Structural and Functional Organization and Evolution of the WD40 Genes Involved in the Regulation of Flavonoid Biosynthesis in the Triticeae Tribe Abstract Flavonoid biosynthesis in plants is regulated by a specific MBW protein complex, which is formed by the interaction of the R2R3-Myb, bHLH, and WD40 transcription factors. The genomes of the representatives of the Triticeae tribe are characterized by the presence of orthologous and homeologous copies of the flavonoid biosynthesis regulatory genes. The structural and functional organization of the R2R3-Myb and bHLH gene families is already well studied, while the genes encoding the third component of the MBW complex in the representatives of Triticeae, the WD40 factor, remain scarcely studied. In the present study, the search and analysis of the WD40 genes in the representatives of Hordeum, Triticum, and Aegilops genera was carried out. Two paralogical groups of genes (WD40-1 and WD40-2), located on the long and short arms of the group 6 chromosomes, were identified. It was demonstrated that conservatism of the identified WD40 sequences was supported by natural selection. High levels of WD40-1 and WD40-2 expression were observed in different organs and tissues of wheat and barley, regardless of their pigmentation. It is suggested that these genes could participate in the biosynthesis of not only flavonoid pigments of anthocyanins but also colorless compounds.

The Characteristics of Primary Hybrids Obtained in Crosses between Common Wheat from China and Cultivated Rye Abstract The gene pool of winter common wheat from China maintained in the VIR collection is unique in the variety of alleles of the genes of selection-valuable traits and properties. Our previous studies have revealed among this wheat the samples that cross well with sowing rye, but in most cases, they had poor winter hardiness. Wheat-rye hybrids were produced in order to involve this material in Russian breeding. A directional selection for winter hardiness and high productivity in several subsequent generations of self-pollinated hybrids was performed. Evaluation of the F1 hybrids in the autumn–winter seeding in the climatic conditions of the Northwest region of the Russian Federation (Pushkin) revealed their differences in viability, winter hardiness, and formation of F2 hybrid caryopses. The subsequent directional individual selection for high overwintering and productivity in F2–F7 hybrid self-pollinated populations led to the production of primary hexaploid wheat-rye lines (2n = 6x = 42, BBAARR). Characteristics of 17 lines are given in the article. The statistically significant heterogeneity of the lines according to the studied traits is shown using the Kruskal–Wallis rank criterion (H). We revealed the elimination of the D genome chromosomes and the presence of the complete genomes B, A, and R in all lines using the method of genomic in situ hybridization. Along with hexaploid plants, forms containing additionally from one to five chromosomes of the D genome were found in one line. The produced primary winter-hardy and highly productive hexaploid wheat-rye lines are a new initial material for wheat and triticale breeding.

Genome-Wide Association Study of Powdery Mildew Resistance in Russian Spring Wheat ( T. aestivum L.) Varieties Abstract Powdery mildew caused by the fungal pathogen Blumeria graminis f. sp. tritici (Bgt) is an econo-mically important disease of common wheat T. aestivum L. One of the most effective and environmentally important ways of protection of wheat against Bgt is cultivation of the varieties with genetic resistance. The aim of this work was to study the genetic diversity of Russian spring wheat varieties for the powdery mildew resistance loci. Phytopathological evaluation of 97 wheat varieties showed that no more than 10% of the varieties have low level of susceptibility to the Bgt population specific to the Western Siberian region. Association mapping carried out on the basis of SNP genotyping and phytopathological testing during three environmental seasons identified eight loci in chromosomes 1AL, 1DS, 2BL, 5AS, 5DS, 6AL, 6DL, and 7AL. A high impact to the phenotypic manifestation of the trait was established for genetic factors localized in chromosomes 5AS, 6AL, and 6DL. The long arm of chromosome 6D contains the gene Pm6Ai=2, which was introduced from wheatgrass Thinopyrum intermedium and provides effective protection against the powdery mildew pathogen. On the basis of comparative analysis of the chromosomal localization of the known Pm resistance genes and loci mapped in this work, it was assumed that QTLs in chromosomes 1DS, 5AS, and 6AL are novel, not previously described resistance loci. The obtained results can be used in breeding programs for selection of target loci and for development of molecular markers specific to Bgt resistance loci.

INVINH1 Gene Alleliс Polymorphism in Maize Accessions from VIR Collection Abstract The sequences of the apoplastic invertase inhibitor gene INVINH1 were identified in 71 maize accessions from the collection of the Vavilov All-Russian Institute of Plant Genetic Resources (VIR). In total, 35 INVINH1 allelic variants were found. In 21 maize accessions, at position –95 from the start codon, INVINH1 contained an extended insertion (143, 190, 192, or 210 bp). In INVINH1 proteins, 21 amino acid substitutions were identified, six of which (A49V, A49G, A65P, S97I, C99R, and D108Y), predicted to be radical, were localized in the PMEI functional domain.

Variability of the North Caucasian Populations of the Greenbug for Host Virulence and Discovered by Molecular Markers Abstract Patterns of the genetic structure dynamics of Krasnodar and Dagestan populations of the greenbug, Schizaphis graminum Rondani, in terms of host virulence and molecular markers were examined. High seasonal polymorphism of two North Caucasian insect populations in terms of virulence frequencies to sorghum accessions protected by the major resistance genes was revealed. It was demonstrated that this variability also depended on the plant resistance genes with weak phenotypic manifestation. During feeding on sorghum, the frequencies of greenbug clones virulent to barley accessions also changed. Moreover, the selection of clones on susceptible and moderately resistant sorghum accessions was differential. On the basis of pyrosequencing of a polymorphic fragment of the mitochondrial ND4 gene, 16 greenbug haplotypes were identified. The heterogeneity and difference of the North Caucasian insect populations by the ratio of the identified haplotypes was demonstrated. In the Krasnodar population of S. graminum, both aphid clone samples sampled simultaneously on the phytophage-susceptible and moderately resistant sorghum genotypes and those sampled at different vegetation periods on the same host plant were different.

Allelic Diversity of Hrd A and Hrd B Hordein-Coding Loci in Wild ( Hordeum spontaneum C. Koch) and Cultivated ( Hordeum vulgare L.) Barley from Israel and Palestine Abstract Polymorphism of hordeins encoded by the Hrd A and Hrd B loci was studied using starch gel electrophoresis in 13 barley landrace accessions and in 31 wild barley populations from Israel and Palestine. In H. spontaneum and H. vulgare, 114 and 11 alleles of the Hrd A locus, as well as 114 and 22 alleles of the Hrd B locus, respectively, were identified. Allele frequencies at the Hrd A and Hrd B loci in the wild barley accessions varied in the range of 0.0019–0.0910 and 0.0019–0.0743, respectively, and in the range of 0.0143–0.4215 and 0.0071–0.200, respectively, in cultivated barley. In the Israeli populations of H. spontaneum and H. vulgare, among 120 alleles of the Hrd A locus, six common alleles were found, and among 135 alleles of the Hrd B locus, only one common allele was detected. At the same time, in H. spontaneum, 18 Hrd A alleles and 15 Hrd B alleles that were found earlier in barley landrace accessions from different countries belonging to or adjacent to the barley center of origin were detected. “Cultural” alleles of the Hrd A and Hrd B loci were found mainly in wild barley populations from the Lake Kinneret region. In the population of H. spontaneum from Susita, the Hrd A3 B162 and Hrd A24 B65 genotypes, which were also found in barley landraces from Syria and Jordan, were identified. In general, analysis of the allelic diversity of hordein-coding loci in the Israeli wild barley populations and the composition and distribution of “cultural” alleles and individual genotypes found in H. spontaneum in barley landrace accessions from 20 countries showed that some populations of H. spontaneum from Israel could have been donors of individual alleles and genotypes of hordein-coding loci for H. vulgare as a result of introgression during spontaneous hybridization in the course of cultivated barley dispersal.

Genetic Diversity of Solanum pinnatisectum Dun. and Solanum chacoense Bitt. by Resistance to Potato Virus Y and Results of DNA Analysis Abstract The potato Solanum tuberosum L. has the greatest diversity of cultivated and wild relatives, whose genetic nature has been studied insufficiently. The aim of the present study was to examine the resistance to PVY in S. chacoense Bitt. and S. pinnatisectum Dun. and to search for DNA markers linked to resistance genes. For the first time, representative populations of two diploid tuber-bearing Solanum species were evaluated by the resistance to PVY and the presence of DNA markers linked to the Ry (extreme resistance) or Ny (hypersensitivity) genes localized on the long arm of chromosome 9. Nine accessions of S. chacoense and six accessions of S. pinnatisectum represented by 168 and 170 genotypes, respectively, from the VIR collection were assessed by resistance to artificial infection with PVY. The differences in segregation of two wild potato species into phenotypic classes with response to PVY infection have been established. The diversity of visible reactions of S. chacoense plants after PVY infection differs from the uniform type of symptoms observed in S. pinnatisectum. DNA analysis was performed in 170 S. chacoense genotypes and 44 S. pinnatisectum genotypes using the Ry186, S1d11, and CT220 markers linked to genes determining viral resistance in potato varieties, breeding clones, or species of the genus Solanum L. Most genotypes of S. chacoense and S. pinnatisectum have amplified CT220 marker linked to the Nxphu gene and the Sw-5 gene in the IvP35 line of the species S. phureja Juz. et Buk. and tomato, respectively. The STS Ry186 marker linked to the Rychc gene in Japanese varieties created on the basis of S. chacoense was identified in a small number of S. chacoense genotypes; however, no association between the DNA marker and resistance phenotype was detected. The CAPS S1d11/AcsI marker, which distinguishes between the PVY resistant and susceptible genotypes of both wild potato species, was developed. The plants of two wild-growing tuber-bearing species of Solanum L. were first examined for the presence of the GBSS gene-specific PCR marker (the gene encoding granules-bound starch synthase). A significant part of the genotypes (15% in S. pinnatisectum and 25% in S. chacoense) did not reveal the genetic marker regulating amylose biosynthesis in the forming starch granules. No significant differences in the ability to form tubers depending on the genotypes with or without GBSS marker, indicating the possible presence of an alternative allelic variant of the GBSSI gene in S. chacoense and S. pinnatisectum species, were detected.

Genetic Analysis of Turkish lynx ( Lynx lynx ) Based on Mitochondrial DNA Sequences Abstract Genetic variability and phylogenetic relationships of the Eurasian lynx (Lynx lynx) have been reported by various researchers from species’ range. As genetic data of Turkish lynx comes from a single genetic study that only contains limited number of lynx samples from the Anatolian part of Turkey, there is still a lack of genetic information for the Eurasian lynx population distributed in Turkey. In this study, mitochondrial Cyt b (1140 bp) and COI (630 bp) sequences were obtained from eight Anatolian samples of the Eurasian lynx. The Anatolian lynx sequences were compared to those of conspecific populations published in GenBank. We found two COI (630 bp) and four Cyt b (1140 bp) haplotypes among the eight Anatolian lynx sequences. Despite the limited number of the Anatolian lynx sequences, Bayesian, Maximum Likelihood, Neighbor-Joining and Network analyses revealed that there was a significant genetic differentiation in the Eurasian lynx, in that at least there were two main mitochondrial lineages within the sampling area. Also, the present study suggested that the Anatolian lynx might have a relatively high genetic variability despite the scarce samples.

Genetic Heterogeneity of a Diploid Grass Aegilops tauschii Revealed by Chromosome Banding Methods and Electrophoretic Analysis of the Seed Storage Proteins (Gliadins) Abstract Genetic diversity of diploid grass Ae. tauschii Coss (2n = 2x = 14, DD), the D-genome progenitor of common wheat, was assessed using fluorescence in situ hybridization (FISH) with eleven DNA probes representing satellite and microsatellite DNA sequences as well as the 45S and 5S rRNA gene families and by electrophoretic (EF) analysis of seed storage proteins (gliadins). A clear genetic differentiation of accessions into groups strangulata (Str) and tauschii (Tau) was observed. The groups differed in the presence of microsatellite repeats GAAn and ACTn and in the distribution of satellite DNA families, especially pAs1. On the basis of similarities of labeling patterns of DNA probes used in the study, we concluded that the Str group was phylogenetically closest to the D genome of common wheat. A comparison of spectra of gliadins revealed the highest similarity of Armenian and Azerbaijani accessions of Ae. tauschii to common wheat, which may indicate a contribution of Transcaucasian members of the Str group in the formation of the genetic pool of common wheat.

Genetic Diversity of Old and Local Apple ( Malus × domestica Borkh.) Cultivars from the Collection of VIR according to AFLP Analysis Abstract The genetic diversity of 123 apple accessions from the collection of the research and production base Pushkin and Pavlovsk Laboratories of VIR, including landraces, Soviet cultivars, and commercial Russian and foreign cultivars, was for the first time estimated using the AFLP technique. A total of 355 fragments were obtained, 319 of which were polymorphic (89.86%), and each of the accessions had a unique set of AFLP fragments. The level of diversity of modern commercial cultivars was lower (74.11%, Не = 0.202, I = 0.302) as compared with landraces (89.20%, Не = 0.238, I = 0.366). A wide range of genetic differences between the studied accessions (0.99–0.63) was demonstrated. The statistical analysis of the data obtained made it possible to divide the studied samples into two groups. The first group included most of the analyzed landraces; with no clear differentiation of these landraces by origin. The second group included modern commercial Russian and foreign apple cultivars, Soviet cultivars, and some landraces.