Taxonomic assessment of the Oxytropis species from South-East of Kazakhstan

The genus Oxytropis DC. is one of the largest genera in the Fabaceae family. The most plant species belonging to the Oxytropis genus have an important medicinal value. Currently the botanical taxonomy of the genus is complicated due to existence of many subgenera and sections that developed based on morphological traits. Also, in the literature there is luck of knowledge on phylogeny of Oxytropis species from Central Asian region. Therefore, the purpose of the present study was the clarification of taxonomic relationship of two Oxytropis species from SouthEast of Kazakhstan (O. almaatensis Bajt. and O. glabra DC.). The study was based on using phylogenetic analysis and haplotype network assessment based on sequences ITS (internal transcribed spacers), which is DNA marker of nuclear genome. Plant materials of O. almaatensis were collected from 2 populations in two neighboring Gorges in Trans Ili Alatau Mountains, O. glabra plant material was obtained from Herbarium of the Department of Biodiversity and Bioresources, al-Farabi Kazakh National University. Based on DNA sequences of ITS the phylogenetic and network relationships were investigated by using Neighbor Joining and Median Joining methods, respectively. The nucleotide sequences of ITS of O. almaatensis and O. glabra were aligned with sequences of 29 Oxytropis references found in the NCBI database. Out of the 601 aligned positions of ITS 33 (5.6 %) sites were found to be polymorphic nucleotides and used in evaluation of the genetic relationship of species. Constructed MJ haplotype network showed a very high congruence with the NJ phylogenetic tree. MJ network provided valuable additional hints in clarification of the taxonomic relationship among species involved in the analysis. In this study phylogenetic NJ tree and MJ network based on the variation of ITS sequences confirmed the monophyletic origin of the genus. The ITS haplotype network suggested that O. glabra is very diverse species and possibly played important role in the evolutionary processes of the genus in Central Asian region. The study is additional contribution in the molecular taxonomy of complex Oxytropis genus

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

New cultivars adapted to major durum wheat growing environments are essential for the cultivation of this crop. The development of new cultivars has required the availability of diverse genetic material and their extensive field trials. In this work, a collection of tetraploid wheat consisting of 85 accessions was tested in the field conditions of Almaty region during 2018 and 2019. The accessions were ranged according to nine agronomic traits studied, and accessions with the highest yield performance for Almaty region of Kazakhstan were revealed. The ANOVA suggested that the performance of agronomic traits were influenced both by Environment and Genotype. Also, the collection was analyzed using seven SSR (simple sequence repeats) markers. From 3 to 6 alleles per locus were revealed, with an average of 4.6, while the effective number of alleles was 2.8. Nei’s genetic diversity was in the range of 0.45–0.69. The results showed high values of polymorphism index content (PIC) in the range of 0.46–0.70, with an average of 0.62, suggesting that 6 out of 7 SSRs were highly informative (PIC > 0.5). Phylogenetic analysis of the collection has allowed the separation of accessions into six clusters. The local accessions were presented in all six clusters with the majority of them grouped in the first three clusters designated as A, B, and C, respectively. The relations between SSR markers and agronomic traits in the collection were studied. The results can be efficiently used for the enhancement of local breeding projects for the improvement of yield productivity in durum wheat

Chromosomal location and mapping of quantitative trait locus determining technological parameters of grain and flour in strong-flour bread wheat cultivar saratovskaya 29

Bread wheat is the primary bread crop in the majority of countries in the world. The most important product that is manufactured from its grain and flour is yeast bread. In order to obtain an excellent bread, grain with high physical properties is needed for flour and dough. The Russian spring wheat cultivar Saratovskaya 29 is characterized by its exclusively high physical properties of flour and dough. The purpose of this work was to identify the chromosomes carrying the main loci for these traits in Saratovskaya 29 and to map them using recombinant substitution lines genotyped with molecular markers. A set of inter-varietal substitution lines Saratovskaya 29 (Yanetzkis Probat) was used to identify the “critical” chromosomes. The donor of individual chromosomes is a spring cultivar with average dough strength and tenacity. Substitution of 1D and 4D*7A chromosomes in the genetic background of Saratovskaya 29 resulted in a significant decrease in the physical properties of the dough. Such a deterioration in the case of 1D chromosome might be related to the variability of gluten protein composition. With the help of recombinant substitution double haploid lines obtained from a Saratovskaya 29 (Yanetzkis Probat 4D*7A) substitution line the region on the 4D chromosome was revealed in the strong-flour cultivar Saratovskaya 29, with the microsatellite locus Xgwm0165 to be associated with the unique physical properties of flour and dough. The detected locus is not related to the composition gluten proteins. These locus may be recommended to breeders for the selection of strong-flour cultivars. Additionally, a QTL associated with vitreousness of grain was mapped in the short arm of chromosome 7A

BREEDING OF EARLY MATURING SOYBEAN VARIETIES IN EAST KAZAKHSTAN

Since 2001, the East Kazakhstan Research Institute of Agriculture has been conducting the work aimed at the development and study of the collection of ultra-early and early soybean accessions in order to obtain new early-maturing and high-yielding cultivars adapted to the soil and climate environment of East Kazakhstan Region. As a result of breeding efforts embracing the whole scheme from hybridization and individual selection to routine and competitive trials, the new soybean cultivars ‘Birlik KV’ (2014) and ‘Vostochnaya Krasavitsa’ (2016), with earlier maturity and higher yield than the references, were submitted for State Variety Trials of the Republic of Kazakhstan. In 2017, the cultivar ‘Birlik KV’ was approved for cultivation in East Kazakhstan Region

GWAS of a soybean breeding collection from South East and South Kazakhstan for resistance to fungal diseases

Soybean (Glycine max (L.) Merr) is an essential food, feed, and technical culture. In Kazakhstan the area under soybean is increasing every year, helping to solve the problem of protein deficiency in human nutrition and animal feeding. One of the main problems of soybean production is fungal diseases causing yields losses of up to 30 %. Modern genomic studies can be applied to facilitate efficient breeding research for improvement of soybean fungal disease tolerance. Therefore, the objective of this genome-wide association study (GWAS) was analysis of a soybean collection consisting of 182 accessions in relation to fungal diseases in the conditions of South East and South Kazakh­stan. Field evaluation of the soybean collection suggested that Fusarium spp. and Cercospora sojina affected plants in the South region (RIBSP), and Septoria glycines – in the South East region (KRIAPP). The major objective of the study was identification of QTL associated with resistance to fusarium root rot (FUS), frogeye leaf spot (FLS), and brown spot (BS). GWAS using 4 442 SNP (single nucleotide polymorphism) markers of Illumina iSelect array allowed for identification of fifteen marker trait associations (MTA) resistant to the three diseases at two different stages of growth. Two QTL both for FUS (chromosomes 13 and 17) and BS (chromosomes 14 and 17) were genetically mapped, including one presumably novel QTL for BS (chromo­some 17). Also, five presumably novel QTL for FLS were genetically mapped on chromosomes 2, 7, and 15. The results can be used for improvement of the local breeding projects based on marker-assisted selection approach

Application of next-generation sequencing technology to study genetic diversity and identify unique SNP markers in bread wheat from Kazakhstan

BACKGROUND: New SNP marker platforms offer the opportunity to investigate the relationships between wheat cultivars from different regions and assess the mechanism and processes that have led to adaptation to particular production environments. Wheat breeding has a long history in Kazakhstan and the aim of this study was to explore the relationship between key varieties from Kazakhstan and germplasm from breeding programs for other regions. RESULTS: The study revealed 5,898 polymorphic markers amongst ten cultivars, of which 2,730 were mapped in the consensus genetic map. Mapped SNP markers were distributed almost equally across the A and B genomes, with between 279 and 484 markers assigned to each chromosome. Marker coverage was approximately 10-fold lower in the D genome. There were 863 SNP markers identified as unique to specific cultivars, and clusters of these markers (regions containing more than three closely mapped unique SNPs) showed specific patterns on the consensus genetic map for each cultivar. Significant intra-varietal genetic polymorphism was identified in three cultivars (Tzelinnaya 3C, Kazakhstanskaya rannespelaya and Kazakhstanskaya 15). Phylogenetic analysis based on inter-varietal polymorphism showed that the very old cultivar Erythrospermum 841 was the most genetically distinct from the other nine cultivars from Kazakhstan, falling in a clade together with the American cultivar Sonora and genotypes from Central and South Asia. The modern cultivar Kazakhstanskaya 19 also fell into a separate clade, together with the American cultivar Thatcher. The remaining eight cultivars shared a single sub-clade but were categorised into four clusters. CONCLUSION: The accumulated data for SNP marker polymorphisms amongst bread wheat genotypes from Kazakhstan may be used for studying genetic diversity in bread wheat, with potential application for marker-assisted selection and the preparation of a set of genotype-specific markers.Yuri Shavrukov, Radoslaw Suchecki, Serik Eliby, Aigul Abugalieva, Serik Kenebayev and Peter Langridg

Conspectus of the genus <i>Juniperus</i> L. growing in Kazakhstan

Background. The genus Juniperus L. is the most numerous in the family Cupressaceae Bartl. and includes about 75 species. There are from 7 to 10 species of this genus in Kazakhstan. All types of juniper are widely used in folk medicine and play an important ecological role. The purpose of our work was to study the current status, systematics and distribution of juniper species. This will help to clarify and expand the information on the current location of Juniperus species in Kazakhstan and will be used in the future to study intra- and interspecific genetic diversity of the genus.Materials and methods. To study the distribution and make a conspectus of the Juniperus spp. growing in Kazakhstan, floristic reports, materials of plant explorations and the herbarium collections for the period from 1890 to 2021 obtained from the herbarium of the Institute of Botany and Phytointroduction (AA), herbarium materials of the Institute of Plant Biology and Biotechnology as well as the digital herbarium of the Lomonosov Moscow State University – Depository of Living Systems “Noah’s Ark” (MW) were analyzed.Results. As a result of the study, 630 herbarium sheets were processed and 70 locations of 7 juniper species growing in Kazakhstan belonging to 2 sections – Juniperus (=Oxycedrus Endl.) and Sabina Endl. – were identified. A conspectus of 7 juniper species identified during the analysis of the three above-mentioned herbarium collections was made. The main division of species is observed in the context of administrative and floristic regions of Kazakhstan. The greatest species concentration occurs in Southern, South-Eastern and Eastern Kazakhstan. The results of the study contribute to the inventory and search for previously forgotten places of growth for the genus Juniperus. Besides, the continuation of comprehensive botanical and molecular genetic studies on junipers will help to examine and preserve the genetic diversity of the species and conserve forest bioresources

SSR-based evaluation of genetic diversity in populations of Agriophyllum squarrosum L. and Agriophyllum minus Fisch. & Mey. collected in South-East Kazakhstan

The development of informative polymorphic DNA markers for poorly studied genera is an important step in population analyses of living organisms, including those that play very important ecological roles in harsh environments, such as desert and semi-desert area. Examples of those poorly studied desert species are Agriophyllum squarrosum L. and Agriophyllum minus Fisch. &amp; Mey. However, a recent RNA-sequencing project in A. squarrosum has proposed a large set of hypothetical SSR (simple sequence repeat) markers. In this work, 11 novel polymorphic SSRs were found due to the screening of 24 randomly selected SSRs for three populations of A. squarrosum and one population of A. minus. The analysis of 11 SSRs revealed 16 polymorphic loci in two Agriophyllum species, 8 polymorphic loci within three populations of A. squarrosum, and 6 polymorphic loci in the population of A. minus. Statistical analyses showed high interspecific, but relatively low intraspecific genetic diversity. The phylogenetic clusterization and population structure analysis have demonstrated a clear segregation of A. minus from A. squarrosum, as well as the separation of population 1 from populations 2 and 3 of A. squarrosum. Thus, we identified the set of novel and informative SSR markers suitable for the study of genetic diversity in Agriophyllum

A study of the genetic diversity in the world soybean collection using microsatellite markers associated with fungal disease resistance

Background. Soybean (Glycine max (L.) Merr.) gradually becomes one of the leading legume crops in Kazakhstan. The area under soybeans in the country has been increasing annually and requires the development of adapted cultivars with a higher yield, improved quality characters, and resistance to emerging fungal diseases. The enlargement of the crop’s gene pool also suggests the need to study and document local soybean accessions to meet the standards of the available world soybean collection by using reliable and informative types of DNA markers.Materials and methods. In this study, the soybean collection consisting of 288 accessions from different countries, including 36 cultivars and promising lines from Kazakhstan, was studied. The molecular genetic analysis was performed using nine polymorphic SSR (simple sequence repeats) markers, seven of which (Satt244, Satt565, Satt038, Satt309, Satt371, Satt570 and Sat_308) were associated with resistance to three main fungal diseases of soybean – frogeye leaf spot, fusarium root rot, and purple seed stain.Results. The average PIC (polymorphism information content) value of the analyzed SSR markers constituted 0.66 ± 0.07, confirming their highlevel polymorphism. The principal coordinate analysis suggested that the local accessions were genetically most close to the accessions from East Asia. As the collection showed a robust resistance to three studied fungal diseases in Almaty Region during 2018–2019, the distribution of the studied SSR markers in the population was not significantly associated with resistance to the analyzed diseases under field conditions.Conclusion. SSR genotyping of the soybean collection helped to identify accessions that potentially possess resistance-associated alleles of fungal disease resistance genes. The data obtained can be further used for the development of DNA documentation and the breeding the promising cultivars and lines of soybean

Identification of QTLs for resistance to leaf and stem rusts in bread wheat (Triticum aestivum L.) using a mapping population of ‘Pamyati Azieva × Paragon’

Leaf rust (LR) and stem rust (SR) are harmful fungal diseases of bread wheat (Triticum aestivum L.). The purpose of this study was to identify QTLs for resistance to LR and SR that are effective in two wheat-growing regions of Kazakhstan. To accomplish this task, a population of recombinant inbred lines (RILs) of ‘Pamyati Azieva × Paragon’ was grown in the northern and southeastern parts of Kazakhstan, phenotyped for LR/SR severities, and analyzed for key yield components. The study revealed a negative correlation between disease severity and plant productivity in both areas. The mapping population was genotyped using a 20,000 Illumina SNP array. A total of 4595 polymorphic SNP markers were further selected for linkage analysis after filtering based on missing data percentage and segregation distortion. Windows QTL Cartographer was applied to identify QTLs associated with LR and SR resistances in the RIL mapping population studied. Two QTLs for LR resistance and eight for SR resistance were found in the north, and the genetic positions of eight of them have matched the positions of the known Lr and Sr genes, while two QTLs for SR were novel. In the southeast, eight QTLs for LR and one for SR were identified in total. The study is an initial step of the genetic mapping of LR and SR resistance loci of bread wheat in Kazakhstan. Field trials in two areas of the country and the genotyping of the selected mapping population have allowed identification of key QTLs that will be effective in regional breeding projects for better bread wheat productivity