A Complete Solution for Dissecting Pure Main and Epistatic Effects of QTL in Triple Testcross Design

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 Z3, calculated from the TTC family means of q...

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Main Authors:	He, Xiao-Hong, Zhang, Yuan-Ming
Format:	Online
Language:	English
Published:	Public Library of Science 2011
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3176238/

id	pubmed-3176238
recordtype	oai_dc
spelling	pubmed-31762382011-09-26 A Complete Solution for Dissecting Pure Main and Epistatic Effects of QTL in Triple Testcross Design He, Xiao-Hong Zhang, Yuan-Ming Research Article 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 Z3, calculated from the TTC family means of quantitative trait, to infer the nature of the collective additive, dominance and epistatic effects of all the genes. Although several quantitative trait loci (QTL) mapping approaches in the TTC design have been developed, these approaches do not provide a complete solution for dissecting pure main and epistatic effects. In this study, therefore, we developed a two-step approach to estimate all pure main and epistatic effects in the F2-based TTC design under the F2 and F∞ metric models. In the first step, with Z1 and Z2 the augmented main and epistatic effects in the full genetic model that simultaneously considered all putative QTL on the whole genome were estimated using empirical Bayes approach, and with Z3 three pure epistatic effects were obtained using two-dimensional genome scans. In the second step, the three pure epistatic effects obtained in the first step were integrated with the augmented epistatic and main effects for the further estimation of all other pure effects. A series of Monte Carlo simulation experiments has been carried out to confirm the proposed method. The results from simulation experiments show that: 1) the newly defined genetic parameters could be rightly identified with satisfactory statistical power and precision; 2) the F2-based TTC design was superior to the F2 and F2:3 designs; 3) with Z1 and Z2 the statistical powers for the detection of augmented epistatic effects were substantively affected by the signs of pure epistatic effects; and 4) with Z3 the estimation of pure epistatic effects required large sample size and family replication number. The extension of the proposed method in this study to other base populations was further discussed. Public Library of Science 2011-09-19 /pmc/articles/PMC3176238/ /pubmed/21949729 http://dx.doi.org/10.1371/journal.pone.0024575 Text en He, Zhang. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	He, Xiao-Hong Zhang, Yuan-Ming
spellingShingle	He, Xiao-Hong Zhang, Yuan-Ming A Complete Solution for Dissecting Pure Main and Epistatic Effects of QTL in Triple Testcross Design
author_facet	He, Xiao-Hong Zhang, Yuan-Ming
author_sort	He, Xiao-Hong
title	A Complete Solution for Dissecting Pure Main and Epistatic Effects of QTL in Triple Testcross Design
title_short	A Complete Solution for Dissecting Pure Main and Epistatic Effects of QTL in Triple Testcross Design
title_full	A Complete Solution for Dissecting Pure Main and Epistatic Effects of QTL in Triple Testcross Design
title_fullStr	A Complete Solution for Dissecting Pure Main and Epistatic Effects of QTL in Triple Testcross Design
title_full_unstemmed	A Complete Solution for Dissecting Pure Main and Epistatic Effects of QTL in Triple Testcross Design
title_sort	complete solution for dissecting pure main and epistatic effects of qtl in triple testcross design
description	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 Z3, calculated from the TTC family means of quantitative trait, to infer the nature of the collective additive, dominance and epistatic effects of all the genes. Although several quantitative trait loci (QTL) mapping approaches in the TTC design have been developed, these approaches do not provide a complete solution for dissecting pure main and epistatic effects. In this study, therefore, we developed a two-step approach to estimate all pure main and epistatic effects in the F2-based TTC design under the F2 and F∞ metric models. In the first step, with Z1 and Z2 the augmented main and epistatic effects in the full genetic model that simultaneously considered all putative QTL on the whole genome were estimated using empirical Bayes approach, and with Z3 three pure epistatic effects were obtained using two-dimensional genome scans. In the second step, the three pure epistatic effects obtained in the first step were integrated with the augmented epistatic and main effects for the further estimation of all other pure effects. A series of Monte Carlo simulation experiments has been carried out to confirm the proposed method. The results from simulation experiments show that: 1) the newly defined genetic parameters could be rightly identified with satisfactory statistical power and precision; 2) the F2-based TTC design was superior to the F2 and F2:3 designs; 3) with Z1 and Z2 the statistical powers for the detection of augmented epistatic effects were substantively affected by the signs of pure epistatic effects; and 4) with Z3 the estimation of pure epistatic effects required large sample size and family replication number. The extension of the proposed method in this study to other base populations was further discussed.
publisher	Public Library of Science
publishDate	2011
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3176238/
_version_	1611476324398923776

A Complete Solution for Dissecting Pure Main and Epistatic Effects of QTL in Triple Testcross Design

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