A simple, cost-effective high-throughput image analysis pipeline improves genomic prediction accuracy for days to maturity in wheat

Morteza Shabannejad,Eslam Majidi-Hervan,Hadi Alipour,Asa Ebrahimi,Mohammad-Reza Bihamta

doi:10.1186/s13007-020-00686-2

Abstract

BackgroundHigh-throughput phenotyping and genomic selection accelerate genetic gain in breeding programs by advances in phenotyping and genotyping methods. This study developed a simple, cost-effective high-throughput image analysis pipeline to quantify digital images taken in a panel of 286 Iran bread wheat accessions under terminal drought stress and well-watered conditions. The color proportion of green to yellow (tolerance ratio) and the color proportion of yellow to green (stress ratio) was assessed for each canopy using the pipeline. The estimated tolerance and stress ratios were used as covariates in the genomic prediction models to evaluate the effect of change in canopy color on the improvement of the genomic prediction accuracy of different agronomic traits in wheat.ResultsThe reliability of the high-throughput image analysis pipeline was proved by three to four times of improvement in the accuracy of genomic predictions for days to maturity with the use of tolerance and stress ratios as covariates in the univariate genomic selection models. The higher prediction accuracies were attained for days to maturity when both tolerance and stress ratios were used as fixed effects in the univariate models. The results of this study indicated that the Bayesian ridge regression and ridge regression-best linear unbiased prediction methods were superior to other genomic prediction methods which were used in this study under terminal drought stress and well-watered conditions, respectively.ConclusionsThis study provided a robust, quick, and cost-effective machine learning-enabled image-phenotyping pipeline to improve the genomic prediction accuracy for days to maturity in wheat. The results encouraged the integration of phenomics and genomics in breeding programs.

Highlights

High-throughput phenotyping and genomic selection accelerate genetic gain in breeding programs by advances in phenotyping and genotyping methods
This study reported the impact of terminal drought stress (TDS) and well-watered (WW) conditions on days to maturity (DTM) in a highly diverse bread wheat germplasm through an machine learning (ML)-based imagephenotyping pipeline
Field conditions Plantings were conducted at the Kheirabad Agricultural Research Station in Zanjan province in the middle of October and weather conditions were recorded during the cropping season (Additional file 4: Figure S2)

Summary

Introduction

High-throughput phenotyping and genomic selection accelerate genetic gain in breeding programs by advances in phenotyping and genotyping methods. Shabannejad et al Plant Methods (2020) 16:146 like canopy color can be recorded with the use of visual assessments. The scoring methods cannot statistically indicate the effect of stress on diverse germplasms [1, 2]. Such barriers in phenotyping have motivated plant breeders to collaborate with engineers and invent modern technologies for high-throughput phenotyping (HTP) in greenhouses and fields [1]. A pipeline with a complete framework for fast feature extraction from high-throughput imaging can be used as a platform for real-time phenotyping [4,5,6,7,8,9,10]

Methods

Results

Discussion

Conclusion