Genome-wide association study reveals 18 QTL for major agronomic traits in a Nordic-Baltic spring wheat germplasm

Abstract

Spring wheat (Triticum aestivum L.) remains an important alternative to winter wheat cultivation at Northern latitudes due to high risk of overwintering or delayed sowing of winter wheat. We studied nine major agronomic traits in a set of 299 spring wheat genotypes in trials across 12-year-site combinations in Lithuania, Latvia, Estonia, and Norway for three consecutive years. The dataset analyzed here consisted of previously published phenotypic data collected in 2021 and 2022, supplemented with additional phenotypic data from the 2023 field season collected in this study. We combined these phenotypic datasets with previously published genotypic data generated using a 25K single nucleotide polymorphism (SNP) array that yielded 18,467 markers with a minor allele frequency above 0.05. Analysis of these datasets via genome-wide association study revealed 18 consistent quantitative trait loci (QTL) replicated in two or more trials that explained more than 5% of phenotypic variance for plant height, grain protein content, thousand kernel weight, or heading date. The most consistent markers across the tested environments were detected for plant height, thousand kernel weight, and days to heading in eight, five, and six trials, respectively. No beneficial effect of the semi-dwarfing alleles Rht-B1b and Rht-D1b on grain yield performance was observed across the 12 tested trials. Moreover, the cultivars carrying these alleles were low yielding in general. Based on principal component analysis, wheat genotypes developed in the Northern European region clustered separately from those developed at the southern latitudes, and markers associated with the clustering were identified. Important phenotypic traits, such as grain yield, days to heading, grain protein content, and thousand kernel weight were associated with this clustering of the genotype sets. Interestingly, despite being adapted to the Nordic environment, genotypes in the Northern set demonstrated lower grain yield performance across all tested environments. The results indicate that spring wheat germplasm harbors valuable QTL/alleles, and the identified trait-marker associations might be useful in improving Nordic-Baltic spring wheat germplasm under global warming conditions.

Keywords: GWAS; Nordic region; QTL; Triticum aestivum; yield-related traits.

Figure 1

Meteorological conditions from April till August in three seasons (2021, 2022, 2023) in four study locations (LT, Lithuania; LV, Latvia; EE, Estonia; NO, Norway) compared to 30-year long-term average (LTA) data (1991–2020): (A) amount of monthly precipitation, (B) average air temperature.

Figure 2

Correlation matrix between the traits using the data from all trials and includes the data from 7,148 plots. All correlations were highly significant with the p-values< 0.001 as indicated by ***. Trait histograms are provided diagonally, while the scatterplots can be observed on the lower left part of the plot. GDD, growing degree days to heading; DH, heading date; PTU, photothermal units to heading; MAT, maturity date; PH, plant height; GY, grain yield; GPC, grain protein content; TKW, thousand kernel weight; TW, test weight.

Figure 3

(A) PCA plot demonstrating the distribution of 299 spring wheat genotypes using 18,467 polymorphic SNPs. The countries of genotype origin are encoded using an ISO 3166–1 alpha-2 two-letter country codes and distinct colors. (B) PCA plot according to the genotype clustering information. “N” letter represents genotypes found in the Northern cluster, while “S” represents genotypes in Southern cluster.

Figure 4

Phenotypic traits (BLUEs) comparison between the Northern and Southern spring wheat genotype clusters. The clusters were compared using Wilcoxon test. **** denotes p-values< 0.001, ns, not significant; GY, grain yield; GPC, grain protein content; DH, days to heading; GDD, growing degree days; MAT, maturity date; TKW, thousand kernel weight; TW, test weight; PH, plant height.

Figure 5

Grain yield (GY) performance of spring wheat lines in Northern and Southern genotype clusters in multiple trials. “S” and “N” denote Southern and Northern genotype clusters respectively. The trial sites were abbreviated as following: LT, Lithuania; LV, Latvia; EE, Estonia; and NO, Norway. The year of the trial is provided next to the site name. *, **, ***, and **** denote p-values of < 0.05, 0.01, 0.001, and 0.0001, respectively, while ns - not significant.

Figure 6

The effect of Rht-B1 and Rht-D1 alleles on plant height (PH). Wt genotypes denotes genotypes harboring no semi-dwarfism-related Rht alleles. The genotypes were compared using Kruskal–Wallis test. The trial sites were abbreviated as following: LT, Lithuania; LV, Latvia; EE, Estonia; and NO, Norway. The year of the trial is provided next to the site name. *, **, ***, and **** denote p-values of < 0.05, 0.01, 0.001, and 0.0001, respectively, while ns - not significant.

Figure 7

The effect of Rht-B1 and Rht-D1 alleles on grain yield (GY). Wt genotypes denotes genotypes harboring no semi-dwarfism-related Rht alleles. The genotypes were compared using Kruskal–Wallis test. The trial sites were abbreviated as following: LT, Lithuania; LV, Latvia; EE, Estonia; and NO, Norway. The year of the trial is provided next to the site name. *, **, ***, and **** denote p-values of < 0.05, 0.01, 0.001, and 0.0001, respectively, while ns - not significant.