Assessment of Genetic Diversity and Relatedness in an Andean Potato Collection from Argentina by High-Density Genotyping

Native potatoes are the most diverse among cultivated potato species and thus constitute a valuable source for identifying genes for potato improvement. Nevertheless, high-density mapping, needed to reveal allelic diversity, has not been performed for native Argentinian potatoes. We present a study of the genetic variability and population structure of 96 Andigena potatoes from Northwestern Argentina performed using a subset of 5035 SNPs with no missing data and full reproducibility. These high-density markers are distributed across the genome and present a good coverage of genomic regions. A Bayesian approach revealed the presence of: (I) a major group comprised of most of the Andean accessions; (II) a smaller group containing the out-group cv. Spunta and the sequenced genotype DM; and (III) a third group containing colored flesh potatoes. This grouping was also consistent when maximum likelihood trees were constructed and further confirmed by a principal coordinate analysis. A group of 19 accessions stored as Andean varieties clustered consistently with group Tuberosum accessions. This was in agreement with previous studies and we hypothesized that they may be reintroductions of European-bred long day-adapted potatoes. The present study constitutes a valuable source for allele mining of genes of interest and thus provides a tool for association mapping studies.

Genotyping of potato samples from the GenAgro ICG SB RAS collection using DNA markers of genes conferring resistance to phytopathogens

Wart (a disease caused by Synchytrium endobioticum) and golden cyst potato nematode (Globodera rostochiensis), which parasitize the roots of the host plant, cause significant damage to potato crop. Both of these disease factors are quarantined in the Russian Federation, and each registered variety is tested for resistance to their most common races and pathotypes. The main method of opposing such diseases is by the development of resistant varieties. An important step in this process is the selection of resistant genotypes from the population and the estimation of the resistance of hybrids obtained by crosses during the breeding process. Conducting a permanent phenotypic evaluation is associated with difficulties, for example, it is not always possible to work with pathogens, and phenotypic evaluation is very costly and time consuming. However, the use of DNA markers linked to resistance genes can significantly speed up and reduce the cost of the breeding process. The aim of the study was to screen the GenAgro potato collection of ICG SB RAS using known diagnostic PCR markers linked to golden potato cyst nematode and wart resistance. Genotyping was carried out on 73 potato samples using three DNA markers 57R, CP113, Gro1-4 associated with nematode resistance and one marker, NL25, associated with wart resistance. The genotyping data were compared with the data on the resistance of the collection samples. Only the 57R marker had a high level of correlation (Spearman R = 0.722008, p = 0.000000, p < 0.05) between resistance and the presence of a diagnostic fragment. The diagnostic efficiency of the 57R marker was 86.11 %. This marker can be successfully used for screening a collection, searching for resistant genotypes and marker-assisted selection. The other markers showed a low correlation between the presence of the DNA marker and resistance. The diagnostic efficiency of the CP113 marker was only 44.44 %. Spearman’s correlation coefficient (Spearman R = –0.109218, p = 0.361104, p < 0.05) did not show significant correlation between resistance and the DNA marker. The diagnostic efficiency of the NL25 marker was 61.11 %. No significant correlation was found between the NL25 marker and resistance (Spearman R = –0.017946, p = 0.881061, p < 0.05). The use of these markers for the search for resistant samples is not advisable.

Wartime activities of the Vavilov Institute

Among the chronicles relating the heroism of the besieged Leningrad, there are pages dedicated to the deeds performed by the staff the world-famous All-Union Research Institute of Plant Industry (VIR, now the N.I. Vavilov All-Russian Institute of Plant Genetic Resources). With the beginning of the war, even before the city was surrounded by the Nazi troops, the government decided to evacuate a number of factories and institutes from Leningrad, including VIR, but the plan failed. Only in winter did the Institute start partial evacuation, although preparations had been going on for a long time. The largest and most important part of the collection was left behind in the besieged city. The remaining employees were forced to work under the hardest conditions of the siege, in unheated premises. In the harsh reality of the winter in 1941–1942, the daily bread rationing was cut down, and hunger raged in the city, killing tens of thousands of city residents, including VIR employees who kept the stored seeds and tubers untouched. The most difficult part was preserving the potato collection. In the spring of 1942, preparations were made for sowing to restore the viability of seeds and tubers in the fields of Leningrad’s suburban area under the fire from the enemy artillery. Only the heroic efforts of VIR’s staff helped to save the collection from destruction and loss of germination. This heroism cost more than 20 experts and scientists their lives. So, the most dangerous period for the Institute was overcome at such price. Immediately after the siege was lifted, a group of experts was sent to Leningrad from Krasnoufimsk to help with selecting seed accessions for urgent reproduction. Working under extreme physical exhaustion in frozen premises, without water or electricity, under continuous shelling, they saved, many at the cost of their own lives, the collection of cultivated plants and their wild relatives, the herbarium, and the scientific library for future generations.

Sanitization of potato varieties from the VIR collection against viruses

Background. VIR’s potato collection is one of the oldest and richest; however, it is constantly exposed to viruses that negatively affect useful agronomic properties of tubers. Close monitoring of the phytosanitary state of potato accessions helps to select the most effective method of therapy for subsequent healing of infected plants and obtaining high-quality planting material.Materials and methods. The research was aimed at improving the health of 18 varieties of Solanum tuberosum L. from the VIR collection. Testing for the presence of viruses was based on the ICA and RTPCR techniques, and the consequent healing was performed using the methods of meristem culture and cryotherapy.Results and conclusions. During the field test of potato plants, PVX, PVS and PVA were found to be the most common viruses. PSTVd was completely absent in all tested accessions. The effectiveness of in vitro healing of potato plants from viruses was assesses using meristem culture. The percentage of healed plants was 0% for PVS, 0% for PVX, 33.4% for PVA, 50% for PLRV, 72.3% for PVY, and 83.4% for PVM. Healing with meristem culture was shown to be the most effective against PVY and PVM. While assessing the effectiveness of post-cryogenic restoration of potato microplants, the level of post-cryogenic regeneration of the shoot tips in potato microplants was determined at 22.3% on average for a sample. The minimum was observed in k-16762 ‘Sagita N’ (5%), and the maximum in k-1378 ‘Marta’ (41.7%). Analysis of the effectiveness of potato recovery from viruses by in vitro cryotherapy showed that the percentage of recovered plants was 100% for PVY, 100% for PVA, 88.9% for PVM, 77.8% for PVS, 44.4% for PVX. Thus, the techniques of apical meristem culture and cryotherapy proved to be effective against PVY, PVA and PVM viruses. However, in the case of multiple infections, it is necessary to combine elements of different healing protocols to increase the effectiveness of the healing procedure.

Polar Experiment Station of VIR: the northernmost outpost of potato research

The establishment and progress of potato cultivation in the Kola Peninsula are closely associated with the Polar Experiment Station of the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR). The data are presented on the development of early-ripening and high-yielding potato cultivars based on the source material from the VIR collection: ‘Imandra’, ‘Sestra Imandry’, ‘Murmansky’, ‘Snezhinka No. 3’, ‘Khibinsky ranny’, etc. Prominent breeders and scientists, who worked at different times at the Polar Station, contributed to the release of unique early-ripening potato cultivars: J. H. Eichfeld, M. N. Veselovskaya, I. A. Veselovsky, F. I. Manykov, M. A. Vavilova, N. N. Ivanova, L. A. Dremlyug, A. M. Kozeletskaya, S. A. Anikina, G. D. Melnichuk, etc. Some of the cultivars developed from 1937 to 1968 are still used in large-scale potato production in Murmansk Province. Every year the cultivar and species diversity of potatoes is planted in the fields of the Arctic North. Today, the extensive material from the potato collection makes it possible to study the impact of environmental factors, identify sources of earliness and productivity, and conduct breeding activities aimed at the release of early cultivars.

SPECIFIC FEATURES OF THE STUDY AND MAINTENANCE OF A POTATO COLLECTION THREATENED BY VIRUSES AND VIRUS¬LIKE DISEASES

Background. The article deals with the problems faced while studying and maintaining a collection of plant genetic resources against a strong virus infection background.Materials and methods. The data obtained during 8 years of monitoring over 1000 potato accessions for the incidence of virus diseases are presented. The work was carried out at Pushkin and Pavlovsk Laboratories of VIR and at the Polar Experiment Station of VIR (Khibiny, Arctic Circle). Visual control of the symptoms of the infection was combined with an enzyme-linked immunosorbent assay (ELISA) for potato mosaic viruses Х, S, M and Y.Results and conclusions. For many years, the global collection of VIR has been studied and maintained under a threat of strong virus infections. Among the viruses that have the widest distribution and cause significant damage to potato, there are viruses M and Y in Pushkin, and Х in Khibiny. Among the infected plant material, accessions with a latent virus infection, manifesting tolerance to the pathogens, have constantly been observed. The conventional point-based principle of scoring field resistance of potato cultivars and hybrids to viruses requires a significant revision. A new alternative approach is proposed for virus resistance assessment, when the clonal reproduction type of the tested accessions is taken into account.

Genetic identity in genebanks: application of the SolCAP 12K SNP array in fingerprinting and diversity analysis in the global in trust potato collection

Breeders rely on genetic integrity of material from genebanks; however, admixture, mislabeling, and errors in original data can occur and be detrimental. Two hundred and fifty accessions, representing paired samples consisting of original mother plants and their in vitro counterparts from the cultivated potato collection at the International Potato Center (CIP) were fingerprinted using the Infinium 12K V2 Potato Array to confirm genetic identity of the accessions and evaluate genetic diversity of the potato collection. Diploid, triploid, and tetraploid accessions were included, representing seven cultivated potato taxa (based on Hawkes, 1990). Fingerprints between voucher mother plants maintained in the field and in vitro clones of the same accession were used to evaluate identity, relatedness, and ancestry using hierarchal clustering and model-based Bayesian admixture analyses. Generally, in vitro and field clones of the same accession grouped together; however, 11 (4.4%) accessions were mismatches genetically, and in some cases the SNP data revealed the identity of the mixed accession. SNP genotypes were used to assess genetic diversity and to evaluate inter- and intraspecific relationships along with determining population structure and hybrid origins. Phylogenetic analyses suggest that the triploids included in this study are genetically similar. Further, some genetic redundancies among individual accessions were also identified along with some putative misclassified accessions. Accessions generally clustered together based on taxonomic classification and ploidy level with some deviations. STRUCTURE analysis identified six populations with significant gene flow among the populations, as well as revealed hybrid taxa and accessions. Overall, the Infinium 12K V2 Potato Array proved useful in confirming identity and highlighting the diversity in this subset of the CIP collection, providing new insights into the accessions evaluated. This study provides a model for genetic identity of plant genetic resources collections as mistakes in conservation of these collections and in genebanks is a reality. For breeders and other users of these collections, confirmed identity is critical, as well as for quality management programs and to provide insights into the accessions evaluated.