Utilizing trait networks and structural equation models as tools to interpret multi-trait genome-wide association studies

Mehdi Momen, Malachy T. Campbell, Harkamal Walia, Gota Morota

Research output: Contribution to journalArticle

Abstract

Background: Plant breeders seek to develop cultivars with maximal agronomic value, which is often assessed using numerous, often genetically correlated traits. As intervention on one trait will affect the value of another, breeding decisions should consider the relationships among traits in the context of putative causal structures (i.e., trait networks). While multi-trait genome-wide association studies (MTM-GWAS) can infer putative genetic signals at the multivariate scale, standard MTM-GWAS does not accommodate the network structure of phenotypes, and therefore does not address how the traits are interrelated. We extended the scope of MTM-GWAS by incorporating trait network structures into GWAS using structural equation models (SEM-GWAS). Here, we illustrate the utility of SEM-GWAS using a digital metric for shoot biomass, root biomass, water use, and water use efficiency in rice. Results: A salient feature of SEM-GWAS is that it can partition the total single nucleotide polymorphism (SNP) effects acting on a trait into direct and indirect effects. Using this novel approach, we show that for most QTL associated with water use, total SNP effects were driven by genetic effects acting directly on water use rather that genetic effects originating from upstream traits. Conversely, total SNP effects for water use efficiency were largely due to indirect effects originating from the upstream trait, projected shoot area. Conclusions: We describe a robust framework that can be applied to multivariate phenotypes to understand the interrelationships between complex traits. This framework provides novel insights into how QTL act within a phenotypic network that would otherwise not be possible with conventional multi-trait GWAS approaches. Collectively, these results suggest that the use of SEM may enhance our understanding of complex relationships among agronomic traits.

Original languageEnglish (US)
Article number107
JournalPlant Methods
Volume15
Issue number1
DOIs
StatePublished - Sep 18 2019

Fingerprint

Genome-Wide Association Study
Structural Models
single nucleotide polymorphism
water use efficiency
quantitative trait loci
phenotype
shoots
plant breeders
water
biomass
breeding value
Water
agronomic traits
Single Nucleotide Polymorphism
rice
Biomass
cultivars
Phenotype
genome-wide association study
Breeding

Keywords

  • Bayesian network
  • Genome-wide association
  • Multi-trait
  • Structural equation modeling

ASJC Scopus subject areas

  • Biotechnology
  • Genetics
  • Plant Science

Cite this

Utilizing trait networks and structural equation models as tools to interpret multi-trait genome-wide association studies. / Momen, Mehdi; Campbell, Malachy T.; Walia, Harkamal; Morota, Gota.

In: Plant Methods, Vol. 15, No. 1, 107, 18.09.2019.

Research output: Contribution to journalArticle

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