The Crimean autochthonous grape varieties are unique by their origin and serve as a valuable source for breeding new cultivars with increased salt and frost resistance, as well as high-quality berries. However, they suffer from fungal pathogens, as the dry and hot summer months contribute to the epiphytotic course of diseases. An increase in the resistance of Crimean grape varieties is currently achieved through interspecific hybridization. In this study, we describe the genetic and agrobiological diversity of three hybrid populations obtained using the Vitis interspecific hybrid ‘Magarach 31-77-10′ as a female parent and Muscadinia rotundifolia × Vitis vinifera BC5 hybrid plants as male parents. The hybrid nature of the populations was assessed using RADseq high-throughput genotyping. We discovered 12,734 SNPs, which were common to all three hybrid populations. We also proved with the SSR markers that the strong powdery and downy mildew resistance of the paternal genotypes is determined by the dominant Run1/Rpv1 locus inherited from M. rotundifolia. As a result, the disease development score (R, %) for both mildew diseases in the female parent ‘Magarach 31-77-10’ was three times higher than in male parents 2000-305-143 and 2000-305-163 over two years of phytopathological assessment. The highest values of yield-contributing traits (average bunch weight ~197 g and 1.3 kg as yield per plant) were detected in the population 4-11 (♀M. No. 31-77-10 × 2000-305-163). Despite the epiphytotic development of PM, the spread of oidium to the vegetative organs of hybrids 4-11 did not exceed 20%. Some hybrid genotypes with high productivity and resistance to pathogens were selected for further assessment as promising candidates for new varieties.

Guar (Cyamopsis tetragonoloba (L.) Taub.) is an annual legume crop native to India and Pakistan. Seeds of the plant serve as a source of galactomannan polysaccharide (guar gum) used in the food industry as a stabilizer (E412) and as a gelling agent in oil and gas fracturing fluids. There were several attempts to introduce this crop to countries of more northern latitudes. However, guar is a plant of a short photoperiod, therefore, its introduction, for example, to Russia is complicated by a long day length during the growing season. Breeding of new guar varieties insensitive to photoperiod slowed down due to the lack of information on functional molecular markers, which, in turn, requires information on guar genome. Modern breeding strategies, e.g., genomic predictions, benefit from integration of multi-omics approaches such as transcriptome, proteome and metabolome assays. Here we present an attempt to use transcriptome-metabolome integration to understand the genetic determination of flowering time variation among guar plants that differ in their photoperiod sensitivity. This study was performed on nine early- and six delayed-flowering guar varieties with the goal to find a connection between 63 metabolites and 1,067 differentially expressed transcripts using Shiny GAM approach. For the key biomarker of flowering in guar myo-inositol we also evaluated the KEGG biochemical pathway maps available for Arabidopsis thaliana. We found that the phosphatidylinositol signaling pathway is initiated in guar plants that are ready for flowering through the activation of the phospholipase C (PLC) gene, resulting in an exponential increase in the amount of myo-inositol in its free form observed on GC-MS chromatograms. The signaling pathway is performed by suppression of myo-inositol phosphate kinases (phosphorylation) and alternative overexpression of phosphatases (dephosphorylation). Our study suggests that metabolome and transcriptome information taken together, provide valuable information about biomarkers that can be used as a tool for marker-assisted breeding, metabolomics and functional genomics of this important legume crop.

Guar gum, a polysaccharide derived from guar seeds, is widely used in a variety of industrial applications, including oil and gas production. Although guar is mostly propagated in India, interest in guar as a new industrial legume crop is increasing worldwide, demanding the development of effective tools for marker-assisted selection. In this paper, we report a wide-ranging set of 4907 common SNPs and 327 InDels generated from RADseq genotyping data of 166 guar plants of different geographical origin. A custom guar reference genome was assembled and used for variant calling. A consensus set of variants was built using three bioinformatic pipelines for short variant discovery. The developed molecular markers were used for genome-wide association study, resulting in the discovery of six markers linked to the variation of an important agronomic trait—percentage of pods matured to the harvest date under long light day conditions. One of the associated variants was found inside the putative transcript sequence homologous to an ABC transporter in Arabidopsis, which has been shown to play an important role in D-myo-inositol phosphates metabolism. Earlier, we suggested that genes involved in myo-inositol phosphate metabolism have significant impact on the early flowering of guar plants. Hence, we believe that the developed SNP set allows for the identification of confident molecular markers of important agrobiological traits.

Амплитуда изменчивости фотопериодической реакции генотипов гуара (Cyamopsis tetragonoloba (L.) Taub.) разного географического происхождения

Leaf-feeding phylloxera decreases the photosynthetic activity of a grape plant, leading to decreasing number of fruit buds. In addition, phylloxera larvae emerging from the leaf galls may colonize the roots, negatively affecting the growth of the grape plant. In this study, we evaluated host tolerance of three grapevine hybrid populations obtained from crossing of the same maternal grapevine M. no. 31-77-10 with interspecific hybrids carrying introgressions from Muscadinia and other North American Vitis species against leaf-feeding grape phylloxera. Combining genotyping data of the populations obtained with 12,734 SNPs and their resistance phenotypes evaluated in the laboratory experiment, we performed an association study. As the result of GWAS, nine SNPs with the lowest significant p-values were discovered in the whole sample of 139 hybrids as associated with variation of the scores ‘the percentage of infested leaves’ and ‘intensity of gall formation’. Three of the SNPs on LG 7 were located in the same chromosome interval where a major QTL (RDV6) for root phylloxera resistance was reported from Muscadine background. Two SNPs on LG 8 were detected within the gene, encoding E3 ubiquitin-protein ligase UPL4 involved in apoptosis. SNPs detected on LG 13 and LG 18 may overlap with the previously reported QTLs for phylloxera resistance inherited from V. cinerea.

Изменение климатических условий оказывает значительное влияние на лесные экосистемы, особенно на хвойные породы, такие как сосна обыкновенная (Pinus sylvestris) и ель европейская (Picea abies), которые составляют основу лесов умеренной зоны. Адаптация этих видов к новым экологическим условиям требует учета генетической изменчивости ключевых адаптивных признаков. Настоящее исследование направлено на изучение однонуклеотидных полиморфизмов (SNP) в генах-кандидатах, регулирующих фотопериодическую реакцию и циркадные ритмы, которые играют важную роль в физиологических процессах деревьев. В работе описываются разработка и тестирование молекулярных маркеров, основанных на методах KASP (Kompetitive Allele Specific PCR) и HRM (High Resolution Melting), для массового генотипирования деревьев. Были идентифицированы SNP в генах фоторецепторов PhyO и CRY1, а также в генах фотопериодической реакции PRR1 и PRR7. Аллельный полиморфизм этих генов демонстрирует географическую клинальность, что свидетельствует об их значительной роли в адаптации деревьев к широтным изменениям фотопериода и температурным градиентам. Результаты исследования подтверждают эффективность методов KASP и HRM для генотипирования, что позволяет использовать разработанные маркеры для мониторинга генетического разнообразия популяций и отбора наиболее адаптивных генотипов в селекционных программах. Такие подходы обеспечивают использование генетически приспособленного посадочного материала в лесовосстановительных мероприятиях, что особенно актуально в условиях меняющегося климата. Climate change significantly impacts forest ecosystems, particularly coniferous species such as Scots pine (Pinus sylvestris) and Norway spruce (Picea abies), which form the basis of temperate forests. The adaptation of these species to new environmental conditions necessitates consideration of the genetic variability of key adaptive traits. This study investigates single nucleotide polymorphisms (SNPs) in candidate genes that regulate photoperiodic response and circadian rhythms, which are critical to tree physiological processes. The research describes the development and testing of molecular markers based on KASP (Kompetitive Allele Specific PCR) and HRM (High Resolution Melting) methods for high-throughput genotyping. SNPs were identified in the photoreceptor genes PhyO and CRY1 and the photoperiodic response genes PRR1 and PRR7. These polymorphisms exhibit geographic clinality, highlighting their significant role in tree adaptation to latitudinal gradients of light and temperature conditions. The findings confirm the efficiency of KASP and HRM methods for genotyping, enabling the use of these markers for monitoring genetic diversity and selecting resilient genotypes in breeding programs. Such approaches ensure the integration of genetically adapted planting material into reforestation efforts, which is particularly relevant in the context of changing climate conditions.