TITLE

Functional mapping of reaction norms to multiple environmental signals through nonparametric covariance estimation

AUTHOR(S)
Yap, John S.; Yao Li; Das, Kiranmoy; Jiahan Li; Rongling Wu
PUB. DATE
January 2011
SOURCE
BMC Plant Biology;2011, Vol. 11 Issue 1, p23
SOURCE TYPE
Academic Journal
DOC. TYPE
Article
ABSTRACT
Background: The identification of genes or quantitative trait loci that are expressed in response to different environmental factors such as temperature and light, through functional mapping, critically relies on precise modeling of the covariance structure. Previous work used separable parametric covariance structures, such as a Kronecker product of autoregressive one [AR(1)] matrices, that do not account for interaction effects of different environmental factors. Results: We implement a more robust nonparametric covariance estimator to model these interactions within the framework of functional mapping of reaction norms to two signals. Our results from Monte Carlo simulations show that this estimator can be useful in modeling interactions that exist between two environmental signals. The interactions are simulated using nonseparable covariance models with spatio-temporal structural forms that mimic interaction effects. Conclusions: The nonparametric covariance estimator has an advantage over separable parametric covariance estimators in the detection of QTL location, thus extending the breadth of use of functional mapping in practical settings.
ACCESSION #
59156321

 

Related Articles

  • Comparisons of quantitative trait locus mapping properties between two methods of recombinant inbred line development. Jixiang Wu; Jenkins, Johnie N.; Jun Zhu; McCarty Jr., Jack C.; Watson, Clarence E. // Euphytica;Jul2003, Vol. 132 Issue 2, p159 

    Theoretical comparisons for quantitative trait loci (QTL) mapping properties were conducted among simulated recombinant inbred (RI) populations developed by single-hill (SH), complete bulk, and single seed descent (SSD) procedures by Monte Carlo simulations based on various population sizes,...

  • Mapping of epistatic quantitative trait loci in four-way crosses. He, Xiao-Hong; Qin, Hongde; Hu, Zhongli; Zhang, Tianzhen; Zhang, Yuan-Ming // Theoretical & Applied Genetics;Jan2011, Vol. 122 Issue 1, p33 

    Four-way crosses (4WC) involving four different inbred lines often appear in plant and animal commercial breeding programs. Direct mapping of quantitative trait loci (QTL) in these commercial populations is both economical and practical. However, the existing statistical methods for mapping QTL...

  • Multi-interval mapping of correlated trait complexes. RONIN †,; NEVO †; HAYES ‡ // Heredity;Mar1998, Vol. 80 Issue 3, p273 

    Employing Monte Carlo simulations, we demonstrate the advantages of multitrait analysis in detection of linked QTL effects within the framework of mixture models. In spite of an increased number of parameters to be estimated, compared to the single-trait formulation, the proposed method allows...

  • A Complete Solution for Dissecting Pure Main and Epistatic Effects of QTL in Triple Testcross Design. Xiao-Hong He; Yuan-Ming Zhang // PLoS ONE;2011, Vol. 6 Issue 9, p1 

    Epistasis plays an important role in genetics, evolution and crop breeding. To detect the epistasis, triple test cross (TTC) design had been developed several decades ago. Classical procedures for the TTC design use only linear transformations Z1, Z2 and Z2, calculated from the TTC family means...

  • R/qtlbim: QTL with Bayesian Interval Mapping in experimental crosses. Brian S. Yandell; Tapan Mehta; Samprit Banerjee; Daniel Shriner; Ramprasad Venkataraman; Jee Young Moon; W. Whipple Neely; Hao Wu; Randy von Smith; Nengjun Yi // Bioinformatics;Mar2007, Vol. 23 Issue 5, p641 

    Summary: R/qtlbim is an extensible, interactive environment for the Bayesian Interval Mapping of QTL, built on top of R/qtl (Broman et al., 2003), providing Bayesian analysis of multiple interacting quantitative trait loci (QTL) models for continuous, binary and ordinal traits in experimental...

  • Using Dominance Relationship Coefficients Based on Linkage Disequilibrium and Linkage With a General Complex Pedigree to Increase Mapping Resolution. Lee, S. H.; Van Der Werf, J. H. J. // Genetics;Oct2006, Vol. 174 Issue 2, p1009 

    Dominance (intralocus allelic interactions) plays often an important role in quantitative trait variation. However, few studies about dominance in QTL mapping have been reported in outbred animal or human populations. This is because common dominance effects can be predicted mainly for many full...

  • Approximating Identity-by-Descent Matrices Using Multiple Haplotype Configurations on Pedigrees. Guimin Gao; Hoeschele, Ina // Genetics;Sep2005, Vol. 171 Issue 1, p365 

    Identity-by-descent (IBD) matrix calculation is an important step in quantitative trait loci (QTL) analysis using variance component models. To calculate IBD matrices efficiently for large pedigrees with large numbers of loci, an approximation method based on the reconstruction of haplotype...

  • Mapping Quantitative Trait Loci Using Naturally Occurring Genetic Variance Among Commercial Inbred Lines of Maize (Zea mays L.). Yuan-Ming Zhang; Yongcai Mao; Chongqing Xie; Smith, Howie; Lang Luo; Shizhong Xu; Walsh, J. B. // Genetics;Apr2005, Vol. 169 Issue 4, p2267 

    Many commercial inbred lines are available in crops. A large amount of genetic variation is preserved among these lines. The genealogical history of the inbred lines is usually well documented. However, quantitative trait loci (QTL) responsible for the genetic variances among the lines are...

  • QTL mapping for combining ability in different population-based NCII designs: a simulation study. LI, LANZHI; SUN, CONGWEI; CHEN, YUAN; DAI, ZHIJUN; QU, ZHEN; ZHENG, XINGFEI; YU, SIBIN; MOU, TONGMIN; XU, CHENWU; HU, ZHONGLI // Journal of Genetics;Dec2013, Vol. 92 Issue 3, p529 

    The NCII design (North Carolina mating design II) has been widely applied in studies of combining ability and heterosis. The objective of our research was to estimate how different base populations, sample sizes, testcross numbers and heritability influence QTL analyses of combining ability and...

Share

Read the Article

Courtesy of VIRGINIA BEACH PUBLIC LIBRARY AND SYSTEM

Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics