GWAS analysis in spring barley (Hordeum vulgare L.) for morphological traits exposed to drought

Abstract

Association analysis based on linkage disequilibrium has become a common and powerful approach for detection of QTLs underlying complex agronomic traits including drought tolerance. To determine marker/trait association, 148 modern European spring barley cultivars were evaluated under drought stress. Associations of morphological traits with AFLP/SSR markers were investigated based on the mixed linear model using the TASSEL3.0. Population structure was estimated using various methods including Bayesian clustering model by STRUCTURE software, PCoA analysis, NJ dendrogram and Hierarchical Clustering. Linkage disequilibrium patterns were explored among the whole genome and each chromosome separately. All the analysis for population structure divided the population into two sub-groups. Linkage disequilibrium analysis showed that by increasing genetic distance, LD decreases. Totally, 167 significant marker trait associations were found which delineated into 65 QTLs in both treatments. Two stable QTLs on 5H at 86.880 cM were detected for Internode Length and on 3H at 126.421 cM for flag leaf length in drought stress treatment. Fourteen QTLs were co-localized with previously reported QTLs and others were novel. The results indicate that these putative genomic regions contain genes that have pleiotropic effects on morphological traits in drought condition.

Genome Wide Association Analysis of Plant Height, Spike and Awn Length in Barley (Hordeum Vulgare L.) Exposed to Mn Stress

“…Thus, it can be proved that MSL and AL have the same controller genomic regions. In non stress conditions, one SSR marker (Bmag0223-170) on chromosome 5H showed significant association with MSL, which was previously reported for plant height (Jabbari et al, 2018). Wang et al (2014) identified four QTLs on chromosomes 1H, 2H, 5H and 7H for spike length.…”

“…For awn length, six markers on chromosomes 1H, 3H, 4H and 5H under non stress conditions and four markers on chromosomes 3H, 4H and 5H under Mn stress conditions were identified. Some of these significant markers have been previously reported for internode length, flag leaf width and flag leaf sheath length (Jabbari et al, 2018). Liller et al (2017) detected twelve significant QTLs for awn length located on all chromosomes.…”

“…The population structure matrix (Q) was defined by ΔK index, the highest value was obtained at K=2, which indicates that there are two sub-groups in this population. The Q-Matrix was extracted based on K value (Falush et al, 2003;Kraakman et al, 2004;Jabbari et al, 2018).…”

“…The significant threshold of P-value for assessing marker-trait-association were calculated. The threshold p-value of 0.03 was used for all traits (Chen et al, 2010;Pasam et al, 2012;Jabbari et al, 2018).…”

Genome-Wide Association Study of Salinity Tolerance During Germination in Barley (Hordeum vulgare L.)

“…The heritability values observed in this study indicated that the variation in tolerance index (germination in salt divided by germination in DI water) was mainly a factor of salinity concentration with a small genetic component. However, salinity tolerance is an important trait in barley that is inherited quantitatively and strongly influenced by environmental conditions (Jabbari et al, 2018), as indicated by the significant interactions among genotypes, salinity tolerance, and location in this study (Table 1). Estimated heritability defines how a trait is affected by genotype; however, it is not a total quantifier of how genes and the environment govern a phenotype, but specific to the population and environment under study.…”