QTL Identification

  • N. Manikanda Boopathi


Most of the important agronomic traits are quantitatively inherited and are controlled by several genes (i.e. polygenic). Thus, the nature of quantitative traits is that their expression is controlled by tens, hundreds or even thousands of quantitative trait loci (QTL), and in general, they are having only a small effect on the trait. QTL is a genomic region that comprises gene(s) which govern(s) the expression of the quantitative trait. Since the advent of molecular markers, researchers and breeders have aimed to identify functional markers (refer chapter x for different kinds of markers) associated with these QTL for implementation of marker-assisted selection. Historically, QTL detection started with linkage mapping in biparental populations (refer chapter x for population types). Identifying a gene or QTL within a plant genome is like finding the proverbial needle in a haystack. However, QTL analysis can be used to divide the haystack in manageable piles and systematically search them. In simple terms, QTL analysis is based on the principle of detecting an association between phenotype and the genotype of markers. Markers are used to partition the mapping population into different genotypic groups based on the presence or absence of a particular marker locus and to determine whether significant differences exist between groups with respect to the quantitative trait being measured. Thus, statistically a significant difference between phenotypic means of the marker groups (either 2 or 3), depending on the marker system and type of population, indicates that the marker locus being used to partition the mapping population is linked to a QTL controlling the trait.


Quantitative Trait Locus Interval Mapping Quantitative Trait Locus Analysis Composite Interval Mapping Quantitative Trait Locus Effect 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


Literature Cited

  1. Churchill GA, Doerge RW (1994) Empirical threshold values for quantitative trait mapping. Genetics 138(3):963–971PubMedGoogle Scholar
  2. Comai L, Young K, Till BJ, Reynolds SH, Greene EA, Codomo CA, Enns LC, Johnson JE, Burtner C, Odden AR, Henikoff S (2004) Efficient discovery of DNA polymorphisms in natural populations by Ecotilling. Plant J 37:778–786PubMedCrossRefGoogle Scholar
  3. Edwards MD, Stuber CW, Wendel JF (1987) Molecular marker facilitated investigation of quantitative trait loci in maize. I. Numbers, genomic distribution and types of gene action. Genetics 116:113–125PubMedGoogle Scholar
  4. Etzel C, Guerra R (2002) Meta-analysis of genetic-linkage of quantitative trait loci. Am J Hum Genet 71:56–65PubMedCrossRefGoogle Scholar
  5. Goffinet B, Gerber S (2000) Quantitative trait loci: a meta-analysis. Genetics 155:463–473PubMedGoogle Scholar
  6. Guo SW, Thompson EA (1992) Performing the exact test of Hardy-Weinberg proportion for multiple alleles. Biometrics 48:361–372PubMedCrossRefGoogle Scholar
  7. Han F, Ullrich SE, Kleinhofs A, Jones BL, Hayes PM, Wesenberg DM (1997) Fine structure mapping of the barley chromosome- 1 centromere region containing malting-quality QTLs. Theor Appl Genet 95:903–910CrossRefGoogle Scholar
  8. Hansen M, Kraft T, Ganestam S, Säll T, Nilsson NO (2001) Linkage disequilibrium mapping of the bolting gene in sea beet using AFLP markers. Genet Res 77:61–66PubMedCrossRefGoogle Scholar
  9. Jansen RC (1993) Interval mapping of multiple quantitative trait loci. Genetics 135:205–211PubMedGoogle Scholar
  10. Jansen J, De Jong AG, Van Ooijen JW (2001) Constructing dense genetic linkage maps. Theor Appl Genet 102:1113–1122CrossRefGoogle Scholar
  11. Jiang C, Zeng ZB (1995) Multiple trait analysis of genetic mapping for quantitative trait loci. Genetics 140:1111–1117PubMedGoogle Scholar
  12. Jiang C, Zengt ZB (1995) Multiple trait analysis of genetic mapping for quantitative trait loci. Genetics 140(3):1111–1127PubMedGoogle Scholar
  13. Kao C-H et al (1999) Multiple interval mapping for quantitative trait loci. Genetics 152:1203–1216PubMedGoogle Scholar
  14. Lander ES, Botstein D (1989) Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121:185–199PubMedGoogle Scholar
  15. Mangin B, Thoquet P, Grimsley N (1998) Pleiotropic QTL analysis. Biometrics 54:88–99CrossRefGoogle Scholar
  16. McCallum CM, Comai L, Greene EA, Henikoff S (2000) Targeting induced local lesions IN genomes (TILLING) for plant functional genomics. Plant Physiol 123:439–442PubMedCrossRefGoogle Scholar
  17. Michelmore RW, Paran I, Kesseli RV (1991) Identification of markers linked to disease-resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic regions by using segregating populations. Proc Natl Acad Sci USA 88:9828–9832PubMedCrossRefGoogle Scholar
  18. Moser G, Muller E, Beeckmann P, Yue G, Geldermann H (1998) Mapping QTL in F2 generations of Wild Boar, Pietrain and Meishanpigs. In: Proceedings of the 6th world congress on genetics applied to livestock production, vol 26, Armidale, pp 478–481Google Scholar
  19. Paterson AH, Lander ES, Hewitt JD, Peterson S, Lincoln SE, Tanksley SD (1988) Resolution of quantitative traits into Mendelian factors by using a complete linkage map of restriction fragment length polymorphisms. Nature 335:521–529CrossRefGoogle Scholar
  20. Rodolphe F, Lefort M (1993) A multi-marker model for detecting chromosomal segments displaying QTL activity. Genetics 134:1277–1288PubMedGoogle Scholar
  21. Sax K (1923) The association of size difference with seed-coat pattern and pigmentation in Phaseolus vulgaris. Genetics 8:552–560PubMedGoogle Scholar
  22. Schena M, Shalon D, Davis RW, Brown PO (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270:467–470PubMedCrossRefGoogle Scholar
  23. Schneider AK, Mary EB, James DK (1997) Marker-assisted selection to improve drought resistance in common bean. Crop Sci 37:51–60CrossRefGoogle Scholar
  24. Thoday JM (1961) Location of polygenes. Nature 191:368–370CrossRefGoogle Scholar
  25. Thornsberry JM, Goodman MM, Doebley J, Kresovich S, Nielsen D et al (2001) Dwarf 8 polymorphisms associate with variation in flowering time. Nat Genet 28:286–289PubMedCrossRefGoogle Scholar
  26. Visscher PM, Thompson R, Haley CS (1996) Confidence intervals in QTL mapping by bootstrapping. Genetics 143:1013–1020PubMedGoogle Scholar
  27. Wolyn DJ, Borevitz JO, Loudet O, Schwartz C, Maloof J, Ecker JR, Berry CC, Chory J (2004) Light-response quantitative trait loci identified with composite interval and eXtreme array mapping in Arabidopsis thaliana. Genetics 167:907–917PubMedCrossRefGoogle Scholar
  28. Yu J, Holland JB, McMullen MD, Buckler ES (2008) Genetic design and statistical power of nested association mapping in maize. Genetics 178:539–551PubMedCrossRefGoogle Scholar
  29. Zeng ZB (1993) Theoretical basis for separation of multiple linked gene effects in mapping quantitative trait loci. Proc Natl Acad Sci 90:10972–10976PubMedCrossRefGoogle Scholar

Further Readings

  1. Asíns MJ (2002) Present and future of quantitative trait locus analysis in plant breeding. Plant Breed 121:281–291CrossRefGoogle Scholar
  2. Broman KW (2001) Review of statistical methods for QTL mapping in experimental crosses. Lab Anim 30(7):44–52Google Scholar
  3. Delvin B, Risch N (1995) A comparison of linkage disequilibrium measures for fine-scale mapping. Genomics 29:311–322CrossRefGoogle Scholar
  4. Doerge RW (2002) Mapping and analysis of quantitative trait loci in experimental populations. Nat Rev 3:43–53Google Scholar
  5. Hospital F (2009) Challenges for effective marker-assisted selection in plants. Genetica 136:303–310, PubMedCrossRefGoogle Scholar
  6. Jorde LB (2000) Linkage disequilibrium and the search for complex disease genes. Genome Res 10:1435–1444PubMedCrossRefGoogle Scholar
  7. Kang MS (2002) Quantitative genetics, genomics, and plant breeding. In: Papers from the symposium on quantitative genetics and plant breeding in the 21st century, Louisiana State University, 26–28 Mar 2001, CAB International 2002Google Scholar
  8. Kendziorski CM et al (2006) Statistical methods for expression quantitative trait loci (eQTL) mapping. Biometrics 62:19–27PubMedCrossRefGoogle Scholar
  9. McMullen MD et al (2009) Genetic properties of the maize nested association mapping population. Science 325:737–740PubMedCrossRefGoogle Scholar
  10. Würschum T (2012) Mapping QTL for agronomic traits in breeding populations. Theor Appl Genet 125:201–210PubMedCrossRefGoogle Scholar
  11. Xu Y, Crouch JH (2008) Marker-assisted selection in plant breeding: from publications to practice. Crop Sci 48:391–407CrossRefGoogle Scholar

Copyright information

© Springer India 2013

Authors and Affiliations

  1. 1.Plant Molecular Biology & BioinformaticsTamil Nadu Agricultural UniversityCoimbatoreIndia

Personalised recommendations