Multi-parent multi-environment QTL analysis: an illustration with the EU-NAM Flint population.

Multi-parent multi-environment QTL analysis: an illustration with the EU-NAM Flint population. Theor Appl Genet. 2020 Jun 09;: Authors: Garin V, Malosetti M, van Eeuwijk F Abstract KEY MESSAGE: Multi-parent populations multi-environment QTL experiments data should be analysed jointly to estimate the QTL effect variation within the population and between environments. Commonly, QTL detection in multi-parent populations (MPPs) data measured in multiple environments (ME) is done by analyzing genotypic values 'averaged' across environments. This method ignores the environment-specific QTL (QTLxE) effects. Running separate single environment analyses is a possibility to measure QTLxE effects, but those analyses do not model the genetic covariance due to the use of the same genotype in different environments. In this paper, we propose methods to analyse MPP-ME QTL experiments using simultaneously the data from several environments and modelling the genotypic covariance. Using data from the EU-NAM Flint population, we show that these methods estimate the QTLxE effects and that they can improve the quality of the QTL detection. Those methods also have a larger inference power. For example, they can be extended to integrate environmental indices like temperature or precipitation to better understand the mechanisms behind the QTLxE effects. Therefore, our methodology allows the exploitation of the full MPP-ME data potential: to estimate QTL ef...
Source: TAG. Theoretical and Applied Genetics - Category: Genetics & Stem Cells Authors: Tags: Theor Appl Genet Source Type: research