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

TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik
Vincent GarinFred van Eeuwijk

Abstract

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...Continue Reading

References

May 20, 2004·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·B Parisseaux, R Bernardo
Aug 21, 2004·Bioinformatics·Marie-Françoise JourjonBrigitte Mangin
Jan 19, 2005·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·H P Piepho
Jun 23, 2006·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·G BlancL Moreau
Feb 26, 2008·Current Opinion in Plant Biology·Colin CavanaghWayne Powell
Aug 8, 2009·Science·Edward S BucklerMichael D McMullen
Aug 8, 2009·Science·Michael D McMullenEdward S Buckler
Feb 9, 2010·Current Opinion in Plant Biology·Fred A van EeuwijkScott C Chapman
Apr 13, 2011·Proceedings of the National Academy of Sciences of the United States of America·Jesse A PolandRebecca J Nelson
May 23, 2012·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Tobias Würschum
Aug 2, 2013·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·N A AlimiF A van Eeuwijk
Sep 21, 2013·Genome Biology·Eva BauerChris-Carolin Schön
Feb 1, 2014·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Damien LerouxBrigitte Mangin
Jun 15, 2014·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Arūnas P VerbylaKlara L Verbyla
Sep 23, 2014·Genetics·Christina LehermeierChris-Carolin Schön
Jul 21, 2016·Plant Physiology·Emilie J MilletFrançois Tardieu
May 27, 2017·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Vincent GarinFred van Eeuwijk
May 22, 2019·Nature Genetics·Emilie J MilletFrançois Tardieu

❮ Previous
Next ❯

Citations

Oct 1, 2020·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Ana L Galiano-CarneiroThomas Miedaner

❮ Previous
Next ❯

Software Mentioned

R package mppR
MPP
R
asreml
R package clusthaplo
ME

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.