Genome-wide Association Studies (GWAS) and Genetic Diversity of Barley (Hordeum vulgare L.) genotypes

Barley (Hardeam valgare L.) is consumed all around the world as the main cereal crop. According to the FAO data, nowadays, it is one of the ancient grain crops cultivated and used worldwide grown over a broader environmental range than any of the cereal, and the average harvested area for barley is estimated at 504,000 ha worldwide (FAO, 2020). Abiotic stress tolerant crops will probably be keys to food security by helping agriculture to cope with climatic changes. Barley has gained particular interest owing to providing a wide range of allelic variants, which could explain the degree of adaptive competence and plasticity of Hordeum and help plant breeding efforts for stress tolerance. It is an excellent model system to study plant response to adverse environmental conditions (Francia et al. 2004). Cold stress in barley is a complex quantitative trait significantly influenced by the environment. Due to this low heritability and dependency on environmental conditions, the direct selection of barley for cold tolerance is time-consuming and less effective (Adhikari et al., 2022). Cold stress can cause foret and spike abortion as well as damage to the developing grain, which could have a significant impact on barley yield and yield components (Tyrka et al., 2015). To reduce the negative effects of cold stress on barley production, it is necessary to identify genomic regions associated with cold tolerance (Fiust et al., 2020).

Plant breeders require access to novel genetic variants to develop barley varieties that can adapt to changing abiotic stressors, such as cold stress. In addition, research on the genetic mechanisms and discovery of genes affecting cold tolerance would be helpful for developing cultivars with strong cold tolerance (Pan et al. 2015). Therefore, efforts to improve cold tolerance need to be continued and strengthened since this improvement has been a major target of global plant breeding programs (Bengtsson et al., 2017). Even though crop-breeding programs have not overtly bred for improving low-stress tolerance traditionally, they have focused on maximizing yield instead when selection pressure for these factors is relatively low (Gilliham et al., 2017). Hence, breeders are extremely interested in new technology offers, such as the possibility to improve the selection strategies in barley breeding by adopting a wide range of novel approaches. Nowadays, the molecular markers system is an effective tool and an important strategy for improving the cold tolerance between various varieties of barley. Information value of the SNPs technique, which is a powerful tool for genetic diversity and association analysis in barley breeding, has been frequently confirmed in several investigations (Lai et al., 2017; Wabila et al., 2019; Jabbari et al. 2021). Moreover, this technique can be valuable for marker-assisted selection to improve cold tolerance in barley breeding (Adhikari et al., 2022). The genetic diversity within and between crop plant species permits the breeders to develop new cold-tolerant varieties with desirable characteristics (Pan et al., 2015). In addition, evaluating the genetic diversity of barley lines using SSR markers is important in barley breeding for successful exploration, genetic stability, and effective conservation, because morphological characters are limited in number and unstable (Teklemariam et al., 2022). QTL mapping is well suited to the detection of genes associated with particular traits, yet is costly and time-consuming for developing the mapping population (just a few cycles of recombination). To overcome these limitations, the identification of molecular markers associated with traits of interest through multiple regression analysis has been adopted in barley so far (Wang et al., 2012; Cheghamirza et al., 2017; Jamali et al., 2017; Beheshtizade et al., 2018). The identification of molecular markers associated with a trait of interest would be an efficient approach to enhancing barley breeding programs (the collections of germplasms, the detection and analysis of potential in specific genotypes, the identification of desirable alleles, the validation of candidate markers linked to quantitative traits, and indirect selection using marker-assisted selection method) (Singh et al., 2020). The objectives of the current study were as follows: