Leveraging breeding values obtained from random regression models for genetic inference of longitudinal traits

Malachy Campbell, Mehdi Momen, Harkamal Walia, Gota Morota

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

Understanding the genetic basis of dynamic plant phenotypes has largely been limited because of a lack of space and labor resources needed to record dynamic traits, often destructively, for a large number of genotypes. However, the recent advent of image-based phenotyping platforms has provided the plant science community with an effective means to nondestructively evaluate morphological, developmental, and physiological processes at regular, frequent intervals for a large number of plants throughout development. The statistical frameworks typically used for genetic analyses (e.g., genomewide association mapping, linkage mapping, and genomic prediction) in plant breeding and genetics are not particularly amenable for repeated measurements. Random regression (RR) models are routinely used in animal breeding for the genetic analysis of longitudinal traits and provide a robust framework for modeling trait trajectories and performing genetic analysis simultaneously. We recently used a RR approach for genomic prediction of shoot growth trajectories in rice (Oryza sativa L.) from 33,674 single nucleotide polymorphisms. In this study, we have extended this approach for genetic inference by leveraging genomic breeding values derived from RR models for rice shoot growth during early vegetative development. This approach provides improvements over conventional single time point analyses for discovering loci associated with shoot growth trajectories. The RR approach uncovers persistent as well as timespecific transient quantitative trait loci. This methodology can be widely applied to understand the genetic architecture of other complex polygenic traits with repeated measurements.

Original languageEnglish (US)
Article number180075
JournalPlant Genome
Volume12
Issue number2
DOIs
StatePublished - Jun 2019

Fingerprint

Genetic Models
breeding value
Breeding
trajectories
Growth
genomics
Multifactorial Inheritance
Physiological Phenomena
chromosome mapping
shoots
genetic techniques and protocols
Plant Development
Chromosome Mapping
Quantitative Trait Loci
phenotype
rice
Single Nucleotide Polymorphism
plant genetics
prediction
animal breeding

ASJC Scopus subject areas

  • Genetics
  • Agronomy and Crop Science
  • Plant Science

Cite this

Leveraging breeding values obtained from random regression models for genetic inference of longitudinal traits. / Campbell, Malachy; Momen, Mehdi; Walia, Harkamal; Morota, Gota.

In: Plant Genome, Vol. 12, No. 2, 180075, 06.2019.

Research output: Contribution to journalArticle

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