Abstract
Many biological phenomena undergo developmental changes in time and space. Functional mapping, which is aimed at mapping genes that affect developmental patterns, is instrumental for studying the genetic architecture of biological changes. Often biological processes are mediated by a network of developmental and physiological components and, therefore, are better described by multiple phenotypes. In this article, we develop a multivariate model for functional mapping that can detect and characterize quantitative trait loci (QTLs) that simultaneously control multiple dynamic traits. Because the true genotypes of QTLs are unknown, the measurements for the multiple dynamic traits are modeled using a mixture distribution. The functional means of the multiple dynamic traits are estimated using the nonparametric regression method, which avoids any parametric assumption on the functional means. We propose the profile likelihood method to estimate the mixture model. A likelihood ratio test is exploited to test for the existence of pleiotropic effects on distinct but developmentally correlated traits. A simulation study is implemented to illustrate the finite sample performance of our proposed method. We also demonstrate our method by identifying QTLs that simultaneously control three dynamic traits of soybeans. The three dynamic traits are the time-course biomass of the leaf, the stem, and the root of the whole soybean. The genetic linkage map is constructed with 950 microsatellite markers. The new model can aid in our comprehension of the genetic control mechanisms of complex dynamic traits over time.
| Original language | English (US) |
|---|---|
| Pages (from-to) | 60-75 |
| Number of pages | 16 |
| Journal | Journal of Agricultural, Biological, and Environmental Statistics |
| Volume | 22 |
| Issue number | 1 |
| DOIs | |
| State | Published - Mar 1 2017 |
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All Science Journal Classification (ASJC) codes
- Statistics and Probability
- Environmental Science(all)
- Agricultural and Biological Sciences (miscellaneous)
- Agricultural and Biological Sciences(all)
- Statistics, Probability and Uncertainty
- Applied Mathematics
Cite this
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Functional Mapping of Multiple Dynamic Traits. / Cao, Jiguo; Wang, Liangliang; Huang, Zhongwen; Gai, Junyi; Wu, Rongling.
In: Journal of Agricultural, Biological, and Environmental Statistics, Vol. 22, No. 1, 01.03.2017, p. 60-75.Research output: Contribution to journal › Article
TY - JOUR
T1 - Functional Mapping of Multiple Dynamic Traits
AU - Cao, Jiguo
AU - Wang, Liangliang
AU - Huang, Zhongwen
AU - Gai, Junyi
AU - Wu, Rongling
PY - 2017/3/1
Y1 - 2017/3/1
N2 - Many biological phenomena undergo developmental changes in time and space. Functional mapping, which is aimed at mapping genes that affect developmental patterns, is instrumental for studying the genetic architecture of biological changes. Often biological processes are mediated by a network of developmental and physiological components and, therefore, are better described by multiple phenotypes. In this article, we develop a multivariate model for functional mapping that can detect and characterize quantitative trait loci (QTLs) that simultaneously control multiple dynamic traits. Because the true genotypes of QTLs are unknown, the measurements for the multiple dynamic traits are modeled using a mixture distribution. The functional means of the multiple dynamic traits are estimated using the nonparametric regression method, which avoids any parametric assumption on the functional means. We propose the profile likelihood method to estimate the mixture model. A likelihood ratio test is exploited to test for the existence of pleiotropic effects on distinct but developmentally correlated traits. A simulation study is implemented to illustrate the finite sample performance of our proposed method. We also demonstrate our method by identifying QTLs that simultaneously control three dynamic traits of soybeans. The three dynamic traits are the time-course biomass of the leaf, the stem, and the root of the whole soybean. The genetic linkage map is constructed with 950 microsatellite markers. The new model can aid in our comprehension of the genetic control mechanisms of complex dynamic traits over time.
AB - Many biological phenomena undergo developmental changes in time and space. Functional mapping, which is aimed at mapping genes that affect developmental patterns, is instrumental for studying the genetic architecture of biological changes. Often biological processes are mediated by a network of developmental and physiological components and, therefore, are better described by multiple phenotypes. In this article, we develop a multivariate model for functional mapping that can detect and characterize quantitative trait loci (QTLs) that simultaneously control multiple dynamic traits. Because the true genotypes of QTLs are unknown, the measurements for the multiple dynamic traits are modeled using a mixture distribution. The functional means of the multiple dynamic traits are estimated using the nonparametric regression method, which avoids any parametric assumption on the functional means. We propose the profile likelihood method to estimate the mixture model. A likelihood ratio test is exploited to test for the existence of pleiotropic effects on distinct but developmentally correlated traits. A simulation study is implemented to illustrate the finite sample performance of our proposed method. We also demonstrate our method by identifying QTLs that simultaneously control three dynamic traits of soybeans. The three dynamic traits are the time-course biomass of the leaf, the stem, and the root of the whole soybean. The genetic linkage map is constructed with 950 microsatellite markers. The new model can aid in our comprehension of the genetic control mechanisms of complex dynamic traits over time.
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U2 - 10.1007/s13253-016-0275-0
DO - 10.1007/s13253-016-0275-0
M3 - Article
AN - SCOPUS:85006783303
VL - 22
SP - 60
EP - 75
JO - Journal of Agricultural, Biological, and Environmental Statistics
JF - Journal of Agricultural, Biological, and Environmental Statistics
SN - 1085-7117
IS - 1
ER -