Genome-wide association study in two-row spring barley landraces identifies QTL associated with plantlets root system architecture traits in well-watered and osmotic stress conditions

Abstract

Water availability is undoubtedly one of the most important environmental factors affecting crop production. Drought causes a gradual deprivation of water in the soil from top to deep layers and can occur at diverse stages of plant development. Roots are the first organs that perceive water deficit in soil and their adaptive development contributes to drought adaptation. Domestication has contributed to a bottleneck in genetic diversity. Wild species or landraces represent a pool of genetic diversity that has not been exploited yet in breeding program. In this study, we used a collection of 230 two-row spring barley landraces to detect phenotypic variation in root system plasticity in response to drought and to identify new quantitative trait loci (QTL) involved in root system architecture under diverse growth conditions. For this purpose, young seedlings grown for 21 days in pouches under control and osmotic-stress conditions were phenotyped and genotyped using the barley 50k iSelect SNP array, and genome-wide association studies (GWAS) were conducted using three different GWAS methods (MLM GAPIT, FarmCPU, and BLINK) to detect genotype/phenotype associations. In total, 276 significant marker-trait associations (MTAs; p-value (FDR)< 0.05) were identified for root (14 and 12 traits under osmotic-stress and control conditions, respectively) and for three shoot traits under both conditions. In total, 52 QTL (multi-trait or identified by at least two different GWAS approaches) were investigated to identify genes representing promising candidates with a role in root development and adaptation to drought stress.

Genome-wide association studies in rice germplasm reveal significant genomic regions for root and yield-related traits under aerobic and irrigated conditions

“…The marker RM22961 associated with traits TSL and SL at the seedling stage at 14 and 21 DAS and also associated with TPL and SL at the PI stage and with grain yield per plant under aerobic conditions. Khodaeiaminjan et al., 2023 identified the MTAs viz., ‘BOPA1_1582-63’ on chromosome 5H for root/shoot ratio and ‘SCRI_RS_192761’ on chromosome 3H for shoot dry weight for control and osmotic stress conditions. In phenotypic correlation analysis also the trait total seedling length showed a significant correlation with the seedling vigour index traits.…”

“…The RSA has implications in plant development, anchorage, nutrient uptake and stress response to specific conditions based on its plasticity. The root system having robust roots and potential branching ability is crucial under the aerobic condition in rice, enabling the plants to extract water from deep soil layers ( Khodaeiaminjan et al., 2023 ). Nevertheless, different soil conditions greatly affect the varietal ability to develop a deep root system ( Sagare et al., 2020 ).…”

Unlocking the genetic diversity and population structure of the newly introduced two-row spring European HerItage Barley collecTion (ExHIBiT)

“…An initial step of data cleaning and processing included outlier removal (for both 2020 and 2021) using Tukey’s method ( Anscombe and Tukey, 1963 ) with outliers removed from both within and across the years according to Khodaeiaminjan et al. (2023) .…”

“…Pairwise Linkage disequilibrium (LD) analysis was carried out according to Khodaeiaminjan et al. (2023) .…”

Crop Landraces and Indigenous Varieties: A Valuable Source of Genes for Plant Breeding

“…During the last two decades, genome-wide association studies (GWAS) have greatly contributed to unraveling the genetic diversity of many landraces [ 27 , 28 , 29 , 30 ]. GWAS facilitates the rapid and accurate identification of alleles linked to preferable traits [ 31 , 32 , 33 , 34 ]. Compared to bi-parental populations, the GWAS panels have greater rates of recombination, which leads to higher mapping resolutions [ 35 ].…”