Genome-Wide Association Mapping for Stomata and Yield Indices in Bread Wheat under Water Limited Conditions

Abstract

Genome-wide association study (GWAS) was performed for stomata- and yield-related attributes with high-density Illumina 90 K Infinium SNP (single nucleotide polymorphism) array in bread wheat to determine genetic potential of germplasm for scarce water resources with sustainable yield potential. Major yield and stomata attributes were phenotyped on a panel of Pakistani and foreign accessions grown in non-stressed and water shortage environments during two seasons. Highly significant variations were shown among accessions in both conditions for examined characteristics. Water shortage conditions reduced the overall wheat yield and strong positive correlation existed among stomatal frequency, leaf venation and grain yield per plant. Population structure analyses based on 90,000 SNP data classified the accessions into four sub-populations which indicated the presence of genetic variability. Marker-trait association (MTA) analyses revealed that 422 significant SNPs at p ≤ 10−3, after crossing the false discovery rate (FDR) <0.05 threshold, were linked with examined attributes. Pleiotropic loci (wsnp_Ex_c8913_14881924 and Tdurum_contig10598_304) were associated with flag leaf area (FLA), stomata size (SS), stomata frequency (SF), leaf venation (LV), number of grain per spike (NGS) and grain yield per plant (GYP), which were located on chromosome 4B and 6B at the positions 173.63cM and 229.64cM, respectively, under water shortage conditions. Pleotropic loci wsnp_Ex_c24167_33416760, wsnp_Ex_c5412_9564046 and Tdurum_contig81797_369 on chromosomes 7A, 2A and 4B at the positions 148.26cM, 261.05cM and 173.63cM, respectively, were significantly linked with stomata and yield indices such as FLA, SS, SF, LV, NGS and GYP under normal and water shortage conditions. The current experiment not only validated several MTAs for studied indices reported in other studies but also discovered novel MTAs significant under water shortage environments. Associated and significant SNPs will be useful in discovering novel genes underpinning water shortage tolerance in bread wheat for producing high-yielding and drought tolerant wheat varieties to fulfill the wheat demand for growing populations.

Genome-wide association mapping of bread wheat genotypes for sustainable food security and yield potential under limited water conditions

“…As the population continues to grow, the demand for wheat is also increasing and it is predicted to be increase up to 40% by 2030. Therefore, there is an urgent need to increase wheat production to ensure sustainable food security [ 1 ]. Various limiting factors leading to the decline in wheat production include low quality wheat seed, late sowing, unapproved sowing practices, poor soil fertility, uneven fertilization, inappropriate weed control, biotic and abiotic stress [ 2 ].…”

“…Although progress has been made in improving wheat breeding under normal water conditions, but little progress has been made for water deficit conditions [ 10 ]. In the context of water shortage, the problem has become more prominent, with large differences in yield between productive areas and rain-fed agricultural areas [ 1 ]. Approaches to decrease this gap include the advancement of genetics for water deficient conditions by determining the causes of water deficient tolerance and subsequent introgression of genes for specific characters associated to cultivated wheat genotypes.…”

“…Selection of wheat genotypes based on these drought-related traits is informal, inexpensive, and less time-consuming. Various efforts have been made to increase wheat yield under drought stress using traditional breeding methods, but these strategies do not contribute more than 1% to the increase in annual yield [ 1 , 17 ].…”

Genome-Wide Association Study of Grain Number in Common Wheat From Shanxi Under Different Water Regimes

“…As Li et al (2021) reported in wheat salt tolerance research, two strategies were used to dissect the basis of stress tolerance: one is to identify loci associated with stress tolerance by comparing the different associated markers identified between stress and normal conditions ( Hoang et al, 2019 ; Pradhan et al, 2019 ; Lin et al, 2020 ; Ahmed et al, 2021 ) and the other is to identify associated loci with stress-tolerant indices of investigated traits ( Hu et al, 2021 ; Jeong et al, 2021 ; Li et al, 2021 ). In this study, we used these two strategies to identify the GNS-associated markers under water stress.…”

“…Among the three main yield components in wheat, GNS is more affected by drought stress during the productive period than TGW ( Fischer, 2008 , 2011 ). Water deficiency directly affects both the vegetative and reproductive growth stages, ultimately reducing fertility parameters, grain yield components, and thus final yield ( Ahmed et al, 2021 ; Jallouli et al, 2021 ). It seems likely that improvements in grain yield may derive from improvements in grain number, particularly under water stress conditions ( Li et al, 2019 ; Sun et al, 2019 ; Zhang et al, 2020 ).…”