Phenotypic Evaluation and Genetic Analysis of Seedling Emergence in a Global Collection of Wheat Genotypes (Triticum aestivum L.) Under Limited Water Availability.

Michael G Francki,Robert J French,Katia T Stefanova,Grantley S Stainer,Gregory J Rebetzke,Esther Walker

doi:10.3389/fpls.2021.796176

Abstract

The challenge in establishing an early-sown wheat crop in southern Australia is the need for consistently high seedling emergence when sowing deep in subsoil moisture (>10 cm) or into dry top-soil (4 cm). However, the latter is strongly reliant on a minimum soil water availability to ensure successful seedling emergence. This study aimed to: (1) evaluate 233 Australian and selected international wheat genotypes for consistently high seedling emergence under limited soil water availability when sown in 4 cm of top-soil in field and glasshouse (GH) studies; (2) ascertain genetic loci associated with phenotypic variation using a genome-wide association study (GWAS); and (3) compare across loci for traits controlling coleoptile characteristics, germination, dormancy, and pre-harvest sprouting. Despite significant (P < 0.001) environment and genotype-by-environment interactions within and between field and GH experiments, eight genotypes that included five cultivars, two landraces, and one inbred line had consistently high seedling emergence (mean value > 85%) across nine environments. Moreover, 21 environment-specific quantitative trait loci (QTL) were detected in GWAS analysis on chromosomes 1B, 1D, 2B, 3A, 3B, 4A, 4B, 5B, 5D, and 7D, indicating complex genetic inheritance controlling seedling emergence. We aligned QTL for known traits and individual genes onto the reference genome of wheat and identified 16 QTL for seedling emergence in linkage disequilibrium with coleoptile length, width, and cross-sectional area, pre-harvest sprouting and dormancy, germination, seed longevity, and anthocyanin development. Therefore, it appears that seedling emergence is controlled by multifaceted networks of interrelated genes and traits regulated by different environmental cues.

Highlights

Wheat crop in Western Australia (WA) has traditionally been sown in moist soils at the beginning of the growing season in late autumn (April–May), after which it grows through the cooler months until flowering and subsequently filling grain in spring (September–November) as rainfall declines and temperature rises
This study aimed to: (1) evaluate 233 global wheat genotypes for high seedling emergence under limited water availability in the field and controlled environments when sown at 4 cm depth; (2) ascertain genetic loci associated with phenotypic variation for seedling emergence at each environment by genome-wide association study (GWAS) using single nucleotide polymorphic (SNP) markers from the iSelect Infinium 90K genotyping array; and (3) compare known loci and genes controlling variation with seed vigor, dormancy, germination, and coleoptile characteristics, and extrapolate their relationship with seed emergence under limited water availability
Analysis of current and historical measurements indicated that lower soil temperature and evaporation rate from mid-April onward in any given season provided suitable sowing opportunities to evaluate the percentage seedling emergence under limited water conditions

Summary

Introduction

Wheat crop in Western Australia (WA) has traditionally been sown in moist soils at the beginning of the growing season in late autumn (April–May), after which it grows through the cooler months until flowering and subsequently filling grain in spring (September–November) as rainfall declines and temperature rises. Decreasing rainfall and the increasing temperature have resulted in water-limited potential across Australia declining by 27% from 1990 to 2015 (Hochman et al, 2017), actual wheat yields in WA have risen slightly since 1990 due to better production technology being developed and adopted over this time. Climate change related rainfall decline in the WA Wheatbelt has been greatest in May and June when crops are traditionally sown, and there has been an increase in March rainfall (Cai and Cowan, 2013; Hochman et al, 2017; Scanlon and Doncon, 2020) This means that soil moisture availability for crop establishment will often be lower in the traditional sowing window than in the past, and there will be more frequent sowing opportunities in March and early April than before. These earlier sowing opportunities will be associated with higher temperatures and evaporation rates than in late April and May, so soil water availability is likely to be limiting for crop establishment more often

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