KASP (KBioscience Competitive Allele Specific PCR) and Amplifluor (Amplification with fluorescence) SNP markers are two prominent technologies based upon a shared identical Allele-specific PCR platform. Amplifluor-like SNP and KASP analysis was carried out using published and own design of Universal probes (UPs) and Gene-specific primers (GSPs). Advantages of the Amplifluor-like system over KASP include the significantly lower costs and much greater flexibility in the adjustment and development of ‘self-designed’ dual fluorescently-labelled UPs and regular GSPs. The presented results include optimisation of ‘tail’ length in UPs and GSPs, protocol adjustment, and the use of various fluorophores in different qPCR instruments. The compatibility of the KASP Master-mix in both original and Amplifluor-like systems has been demonstrated in the presented results, proving their similar principles. Results of SNP scoring with rare alleles in addition to more frequently occurring alleles are shown. The Amplifluor-like system produces SNP genotyping results with a level of sensitivity and accuracy comparable to KASP but at a significantly cheaper cost and with much greater flexibility for UPs with self-designed GSPs.

Two genes, HvSAP8 and HvSAP16, encoding Zinc-finger proteins, were identified earlier as active in barley plants. Based on bioinformatics and sequencing analysis, six SNPs were found in the promoter regions of HvSAP8 and one in HvSAP16, among parents of two barley segregating populations, Granal × Baisheshek and Natali × Auksiniai-2. ASQ and Amplifluor markers were developed for HvSAP8 and HvSAP16, one SNP in each gene, and in each of two populations, showing simple Mendelian segregation. Plants of F₆ selected breeding lines and parents were evaluated in a soil-based drought screen, revealing differential expression of HvSAP8 and HvSAP16 corresponding with the stress. After almost doubling expression during the early stages of stress, HvSAP8 returned to pre-stress level or was strongly down-regulated in plants with Granal or Baisheshek genotypes, respectively. For HvSAP16 under drought conditions, a high expression level was followed by either a return to original levels or strong down-regulation in plants with Natali or Auksiniai-2 genotypes, respectively. Grain yield in the same breeding lines and parents grown under moderate drought was strongly associated with their HvSAP8 and HvSAP16 genotypes. Additionally, Granal and Natali genotypes with specific alleles at HvSAP8 and HvSAP16 were associated with improved performance under drought via higher 1000 grain weight and more shoots per plant, respectively.

Salinity tolerance was studied in chickpea accessions from a germplasm collection and in cultivars from Kazakhstan. After NaCl treatment, significant differences were found between genotypes, which could be arranged into three groups. Those that performed poorest were found in group 1, comprising five ICC accessions with the lowest chlorophyll content, the highest leaf necrosis (LN), Na⁺ accumulation, malondialdehyde (MDA) content, and a low glutathione ratio GSH/GSSG. Two cultivars, Privo-1 and Tassay, representing group 2, were moderate in these traits, while the best performance was for group 3, containing two other cultivars, Krasnokutsky-123 and Looch, which were found to have mostly green plants and an exact opposite pattern of traits. Marker–trait association (MTA) between 6K DArT markers and four traits (LN, Na⁺, MDA, and GSH/GSSG) revealed the presence of four possible candidate genes in the chickpea genome that may be associated with the three groups. One gene, ATP-binding cassette, CaABCC6, was selected, and three haplotypes, A, D1, and D2, were identified in plants from the three groups. Two of the most salt-tolerant cultivars from group 3 were found to have haplotype D2 with a novel identified SNP. RT-qPCR analysis confirmed that this gene was strongly expressed after NaCl treatment in the parental- and breeding-line plants of haplotype D2. Mass spectrometry of seed proteins showed a higher accumulation of glutathione reductase and S-transferase, but not peroxidase, in the D2 haplotype. In conclusion, the CaABCC6 gene was hypothesized to be associated with a better response to oxidative stress via glutathione metabolism, while other candidate genes are likely involved in the control of chlorophyll content and Na⁺ accumulation.

Stem internode length determines height to first pod (HFP), an important trait for mechanical harvesting in legume crops. In the present study, this trait in lentil was (Lens culinaris Medik.) examined using scanning electron microscopy (SEM) of epidermal cells in stem internodes of two parents, Flip92-36L and ILL-1552, with long and short HFP, respectively. No significant differences in cell length, but differences in cell width were seen. This indicates that HFP was determined by cell number rather than cell length. The candidate gene family for HFP, Suppressor of Overexpression of Constans 1 (SOC1), a member of the MADS-box transcription factor family, controls both flowering time (FT) and HFP traits. Six LcSOC1 genes were identified in this study, and their expression was analysed. Most of the genes studied showed constitutive expression during vegetative growth, flowering, and seed development stages. Expression of LcSOC1-a seems to be involved in the transition to flowering and FT, whereas expression of LcSOC1-b2 was strongly associated with HFP but not FT. Two haplotypes with two SNP each were identified in LcSOC1-b2 among eight sequenced lentil accessions, and an SNP-based ASQ marker was developed and used for genotyping of a lentil germplasm collection. Significant association between LcSOC1-b2 haplotypes and HFP was found in this study, indicating a primary role for this gene in internode length, potentially by regulating cell number.

Drought poses a significant challenge to plant growth and productivity, particularly in arid regions like northern Kazakhstan. Dehydration-responsive element-binding (DREB) transcription factors play an important role in plant response to drought and other abiotic stresses. In Arabidopsis thaliana, the DREB subfamily consists of six groups, designated DREB1 to DREB6. Among these, DREB2 is primarily associated with drought and salinity tolerance. In the chickpea genome, two DREB genes, CaDREB2c and CaDREB2h, have been identified, exhibiting high sequence similarity to Arabidopsis DREB2 genes. We investigated the nucleotide sequences of CaDREB2c and CaDREB2h genes in several chickpea cultivars commonly grown in northern Kazakhstan. Interestingly, the CaDREB2h gene sequence was identical across all varieties and corresponded to the sequence deposited in the GenBank. However, the CaDREB2c gene sequence exhibited variations among the studied varieties, categorized into three groups: the first group (I), comprising 20 cultivars, contained a CaDREB2c gene sequence identical to the GenBank (Indian cultivar CDC Frontier). The second group (II), consisting of 4 cultivars, had a single synonymous substitution (T to C) compared to the deposited CaDREB2c gene sequence. The third group, encompassing 5 cultivars, displayed one synonymous substitution (C to T) and two non-synonymous substitutions (G to T and G to A). Furthermore, we assessed the gene expression patterns of CaDREB2c and CaDREB2h in different chickpea varieties under drought conditions. Chickpea cultivars 8 (III), 37 (I), 6 (III), and 43 (I) exhibited the highest drought resistance. Our analysis revealed a strong positive correlation between drought resistance and CaDREB2h gene expression under drought stress. Our findings suggest that the chickpea’s adaptive responses to water deprivation are associated with changes in CaDREB2 gene expression. To further elucidate the mechanisms underlying drought tolerance, we propose future research directions that will delve into the molecular interactions and downstream targets of CaDREB2 genes.

The technological properties of durum wheat grain are determined by prolamins (gliadins and glutenins). Information on the allelic composition of key loci remains incomplete despite existing global studies examining prolamin variability. This highlighted the need to study these traits in durum wheat in Kazakhstan. The effects of specific gliadin components with high- and low-molecular-weight glutenin fractions on gluten quality are also not fully clarified. This study aimed to characterise allelic diversity at prolamin-coding loci and evaluate associated grain quality traits. Using native and denaturing SDS-electrophoresis, 181 tetraploid wheat accessions from Kazakhstan, an International germplasm collection, and 26 breeding lines were analysed for allelic variation and associations with protein content, gluten content, gluten index, and SDS-sedimentation. The γ45 gliadin component and Glu-A3a allele were positively associated with SDS-sedimentation and gluten index, while Glu-B3b had a negative effect. Distinct prolamin profiles were observed among accessions from different ecological and geographical locations. These results support the selection of superior durum wheat genotypes and enable the identification of favourable allele combinations at the Gli-1, Gli-2, Glu-1, and Glu-3 loci in cultivars from Kazakhstan. Comparison with global tetraploid wheat germplasm collections demonstrates unique genetic diversity in genotypes, providing a valuable basis for breeding programs aimed at improving grain and gluten quality in durum wheat in Kazakhstan and Central Asian countries.