Kompetitive Allele Specific PCR (KASP) Markers for Potato: An Effective Tool for Increased Genetic Gains

Potato virus Y (PVY) and Phytophthora infestans (Mont.) de Bary that causes potato late blight (LB), pose serious constraints to cultivated potatoes due to significant yield reduction, and phenotyping for resistance remains challenging. Breeding operations for vegetatively propagated crops can lead to genotype mislabeling that, in turn, reduces genetic gains. Low-density and low-cost molecular marker assessment for phenotype prediction and quality control is a viable option for breeding programs. Here, we report on the development of kompetitive allele specific PCR (KASP) markers for LB and PVY resistance, and for routine quality control assessment of different breeding populations. Two KASP markers for LB resistance and two for PVY Ryadg were validated with an estimated assay power that ranged between 0.65 and 0.88. The developed QC KASP markers demonstrated the capability of discriminating tetraploid calls in breeding materials, including full-sibs and half-sibs. Routine implementation of the developed markers in a breeding program would assist with better allocation of resources and enable precise characterization of breeding material, thereby leading to increased genetic gains.

Pectobacterium brasiliense (soft rot and blackleg of ornamentals and potato).

Pectobacterium brasiliense is a bacterial pathogen primarily infecting potato and other vegetables and ornamentals. The earliest reports of the bacterium causing disease were from Brazil in 2004 (El-Tassa and Duarte, 2004; Duarte et al., 2004). This pathogen was reported for the first time in Europe (Belgium) in 2012 (van der Wolf et al., 2017). Since then, the pathogen has been reported in many regions of Europe, Asia, Africa, Australia, North and South America. The bacterium has adapted itself to a wide range of temperatures and host species, thus it is considered a culprit for significant losses in China, South Africa, Brazil, Netherlands, Switzerland and UK (Meng et al., 2017; van der Wolf et al., 2017). Symptoms caused by P. brasiliense are indistinguishable from other soft rot Pectobacterium and Dickeya, therefore it is impossible to identify this species on the basis of field and laboratory symptoms. Unfortunately, there is no evidence of curative measures and varietal resistance (in cultivated potatoes) against this group of bacteria, so farmers rely on seed certification, exclusion and sanitation to mitigate its worst effects.

Influence of various factors on crop formation and potato quality

The purpose of the research was to study the effect of fertilizer rates depending on drainage and weather conditions on the yield and quality of potatoes, their payback with an increase in yield. Methodology and methods of research. The studies were conducted in a two-factor field experiment in 2012–2020, factor A – drainage (drained by closed potter drainage and non-drained soil), factor B – various fertilizer rates (without fertilizers; multi-purpose compost (KMN) 10 t/ha + K90; KMN 10 t/ha + N70K180). The soil of experimental plot of sod-podzolic light loamy are predominant, well-cultivated. Potatoes were cultivated according to the ridge technology developed at VNIIMZ, the predecessor of winter grain crops. According to weather conditions, the years of research are divided into excessively humid, humid and arid. Analyses and observations were carried out according to the generally accepted methods of experimental work, calculations using statistical analysis. Results. The tendencies of changes in the indicators of the water-air regime of the arable layer of soil (moisture, total porosity, porosity of aeration, bulk density) depending on drainage and weather conditions were revealed. The influence of fertilizer rates on drained and non-drained areas, depending on weather conditions, on the content of mineral nitrogen in the soil, yield and its structure, the quality of potato production (content of nitrates, starch in tubers), the use of photosynthetically active solar radiation, payback of fertilizers by an increase in yield has been established. The share of the influence of fertilizers and drainage on the variability of the yield in different weather conditions has been determined. Scientific novelty. The share of the participation of the studied factors in the variability of the potato yield and the rational rates of the use of fertilizers, depending on soil and weather conditions, have been established.

Natural and Cultural Processes Influencing Gene Flow Among Wild (atoq papa), Weedy (araq papa and k’ipa papa), and Crop Potatoes in the Andean Region of Southern Peru

The Andean region is one of the areas with the earliest signs of food production systems and highest agrobiodiversity of the world, which resulted from millennia of domestication in a context of high ecosystem heterogeneity and human cultures valuing diversity for risk management. FAO has reported nearly 4000 varieties of cultivated potatoes still grown in the Andes, 3000 of them currently occurring in Peru. Such diversity has enormous sources of variation in wild (atoq papa) and weedy (araq papa and k’ipa papa) potatoes that coexist with crops, but their variation, interactions and mechanisms influencing diversification processes still require studies. In order to have a panorama of the variation and mechanisms influencing it in a regional setting, we studied biocultural factors favoring potatoes diversity in communities of Cusco and Apurimac, Peru. Our study documented the regional variation of wild, weedy, and cultivated potatoes recognized by local Quechua people and conducted semi-structured interviews to document their use, cultural value, and strategies of gene flow management implemented. We also studied their phenology, floral biology, flower visitors, and conducted experimental crosses between the wild S. candolleanum and 30 varieties of cultivated potatoes. We identified the wild potatoes S. acaule, S. brevicaule and S. candolleanum and 53 varieties of araq papa used and managed by local people. The latter provide nearly one third of the annual consumption of tubers by people interviewed and are, therefore, highly valued, maintained and managed in crop fields (chacras). People recognized that crosses between wild, weedy, and cultivated potatoes occur, and identified flower visitors and frugivores consuming their berries. Overlap of blooming periods and flower visitors of wild, weedy, and cultivated potatoes was recorded. Almost all flower visitors are shared among the different potato species and varieties, the bumble bees being particularly relevant in pollination of all taxa studied. We recorded seed production in nearly 35% of the experimental crosses. K’ipa papas are sets of mixtures of plants resulting from remaining tubers of cultivated potatoes, but also those from seeds that may result from hybridization of wild, weedy, and cultivated potatoes. Since local people commonly use k’ipa papa varieties and some of them are kept for planting in chacras, sexual reproduction in k’ipa papas is possibly one main mechanism of variation and source of new varieties of crops. Maintaining wild and weedy potatoes, and the natural and cultural mechanisms of gene flow is crucial for in situ conservation and generation of potato variation.

Potato Landraces and Their Wild Relatives in 3 Micro-centers of Diversity in Ecuador: Farmers' Perception and Ecogeography

Ecuador is one of the centers of diversity for wild and cultivated potatoes. Three micro-centers of diversity were previously identified based on germplasm collecting passport data of potato landraces and their wild relatives. The objective of this study was to understand the potential hybridization dynamic of the genetic diversity present in situ in these micro-centers (provinces of Carchi, Chimborazo and Loja in Ecuador) by means of: 1. Reviewing the possibility of an eventual genetic cross within intercropped potato landraces through surveys to local producers; 2. Reviewing the possibility of potato landraces crossing with their wild relatives, also according to local producers; and 3. Map the actual geographic location of recent collections of potato landrace and wild potato relatives in the study areas. Information from farmers and eco-geographic data demonstrated that there is no potential crossing between wild and cultivated potato species. Probably the existing genetic variability in Ecuador has been accumulated since the historical movement of potato landraces by American ancestors from the center of origin in Peru and Bolivia and the continuum knowledge and seed sharing besides the conscious and unconscious selection of potato landraces by local farmers for centuries. Additionally, we discuss options to conserve both cultivated and wild potato species in Ecuador due to apparent current genetic erosion processes.

Pectobacterium brasiliense (soft rot and blackleg of ornamentals and potato).

Pectobacterium brasiliense is a bacterial pathogen primarily of potato and other vegetables and ornamentals. The earliest reports of the bacterium causing disease were from Brazil in 2004 (El-Tassa and Duarte, 2004). This pathogen was reported for the first time in Europe (Belgium) in 2012 (van der Wolf et al., 2017). Since then, the pathogen has been reported in many regions of Europe, Asia, Africa, Australia, North and South America. The bacterium has adapted itself to a wide range of temperatures and host species, thus it is considered a culprit for significant losses in China, South Africa, Brazil, Netherlands, Switzerland and UK (Meng et al., 2017; van der Wolf et al., 2017). Symptoms caused by P. brasiliense are indistinguishable from other soft rot Pectobacterium and Dickeya, therefore it is impossible to identify this species on the basis of field and laboratory symptoms. Unfortunately, there is no evidence of curative measures and varietal resistance (in cultivated potatoes) against this group of bacteria, so farmers rely on seed certification, exclusion and sanitation to mitigate its worst effects.

Yield Prediction in Sorghum (Sorghum bicolor (L.) Moench) and Cultivated Potato (Solanum tuberosum L.)

Sorghum and potato pilots were conducted in this work to provide a solution to current limitations (dependability, cost) in crop monitoring in Europe. These limations include yield forecasting based mainly on field surveys, sampling, censuses, and the use of coarser spatial resolution satellites. We used the indexes decribing the fraction of absorbed photosynthetically active radiation as well as the leaf areas derived from Sentinel-2 satellites to predict yields and provide farmers with actionable advice in sorghum biomass and, in combination with WOFOST crop growth model, in cultivated potatoes. Overall, the Bayesian additive regression trees method modelled best sorghum biomass yields. The best explanatory variables were days 150 and 165 of the year. In potato, the use of earth observation information allowed to improve the growth model, resulting in better yield prediction with a limited number of field trials. The online platform provided the potato farmers more insight through benchmarking among themselves across cropping seasons, and observing in-field variability Site-specific management became easier based on the field production potential and its performance relative to surrounding fields. The extensive pilots run in this work showed that farming is a business with several variables which not all can be controlled by the farmer. The technologies developed herein are expected to inform about the farming operations, giving rise to well-informed farmers with the advantage to be able to adapt to the circumstances, mitigating production risks, and ultimately staying longer in the business.

Screening of Wild Potatoes Identifies New Sources of Late Blight Resistance

Late blight (LB) of potato is considered one of the most devastating plant diseases in the world. Most cultivated potatoes are susceptible to this disease. However, wild relatives of potatoes are an excellent source of LB resistance. We screened 384 accessions of 72 different wild potato species available from the U.S. Potato GeneBank against the LB pathogen Phytophthora infestans in a detached leaf assay (DLA). P. infestans isolates US-23 and NL13316 were used in the DLA to screen the accessions. Although all plants in 273 accessions were susceptible, all screened plants in 39 accessions were resistant. Resistant and susceptible plants were found in 33 accessions. All tested plants showed a partial resistance phenotype in two accessions, segregation of resistant and partial resistant plants in nine accessions, segregation of partially resistant and susceptible plants in four accessions, and segregation of resistant, partially resistant, and susceptible individuals in 24 accessions. We found several species that were never before reported to be resistant to LB: Solanum albornozii, S. agrimoniifolium, S. chomatophilum, S. ehrenbergii, S. hypacrarthrum, S. iopetalum, S. palustre, S. piurae, S. morelliforme, S. neocardenasii, S. trifidum, and S. stipuloideum. These new species could provide novel sources of LB resistance. P. infestans clonal lineage-specific screening of selected species was conducted to identify the presence of RB resistance. We found LB resistant accessions in Solanum verrucosum, Solanum stoloniferum, and S. morelliforme that were susceptible to the RB overcoming isolate NL13316, indicating the presence of RB-like resistance in these species.

Composition of the collection of primitive cultivated species within the Solanum L. section Petota Dumort. and contemporary trends in their research

The diversity of potato genetic resources in the VIR genebank harbors one of the world’s first collections of primitive cultivated species. These accessions are native potato varieties cultivated by the indigenous population of South America. The oldest accessions in the collection are traced back to 1927. Approximately one fifth of the collection (106 accessions out of 573) is the unique material procured by VIR’s collecting missions to Bolivia, Colombia, Ecuador, and Peru. According to S. Bukasov’s potato classification, the diversity of South American highland potatoes explored by VIR’s collectors belongs to spp. Solanum ajanhuiri Juz. et Buk., S. × chaucha Juz. et Buk., S. mammilliferum Juz. et Buk., S. phureja Juz. et Buk., S. rybinii Juz. et Buk., S. goniocalyx Juz. et Buk., S. stenotomum Juz. et Buk., S. tenuifilamentum Juz. et Buk., S.× juzepczukii Buk., and S. × curtilobum Juz. et Buk. Within this group of species, S. × ajanhuiri, S. phureja and S. stenostomum are the closest in their characteristics to ancient domesticated forms of tuber-bearing Solanum spp. This publication is an analytical review of the current composition of the primitive cultivated potato species collection and the results of its earlier studies. Ecogeographic descriptions of the sites native for cultivated potatoes and information on the sources of the accessions are presented. A large-scale evaluation of primitive cultivated potato accessions by a set of characters, carried out in field and laboratory experiments, uncovers their breeding potential and serves as the primary information platform for further indepth research. Studying S. phureja and closely related cultivated potato species is important for finding solutions of fundamental problems in plant biology. The data arrays accumulated today would facilitate targeted selection among accessions to identify most promising ones for molecular genetic studies into the gene pool diversity of potato species.

Development of chromosome-specific markers for a study on introgressive hybridization of potato with the wild Mexican allotetraploid species Solanum stoloniferum Schltdl

In order to involve valuable germplasm of the wild Mexican allotetraploid potato species Solanum stoloniferum Schltdl. (genomic composition ААВВ) into breeding, pentaploid interspecific hybrids (ААAAВ) with cultivated potato S. tuberosum L. (АААА) and their backcross progenies are usually used. Homologous synapsis in meiosis of such hybrids is expected only between chromosomes of the A subgenome, therefore a question arose about a possibility of introgressing genetic material of the subgenome B into the A genome of cultivated potato. In this connection, development of various schemes for the B subgenome introgression into the genome of cultivated potato is considered as a topical issue. The previous research has yielded four schemes of S. stoloniferum involvement into breeding, which imply backcrossing with cultivated potato of the following interspecific hybrids: (1) hexaploids (genomic composition ААААВВ, the conventional introgression scheme), (2) tetraploids (putatively, АААВ), (3) self-pollination progeny of a 4x hybrid and (4) pentaploid hybrids with a putative genome composition of АААВВ. The present paper presents the first results of the development of chromosome-specific DNA markers for the identification of S. stoloniferum chromosomes in interspecific hybrids. An S. stoloniferum accession PI 205522 with a high degree of resistance to late blight and PVY had been found to possess several DNA-markers of the R-genes conferring resistance to these pathogens and was used in hybridization as a promising parent. A set of 23 SSR- and CAPS markers with the known chromosome location in S. tuberosum was generated. These markers detect polymorphism between parent genotypes, i.e., the diploid clone IGC 10/1.21 of cultivated potatoes S. tuberosum, and accession PI 205522 of S. stoloniferum. All the markers specific for the wild species were found in triploid (ААВ) and pentaploid (АААВВ) hybrids of S. stoloniferum × S. tuberosum. This set of markers will be used for efficiency assessment of different schemes for S. stoloniferum genetic material introgression into the obtained BC2-BC3 generations after crossing the interspecific hybrids with cultivated potato.