Ecogeography of ploidy variation in cultivated potato (Solanum sect. Petota)

Analysis of Genome Structure and Its Variations in Potato Cultivars Grown in Russia

Solanum tuberosum L. (common potato) is one of the most important crops produced almost all over the world. Genomic sequences of potato opens the way for studying the molecular variations related to diversification. We performed a reconstruction of genomic sequences for 15 tetraploid potato cultivars grown in Russia using short reads. Protein-coding genes were identified; conserved and variable parts of pan-genome and the repertoire of the NBS-LRR genes were characterized. For comparison, we used additional genomic sequences for twelve South American potato accessions, performed analysis of genetic diversity, and identified the copy number variations (CNVs) in two these groups of potato. Genomes of Russian potato cultivars were more homogeneous by CNV characteristics and have smaller maximum deletion size in comparison with South American ones. Genes with different CNV occurrences in two these groups of potato accessions were identified. We revealed genes of immune/abiotic stress response, transport and five genes related to tuberization and photoperiod control among them. Four genes related to tuberization and photoperiod were investigated in potatoes previously (phytochrome A among them). A novel gene, homologous to the poly(ADP-ribose) glycohydrolase (PARG) of Arabidopsis, was identified that may be involved in circadian rhythm control and contribute to the acclimatization processes of Russian potato cultivars.

Defining a diverse core collection of the Colombian Central Collection of potatoes: a tool to advance research and breeding

The highly diverse Colombian Central Collection (CCC) of cultivated potatoes is the most important source of genetic variation for breeding and the agricultural development of this staple crop in Colombia. Potato is the primary source of income for more than 100.000 farming families in Colombia. However, biotic and abiotic challenges limit crop production. Furthermore, climate change, food security, and malnutrition constraints call for adaptive crop development to be urgently addressed. The clonal CCC of potatoes contains 1,255 accessions - an extensive collection size that limits its optimal assessment and use. Our study evaluated different collection sizes from the whole clonal collection to define the best core collection that captures the total genetic diversity of this unique collection, to support a characterization more cost-effectively. Initially, we genotyped 1,141 accessions from the clonal collection and 20 breeding lines using 3,586 genome-wide polymorphic markers to study CCC's genetic diversity. The analysis of molecular variance confirmed the CCC's diversity with a significant population structure (Phi=0.359; p-value=0.001). Three main genetic pools were identified within this collection (CCC_Group_A, CCC_Group_B1, and CCC_Group_B2), and the commercial varieties were located across the pools. The ploidy level was the main driver of pool identification, followed by a robust representation of accessions from Phureja and Andigenum cultivar groups based on former taxonomic classifications. We also found divergent heterozygosity values within genetic groups, with greater diversity in genetic groups with tetraploids (CCC_Group_B1: 0.37, and CCC_Group_B2: 0.53) than in diploid accessions (CCC_Group_A: 0.14). We subsequently generated one mini-core collection size of 3 percent (39 entries) and three further core collections sizes of 10, 15, and 20 percent (i.e., 129, 194, and 258 entries, respectively) from the total samples genotyped. As our results indicated that genetic diversity was similar across the sampled core collection sizes compared to the main collection, we selected the smallest core collection size of 10 percent. We expect this 10 percent core collection to be an optimal tool for discovering and evaluating functional diversity in the genebank to advance potato breeding and agricultural-related studies. This study also lays the foundations for continued CCC curation by evaluating duplicity and admixing between accessions, completing the digitalization of data, and ploidy determination using chloroplast count.

Comparative Analysis of the Genetic Diversity of Chilean Cultivated Potato Based on a Molecular Study of Authentic Herbarium Specimens and Present-Day Gene Bank Accessions

At the end of the 1920s, Vavilov organized several potato-collecting missions in South and Central America. Vavilov and his colleagues, Juzepczuk and Bukasov, participated in these expeditions and worked on gathered material, designated two centers of potato varietal riches and diversity-the Peru-Bolivia high-mountain center and the southern coast of Chile. The WIR Herbarium holds authentic specimens of many taxa described by Russian taxonomists. Here, a set of 20 plastid DNA-specific markers was applied for 49 authentic herbarium specimens of Solanum tuberosum L. from the WIR Herbarium to analyze the genetic diversity of the landrace population collected by Juzepczuk in 1928 in southern-central Chile. Two plastid DNA types, T and A, and two chlorotypes were identified in herbarium specimens, with a clear predominance (96%) of chlorotype cpT_III. In addition, we analyzed 46 living Chilean accessions from the VIR field potato gene bank that were collected after the appearance of Phytophthora infestans in Chile. These living accessions were differentiated into four chlorotypes. Finding a D-type cytoplasm in living Chilean accessions that possess two new chlorotypes indicates a replacement of native cultivars and introgression from the wild Mexican species S. demissum that was actively used in breeding as a source of race-specific resistance to late blight.

Understanding SUMO-mediated adaptive responses in plants to improve crop productivity

The response to abiotic and biotic stresses in plants and crops is considered a multifaceted process. Due to their sessile nature, plants have evolved unique mechanisms to ensure that developmental plasticity remains during their life cycle. Among these mechanisms, post-translational modifications (PTMs) are crucial components of adaptive responses in plants and transduce environmental stimuli into cellular signalling through the modulation of proteins. SUMOylation is an emerging PTM that has received recent attention due to its dynamic role in protein modification and has quickly been considered a significant component of adaptive mechanisms in plants during stress with great potential for agricultural improvement programs. In the present review, we outline the concept that small ubiquitin-like modifier (SUMO)-mediated response in plants and crops to abiotic and biotic stresses is a multifaceted process with each component of the SUMO cycle facilitating tolerance to several different environmental stresses. We also highlight the clear increase in SUMO genes in crops when compared with Arabidopsis thaliana. The SUMO system is understudied in crops, given the importance of SUMO for stress responses, and for some SUMO genes, the apparent expansion provides new avenues to discover SUMO-conjugated targets that could regulate beneficial agronomical traits.

Distribution and Climatic Adaptation of Wild Tomato (Solanum lycopersicum L.) Populations in Mexico

Tomato (Solanum lycopersicum L.) is a vegetable with worldwide importance. Its wild or close related species are reservoirs of genes with potential use for the generation of varieties tolerant or resistant to specific biotic and abiotic factors. The objective was to determine the geographic distribution, ecological descriptors, and patterns of diversity and adaptation of 1296 accessions of native tomato from Mexico. An environmental information system was created with 21 climatic variables with a 1 km² spatial resolution. Using multivariate techniques (Principal Component Analysis, PCA; Cluster Analysis, CA) and Geographic Information Systems (GIS), the most relevant variables for accession distribution were identified, as well as the groups formed according to the environmental similarity among these. PCA determined that with the first three PCs (Principal Components), it is possible to explain 84.1% of the total variation. The most relevant information corresponded to seasonal variables of temperature and precipitation. CA revealed five statistically significant clusters. Ecological descriptors were determined and described by classifying accessions in Physiographic Provinces. Temperate climates were the most frequent among tomato accessions. Finally, the potential distribution was determined with the Maxent model with 10 replicates by cross-validation, identifying areas with a high probability of tomato presence. These results constitute a reliable source of useful information for planning accession sites collection and identifying accessions that are vulnerable or susceptible to conservation programs.

Edaphoclimatic Descriptors of Wild Tomato Species (Solanum Sect. Lycopersicon) and Closely Related Species (Solanum Sect. Juglandifolia and Sect. Lycopersicoides) in South America

Wild species related to cultivated tomato are essential genetic resources in breeding programs focused on food security to face future challenges. The ecogeographic analysis allows identifying the species adaptive ranges and most relevant environmental variables explaining their patterns of actual distribution. The objective of this research was to identify the diversity, ecological descriptors, and statistical relationship of 35 edaphoclimatic variables (20 climatic, 1 geographic and 14 edaphic variables) from 4,649 accessions of 12 wild tomato species and 4 closely related species classified in Solanum sect. Lycopersicon and clustered into four phylogenetic groups, namely “Lycopersicon group” (S. pimpinellifolium, S. cheesmaniae, and S. galapagense), “Arcanum group” (S. arcanum, S. chmielewskii, and S. neorickii), “Eriopersicon group” (S. habrochaites, S. huaylasense, S. corneliomulleri, S. peruvianum, and S. chilense), “Neolycopersicon group” (S. pennellii); and two phylogenetically related groups in Solanum sect. Juglandifolia (S. juglandifolium and S. ochranthum), and section Lycopersicoides (S. lycopersicoides and S. sitiens). The relationship between the climate and edaphic variables were determined by the canonical correlation analysis, reaching 89.2% of variation with the first three canonical correlations. The most significant climatic variables were related to humidity (annual evapotranspiration, annual precipitation, and precipitation of driest month) and physicochemical soil characteristics (bulk density, pH, and base saturation percentage). In all groups, ecological descriptors and diversity patterns were consistent with previous reports. Regarding edaphoclimatic diversity, 12 climate types and 17 soil units were identified among all species. This approach has promissory applications for biodiversity conservation and uses valuable genetic resources related to a leading crop.

Genomic regions associated with physiological, biochemical and yield-related responses under water deficit in diploid potato at the tuber initiation stage revealed by GWAS

Water deficit, which is increasing with climate change, is a serious threat to agricultural sustainability worldwide. Dissection of the genetic architecture of water deficit responses is highly desirable for developing water-deficit tolerant potato cultivars and enhancing the resilience of existing cultivars. This study examined genetic variation in response to water deficit in a panel of diploid potato and identified the QTL governing this trait via a genome-wide association study (GWAS). A panel of 104 diploid potato accessions were evaluated under both well-watered and water deficit treatments at tuber initiation stage. Drought stress index (DTI) was calculated to assess tolerance of the diploid potato genotypes to water deficit. The GWAS was conducted using a matrix of 47K single nucleotide polymorphisms (SNP), recently available for this population. We are reporting 38 QTL, seven for well-watered conditions, twenty-two for water deficit conditions and nine for DTI which explain between 12.6% and 44.1% of the phenotypic variance. A set of 6 QTL were found to be associated with more than one variable. Marker WDP-9.21 was found associated with tuber fresh weigh under WD and gene annotation analysis revealed co-localization with the Glucan/water dikinase (GWD) gene. Of the nine QTL detected from DTI on chromosomes 2,3,5,8,10 and 12, three candidate genes with a feasible role in water deficit response were identified. The findings of this study can be used in marker-assisted selection (MAS) for water- deficit tolerance breeding in potato.

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.

Genetic analysis of a potato (Solanum tuberosum L.) breeding collection for southern Colombia using Single Nucleotide Polymorphism (SNP) markers

Detailed knowledge on genetic parameters such as diversity, structure, and linkage disequilibrium (LD) and identification of duplicates in a germplasm bank and/or breeding collection are essential to conservation and breeding strategies in any crop. Therefore, the potato genetic breeding collection at the Universidad de Nariño in Colombia, which is made up of diploid and tetraploid genotypes in two of the more diverse genebanks in the world, was analyzed with 8303 single nucleotide polymorphisms (SNP) from SolCAP version 1. In total, 144 genotypes from this collection were analyzed identifying an 57.2% of the polymorphic markers that allowed establishing two and three subpopulations that differentiated the diploid genotypes from the tetraploids. These subpopulations had high levels of heterozygosity and linkage disequilibrium. The diversity levels were higher in the tetraploid genotypes, while the LD levels were higher in the diploid genotypes. For the tetraploids, the genotypes from Peru had greater diversity and lower linkage disequilibrium than those from Colombia, which had slightly lower diversity and higher degrees of LD. The genetic analysis identified, adjusted and/or selected diploid and tetraploid genotypes under the following characteristics: 1) errors in classification associated with the level of ploidy; 2) presence of duplicates; and 3) genotypes with broad genetic distances and potential use in controlled hybridization processes. These analyses suggested that the potato genetic breeding collection at the Universidad de Nariño has a genetic base with a potential use in breeding programs for this crop in the Department of Nariño, in southern Colombia.

Holocene land and sea-trade routes explain complex patterns of pre-Columbian crop dispersion

Pre-Columbian crop movement remains poorly understood, hampering a good interpretation of the domestication and diversification of Neotropical crops. To provide new insights into pre-Columbian crop movement, we applied spatial genetics to identify and compare dispersal routes of three American crops between Mesoamerica and the Andes, two important centres of pre-Columbian crop and cultural diversity. Our analysis included georeferenced simple-sequence repeats (SSR) marker datasets of 1852 genotypes of cherimoya (Annona cherimola Mill.), a perennial fruit crop that became underutilised in the Americas after the European conquest, 770 genotypes of maize (Zea mays L.) and 476 genotypes of common bean (Phaseolus vulgaris L.). Our findings show that humans brought cherimoya from Mesoamerica to present Peru through long-distance sea-trade routes across the Pacific Ocean at least 4700 yr bp, after more ancient dispersion of maize and other crops through the Mesoamerican isthmus over land and near-coastal waters. To our knowledge, this is the first evidence of pre-Columbian crop movement between Mesoamerica and the Andes across the Pacific Ocean providing new insights into pre-Columbian crop exchange in the Americas. We propose that cherimoya represents a wider group of perennial fruit crops dispersed by humans via sea-trade routes between Mesoamerica and the Andes across the Pacific Ocean.

Estimation of Potato Yield Using Satellite Data at a Municipal Level: A Machine Learning Approach

Crop growth modeling and yield forecasting are essential to improve food security policies worldwide. To estimate potato (Solanum tubersum L.) yield over Mexico at a municipal level, we used meteorological data provided by the ERA5 (ECMWF Re-Analysis) dataset developed by the Copernicus Climate Change Service, satellite imagery from the TERRA platform, and field information. Five different machine learning algorithms were used to build the models: random forest (rf), support vector machine linear (svmL), support vector machine polynomial (svmP), support vector machine radial (svmR), and general linear model (glm). The optimized models were tested using independent data (2017 and 2018) not used in the training and optimization phase (2004–2016). In terms of percent root mean squared error (%RMSE), the best results were obtained by the rf algorithm in the winter cycle using variables from the first three months of the cycle (R2 = 0.757 and %RMSE = 18.9). For the summer cycle, the best performing model was the svmP which used the first five months of the cycle as variables (R2 = 0.858 and %RMSE = 14.9). Our results indicated that adding predictor variables of the last two months before the harvest did not significantly improved model performances. These results demonstrate that our models can predict potato yield by analyzing the yield of the previous year, the general conditions of NDVI, meteorology, and information related to the irrigation system at a municipal level.

Genetic structure and diversity analysis of tall fescue populations by EST-SSR and ISSR markers

Tall fescue is a perennial cool-season grass with economic importance especially in temperate regions of the northern hemisphere. This study was done to assess the genetic diversity and population structure of 90 tall fescue populations and cultivars using ISSR and EST-SSR markers in order to categorize valuable populations for breeding programs and to construct the core collection of tall fescue collection in Iran. The 10 EST-SSR primer pairs amplified 92 alleles. The allele numbers varied from 4 to 13 alleles per locus with an average of 9.2 alleles, of which 84 (90.6%) were polymorphic with an average of 8.4 polymorphic bands per primer. The 39 ISSR primers totally produced 387 scorable bands, of which 335 (86.6%) were polymorphic with an average of 8.6 polymorphic bands per primer. The amplified markers by ISSR primers varied from 6 to 14 markers per primer with an average of 9.92 markers per primer. The 90 tall fescue populations using both EST-SSR and ISSR data were classified into two clusters by UPGMA method that was coincide with PCA and structure analysis results. The turf-type and forage-type populations were clearly separated. Based on the results, the Iranian populations provide a valuable and novel germplasm to employ in tall fescue varietal improvement programs for both forage and turf-type applications. This progression is an important step to introduce this collection for development of a core collection of tall fescue germplasm in Iran.

Novel organ-specific genetic factors for quantitative resistance to late blight in potato

Potato, Solanum tuberosum, is one of the major consumed food in the world, being the basis of the diet of millions of people. The main limiting and destructive disease of potato is late blight, caused by Phytophtora infestans. Here, we present a multi-environmental analysis of the response to P. infestans using an association panel of 150 accessions of S. tuberosum Group Phureja, evaluated in two localities in Colombia. Disease resistance data were merged with a genotyping matrix of 83,862 SNPs obtained by 2b-restriction site–associated DNA and Genotyping by sequencing approaches into a Genome-wide association study. We are reporting 16 organ-specific QTL conferring resistance to late blight. These QTL explain between 13.7% and 50.9% of the phenotypic variance. Six and ten QTL were detected for resistance response in leaves and stem, respectively. In silico analysis revealed 15 candidate genes for resistance to late blight. Four of them have no functional genome annotation, while eleven candidate genes code for diverse proteins, including a leucine-rich repeat kinase.

Novel organ-specific genetic factors for quantitative resistance to late blight in potato

Potato, Solanum tuberosum, is one of the major consumed food in the world, being the basis of the diet of millions of people. The main limiting and destructive disease of potato is late blight, caused by Phytophtora infestans. Here, we present a multi-environmental analysis of the response to P. infestans using an association panel of 150 accessions of S. tuberosum Group Phureja, evaluated in two localities in Colombia. Disease resistance data were merged with a genotyping matrix of 83,862 SNPs obtained by 2b-restriction site-associated DNA and Genotyping by sequencing approaches into a Genome-wide association study. We are reporting 16 organ-specific QTL conferring resistance to late blight. These QTL explain between 13.7% and 50.9% of the phenotypic variance. Six and ten QTL were detected for resistance response in leaves and stem, respectively. In silico analysis revealed 15 candidate genes for resistance to late blight. Four of them have no functional genome annotation, while eleven candidate genes code for diverse proteins, including a leucine-rich repeat kinase.

Application and development of genome editing technologies to the Solanaceae plants

Genome editing technology using artificial nucleases, including zinc finger nuclease (ZFN), transcription activator-like effector nuclease (TALEN), and clustered regulatory interspaced short palindromic repeats (CRISPR)-Cas9, can mutagenize the target sites of genes of interest. This technology has been successfully applied in several crops, including the Solanaceae plants, such as tomato, potato, tobacco, and petunia. Among the three nucleases, CRISPR-Cas9 is the best for breeding, crop improvement, and the functional analysis of genes of interest, because of its simplicity and high efficiency. Although the technology is useful for reverse genetics, its use in plants is limited due to a lack of regeneration protocols and sequence information. In this review, the present status of genome editing technology in Solanaceae plants is described, and techniques that may improve genome editing technologies are discussed.

Ecological niche modeling for a cultivated plant species: a case study on taro (Colocasia esculenta) in Hawaii

Under the threat of ongoing and projected climate change, communities in the Pacific Islands face challenges of adapting culture and lifestyle to accommodate a changing landscape. Few models can effectively predict how biocultural livelihoods might be impacted. Here, we examine how environmental and anthropogenic factors influence an ecological niche model (ENM) for the realized niche of cultivated taro (Colocasia esculenta) in Hawaii. We created and tuned two sets of ENMs: one using only environmental variables, and one using both environmental and cultural characteristics of Hawaii. These models were projected under two different Intergovernmental Panel on Climate Change (IPCC) Representative Concentration Pathways (RCPs) for 2070. Models were selected and evaluated using average omission rate and area under the receiver operating characteristic curve (AUC). We compared optimal model predictions by comparing the percentage of taro plots predicted present and measured ENM overlap using Schoener's D statistic. The model including only environmental variables consisted of 19 Worldclim bioclimatic variables, in addition to slope, altitude, distance to perennial streams, soil evaporation, and soil moisture. The optimal model with environmental variables plus anthropogenic features also included a road density variable (which we assumed as a proxy for urbanization) and a variable indicating agricultural lands of importance to the state of Hawaii. The model including anthropogenic features performed better than the environment-only model based on omission rate, AUC, and review of spatial projections. The two models also differed in spatial projections for taro under anticipated future climate change. Our results demonstrate how ENMs including anthropogenic features can predict which areas might be best suited to plant cultivated species in the future, and how these areas could change under various climate projections. These predictions might inform biocultural conservation priorities and initiatives. In addition, we discuss the incongruences that arise when traditional ENM theory is applied to species whose distribution has been significantly impacted by human intervention, particularly at a fine scale relevant to biocultural conservation initiatives.

Molecular and biochemical characterization of a potato collection with contrasting tuber carotenoid content

After wheat and rice, potato is the third most important staple food worldwide. A collection of ten tetraploid (Solanum tuberosum) and diploid (S. phureja and S. chacoense) genotypes with contrasting carotenoid content was subjected to molecular characterization with respect to candidate carotenoid loci and metabolic profiling using LC-HRMS. Irrespective of ploidy and taxonomy, tubers of these genotypes fell into three groups: yellow-fleshed, characterized by high levels of epoxy-xanthophylls and xanthophyll esters and by the presence of at least one copy of a dominant allele of the β-Carotene Hydroxylase 2 (CHY2) gene; white-fleshed, characterized by low carotenoid levels and by the presence of recessive chy2 alleles; and orange-fleshed, characterized by high levels of zeaxanthin but low levels of xanthophyll esters, and homozygosity for a Zeaxanthin Epoxidase (ZEP) recessive allele. Novel CHY2 and ZEP alleles were identified in the collection. Multivariate analysis identified several groups of co-regulated non-polar compounds, and resulted in the grouping of the genotypes according to flesh color, suggesting that extensive cross-talk exists between the carotenoid pathway and other metabolite pathways in tubers. Postharvest traits like tuber dormancy and weight loss during storage showed little correlation with tuber carotenoid content, with the exception of zeaxanthin and its esters. Other tuber metabolites, such as glucose, monogalactosyldiacyglycerol (a glycolipid), or suberin precursors, showed instead significant correlations with both traits.

Genetic diversity and association mapping in the Colombian Central Collection of Solanum tuberosum L. Andigenum group using SNPs markers

The potato (Solanum tuberosum L.) is the fourth most important crop food in the world and Colombia has one of the most important collections of potato germplasm in the world (the Colombian Central Collection-CCC). Little is known about its potential as a source of genetic diversity for molecular breeding programs. In this study, we analyzed 809 Andigenum group accessions from the CCC using 5968 SNPs to determine: 1) the genetic diversity and population structure of the Andigenum germplasm and 2) the usefulness of this collection to map qualitative traits across the potato genome. The genetic structure analysis based on principal components, cluster analyses, and Bayesian inference revealed that the CCC can be subdivided into two main groups associated with their ploidy level: Phureja (diploid) and Andigena (tetraploid). The Andigena population was more genetically diverse but less genetically substructured than the Phureja population (three vs. five subpopulations, respectively). The association mapping analysis of qualitative morphological data using 4666 SNPs showed 23 markers significantly associated with nine morphological traits. The present study showed that the CCC is a highly diverse germplasm collection genetically and phenotypically, useful to implement association mapping in order to identify genes related to traits of interest and to assist future potato genetic breeding programs.

Do floral and niche shifts favour the establishment and persistence of newly arisen polyploids? A case study in an Alpine primrose

BACKGROUND AND AIMS

Polyploidization plays a key role in plant evolution. Despite the generally accepted 'minority-cytotype exclusion' theory, the specific mechanisms leading to successful establishment and persistence of new polyploids remain controversial. The majority of newly formed polyploids do not become established, because they are less common, have fewer potential mates or may not be able to compete successfully with co-occurring progenitors at lower ploidy levels. Changes in floral traits and ecological niches have been proposed as important mechanisms to overcome this initial frequency-dependent disadvantage. The aim of this study was to determine whether dodecaploids of the heterostylous P. marginata differ from their hexaploid progenitors in P. marginata and P. allionii for selected floral traits and ecological preferences that might be involved in establishment and persistence, providing a possible explanation for the origin of polyploidized populations.

METHODS

Floral morphological traits and ecological niche preferences among dodecaploids and their hexaploid progenitors in P. marginata and P. allionii ,: all restricted to the south-western Alps, were quantified and compared KEY RESULTS: Differences in floral traits were detected between dodecaploids and their closest relatives, but such differences might be too weak to counter the strength of minority cytotype disadvantage and are unlikely to enable the coexistence of different cytotypes. Furthermore, the results suggest the preservation of full distyly and no transition to selfing in dodecaploids. Finally, dodecaploids occur almost exclusively in environments that are predicted to be suitable also for their closest hexaploid relatives.

CONCLUSIONS

In light of the results, P. marginata dodecaploids have probably been able to establish and persist by occupying geographical areas not yet filled by their closest relatives without significant evolution in their climatic and pollination niches. Dispersal limitation and minority-cytotype exclusion probably maintain their current range disjunct from those of its close relatives.

Late Archaic-Early Formative period microbotanical evidence for potato at Jiskairumoko in the Titicaca Basin of southern Peru

The data presented in this paper provide direct microbotanical evidence concerning the early use of potato (Solanum tuberosum) within its botanical locus of origin in the high south-central Andes. The data derive from Jiskairumoko, an early village site in the western Titicaca Basin dating to the Late Archaic to Early Formative periods (∼3,400 cal y BC to 1,600 cal y BC). Because the site reflects the transition to sedentism and food production, these data may relate to potato domestication and early cultivation. Of 141 starch microremains recovered from 14 groundstone tools from Jiskairumoko, 50 are identified as consistent with cultivated or domesticated potato, based on reference to published materials and a study of wild and cultivated potato starch morphology. Along with macro- and microbotanical evidence for chenopod consumption and grinding tool data reflecting intensive use of this technology throughout site occupation, the microbotanical data reported here suggest the intensive exploitation, if not cultivation, of plant resources at Jiskairumoko. Elucidating the details of the trajectory of potato domestication is necessary for an overall understanding of the development of highland Andean agriculture, as this crop is central to the autochthonous agricultural suite. A paucity of direct botanical evidence, however, has hindered research efforts. The results of the modern and archaeological starch analyses presented here underscore the utility of this method in addressing questions related to the timing, mode, and context of potato origins.

Outcrossing potential between 11 important genetically modified crops and the Chilean vascular flora

The potential impact of genetically modified (GM) crops on biodiversity is one of the main concerns in an environmental risk assessment (ERA). The likelihood of outcrossing and pollen-mediated gene flow from GM crops and non-GM crops are explained by the same principles and depend primarily on the biology of the species. We conducted a national-scale study of the likelihood of outcrossing between 11 GM crops and vascular plants in Chile by use of a systematized database that included cultivated, introduced and native plant species in Chile. The database included geographical distributions and key biological and agronomical characteristics for 3505 introduced, 4993 native and 257 cultivated (of which 11 were native and 246 were introduced) plant species. Out of the considered GM crops (cotton, soya bean, maize, grape, wheat, rice, sugar beet, alfalfa, canola, tomato and potato), only potato and tomato presented native relatives (66 species total). Introduced relative species showed that three GM groups were formed having: a) up to one introduced relative (cotton and soya bean), b) up to two (rice, grape, maize and wheat) and c) from two to seven (sugar beet, alfalfa, canola, tomato and potato). In particular, GM crops presenting introduced noncultivated relative species were canola (1 relative species), alfalfa (up to 4), rice (1), tomato (up to 2) and potato (up to 2). The outcrossing potential between species [OP; scaled from 'very low' (1) to 'very high' (5)] was developed, showing medium OPs (3) for GM-native relative interactions when they occurred, low (2) for GMs and introduced noncultivated and high (4) for the grape-Vitis vinifera GM-introduced cultivated interaction. This analytical tool might be useful for future ERA for unconfined GM crop release in Chile.

Diversity of potato genetic resources

A considerable number of highly diverse species exist in genus Solanum. Because they can adapt to a broad range of habitats, potato wild relatives are promising sources of desirable agricultural traits. Potato taxonomy is quite complex because of introgression, interspecific hybridization, auto- and allopolyploidy, sexual compatibility among many species, a mixture of sexual and asexual reproduction, possible recent species divergence, phenotypic plasticity, and the consequent high morphological similarity among species. Recent researchers using molecular tools have contributed to the identification of genes controlling several types of resistance as well as to the revision of taxonomical relationships among potato species. Historically, primitive forms of cultivated potato and its wild relatives have been used in breeding programs and there is still an enormous and unimaginable potential for discovering desirable characteristics, particularly in wild species Different methods have been developed to incorporate useful alleles from these wild species into the improved cultivars. Potato germplasm comprising of useful alleles for different breeding objectives is preserved in various gene banks worldwide. These materials, with their invaluable information, are accessible for research and breeding purposes. Precise identification of species base on the new taxonomy is essential for effective use of the germplasm collection.

A genetic approach to the species problem in wild potato

Wild potatoes are native to the Americas, where they present very wide geographical and ecological distribution. Most are diploid, obligate out-crossers due to a multiallelic gametophytic self-incompatibility (S) locus that prevents self-fertilisation and crossing between individuals carrying identical S-alleles. They have two alternative modes of reproduction: sexual (by seeds) and asexual (by stolons and tubers), which provide, respectively, for genetic flexibility in changing environments and high fitness of adapted genotypes under stable conditions. Since the early twentieth century, their taxonomic classification has been mostly based on morphological phenotypes (Taxonomic Species Concept). More recently, attempts have been made to establish phylogenetic relationships, applying molecular tools in samples of populations (accessions) with a previously assigned specific category. However, neither the reproductive biology and breeding relations among spontaneous populations nor the morphological and genetic variability expected in obligate allogamous populations are considered when the taxonomic species concept is applied. In nature, wild potato populations are isolated through external and internal hybridisation barriers; the latter, which are genetically determined, can be either pre-zygotic (pollen-pistil incompatibility) or post-zygotic (abortion of embryo, endosperm or both tissues, sterility, and hybrid weakness and breakdown in segregating generations). The internal barriers, however, can be incomplete, providing opportunities for hybridisation and introgression within and between populations and ploidy levels in areas of overlap. The widespread occurrence of spontaneous hybrids in nature was recognised in the mid-twentieth century. Using genetic approaches, results have been obtained that provide strong support to the assertion that populations are at different stages of genetic divergence and are not at the end of the evolutionary process, as presupposed by the Taxonomic Species Concept. Furthermore, since wild potatoes have uniparental and biparental overlapping generations, the Biological Species Concept - developed for sexually reproducing biparental organisms - cannot be applied to them. In this paper, morphological, genetic, molecular and taxonomic studies in wild potato are reviewed, considering the genetic consequences of their reproductive biology, in an attempt to shed light on the species problem, because of its relevance in germplasm conservation and breeding.