Genome-wide association study reveals a genomic region on 5AL for salinity tolerance in wheat

Abstract

Soil salinity is a major threat to crop productivity and quality worldwide. In order to reduce the negative effects of salinity stress, it is important to understand the genetic basis of salinity tolerance. Identifying new salinity tolerance QTL or genes is crucial for breeders to pyramid different tolerance mechanisms to improve crop adaptability to salinity. Being one of the major cereal crops, wheat is known as a salt-sensitive glycophyte and subject to substantial yield losses when grown in the presence of salt. In this study, both pot and tank experiments were conducted to investigate the genotypic variation present in 328 wheat varieties in their salinity tolerance at the vegetative stage. A Genome-Wide Association Studies (GWAS) were carried out to identify QTL conferring salinity tolerance through a mixed linear model. Six, five and eight significant marker-trait associations (MTAs) were identified from pot experiments, tank experiments and average damage scores, respectively. These markers are located on the wheat chromosomes 1B, 2B, 2D, 3A, 4B, and 5A. These tolerance alleles were additive in their effects and, when combined, increased tolerance to salinity. Candidate genes identified in these QTL regions encoded a diverse class of proteins involved in salinity tolerance in plants. A Na + /H + exchanger and a potassium transporter on chromosome 5A (IWB30519) will be of a potential value for improvement of salt tolerance of wheat cultivars using marker assisted selection programs. Some useful genotypes, which showed consistent tolerance in different trials, can also be effectively used in breeding programs.

Multidimensional screening and evaluation of morpho‐physiological indices for salinity stress tolerance in wheat

“…Plants employ various types of salt stress tolerance mechanisms (Deinlein et al, 2014; Gupta & Huang, 2014), but their ability to resist salt stress varies widely amongst different species and cultivars (Quamruzzaman, Manik, Shabala, Cao, et al, 2021a; Quamruzzaman, Manik, Shabala, & Zhou, 2021b). Wheat is a moderately salt‐tolerant crop and has a certain level of salt tolerance criteria (Maas & Hoffman, 1977).…”

“…A total of eight different wheat accessions were obtained from Australian and Chinese National GeneBanks. These were selected based on the salinity damage scores from our previous GWAS experiment (Quamruzzaman, Manik, Shabala, Cao, et al, 2021a;Quamruzzaman, Manik, Shabala, & Zhou, 2021b). The full list and a short description of these genotypes are given in Table S1.…”

“…Salinity tolerance is a complex of traits that affects various physiological processes, such as osmotic adjustment, ionic homeostasis (mainly Na + /K + ), oxidative homeostasis (ROS) and efficient stomata operation (Quamruzzaman et al, 2021a, 2021b; Zhao et al, 2020). Osmotic tolerance is associated with improving water uptake capacity of plants, thus enhancing cell expansion.…”

“…Salinity tolerance is a complex of traits that affects various physiological processes, such as osmotic adjustment, ionic homeostasis (mainly Na + /K + ), oxidative homeostasis (ROS) and efficient stomata operation (Quamruzzaman et al, 2021a(Quamruzzaman et al, , 2021bZhao et al, 2020).…”

Genome-Wide Association Study Reveals Marker Trait Associations (MTA) for Waterlogging-Triggered Adventitious Roots and Aerenchyma Formation in Barley

“…Genome-wide association studies (GWAS) have been applied in the trait-associated genetic studies with a large number of single nucleotide polymorphisms (SNPs) in many plant species, such as Arabidopsis thaliana [ 27 ], rice [ 28 ], and wheat [ 29 , 30 ]. Many QTL for waterlogging tolerance in barley have been detected [ 31 , 32 , 33 ], including those for aerenchyma formation [ 32 , 34 ], total root dry weight [ 35 , 36 ], root porosity [ 34 ], and ROS formation [ 37 ].…”