Barley (Hordeum vulgare L.) is a major cereal in Kazakhstan, where diverse breeding material supports crop improvement. We characterized 86 two-row spring barley accessions from six breeding organizations using the Illumina Infinium 50K Barley SNP Array. Analysis of 29,920 high-quality SNPs revealed moderate diversity (He = 0.346, PIC = 0.278, Shannon = 0.752), with 80.84% of molecular variation occurring within and 19.16% among breeding organizations. A minor allele frequency-free (MAF-free) analysis showed that 95.61% of marker–allele combinations at polymorphic loci were shared by at least two organizations. Although PCA, kinship, and neighbor-joining analyses indicated extensive overlap, discriminant analysis of principal components (DAPC) cluster membership was significantly associated with breeding origin (χ2 = 106.38, Monte Carlo p = 1 × 10–5; bias-corrected Cramér’s V = 0.513), demonstrating substantial but incomplete differentiation among breeding programs. Phenotypic differentiation was evaluated using environment-adjusted genotype BLUPs. All seven traits differed significantly among five DAPC clusters. In a reduced six-trait linear discriminant analysis (LDA) excluding vegetation period, LD1 was associated most strongly with number of kernels per spike, followed by heading time, spike length, and heading-to-maturity time. Leave-one-out cross-validation (LOOCV) accuracy was 36.47%, exceeding the permutation mean of 19.83% but indicating considerable phenotypic overlap. The examined materials therefore constitute a diverse, interconnected breeding panel that may support germplasm management and parent selection and provide a genomic and phenotypic framework for future GWAS, genomic selection, and targeted validation of molecular markers within the represented collections.
Y. Genievskaya, V. Chudinov, G. Sereda et al.· International Journal of Mol...· 0 citations
Net form net blotch (NFNB), caused by
Pyrenophora teres
f.
teres
(
Ptt
), is a major constraint to barley production. However, the genetic basis of adult plant resistance (APR) and seedling resistance remains incompletely understood. This study aimed to dissect the genetic architecture of NFNB resistance in a diverse panel of 273 spring barley accessions.
APR was evaluated in two contrasting field environments in Kazakhstan, whereas seedling resistance was assessed under greenhouse conditions using two
Ptt
races. Genotyping with the 50K SNP array yielded 31,834 high-quality SNPs. Genome-wide association analyses were performed using four models – MLM, MLMM, FarmCPU, and BLINK – that accounted for population structure and kinship. Candidate genes within QTL intervals were prioritized using transcriptomic data from 16 barley tissues and co-expression network analysis.
Substantial phenotypic variation was observed, with moderate heritability for APR (
h
2
= 50.6%) and seedling resistance (
h
2
= 41.3%), together with strong genotype × environment and genotype × race interactions. In total, 275 marker–trait associations were detected for APR and 48 for seedling resistance. These associations were consolidated into 57 genome-wide significant (P < 1.57E–6) or multi-model-supported QTLs across all seven barley chromosomes, including 39 APR and 18 seedling-resistance QTLs. Forty QTLs co-localized with known resistance genes (
Rpt1
,
Rpt2
,
Rpt3
,
Rpt4
,
Rpt6
,
Rpt8
,
Rpt9
, and
SPN1
) or previously reported net blotch QTLs, whereas 17 were potentially novel. Transcriptomic integration identified 87 highly expressed genes within APR QTL regions and 42 within seedling-resistance QTLs. The potentially novel QTLs
Q_NB_1H.6
,
Q_NB_2H.3
, and
Q_NB_3H.1
harbored genes encoding proteins previously associated with pathogen resistance and stress responses. Co-expression analysis revealed stage-specific transcriptional patterns, with APR-associated genes enriched in regulatory functions and seedling-resistance genes enriched in metabolic and structural functions.
The results demonstrate that NFNB resistance is polygenic and developmentally stage-dependent, with partly distinct mechanisms underlying adult plant and seedling resistance. The identified QTLs and prioritized candidate genes provide targets for independent validation, functional characterization, and the development of molecular markers to support breeding for durable NFNB resistance in barley.
Y. Genievskaya, A. Maulenbay, A. Zatybekov et al.· Frontiers in Agronomy· 0 citations
