Multi-QTL Mapping for Quantitative Traits Using Epistatic Distorted Markers

Overview

Journal PLoS One

Specialties General Medicine
Science

Date 2013 Jul 23

PMID 23874647

Citations 4

Authors

Shang-Qian Xie

Jia Wen

Yuan-Ming Zhang

Affiliations

Soon will be listed here.

Abstract

The interaction between segregation distortion loci (SDL) has been often observed in all kinds of mapping populations. However, little has been known about the effect of epistatic SDL on quantitative trait locus (QTL) mapping. Here we proposed a multi-QTL mapping approach using epistatic distorted markers. Using the corrected linkage groups, epistatic SDL was identified. Then, these SDL parameters were used to correct the conditional probabilities of QTL genotypes, and these corrections were further incorporated into the new QTL mapping approach. Finally, a set of simulated datasets and a real data in 304 mouse F2 individuals were used to validate the new method. As compared with the old method, the new one corrects genetic distance between distorted markers, and considers epistasis between two linked SDL. As a result, the power in the detection of QTL is higher for the new method than for the old one, and significant differences for estimates of QTL parameters between the two methods were observed, except for QTL position. Among two QTL for mouse weight, one significant difference for QTL additive effect between the above two methods was observed, because epistatic SDL between markers C66 and T93 exists (P = 2.94e-4).

Citing Articles

Construction of a high density genetic map of an interspecific cross of Capsicum chinense and Capsicum annuum and QTL analysis of floral traits.

Zhu Z, Sun B, Wei J, Cai W, Huang Z, Chen C Sci Rep. 2019; 9(1):1054.

PMID: 30705330 PMC: 6355862. DOI: 10.1038/s41598-018-38370-0.

Molecular Mapping of Restriction-Site Associated DNA Markers In Allotetraploid Upland Cotton.

Wang Y, Ning Z, Hu Y, Chen J, Zhao R, Chen H PLoS One. 2015; 10(4):e0124781.

PMID: 25894395 PMC: 4403916. DOI: 10.1371/journal.pone.0124781.

Ngoma E, Reichwald K, Dorn A, Wittig M, Balschun T, Franke A Aging (Albany NY). 2014; 6(6):468-80.

PMID: 25093339 PMC: 4100809. DOI: 10.18632/aging.100660.

Multi-QTL mapping for quantitative traits using epistatic distorted markers.

Xie S, Wen J, Zhang Y PLoS One. 2013; 8(7):e68510.

PMID: 23874647 PMC: 3706401. DOI: 10.1371/journal.pone.0068510.

References

Lorieux M, Perrier X, Goffinet B, Lanaud C, de Leon D . Maximum-likelihood models for mapping genetic markers showing segregation distortion. 2. F2 populations. Theor Appl Genet. 2013; 90(1):81-9. DOI: 10.1007/BF00220999. View

Jiang C, Zeng Z . Mapping quantitative trait loci with dominant and missing markers in various crosses from two inbred lines. Genetica. 1997; 101(1):47-58. DOI: 10.1023/a:1018394410659. View

Li X, Wang X, Wei Y, Brummer E . Prevalence of segregation distortion in diploid alfalfa and its implications for genetics and breeding applications. Theor Appl Genet. 2011; 123(4):667-79. DOI: 10.1007/s00122-011-1617-5. View

Chang A, Noor M . Epistasis modifies the dominance of loci causing hybrid male sterility in the Drosophila pseudoobscura species group. Evolution. 2009; 64(1):253-60. PMC: 2827646. DOI: 10.1111/j.1558-5646.2009.00823.x. View

Kubo T, Yamagata Y, Eguchi M, Yoshimura A . A novel epistatic interaction at two loci causing hybrid male sterility in an inter-subspecific cross of rice (Oryza sativa L.). Genes Genet Syst. 2009; 83(6):443-53. DOI: 10.1266/ggs.83.443. View

Yang J, Zhao X, Cheng K, Du H, Ouyang Y, Chen J . A killer-protector system regulates both hybrid sterility and segregation distortion in rice. Science. 2012; 337(6100):1336-40. DOI: 10.1126/science.1223702. View

Baumbach J, Rogers J, Slattery R, Narayanan N, Xu M, Palmer R . Segregation distortion in a region containing a male-sterility, female-sterility locus in soybean. Plant Sci. 2012; 195:151-6. DOI: 10.1016/j.plantsci.2012.07.003. View

Zhang L, Wang S, Li H, Deng Q, Zheng A, Li S . Effects of missing marker and segregation distortion on QTL mapping in F2 populations. Theor Appl Genet. 2010; 121(6):1071-82. DOI: 10.1007/s00122-010-1372-z. View

Xu Y, Li H, Li G, Wang X, Cheng L, Zhang Y . Mapping quantitative trait loci for seed size traits in soybean (Glycine max L. Merr.). Theor Appl Genet. 2010; 122(3):581-94. DOI: 10.1007/s00122-010-1471-x. View

10.

Xu S . Quantitative trait locus mapping can benefit from segregation distortion. Genetics. 2008; 180(4):2201-8. PMC: 2600952. DOI: 10.1534/genetics.108.090688. View

11.

Torjek O, Witucka-Wall H, Meyer R, von Korff M, Kusterer B, Rautengarten C . Segregation distortion in Arabidopsis C24/Col-0 and Col-0/C24 recombinant inbred line populations is due to reduced fertility caused by epistatic interaction of two loci. Theor Appl Genet. 2006; 113(8):1551-61. DOI: 10.1007/s00122-006-0402-3. View

12.

Doerge R . Mapping and analysis of quantitative trait loci in experimental populations. Nat Rev Genet. 2002; 3(1):43-52. DOI: 10.1038/nrg703. View

13.

Lyttle T . Segregation distorters. Annu Rev Genet. 1991; 25:511-57. DOI: 10.1146/annurev.ge.25.120191.002455. View

14.

Carr D, Dudash M . Recent approaches into the genetic basis of inbreeding depression in plants. Philos Trans R Soc Lond B Biol Sci. 2003; 358(1434):1071-84. PMC: 1693197. DOI: 10.1098/rstb.2003.1295. View

15.

Paterson A, Damon S, Hewitt J, Zamir D, Rabinowitch H, Lincoln S . Mendelian factors underlying quantitative traits in tomato: comparison across species, generations, and environments. Genetics. 1991; 127(1):181-97. PMC: 1204303. DOI: 10.1093/genetics/127.1.181. View

16.

Zhu C, Wang C, Zhang Y . Modeling segregation distortion for viability selection. I. Reconstruction of linkage maps with distorted markers. Theor Appl Genet. 2006; 114(2):295-305. DOI: 10.1007/s00122-006-0432-x. View

17.

Lander E, Green P, ABRAHAMSON J, Barlow A, Daly M, Lincoln S . MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics. 1987; 1(2):174-81. DOI: 10.1016/0888-7543(87)90010-3. View

18.

Phillips P . Epistasis--the essential role of gene interactions in the structure and evolution of genetic systems. Nat Rev Genet. 2008; 9(11):855-67. PMC: 2689140. DOI: 10.1038/nrg2452. View

19.

Luo L, Zhang Y, Xu S . A quantitative genetics model for viability selection. Heredity (Edinb). 2004; 94(3):347-55. DOI: 10.1038/sj.hdy.6800615. View

20.

Kao C, Zeng Z, Teasdale R . Multiple interval mapping for quantitative trait loci. Genetics. 1999; 152(3):1203-16. PMC: 1460657. DOI: 10.1093/genetics/152.3.1203. View