A comprehensive image-based phenomic analysis reveals the complex genetic architecture of shoot growth dynamics in rice (Oryza sativa)

Malachy T. Campbell, Qian Du, Kan Liu, Chris J. Brien, Bettina Berger, Chi Zhang, Harkamal Walia

Research output: Contribution to journalArticle

11 Citations (Scopus)

Abstract

Early vigor is an important trait for many rice (Oryza sativa L.)-growing environments. However, genetic characterization and improvement for early vigor is hindered by the temporal nature of the trait and strong genotype × environment effects. We explored the genetic architecture of shoot growth dynamics during the early and active tillering stages by applying a functional modeling and genomewide association (GWAS) mapping approach on a diversity panel of ~360 rice accessions. Multiple loci with small effects on shoot growth trajectory were identified, indicating a complex polygenic architecture. Natural variation for shoot growth dynamics was assessed in a subset of 31 accessions using RNA sequencing and hormone quantification. These analyses yielded a gibberellic acid (GA) catabolic gene, OsGA2ox7, which could influence GA levels to regulate vigor in the early tillering stage. Given the complex genetic architecture of shoot growth dynamics, the potential of genomic selection (GS) for improving early vigor was explored using all 36,901 single-nucleotide polymorphisms (SNPs) as well as several subsets of the most significant SNPs from GWAS. Shoot growth trajectories could be predicted with reasonable accuracy using the 50 most significant SNPs from GWAS (0.37–0.53); however, the accuracy of prediction was improved by including more markers, which indicates that GS may be an effective strategy for improving shoot growth dynamics during the vegetative growth stage. This study provides insights into the complex genetic architecture and molecular mechanisms underlying early shoot growth dynamics and provides a foundation for improving this complex trait in rice.

Original languageEnglish (US)
JournalPlant Genome
Volume10
Issue number2
DOIs
StatePublished - Jan 1 2017

Fingerprint

Oryza sativa
rice
shoots
Growth
vigor
single nucleotide polymorphism
Single Nucleotide Polymorphism
tillering
gibberellic acid
marker-assisted selection
trajectories
RNA Sequence Analysis
phenomics
Oryza
chromosome mapping
vegetative growth
sequence analysis
Molecular Biology
hormones
developmental stages

ASJC Scopus subject areas

  • Genetics
  • Agronomy and Crop Science
  • Plant Science

Cite this

A comprehensive image-based phenomic analysis reveals the complex genetic architecture of shoot growth dynamics in rice (Oryza sativa). / Campbell, Malachy T.; Du, Qian; Liu, Kan; Brien, Chris J.; Berger, Bettina; Zhang, Chi; Walia, Harkamal.

In: Plant Genome, Vol. 10, No. 2, 01.01.2017.

Research output: Contribution to journalArticle

Campbell, Malachy T. ; Du, Qian ; Liu, Kan ; Brien, Chris J. ; Berger, Bettina ; Zhang, Chi ; Walia, Harkamal. / A comprehensive image-based phenomic analysis reveals the complex genetic architecture of shoot growth dynamics in rice (Oryza sativa). In: Plant Genome. 2017 ; Vol. 10, No. 2.
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