A Comprehensive Image-based Phenomic Analysis Reveals the Complex Genetic Architecture of Shoot Growth Dynamics in Rice (Oryza sativa)

Authors

Malachy T. Campbell, University of Nebraska-LincolnFollow
Qian Du, University of Nebraska-LincolnFollow
Kan Liu, University of Nebraska-Lincoln
Chris J. Brien, University of South Australia
Bettina Berger, University of Adelaide
Chi Zhang, University of Nebraska-LincolnFollow
Harkamal Walia, University of Nebraska-LincolnFollow

Document Type

Article

Date of this Version

2017

Citation

the plant genome, july 2017, vol. 10, no. 2

Comments

© Crop Science Society of America

Open access

doi: 10.3835/plantgenome2016.07.0064

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.