Skip to main content
PMC home page
Genetics logoLink to Genetics
. 1998 Jun;149(2):1139–1146. doi: 10.1093/genetics/149.2.1139

Combining different line crosses for mapping quantitative trait loci using the identical by descent-based variance component method.

C Xie 1, D D Gessler 1, S Xu 1
PMCID: PMC1460169  PMID: 9611221

Abstract

Mapping quantitative trait loci (QTLs) is usually conducted with a single line cross. The power of such QTL mapping depends highly on the two parental lines. If the two lines are fixed for the same allele at a putative QTL, the QTL is undetectable. On the other hand, if a QTL is segregating in the line cross and is detected, the estimated variance of the QTL cannot be extrapolated beyond the statistical inference space of the two parental lines. To reduce the likelihood of missing a QTL and to increase the statistical inference space of the estimated QTL variance, we present a consensus QTL mapping strategy. We adopt the identical by descent (IBD)-based variance component method originally applied to human linkage analysis by combining multiple line crosses as independent families. We explore the properties of consensus QTL mapping and demonstrate the method with F2, backcross (BC), and full-sib (FS) families. In addition, we examine the effects of the QTL heritability, marker informativeness, QTL position, the number of families, and family size. We show that F2 families notably outperform BC and FS families in detecting a QTL. There is a substantial reduction in the standard deviation of the estimated QTL position and the separation of the QTL and polygenic variance. Finally, we show that the power to detect a QTL is greater when using a small number of large families than a large number of small families.

Full Text

The Full Text of this article is available as a PDF (165.8 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Edwards M. D., Stuber C. W., Wendel J. F. Molecular-marker-facilitated investigations of quantitative-trait loci in maize. I. Numbers, genomic distribution and types of gene action. Genetics. 1987 May;116(1):113–125. doi: 10.1093/genetics/116.1.113. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Fulker D. W., Cherny S. S., Cardon L. R. Multipoint interval mapping of quantitative trait loci, using sib pairs. Am J Hum Genet. 1995 May;56(5):1224–1233. [PMC free article] [PubMed] [Google Scholar]
  3. Gessler D. D., Xu S. Using the expectation or the distribution of the identity by descent for mapping quantitative trait loci under the random model. Am J Hum Genet. 1996 Dec;59(6):1382–1390. [PMC free article] [PubMed] [Google Scholar]
  4. Goldgar D. E. Multipoint analysis of human quantitative genetic variation. Am J Hum Genet. 1990 Dec;47(6):957–967. [PMC free article] [PubMed] [Google Scholar]
  5. HARRIS D. L. GENOTYPIC COVARIANCES BETWEEN INBRED RELATIVES. Genetics. 1964 Dec;50:1319–1348. doi: 10.1093/genetics/50.6.1319. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Haseman J. K., Elston R. C. The investigation of linkage between a quantitative trait and a marker locus. Behav Genet. 1972 Mar;2(1):3–19. doi: 10.1007/BF01066731. [DOI] [PubMed] [Google Scholar]
  7. Jansen R. C. Interval mapping of multiple quantitative trait loci. Genetics. 1993 Sep;135(1):205–211. doi: 10.1093/genetics/135.1.205. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Jiang C., Zeng Z. B. Multiple trait analysis of genetic mapping for quantitative trait loci. Genetics. 1995 Jul;140(3):1111–1127. doi: 10.1093/genetics/140.3.1111. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Kempthorne O. The Correlations between Relatives in Inbred Populations. Genetics. 1955 Sep;40(5):681–691. doi: 10.1093/genetics/40.5.681. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Kruglyak L., Lander E. S. Complete multipoint sib-pair analysis of qualitative and quantitative traits. Am J Hum Genet. 1995 Aug;57(2):439–454. [PMC free article] [PubMed] [Google Scholar]
  11. Lander E. S., Botstein D. Mapping mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics. 1989 Jan;121(1):185–199. doi: 10.1093/genetics/121.1.185. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Olson J. M. Robust multipoint linkage analysis: an extension of the Haseman-Elston method. Genet Epidemiol. 1995;12(2):177–193. doi: 10.1002/gepi.1370120206. [DOI] [PubMed] [Google Scholar]
  13. Xu S., Atchley W. R. A random model approach to interval mapping of quantitative trait loci. Genetics. 1995 Nov;141(3):1189–1197. doi: 10.1093/genetics/141.3.1189. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Xu S. Computation of the full likelihood function for estimating variance at a quantitative trait locus. Genetics. 1996 Dec;144(4):1951–1960. doi: 10.1093/genetics/144.4.1951. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Zeng Z. B. Precision mapping of quantitative trait loci. Genetics. 1994 Apr;136(4):1457–1468. doi: 10.1093/genetics/136.4.1457. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Genetics are provided here courtesy of Oxford University Press

RESOURCES