedings of the 5th international crop science congress, April 13–18, 2008, Jeju, Korea. Published on CDROM, Website http://www.cropscience2008.com.
Zamir D, Tadmor Y (1986) Unequal segregation of nuclear genes in plants. Bot Gaz 147:355–358
Zhang LP, Lin GY, Niño D, Foolad MR (2003) Mapping QTLs conferring early blight (Alternaria solani) resistance in a Lycopersicon esculentum × L. hirsutum cross by selective genotyping. Mol Breed 12:3–19
This research was conducted with financial support from research grants provided by the Canadian International Development Agency, Natural Sciences and Engineering Research Council of Canada, the Alberta Agricultural Research Institute, and the Alberta Crop Industry Development Fund. Genetic simulation experiments were conducted in part by using Perl scripts written by Hai Pham. We thank Hai Pham and Nicholas Tinker for providing access to this unpublished software and we thank Hai Pham for helping with computer programming. We are also grateful to Chris-Carolin Schön for critical review of an earlier version of the manuscript. We are grateful for the insightful suggestions of several anonymous reviewers.
Communicated by M. Sillanpaa.
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Navabi, A., Mather, D.E., Bernier, J. et al. QTL detection with bidirectional and unidirectional selective genotyping: marker-based and trait-based analyses. Theor Appl Genet 118, 347–358 (2009). https://doi.org/10.1007/s00122-008-0904-2
- Quantitative Trait Locus
- Segregation Distortion
- Quantitative Trait Locus Effect
- Quantitative Trait Locus Detection
- Quantitative Trait Locus Allele