Plant height variation and genetic diversity between Prunus ledebouriana (Schlecht.) YY Yao and Prunus tenella Batsch based on using SSR markers in East Kazakhstan.

Background: Genetic differences between isolated endemic populations of plant species and those with widely known twin species are relevant for conserving the biological diversity of our planet's flora. Prunus ledebouriana (Schlecht.) YY Yao is an endangered and endemic species of shrub almond from central Asia. Few studies have explored this species, which is closely related and morphologically similar to the well-known Prunus tenella Batsch. In this article, we present a comparative analysis of studies of three P. ledebouriana populations and one close population of P. tenella in Eastern Kazakhstan in order to determine the particular geographic mutual replacement of the two species. Methods: The populations were collected from different ecological niches, including one steppe population near Ust-Kamenogorsk (P. tenella) and three populations (P. ledebouriana) in the mountainous area. Estimation of plant height using a t-test suggested a statistically significant difference between the populations and the two species (P < 0.0001). DNA simple sequence repeat (SSR) markers were applied to study the two species' genetic diversity and population structure. Results: A total of 19 polymorphic SSR loci were analyzed, and the results showed that the population collected in mountainous areas had a lower variation level than steppe populations. The highest level of Nei's genetic diversity index was demonstrated in the 4-UK population (0.622) of P. tenella. The lowest was recorded in population 3-KA (0.461) of P. ledebouriana, collected at the highest altitude of the four populations (2,086 meters above sea level). The total genetic variation of P. ledebouriana was distributed 73% within populations and 27% between populations. STRUCTURE results showed that two morphologically similar species diverged starting at step K = 3, with limited population mixing. The results confirmed the morphological and genetic differences between P. tenella and P. ledebouriana and described the level of genetic variation for P. ledebouriana. The study's results proved that the steppe zone and mountain altitude factor between P. tenella and isolated mountain samples of P. ledebouriana.

Comparative analysis of chloroplast genomes of seven Juniperus species from Kazakhstan.

Juniperus species are shrubs or trees in the family Cupressaceae that play an important role in forest ecosystems. In this study, we report the complete sequences of the plastid (pt) genomes of five Juniperus species collected in Kazakhstan (J. communis, J. sibirica, J. pseudosabina, J. semiglobosa, and J. davurica). The sequences of the pt genomes of the five species were annotated in addition to two full pt genome sequences from J. sabina and J. seravschanica, which we have previously reported. The pt genome sequences of these seven species were compared to the pt genomes of Juniperus species available in the public NCBI database. The total length of the pt genomes of Juniperus species, including previously published pt genome data, ranged from 127,469 bp (J. semiglobosa) to 128,097 bp (J. communis). Each Juniperus plastome consisted of 119 genes, including 82 protein-coding genes, 33 transfer RNA and 4 ribosomal RNA genes. Among the identified genes, 16 contained one or two introns, and 2 tRNA genes were duplicated. A comparative assessment of pt genome sequences suggested the identification of 1145 simple sequence repeat markers. A phylogenetic tree of 26 Juniperus species based on the 82 protein-coding genes separated the Juniperus samples into two major clades, corresponding to the Juniperus and Sabina sections. The analysis of pt genome sequences indicated that accD and ycf2 were the two most polymorphic genes. The phylogenetic evaluation of 26 Juniperus species using these two genes confirmed that they can be efficiently used as DNA barcodes for phylogenetic analyses in the genus. The sequenced plastomes of these Juniperus species have provided a large amount of genetic data that will be valuable for future genomic studies of this genus.

Genetic Diversity and Population Structure of Juniperus seravschanica Kom. Collected in Central Asia.

Juniperus seravschanica Kom. is a species that grows widely in the mountain ranges from Central Asia to Oman. It is an important tree for the formation of shrub-forest massifs in mountainous areas and for draining and fixing soils from middle to high altitudes. A comprehensive study of the species' genetic diversity and population structure is a basic approach to understanding the current status of J. seravschanica resources for the development of future conservation strategies. Samples from 15 populations of J. seravschanica were collected from the mountain ranges of Uzbekistan, Kyrgyzstan, and Kazakhstan. The genetic diversity and population structure of 15 Central Asian populations of J. seravschanica were assessed using 11 polymorphic simple sequence repeat (SSR) markers. Genetic diversity parameters, including the number of alleles (na), the effective number of alleles (ne), Shannon's information index (I), the percentage of polymorphic loci (PPL), Nei's genetic diversity index (Nei), principal coordinate analysis (PCoA), etc., were evaluated. The analysis of 15 J. seravschanica populations based on 11 polymorphic SSRs detected 35 alleles. The average PIC value was 0.432, and the highest value (0.662) was found in the JT_40 marker. Nei's genetic diversity index for the J. seravschanica populations was 0.450, ranging from 0.407 (population 14) to 0.566 (population 4). The analysis of molecular variance (AMOVA) showed that 90.3% of total genetic variation is distributed within the population. Using the alleles of all the populations, the gene flow (Nm) was found to be 4.654. Population structure analysis revealed poor clustering in the studied populations and confirmed our AMOVA results. The output of this work can be efficiently used for the maintenance of the species across the Central Asian region.

Illumina sequencing data of the complete chloroplast genome of rare species Juniperus seravschanica (Cupressaceae) from Kazakhstan.

The species of the genus Juniperus L. play an important role in Kazakhstan forest ecosystems and one of them is Juniperus seravschanica Kom. which has been listed as a rare species in the Red Book of Kazakhstan. The distribution area of J. seravschanica extends from Central Asia (Kazakhstan, Uzbekistan, Kyrgyzstan, Tajikistan, and Turkmenistan) to northern and eastern Afghanistan, northern Pakistan, Kashmir, southeastern Iran, and Oman. J. seravschanica occurred in the southern part of Kazakhstan along with the ranges Karatau, Talas Alatau, Kyrgyz Alatau, Chu-Ili, Karzhantau, and Ugam. The distribution area of J. seravschanica is constantly decreasing due to intensive logging, forest fires, and excessive cattle grazing. The species has ecological importance in the stabilization of mountain slopes against erosion, for hydrobiological regulation, and as a significant medicinal herb. The species J. excelsa M. Bieb., J. polycarpos K.Koch (var. polycarpos and var. turcomanica R.P.Adams), and J. seravschanica are morphologically very similar with some difficulties in species identification. For a better understanding of the evolutionary relationship of these species in the Juniperus genus, it is important to obtain genetic information on the highly conserved chloroplast (cp) genome. Due to the conserved genomic structure, the cp genome nucleotide sequences are widely used in species distinguishing and reconstructing phylogenetic relationships. Unfortunately, there are no publicly available nucleotide sequences of cp genomes data for J. polycarpos (var. polycarpos and var. turcomanica), J. excelsa and J. seravschanica. We report the de novo assembly of the J. seravschanica chloroplast genome by applying next-generation sequencing technology based on Illumina NovaSeq 6000. The assembled cp genome of J. seravschanica is 127,609 bp in length and contained 118 genes, including 82 protein-coding genes, 32 transfer RNA genes, and 4 ribosomal RNA genes. In total 152 simple sequence repeats were identified in the chloroplast genome sequence of J. seravschanica. The Bioproject (PRJNA883033), Sequence Read Archive (SRR21673293), and GenBank (OL684343) data were deposited at National Center for Biotechnology Information.

The complete chloroplast genome sequencing data of Juniperus sabina L. (Cupressaceae Bartl.) from Kazakhstan.

The genus Juniperus L. (Cupressaceae Bartl.) is consisting of about 75 species that are divided into sections Caryocedrus Endlicher, Sabina (Miller) Spach, and Juniperus (syn: sect. Oxycedrus Spach). Juniperus sabina L. from section Sabina is an important shrub for the maintenance of the ecosystem in mountainous regions and a source of medicinal compounds. The species is monoecious, rarely dioecious, and distributed in Europe, Central Asia, China, and Mongolia. The goal of the present study was to sequence and reconstruct the complete chloroplast genome of J. sabina. De novo chloroplast (cp) genome assembly for J. sabina was conducted using Illumina paired-end reads. The assembled cp genome size is 127,646 bp in length and has a typical circular DNA molecule. The genome encodes 118 genes, including 82 protein-coding genes, 32 tRNA genes, and 4 rRNA genes, the overall GC content is 34,36%. The complete cp genome nucleotide sequence of J. sabina was deposited to the NCBI (National Center for Biotechnology Information) under accession number OL467323. The raw data in fastq format was deposited to the NCBI sequence read archive under accession number SRR21515769.

Innate Immunomodulatory Activity of Cedrol, a Component of Essential Oils Isolated from Juniperus Species.

Little is known about the immunomodulatory activity of essential oils isolated from Juniperus species. Thus, we isolated essential oils from the cones and leaves of eight juniper species found in Montana and in Kazakhstan, including J. horizontalis, J. scopolorum, J. communis, J. seravschanica, J. sabina, J. pseudosabina, J. pseudosabina subsp. turkestanica, and J. sibirica. We report here the chemical composition and innate immunomodulatory activity of these essential oils. Compositional analysis of the 16 samples of Juniper essential oils revealed similarities and differences between our analyses and those previously reported for essential oils from this species. Our studies represent the first analysis of essential oils isolated from the cones of four of these Juniper species. Several essential oil samples contained high levels of cedrol, which was fairly unique to three Juniper species from Kazakhstan. We found that these essential oils and pure (+)-cedrol induced intracellular Ca2+ mobilization in human neutrophils. Furthermore, pretreatment of human neutrophils and N-formyl peptide receptor 1 and 2 (FPR1 and FPR2) transfected HL60 cells with these essential oils or (+)-cedrol inhibited agonist-induced Ca2+ mobilization, suggesting these responses were desensitized by this pretreatment. In support of this conclusion, pretreatment with essential oils from J. seravschanica cones (containing 16.8% cedrol) or pure (+)-cedrol inhibited human neutrophil chemotaxis to N-formyl peptide. Finally, reverse pharmacophore mapping predicted several potential kinase targets for cedrol. Thus, our studies have identified cedrol as a novel neutrophil agonist that can desensitize cells to subsequent stimulation by N-formyl peptide.

Population Structure and Genetic Diversity of Two-Rowed Barley Accessions from Kazakhstan Based on SNP Genotyping Data.

The genetic relationship and population structure of two-rowed barley accessions from Kazakhstan were assessed using single-nucleotide polymorphism (SNP) markers. Two different approaches were employed in the analysis: (1) the accessions from Kazakhstan were compared with barley samples from six different regions around the world using 1955 polymorphic SNPs, and (2) 94 accessions collected from six breeding programs from Kazakhstan were studied using 5636 polymorphic SNPs using a 9K Illumina Infinium assay. In the first approach, the neighbor-joining tree showed that the majority of the accessions from Kazakhstan were grouped in a separate subcluster with a common ancestral node; there was a sister subcluster that comprised mainly barley samples that originated in Europe. The Pearson's correlation analysis suggested that Kazakh accessions were genetically close to samples from Africa and Europe. In the second approach, the application of the STRUCTURE package using 5636 polymorphic SNPs suggested that Kazakh barley samples consisted of five subclusters in three major clusters. The principal coordinate analysis plot showed that, among six breeding origins in Kazakhstan, the Krasnovodopad (KV) and Karaganda (KA) samples were the most distant groups. The assessment of the pedigrees in the KV and KA samples showed that the hybridization schemes in these breeding stations heavily used accessions from Ethiopia and Ukraine, respectively. The comparative analysis of the KV and KA samples allowed us to identify 214 SNPs with opposite allele frequencies that were tightly linked to 60 genes/gene blocks associated with plant adaptation traits, such as the heading date and plant height. The identified SNP markers can be efficiently used in studies of barley adaptation and deployed in breeding projects to develop new competitive cultivars.

The molecular taxonomy of three endemic Central Asian species of Ranunculus(Ranunculaceae).

Worldwide, the genus Ranunculus includes approximately 600 species and is highly genetically diverse. Recent taxonomic reports suggest that the genus has a monophyletic origin, divided into two subgenera, and consists of 17 sections. The Central Asian country of Kazakhstan has 62 species of the genus that have primarily been collected in the central part of the country. The latest collection trips in southern parts of the country have led to the description of a wider distribution area for Ranunculus and the identification of a new species Ranunculus talassicus Schegol. et A.L. Ebel from Western Tien Shan. Therefore, in this study, attempts were made to assess the molecular taxonomic positions of R. talassicus and two other species endemic to the Central Asian region R. karkaralensis Schegol. and R. pskemensis V.N. Pavlov in relation to other species of the genus, using internal transcribed spacer (ITS) molecular genetic markers. The ITS-aligned sequences of 22 local Central Asian accessions and 43 accession sequences available in the National Center for Biotechnology Information (NCBI) database allowed the construction of a maximum parsimony phylogenetic tree and a Neighbor-Net network. The results indicated that R. talassicus and R. pskemensis could be assigned to section Ranunculastrum. Additionally, an assessment of the network suggested that R. pskemensis was the rooting taxon for the group of species containing R. talassicus, and that R. illyricus L. and R. pedatus Waldst. & Kit. were founders of a prime rooting node for the Ranunculastrum section of the genus. The ITS-aligned sequences showed that R. karkaralensis was indifferent with respect to three other species in the Ranunculus section of the genus, i.e., R. acris L., R. grandifolius C.A. Mey., and R. subborealis Tzvelev. The study indicated that the assessments of ITS-based phylogenetic tree and Neighbor-Net network provided new insights into the taxonomic positions of three endemic species from Central Asia.

Association mapping for agronomic traits in six-rowed spring barley from the USA harvested in Kazakhstan.

In barley, six-rowed barley is advantageous over two-rowed barley for feed due to the larger number of seeds per spike and the higher seed protein content. The growth of six-rowed barley is potentially important for breeding in agriculturally oriented countries, such as Kazakhstan. Nevertheless, until recently, very little attention was given to six-rowed barley in breeding projects in Kazakhstan, one of the largest countries in the world. In this study, phenotyping and single nucleotide polymorphism (SNP) genotyping data were generated from 275 accessions originating from six different breeding organizations in the USA as well as 9 accessions from Kazakhstan in field trials at six breeding institutions. The USA six-rowed barley was tested in comparison to local accessions over three years (2009-2011) based on analyses of key agronomic traits. It was determined that the average yield in the USA accessions in comparison to local lines showed heavier yield in all six tested sites. Principal Coordinate Analysis based on 1618 polymorphic SNP markers separated Kazakh lines from six USA barley origin groups based on PC1 (77.9%), and Montana lines from the remaining five USA groups based on PC2 (15.1%). A genome-wide association study based on eighteen field trials allowed the identification of 47 stable marker-trait associations (MTA) for ten agronomic traits, including key yield related characters such as yield per square meter, thousand grain weight, number of kernels per spike, and productive tillers. The comparison of chromosomal positions of identified MTA with positions of known genes and quantitative trait loci suggests that 25 out of those 47 MTAs are presumably novel. The analysis of 42 SNPs associated with 47 MTAs in the Ensemble genome annotation system (http://ensemblgenomes.org) suggested that 40 SNPs were in genic positions of the genome, as their sequences successfully aligned with corresponding Gen ID.

Isolation and characterization of 15 SSR loci for the endangered European tetraploid species Gladiolus palustris (Iridaceae).

PREMISE: Gladiolus palustris (Iridaceae) is an endangered European perennial tetraploid herb with special conservation interest in the European Union. Microsatellite markers can serve as effective tools for the conservation genetics of this species. METHODS AND RESULTS: We utilized a 454 pyrosequencing approach to identify simple sequence repeat (SSR) regions in a microsatellite-enriched library. Of all SSR regions, 46 were screened for specific PCR amplification, and 15 were found to be applicable in the target species. We found 1.62-3.08 alleles per population (effective alleles: 1.58-2.08) that indicated moderate to high genetic diversity values (0.28-0.44) in three pilot populations. Cross-species amplification was less effective in G. imbricatus and G. tenuis. CONCLUSIONS: The primers reported here can be used for the population genetic characterization of G. palustris. They will help us to better understand the conservation genetics of this highly endangered species.

Marker-trait associations in two-rowed spring barley accessions from Kazakhstan and the USA.

In this study, phenotyping and single nucleotide polymorphism (SNP) genotyping data of 272 accessions of two-rowed spring barley from the USA along with 94 accessions from Kazakhstan were assessed in field trials at six breeding organizations in Kazakhstan to evaluate the performance of the USA samples over three years (2009-2011). The average grain yield over the six locations was not significantly higher in Kazakh accessions in comparison to the USA samples. Twenty four samples from Montana, Washington, the USDA station in Aberdeen Idaho, and the Anheuser-Busch breeding programs showed heavier average yield than the local standard cultivar "Ubagan". Principal Coordinate analysis based on two sets of SNP data suggested that Kazakh accessions were closest to the USA accessions among eight groups of samples from different parts of the World, and within five US barley origin groups the samples from Montana and Washington perfectly matched six groups of Kazakh breeding origins. A genome-wide association study (GWAS) using data from eighteen field trials allowed the identification of ninety one marker-trait associations (MTA) in two or more environments for nine traits, including key characters such as heading time (HT), number of kernels per spike (NKS), and thousand grain weight (TGW). Our GWAS allowed the identification of eight MTA for HT and NKS, and sixteen MTA for TGW, when those MTA were linked to mapped SNPs. Based on comparisons of chromosomal positions of MTA identified in this study, and positions of known genes and quantitative trait loci for HT, NKS and TGW, it was suggested that MTA for HT on chromosome 2H (at 158.2 cM, 11_21414), MTA for NKS on 5H (at 118.6 cM, 11_20298), and two MTA for TGW on chromosome 4H (at 94.7 cM, 12_30718, and at 129.3 cM, 11_20013) were potentially new associations in barley. GWAS suggested that six MTA for HT, including two on chromosome 1H, two on chromosome 3H, and one each on chromosomes 4H and 6H, had useful pleiotropic effects for improving barley spike traits.

Phylogenetic study of the endemic species Oxytropis almaatensis (Fabaceae) based on nuclear ribosomal DNA ITS sequences.

BACKGROUND: Oxytropis almaatensis Bajt. is a rare, narrow endemic species of the Trans-Ili Alatau mountains in Kazakhstan. Up to now, no studies regarding the taxonomy and variation of key morphological traits of O. almaatensis were undertaken. The purpose of this analysis was to evaluate phenotypic variation of O. almaatensis and assess the position of the species within the genus based on nucleotide sequences of the nuclear ribosomal DNA internal transcribed spacer (ITS) region. RESULTS: Two populations of O. almaatensis were collected in neighboring gorges of the Trans-Ili Alatau Mountains. The ITS sequences from the samples of two populations of O. almaatensis were identical. The phylogenetic analysis indicated that O. almaatensis is within Oxytropis genetically close to O. glabra as these species formed a separate subclade. The phenotypic variation of populations was assessed using nine morphological traits and compared to descriptions of O. glabra. The range of variation for the traits between two populations was established. A clear morphological difference of O. almaatensis and O. glabra was found in peduncle length to leaf length ratio. This was in O. almaatensis 1.56, while in O. glabra, it was 1.0. CONCLUSIONS: The study provides the first phenotypic description and phylogenetic placement of the rare endemic species O. almaatensis. The morphological traits in two O. almaatensis populations showed a high level of phenotypic variability. Although clearly different from O. glabra, the ITS phylogeny grouped these species in a subclade within the genus.