Genome-wide association study of agronomic traits in bread wheat reveals novel putative alleles for future breeding programs

Abstract

BackgroundIdentification of loci for agronomic traits and characterization of their genetic architecture are crucial in marker-assisted selection (MAS). Genome-wide association studies (GWAS) have increasingly been used as potent tools in identifying marker-trait associations (MTAs). The introduction of new adaptive alleles in the diverse genetic backgrounds may help to improve grain yield of old or newly developed varieties of wheat to balance supply and demand throughout the world. Landraces collected from different climate zones can be an invaluable resource for such adaptive alleles.ResultsGWAS was performed using a collection of 298 Iranian bread wheat varieties and landraces to explore the genetic basis of agronomic traits during 2016–2018 cropping seasons under normal (well-watered) and stressed (rain-fed) conditions. A high-quality genotyping by sequencing (GBS) dataset was obtained using either all original single nucleotide polymorphism (SNP, 10938 SNPs) or with additional imputation (46,862 SNPs) based on W7984 reference genome. The results confirm that the B genome carries the highest number of significant marker pairs in both varieties (49,880, 27.37%) and landraces (55,086, 28.99%). The strongest linkage disequilibrium (LD) between pairs of markers was observed on chromosome 2D (0.296). LD decay was lower in the D genome, compared to the A and B genomes. Association mapping under two tested environments yielded a total of 313 and 394 significant (−log10 P >3) MTAs for the original and imputed SNP data sets, respectively. Gene ontology results showed that 27 and 27.5% of MTAs of SNPs in the original set were located in protein-coding regions for well-watered and rain-fed conditions, respectively. While, for the imputed data set 22.6 and 16.6% of MTAs represented in protein-coding genes for the well-watered and rain-fed conditions, respectively.ConclusionsOur finding suggests that Iranian bread wheat landraces harbor valuable alleles that are adaptive under drought stress conditions. MTAs located within coding genes can be utilized in genome-based breeding of new wheat varieties. Although imputation of missing data increased the number of MTAs, the fraction of these MTAs located in coding genes were decreased across the different sub-genomes.

Phenotypic and genetic variability of a tetraploid wheat collection grown in Kazakhstan

“…The significance of each SSR marker for studied traits was assessed using a two-tailed t-test (Lüders et al, 2016;Rahimi et al, 2019). The results of the test suggested that five out of seven SSRs were significant at least for one studied trait (see Table 5).…”

Tackling microbial threats in agriculture with integrative imaging and computational approaches

“…Downstream applications included functional genetic studies for drought tolerance and GWAS applications, which in turn can feed into marker-assisted breeding efforts. In a different application, chlorophyll fluorescence and thermal (infrared) phenotyping of ~300 Iranian wheat cultivars combined with GWAS revealed adaptive alleles for drought stress useful for marker-assisted selection [91] .…”

A simple, cost-effective high-throughput image analysis pipeline improves genomic prediction accuracy for days to maturity in wheat

“…The Persian farmers irrigate their farms two to four more times with the stored water after spike appearance to avoid yield loss due to late-season drought stress. This strategy leads to a significant increase in wheat grain yield [ 27 ]. The impact of drought stress and irrigation at the end of the growing season on different genotypes needs further investigations.…”