Multi-environment genome -wide association mapping of culm morphology traits in barley

Gianluca Bretani; Salar Shaaf; Alessandro Tondelli; Luigi Cattivelli; Stefano Delbono; Robbie Waugh; William Thomas; Joanne Russell; Hazel Bull; Ernesto Igartua; Ana M Casas; Pilar Gracia; Roberta Rossi; Alan H Schulman; Laura Rossini

doi:10.3389/fpls.2022.926277

Multi-environment genome -wide association mapping of culm morphology traits in barley

Front Plant Sci. 2022 Sep 23:13:926277. doi: 10.3389/fpls.2022.926277. eCollection 2022.

Authors

Affiliations

¹ Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, Università degli Studi di Milano, Milan, Italy.
² Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, Fiorenzuola d'Arda, Italy.
³ Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom.
⁴ Aula Dei Experimental Station (EEAD-CSIC), Spanish Research Council, Zaragoza, Spain.
⁵ Viikki Plant Sciences Centre, Natural Resources Institue (LUKE), HiLIFE Institute of Biotechnology, University of Helsinki, Helsinki, Finland.

Abstract

In cereals with hollow internodes, lodging resistance is influenced by morphological characteristics such as internode diameter and culm wall thickness. Despite their relevance, knowledge of the genetic control of these traits and their relationship with lodging is lacking in temperate cereals such as barley. To fill this gap, we developed an image analysis-based protocol to accurately phenotype culm diameters and culm wall thickness across 261 barley accessions. Analysis of culm trait data collected from field trials in seven different environments revealed high heritability values (>50%) for most traits except thickness and stiffness, as well as genotype-by-environment interactions. The collection was structured mainly according to row-type, which had a confounding effect on culm traits as evidenced by phenotypic correlations. Within both row-type subsets, outer diameter and section modulus showed significant negative correlations with lodging (<-0.52 and <-0.45, respectively), but no correlation with plant height, indicating the possibility of improving lodging resistance independent of plant height. Using 50k iSelect SNP genotyping data, we conducted multi-environment genome-wide association studies using mixed model approach across the whole panel and row-type subsets: we identified a total of 192 quantitative trait loci (QTLs) for the studied traits, including subpopulation-specific QTLs and 21 main effect loci for culm diameter and/or section modulus showing effects on lodging without impacting plant height. Providing insights into the genetic architecture of culm morphology in barley and the possible role of candidate genes involved in hormone and cell wall-related pathways, this work supports the potential of loci underpinning culm features to improve lodging resistance and increase barley yield stability under changing environments.

Keywords: Hordeum vulgare; barley; culm morphology; image-analysis; lodging; multi-environment GWAS.