Identification, deployment, and transferability of quantitative trait loci from genome-wide association studies in plants

Mohsen Mohammadi; Alencar Xavier; Travis Beckett; Savannah Beyer; Liyang Chen; Habte Chikssa; Valerie Cross; Fabiana Freitas Moreira; Elizabeth French; Rupesh Gaire; Stefanie Griebel; Miguel Angel Lopez; Samuel Prather; Blake Russell; Weidong Wang

Current Plant Biology (Dec 2020)

Identification, deployment, and transferability of quantitative trait loci from genome-wide association studies in plants

Mohsen Mohammadi,
Alencar Xavier,
Travis Beckett,
Savannah Beyer,
Liyang Chen,
Habte Chikssa,
Valerie Cross,
Fabiana Freitas Moreira,
Elizabeth French,
Rupesh Gaire,
Stefanie Griebel,
Miguel Angel Lopez,
Samuel Prather,
Blake Russell,
Weidong Wang

Affiliations

Mohsen Mohammadi: Department of Agronomy, Purdue University, 915 West State Street, West Lafayette, IN, 47907, USA; Corresponding author at: Wheat Breeding and Quantitative Genetics, Department of Agronomy, College of Agriculture, Purdue University, 915 West State Street, West Lafayette, IN, 47907, USA.
Alencar Xavier: Department of Agronomy, Purdue University, 915 West State Street, West Lafayette, IN, 47907, USA; Whole-genome Analytics, Corteva Agrisciences, 7000 NW 62nd Avenue, Johnston, IA, 50131, USA
Travis Beckett: Department of Agronomy, Purdue University, 915 West State Street, West Lafayette, IN, 47907, USA
Savannah Beyer: Department of Agronomy, Purdue University, 915 West State Street, West Lafayette, IN, 47907, USA
Liyang Chen: Department of Agronomy, Purdue University, 915 West State Street, West Lafayette, IN, 47907, USA
Habte Chikssa: Department of Botany and Plant Pathology, Purdue University, 915 West State Street, West Lafayette, IN, 47907, USA
Valerie Cross: Department of Agronomy, Purdue University, 915 West State Street, West Lafayette, IN, 47907, USA
Fabiana Freitas Moreira: Department of Agronomy, Purdue University, 915 West State Street, West Lafayette, IN, 47907, USA
Elizabeth French: Department of Botany and Plant Pathology, Purdue University, 915 West State Street, West Lafayette, IN, 47907, USA
Rupesh Gaire: Department of Agronomy, Purdue University, 915 West State Street, West Lafayette, IN, 47907, USA
Stefanie Griebel: Department of Agronomy, Purdue University, 915 West State Street, West Lafayette, IN, 47907, USA
Miguel Angel Lopez: Department of Agronomy, Purdue University, 915 West State Street, West Lafayette, IN, 47907, USA
Samuel Prather: Department of Agronomy, Purdue University, 915 West State Street, West Lafayette, IN, 47907, USA
Blake Russell: Department of Agronomy, Purdue University, 915 West State Street, West Lafayette, IN, 47907, USA
Weidong Wang: Department of Agronomy, Purdue University, 915 West State Street, West Lafayette, IN, 47907, USA

Journal volume & issue: Vol. 24
p. 100145

Abstract

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Over the past decade, the use of genome-wide association studies (GWAS) in plant breeding for discovery and validation of quantitative trait loci (QTL) has vastly increased. Successful deployment and transferability of these findings, however, have been limited. To increase the value of GWAS for plant breeding, experimental and methodological aspects must be addressed and refined. Population designs and statistical techniques are necessary to properly account for the effect of long-range linkage disequilibrium. Success of current methods has been restricted to the detection of common-variants with moderate additive effects; discovery of rare variants or QTL that depart from additivity has been elusive. Pleiotropy casts doubt on the cause-effect relationships between markers and multiple traits. Major criticisms of association studies center on reproducibility of results and the lack of transferability to other environments and populations. We also discuss population structure, phenotypic plasticity, epistasis, and genotype-by-environment interactions as they apply to GWAS. Perspectives are given for environment-dependent QTL, experimental settings, use of next-generation populations, and deployment of GWAS results for breeding applications and strategic exploitation of genotype-by-environment interactions. In summary, we present an overview of contemporary issues in identification and deployment of marker-trait associations and suggest future avenues of research towards new methods and new sources of data.

Published in Current Plant Biology

ISSN: 2214-6628 (Online)
Publisher: Elsevier
Country of publisher: Netherlands
LCC subjects: Science: Botany
Website: http://www.journals.elsevier.com/current-plant-biology/

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