Ekaterina Sokolova

Scopus Publications

Expression of late blight resistance gene markers in potato varieties and wild Solanum species
Ekaterina Sokolova, Mariya Beketova, Oleg Kazakov, and Viktor Martynov
Open Science Publishers LLP
DNA markers are increasingly used in potato breeding for resistance to late blight. Such markers are generally based on polymerase chain reaction amplification of sequences of resistance genes introduced into cultivated potato varieties from wild tuber-bearing Solanum species. However, if nonfunctional homologues of resistance genes are being revealed with DNA markers, there will be no association between plant resistance and the occurrence/ absence of these markers. In order to increase the reliability of such DNA markers, it would be desirable to test the functionality of the genetic targets used to develop these markers. It makes sense to begin testing functionality by assessing the expression of these genetic targets, because the absence of expression will clearly indicate the absence of function, and this, in turn, will make it possible to immediately reject markers of inactive homologues of resistance (R) genes. The present study is dedicated to the examination of expression of 10 R genes: R1, R2, Rpi-blb3, R3a, R3b, Rpi-blb1, Rpi-sto1, Rpi-blb2, Rpi-vnt1.3, and Rpi-chc1, detected using 11 sequence-characterized amplified region markers of these genes in wild Solanum species and potato cultivars. As a result of this study, most markers were shown to be associated with expressed R genes, and these markers can be recommended for further use in marker-assisted selection for resistance to late blight. On the other hand, the revealed homologues of the R3a and Rpi-blb2 genes seem to be inactive outside the species in which these genes were originally discovered, and the Rpi-sto1 gene has both expressed and non-expressed variants.

Diversity of Late Blight Resistance Genes in the VIR Potato Collection
Elena V. Rogozina, Alyona A. Gurina, Nadezhda A. Chalaya, Nadezhda M. Zoteyeva, Mariya A. Kuznetsova, Mariya P. Beketova, Oksana A. Muratova, Ekaterina A. Sokolova, Polina E. Drobyazina, and Emil E. Khavkin
MDPI AG
Late blight (LB) caused by the oomycete Phytophthora infestans (Mont.) de Bary is the greatest threat to potato production worldwide. Current potato breeding for LB resistance heavily depends on the introduction of new genes for resistance to P. infestans (Rpi genes). Such genes have been discovered in highly diverse wild, primitive, and cultivated species of tuber-bearing potatoes (Solanum L. section Petota Dumort.) and introgressed into the elite potato cultivars by hybridization and transgenic complementation. Unfortunately, even the most resistant potato varieties have been overcome by LB due to the arrival of new pathogen strains and their rapid evolution. Therefore, novel sources for germplasm enhancement comprising the broad-spectrum Rpi genes are in high demand with breeders who aim to provide durable LB resistance. The Genbank of the N.I. Vavilov Institute of Plant Genetic Resources (VIR) in St. Petersburg harbors one of the world’s largest collections of potato and potato relatives. In this study, LB resistance was evaluated in a core selection representing 20 species of seven Petota series according to the Hawkes (1990) classification: Bulbocastana (Rydb.) Hawkes, Demissa Buk., Longipedicellata Buk., Maglia Bitt., Pinnatisecta (Rydb.) Hawkes, Tuberosa (Rydb.) Hawkes (wild and cultivated species), and Yungasensa Corr. LB resistance was assessed in 96 accessions representing 18 species in the laboratory test with detached leaves using a highly virulent and aggressive isolate of P. infestans. The Petota species notably differed in their LB resistance: S. bulbocastanum Dun., S. demissum Lindl., S. cardiophyllum Lindl., and S. berthaultii Hawkes stood out at a high frequency of resistant accessions (7–9 points on a 9-point scale). Well-established specific SCAR markers of ten Rpi genes—Rpi-R1, Rpi-R2/Rpi-blb3, Rpi-R3a, Rpi-R3b, Rpi-R8, Rpi-blb1/Rpi-sto1, Rpi-blb2, and Rpi-vnt1—were used to mine 117 accessions representing 20 species from seven Petota series. In particular, our evidence confirmed the diverse Rpi gene location in two American continents. The structural homologs of the Rpi-R2, Rpi-R3a, Rpi-R3b, and Rpi-R8 genes were found in the North American species other than S. demissum, the species that was the original source of these genes for early potato breeding, and in some cases, in the South American Tuberosa species. The Rpi-blb1/Rpi-sto1 orthologs from S. bulbocastanum and S. stoloniferum Schlechtd et Bché were restricted to genome B in the Mesoamerican series Bulbocastana, Pinnatisecta, and Longipedicellata. The structural homologs of the Rpi-vnt1 gene that were initially identified in the South American species S. venturii Hawkes and Hjert. were reported, for the first time, in the North American series of Petota species.

Polymorphism of avirulence genes in potato late blight pathogen Phytophthora infestans as characterized by SSCP analysis
Viktor Martynov, Vera Chizhik, Ekaterina Sokolova, Mariya Kuznetsova, and Emil Khavkin
Elsevier BV

Discerning strains of Phytophthora infestans the causative agent of potato late blight by SSCP analysis of virulence genes
V.K. Chizhik, , E.A. Sokolova, V.V. Martynov, M.A. Kuznetsova, E.E. Khavkin, , , , and

Two orthologs of late blight resistance gene R1 in wild and cultivated potato
M. P. Beketova, E. A. Sokolova, E. V. Rogozina, M. A. Kuznetsova, and E. E. Khavkin
Pleiades Publishing Ltd

Anticipatory breeding: Molecular markers as a tool in developing donors of potato (Solanum Tuberosum L.) Late blight resistance from complex interspecific hybrids
O.A. Fadina, , M.P. Beketova, E.A. Sokolova, M.A. Kuznetsova, T.I. Smetanina, E.V. Rogozina, E.E. Khavkin, , ,et al.
Sel'skokhozyaistvennaya Biologiya Editorial Office (SBEO), NPO
Potato late blight caused by oomycete Phytophthora infestans Mont de Bary remains the most significant agronomic and economic problem of potato husbandry. The unique rate of evolution of this pathogen as well as its migration are a major obstacle to producing varieties with durable late blight resistance. The best way to counter this threat is the anticipatory breeding based on donors that carry genes of resistance to a wide range of pathogen races. Combining multiple genes for late blight resistance in the same plant (pyramiding of genes) makes such resistance durable. The most promising way of obtaining such donors is introgression breeding of interspecific potato hybrids with resistance genes transferred from potato wild relatives — the tuber-bearing species of Solanum L. Molecular markers allowing to reliably distinguish between resistance genes of diverse specificity and successfully control their transfer in the process of crossing and selecting, dramatically increase the efficiency of introgression breeding for late blight resistance. We examined about 40 complex hybrids bred in the A.G. Lorkh All-Russian Research Institute of Potato Husbandry, the N.I. Vavilov AllRussian Institute of Plant Genetic Resources and the All-Russian Research Institute of Plant Protection using the germplasm of 16 species of tuber-bearing Solanum, and further maintained as clones. Each of these clones carries the genetic material introgressed from two to eight wild species established as the sources of resistance to late blight. Most of these clones have manifested, from year to year, high late blight resistance in field trials under natural infection and in vitro studies when detached leaves were infected with a highly virulent and aggressive isolate of P. infestans. SCAR (sequence-characterized amplified region) markers, the fragments of R genes of race-specific (vertical) resistance to late blight discerned in various Solanum species, were employed to screen the clones of interspecific hybrids. The information on the presence of SCAR markers for six R genes, i.e. R1 (chromosome 5), R2/Rpi-blb3 (chromosome 4), R3a and R3b (chromosome 11), RB/Rpi-blb1 = Rpisto1 (chromosome 8), and Rpi-vnt1.3 (chromosome 9), was juxtaposed against the indices of late blight resistance. Comparison of the resistance of the clones of interspecific hybrids and potato varieties devoid of R gene marker presumes a significant contribution of these genes to general late blight resistance of potato plants. The higher number of R gene markers per plant corresponded to superior late blight resistance. Presumably, future use of these clones for pyramiding resistance genes under the control of molecular markers will enable target introgression breeding. Such approach will

Molecular analysis of polymorphisms in differentiating phytophthora infestans races
E.A. Sokolova, , E.V. Morozova, T.I. Ulanova, O.P. Malychenko, Ya.I. Alekseev, M.A. Kuznetsova, E.E. Khavkin, , ,et al.
Sel'skokhozyaistvennaya Biologiya Editorial Office (SBEO), NPO
Potato late blight caused by oomycete Phytophthora infestans (Mont.) de Bary is economically significant disease of worldwide importance. The traditional classification of specialized races of P. infestans is based on eleven resistance genes (R genes) introgressed from Solanum demissum to cultivated potato S. tuberosum. The selection of potato varieties, each comprising one of these R genes, is referred to as the Mastenbroek-Black set of differential plants. This set has been employed to establish the virulence genes (r genes) in isolates and strains of P. infestans, and collections of such individual strains have been maintained as tool sets of differential races for discerning R genes in cultivated and wild Solanum plants. While widely used in potato breeding for late blight resistance, these differential races have not been sufficiently explored by present-day molecular methods. We studied 11 differential races (1; 3; 4; 10; 11; 1.2; 1.3; 1.4; 1.2.3; 1.2.4; 1.2.3.4) maintained in the Institute of Phytopathology for over forty years and isolate 161 possessing all 11 genes of virulence. When the differential races of P. infestans were genotyped with the standard set of 12 microsatellite (simple sequence repeat, SSR) loci, these races were distinct from reference A1 strains and highly aggressive lines lately dominant in the Western and Central Europe. SSR clusters of differential races did not match their r gene profiles. To assess the profiles of virulence genes in the differential races of P. infestans, we cloned three avirulence genes (Avr genes): ipiO = Avr-blb1, which recognizes the Rpi-blb1 = Rpi-sto1 gene of S. bulbocastanum and S. stoloniferum characterized by broad resistance to P. infestans races, and also Avr3a and Avr4 corresponding to R3a and R4 of S. demissum. These Avr genes were found in all differential races under study, and each gene was represented by several alleles. The complex patterns of Avr genes are in sharp contrast with the conventional concept of «simple» monogenic races. In the case of ipiO (NCBI GenBank accession numbers KP308170-KP308174, KF154431-KF154433 and KF154434-KF154439) race 1 was represented by the alleles of classes I and II, whereas races 3 and 4 comprised only the class I genes. None of three races contained the most virulent class III ipiO gene. The virulent allele Avr3a_EM was found in all investigated races, while the avirulent allele Avr3a_KI was discerned only in races 1, 3 and 1.2.3 (KF154421KF154426, KF154430, KP317568, KP317572, KP317580-KP317584, KP317588, KP317589). The Avr4 gene was cloned from differential races 1, 3, 1.4 and 11 (KF188215-KF188223). All these races contained the virulent allele, and race 11 comprised both avirulent and virulent alleles. The molecular and phytopathological evidence for Avr and r genes, respectively, matched only in 30 % of races. Probably, these discrepancies are due to the accumulation of mutations in the Avr genes of differential races in the course of their long-term maintenance in the collection and more complex composition of R genes in plants which were initially to select the differentiating races.

Phytopathological and molecular characteristics of Phytophthora infestans isolates collected on resistant and susceptible potato genotypes

SCAR markers of the R-genes and germplasm of wild Solanum species for breeding late blight-resistant potato cultivars
Ekaterina Sokolova, Artem Pankin, Maria Beketova, Maria Kuznetsova, Svetlana Spiglazova, Elena Rogozina, Isol'da Yashina, and Emil Khavkin
Cambridge University Press (CUP)
New races of Phytophthora infestans rapidly defeat potato late blight (LB) resistance based on Solanum demissum germplasm, and breeders search for new sources of durable LB resistance. We developed and verified six sequence characterized amplified region markers recognizing the race-specific genes R1 and R3 of S. demissum and the broad-spectrum resistance gene RB of S. bulbocastanum and the germplasms of these species and used them to screen 209 accessions of 21 wild Solanum species. In addition to S. demissum, homologues of R1 and R3 were found in several species of series Demissa,Longipedicellata and diploid Tuberosa; R3 homologues were also detected in S. bulbocastanum,S. cardiophyllum and S. ehrenbergii. The RB homologues were found in a wider range of Solanum species. The markers of R1 and R3 genes reliably discerned between germplasms of S. tuberosum ssp. tuberosum and wild sources of LB resistance. Following introgression, the species-specific markers of demissum and bulbocastanum germplasm were rapidly lost, whereas the markers of R1 and R3 genes lasted through several meiotic generations and were maintained at high frequencies in modern potato cultivars. The presence of these markers in demissoid potato cultivars was significantly associated with LB resistance, presuming that both genes contribute to overall defence response.

Allele mining in the gene pool of wild Solanum species for homologues of late blight resistance gene RB/Rpi-blb1
Artem Pankin, Ekaterina Sokolova, Elena Rogozina, Maria Kuznetsova, Kenneth Deahl, Richard Jones, and Emil Khavkin
Cambridge University Press (CUP)
A coiled coil-nucleotide binding site-leucine-rich repeat gene RB/Rpi-blb1 isolated from Solanum bulbocastanum confers broad-spectrum resistance to Phytophthora infestans and is currently employed in potato breeding for durable late blight (LB) resistance. RB homologues were reported in several Solanum species; some of them retained defence function. Here, we report additional evidence on RB-like sequences in 21 Solanum species of the section Petota. The panel of Solanum species was screened with three RB-related PCR markers. RB-like sequences were found in every tested Solanum accession, suggesting universal distribution of RB structural homologues among Solanum genomes, while locus-specific RB-629 was found only in 15 species. Phylogenetic analysis of RB-629 sequences suggested a highly conservative pattern of polymorphisms that was neither species- nor series-specific. Apparently, duplication and evolution of RB-like loci preceded Solanum speciation. Marker presence and particular haplotypes were not immediately associated with high LB resistance.

DNA markers for potato introgression breeding
A. Haverkort and B. Anisimov
Brill | Wageningen Academic

Ekaterina Sokolova

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Scopus Publications