Full Text:   <1355>

CLC number: TP391.41

On-line Access: 

Received: 2006-03-20

Revision Accepted: 2006-07-23

Crosschecked: 0000-00-00

Cited: 1

Clicked: 3555

Citations:  Bibtex RefMan EndNote GB/T7714

-   Go to

Article info.
1. Reference List
Open peer comments

Journal of Zhejiang University SCIENCE A 2007 Vol.8 No.4 P.563~567

10.1631/jzus.2007.A0563


3D graphical visualization of the genetic architectures underlying complex traits in multiple environments


Author(s):  HU Cheng-cheng, YE Xiu-zi, ZHANG Yin, YU Rong-dong, YANG Jian, ZHU Jun

Affiliation(s):  College of Computer Science, Zhejiang University, Hangzhou 310027, China; more

Corresponding email(s):   cechu@ucdavis.edu, yxz@zju.edu.cn

Key Words:  Quantitative trait locus (QTL), Visualization, 3D graphical, Interactive visualization


HU Cheng-cheng, YE Xiu-zi, ZHANG Yin, YU Rong-dong, YANG Jian, ZHU Jun. 3D graphical visualization of the genetic architectures underlying complex traits in multiple environments[J]. Journal of Zhejiang University Science A, 2007, 8(4): 563~567.

@article{title="3D graphical visualization of the genetic architectures underlying complex traits in multiple environments",
author="HU Cheng-cheng, YE Xiu-zi, ZHANG Yin, YU Rong-dong, YANG Jian, ZHU Jun",
journal="Journal of Zhejiang University Science A",
volume="8",
number="4",
pages="563~567",
year="2007",
publisher="Zhejiang University Press & Springer",
doi="10.1631/jzus.2007.A0563"
}

%0 Journal Article
%T 3D graphical visualization of the genetic architectures underlying complex traits in multiple environments
%A HU Cheng-cheng
%A YE Xiu-zi
%A ZHANG Yin
%A YU Rong-dong
%A YANG Jian
%A ZHU Jun
%J Journal of Zhejiang University SCIENCE A
%V 8
%N 4
%P 563~567
%@ 1673-565X
%D 2007
%I Zhejiang University Press & Springer
%DOI 10.1631/jzus.2007.A0563

TY - JOUR
T1 - 3D graphical visualization of the genetic architectures underlying complex traits in multiple environments
A1 - HU Cheng-cheng
A1 - YE Xiu-zi
A1 - ZHANG Yin
A1 - YU Rong-dong
A1 - YANG Jian
A1 - ZHU Jun
J0 - Journal of Zhejiang University Science A
VL - 8
IS - 4
SP - 563
EP - 567
%@ 1673-565X
Y1 - 2007
PB - Zhejiang University Press & Springer
ER -
DOI - 10.1631/jzus.2007.A0563


Abstract: 
An approach for generating interactive 3D graphical visualization of the genetic architectures of complex traits in multiple environments is described. 3D graphical visualization is utilized for making improvements on traditional plots in quantitative trait locus (QTL) mapping analysis. Interactive 3D graphical visualization for abstract expression of QTL, epistasis and their environmental interactions for experimental populations was developed in framework of user-friendly software QTLNetwork (http://ibi.zju.edu.cn/software/qtlnetwork). Novel definition of graphical meta system and computation of virtual coordinates are used to achieve explicit but meaningful visualization. Interactive 3D graphical visualization for QTL analysis provides geneticists and breeders a powerful and easy-to-use tool to analyze and publish their research results.

Darkslateblue:Affiliate; Royal Blue:Author; Turquoise:Article

Reference

[1] Broman, K.W., Wu, H., Sen, S., Churchill, G.A., 2003. R/qtl: QTL mapping in experimental crosses. Bioinformatics, 19(7):889-890.

[2] Chesler, E.J., Lu, L., Shou, S., Qu, Y.H., Gu, J., Wang, J.T., Hsu, H.C., Mountz, J.D., Baldwin, N.E., Langston, M.A., et al., 2005. Complex trait analysis of gene expression uncovers polygenic and pleiotropic networks that modulate nervous system function. Nat. Genet., 37(3):233-242.

[3] Doerge, R.W., 2002. Mapping and analysis of quantitative trait loci in experimental populations. Nat. Rev. Genet., 3(1):43-52.

[4] Fischer, G., Ibrahim, S.M., Brockmann, G.A., Pahnke, J., Bartocci, E., Thiesen, H.J., Serrano-Fernández, P., Möller, S., 2003. Expressionview: visualization of quantitative trait loci and gene-expression data in ensembl. Genome Biology, 4(11):R77.

[5] Haley, C.S., Knott, S.A., 1992. A simple regression method for mapping quantitative trait loci in line crosses using flanking markers. Heredity, 69:315-324.

[6] Kao, C.H., Zeng, Z.B., Teasdale, R.D., 1999. Multiple interval mapping for quantitative trait loci. Genetics, 152:1203-1216.

[7] Lander, E.S., Botstein, D., 1989. Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics, 121:185-199.

[8] Mauricio, R., 2001. Mapping quantitative trait loci in plants: uses and caveats for evolutionary biology. Nat. Rev. Genet., 2(5):370-381.

[9] Piepho, H.P., Gauch, H.G., 2001. Marker pair selection for mapping quantitative trait loci. Genetics, 157:433-444.

[10] Wang, D.L., Zhu, J., Li, Z.K., Paterson, A.H., 1999. Mapping QTLs with epistatic effects and QTL environment interactions by mixed linear model approaches. Theor. Appl. Genet., 99:1255-1264.

[11] Wang, S.C., Basten, J., Zeng, Z.B., 2005. Windows QTL Cartographer 2.5. Department of Statistics, North Carolina State University, Raleigh, NC. Http://statgen.ncsu.edu/qtlcart/WQTLCart.htm

[12] Yang, J., Zhu, J., 2005. Methods for predicting superior genotypes under multiple environments based on QTL effects. Theor. Appl. Genet., 110(7):1268-1274.

[13] Yang, J., Zhu, J., Williams, R., 2006. Mapping genetic architecture of complex trait in experimental populations. Bioinformatics, under revision.

[14] Zeng, Z.B., 1994. Precision mapping of quantitative trait loci. Genetics, 136:1457-1468.

[15] Zhu, J., 1999. Mixed model approaches of mapping genes for complex quantitative traits. J. Zhejiang Univ. (Natural Science), 33:327-335 (in Chinese).

Open peer comments: Debate/Discuss/Question/Opinion

<1>

Please provide your name, email address and a comment





Journal of Zhejiang University-SCIENCE, 38 Zheda Road, Hangzhou 310027, China
Tel: +86-571-87952783; E-mail: cjzhang@zju.edu.cn
Copyright © 2000 - Journal of Zhejiang University-SCIENCE