Tomato is one of the most prominent crops in global horticulture and an important vegetable crop in Kazakhstan. The lack of data on the genetic background of local varieties limits the development of tomato breeding in the country. This study aimed to perform an initial evaluation of the breeding collection of tomato varieties from the point of view of their genetic structure and pathogen resistance using a set of PCR based molecular markers, including 13 SSR markers for genetic structure analysis, and 14 SCAR and CAPS markers associated with resistance to five pathogens: three viruses, fungus Fusarium oxysporum, and oomycete P hytophthora infestans. Nine SSR markers were with a PIC value varying from 0.0562 (low information content) to 0.629 (high information content). A weak genetic structure was revealed in the samples of varieties including local cultivars and, predominantly, varieties from Russia and other ex-USSR countries. The local varieties were closely related to several groups of cultivars of Russian origin. Screening for a set of resistance markers revealed the common occurrence of the resistance locus I against Fusarium oxysporum and only the occasional presence of resistance alleles of other markers. No markers of resistance to the three considered viruses were revealed in local tomato varieties. Only two local cultivars had markers of resistance to P. infestans, and only the ‘Meruert’ cultivar had a combination of resistance markers against P. infestans and F. oxysporum. The obtained results have demonstrated the need for further studies of local tomato varieties with a wider range of molecular markers and source germplasm to lay a foundation for the development of tomato breeding in Kazakhstan.

Horses are traditionally used in Kazakhstan as a source of food and as working and saddle animals as well. Here, for the first time, microarray-based medium-density SNP genotyping of six traditionally defined types and breeds of indigenous Kazakh horses was conducted to reveal their genetic structure and find markers associated with animal size and weight. The results showed that the pre-defined separation between breeds and sampled populations was not supported by the molecular data. The lack of genetic variation between breeds and populations was revealed by the principal component analysis (PCA), ADMIXTURE, and distance based analyses, as well as the general population parameters expected and observed heterozygosity (He and Ho) and between group fixation index (Fst). The comparison with previously published data on global horse breed diversity revealed the relatively high level of individual diversity of Kazakh horses in comparison with the well-known foreign breeds. The Mongolian and Tuva breeds were identified as the closest horse landraces, demonstrating similar patterns of internal variability. The genome-wide association analysis was performed for animal size and weight as the traits directly related with meat productivity of horses. The analysis identified a set of 60 SNPs linked with horse genes involved in the regulation of processes of development of connective tissues and the bone system, neural system, immune system regulation, and other processes. The present study is novel and introduces Kazakh horses as a promising genetic source for horse breeding and selection.

No abstract

Raspberry bushy dwarf virus (RBDV) is an economically significant pathogen of raspberry and grapevine, and it has also been found in cherry. Most of the currently available RBDV sequences are from European raspberry isolates. This study aimed to sequence genomic RNA2 of both cultivated and wild raspberry in Kazakhstan and compare them to investigate their genetic diversity and phylogenetic relationships, as well as to predict their protein structure. Phylogenetic and population diversity analyses were performed on all available RBDV RNA2, MP and CP sequences. Nine of the isolates investigated in this study formed a new, well-supported clade, while the wild isolates clustered with the European isolates. Predicted protein structure analysis revealed two regions that differed between α- and β-structures among the isolates. For the first time, the genetic composition of Kazakhstani raspberry viruses has been characterized.

Beekeeping as a staple of agriculture in Kazakhstan is believed to have emerged when external bee specimens were introduced into the country. The Central Russian bee (Apis mellifera mellifera) has been present throughout Kazakhstanian apiaries for a long time since its import into Eastern Kazakhstan at the end of the 18th century. To date, six subspecies have been distributed across the country (A.m. sossimai, A.m. carpatica, A.m. mellifera, A.m. ligustica, A.m. caucasica, and A.m. carnica). According to mitochondrial haplotype analysis based on DraI mtDNA COI-COII (DmCC) test, local samples were represented by C2 (316), C1 (99), and M4 (7) haplotypes. The results of simple sequence repeats (SSR) genotyping revealed a large polymorphism at nine microsatellite loci, with the number of alleles amounting to 35 (AP55), 32 (AP43), 25 (A124), 18 (A113), 13 (A88), 12 (A43), 11 (A007), 7 (A28), and 5 (A24). Relative to the expected heterozygosity (He), the observed heterozygosity (Ho) was slightly higher for most markers considering both the overall samples and individual populations. The inbreeding coefficient confirmed the excess outbreeding for the geographical populations of car-Shym-T (-0,105), car-zham-A (-0,114), Zhet-Alakol (-0,008), and Zhet-Ushbulak (-0,028). The admixture of honeybee local populations was confirmed by the research presented here.The differentiation of populations was only possible by geographical location according to clustering analysis. A considerable degree of genetic admixtures among subspecies was identified in every population. The subspecies were not separated from each other. None of the groups formed by the neighbor-joining tree based on Nei's genetic distance included a precise subspecies or population. All groups represented an admixture of subspecies from different populations. Unregulated cross-breeding for the past 50 years has laid the foundation for the promiscuous genetic nature of honeybee populations in Kazakhstan. It could be concluded that some samples were the result of cross-breeding with endemic bee Apis mellifera pomonella since most apiaries were located in areas of endemic bee distribution.