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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. [ABSTRACT FROM AUTHOR]

Genotyping-by-sequencing (GBS) potentially offers a cost-effective alternative for SNP discovery and genotyping. Here, we report the exploration of GBS in tetraploid potato. Both ApeKI and PstI/ MspI enzymes were used for library preparation on eight diverse potato genotypes. ApeKI yielded more markers than PstI/ MspI but provided a lower read coverage per marker, resulting in more missing data and limiting effective genotyping to the tetraploid mode. We then assessed the accuracy of these SNPs by comparison with SolCAP data (5824 data points in diploid mode and 3243 data points in tetraploid mode) and found the match rates between genotype calls was 90.4% and 81.3%, respectively. Imputation of missing data did not prove very accurate because of incomplete haplotype discovery, suggesting caution in setting the allowance for missing data. To further assess the quality of GBS-derived data, a genome-wide association analysis was performed for flower color on 318 clones (with ApeKI). A strong association signal on chromosome 2 was obtained with the most significant SNP located in the middle of the dihydroflavonol 4-reductase ( DFR) gene. We conclude that an appropriate choice of enzyme for GBS library preparation makes it possible to obtain high-quality SNPs in potato and will be helpful for marker-assisted genomics. [ABSTRACT FROM AUTHOR]

Genes involved in photoassimilate partitioning and changes in hormonal balance are important for potato tuberization. In the present study, we investigated gene expression patterns in the tuber-bearing potato somatic hybrid (E1-3) and control non-tuberous wild species Solanum etuberosum (Etb) by microarray. Plants were grown under controlled conditions and leaves were collected at eight tuber developmental stages for microarray analysis. A t-test analysis identified a total of 468 genes (94 up-regulated and 374 down-regulated) that were statistically significant ( p ≤ 0.05) and differentially expressed in E1-3 and Etb. Gene Ontology (GO) characterization of the 468 genes revealed that 145 were annotated and 323 were of unknown function. Further, these 145 genes were grouped based on GO biological processes followed by molecular function and (or) PGSC description into 15 gene sets, namely (1) transport, (2) metabolic process, (3) biological process, (4) photosynthesis, (5) oxidation-reduction, (6) transcription, (7) translation, (8) binding, (9) protein phosphorylation, (10) protein folding, (11) ubiquitin-dependent protein catabolic process, (12) RNA processing, (13) negative regulation of protein, (14) methylation, and (15) mitosis. RT-PCR analysis of 10 selected highly significant genes ( p ≤ 0.01) confirmed the microarray results. Overall, we show that candidate genes induced in leaves of E1-3 were implicated in tuberization processes such as transport, carbohydrate metabolism, phytohormones, and transcription/translation/binding functions. Hence, our results provide an insight into the candidate genes induced in leaf tissues during tuberization in E1-3. [ABSTRACT FROM AUTHOR]

MicroRNA (miRNA) mediated changes in gene expression by post-transcriptional modulation of major regulatory transcription factors is a potent mechanism for integrating growth and stress-related responses. Exotic plants including many traditional varieties of Andean potatoes ( Solanum tuberosum subsp. andigena) are known for better adaptation to marginal environments. Stress physiological studies confirmed earlier reports on the salinity tolerance potentials of certain andigena cultivars. Guided by the hypothesis that certain miRNAs play important roles in growth modulation under suboptimal conditions, we identified and characterized salinity stress-responsive miRNA-target gene pairs in the andigena cultivar Sullu by parallel analysis of noncoding and coding RNA transcriptomes. Inverse relationships were established by the reverse co-expression between two salinity stress-regulated miRNAs ( miR166, miR159) and their target transcriptional regulators HD-ZIP-Phabulosa/Phavulota and Myb101, respectively. Based on heterologous models in Arabidopsis, the miR166-HD-ZIP-Phabulosa/Phavulota network appears to be involved in modulating growth perhaps by mediating vegetative dormancy, with linkages to defense-related pathways. The miR159-Myb101 network may be important for the modulation of vegetative growth while also controlling stress-induced premature transition to reproductive phase. We postulate that the induction of miR166 and miR159 under salinity stress represents important network hubs for balancing gene expression required for basal growth adjustments. [ABSTRACT FROM AUTHOR]

Wild potato ( Solanum L. sect. Petota Dumort.) species contain diploids (2 n = 2 x = 24) to hexaploids (2 n = 6 x = 72). J.G. Hawkes classified all hexaploid Mexican species in series Demissa Bukasov and, according to a classic five-genome hypothesis of M. Matsubayashi in 1991, all members of series Demissa are allopolyploids. We investigated the genome composition of members of Hawkes's series Demissa with genomic in situ hybridization (GISH), using labeled DNA of their putative progenitors having diploid AA, BB, or PP genome species or with DNA of tetraploid species having AABB or AAAaAa genomes. GISH analyses support S. hougasii Correll as an allopolyploid with one AA component genome and another BB component genome. Our results also indicate that the third genome of S. hougasii is more closely related to P or a P genome-related species. Solanum demissum Lindl., in contrast, has all three chromosome sets related to the basic A genome, similar to the GISH results of polyploid species of series Acaulia Juz. Our results support a more recent taxonomic division of the Mexican hexaploid species into two groups: the allopolyploid Iopetala group containing S. hougasii, and an autopolyploid Acaulia group containing S. demissum with South American species S. acaule Bitter and S. albicans (Ochoa) Ochoa. [ABSTRACT FROM AUTHOR]

Potato chromosome 5 harbours numerous genes for important qualitative and quantitative traits, such as resistance to the root cyst nematode Globodera pallida and the late blight fungus, Phytophthora infestans. The genes make up part of a “hot spot” for resistances to various pathogens covering a genetic map length of 3 cM between markers GP21 and GP179. We established the physical size and position of this region on chromosome 5 in potato and tomato using fluorescence in situ hybridization (FISH) on pachytene chromosomes. Five potato bacterial artificial chromosome (BAC) clones with the genetically anchored markers GP21, R1-contig (proximal end), CosA, GP179, and StPto were selected, labeled with different fluorophores, and hybridized in a five-colour FISH experiment. Our results showed the location of the BAC clones in the middle of the long arm of chromosome 5 in both potato and tomato. Based on chromosome measurements, we estimate the physical size of the GP21-GP179 interval at 0.85 Mb and 1.2 Mb in potato and tomato, respectively. The GP21-GP179 interval is part of a genome segment known to have inverted map positions between potato and tomato. [ABSTRACT FROM AUTHOR]

The European cultivated potato, Solanum tuberosum subsp. tuberosum, has 6 related cultivated species and more than 200 wild relatives. In Solanum spp., studies of cytoplasmic organelles have been mainly confined to the plastid DNA composition of cultivated and wild species. In this study, 53 genotypes of 30 potato species belonging to the subsections Estolonifera and Potatoe, 2 tomato species, and a black nightshade genotype were examined using PCR markers to evaluate mitochondrial DNA diversity and assess whether mtDNA variability was correlated with series classification, geographical origin, ploidy, and endosperm balance number (EBN). The markers used revealed interspecific mtDNA variability in Solanum spp. and identified 13 different haplotypes. Intraspecific variability was also observed in a few species and genomic regions. Cluster analysis allowed arrangement of the 13 haplotypes into 7 subgroups, and statistical association tests showed significant relationships between mitochondrial patterns detected by molecular analysis and ploidy, EBN, and geographical origin. On the whole, the evolutionary patterns for the genomic regions analyzed reflected the species relationships established on the basis of morphological and molecular (nuclear and plastidial DNA) data. The mtDNA variability shown is also important for better characterization of genetic resources for potato breeding. La pomme de terre cultivée en Europe, Solanum tuberosum subsp. tuberosum, compte 6 espèces cultivées et plus de 200 espèces sauvages apparentées. Chez les Solanum spp., les études sur les organites cytoplasmiques ont principalement porté sur la composition de l’ADN plastidique chez les espèces cultivées et sauvages. Dans ce travail, 53 génotypes appartenant à 30 espèces des sous-sections Estolonifera et Potatoe, 2 espèces de tomates, et un génotype de morelle ont été examinées à l’aide de marqueurs PCR pour évaluer la diversité génétique de l’ADN mitochondrial et déterminer si la variabilité de l’ADNmt était corrélée avec leur classification, origine géographique, ploïdie et EBN. Les marqueurs employés ont révélé une variabilité mitochondriale interspécifique chez les Solanum spp. et ont permis d’identifier 13 haplotypes différents. De la variabilité intraspécifique a également été observée chez quelques espèces au sein de certaines régions génomiques. Des analyses de groupement ont permis de séparer les 13 haplotypes en 7 sous-groupes et des tests statistiques d’association ont montré des relations significatives entre les empreintes moléculaires des ADN mitochondriaux et les niveaux de ploïdie/EBN ou l’origine géographique. Globalement, l’évolution des régions génomiques analysées reflétait les relations entre espèces établies sur la base de données morphologiques et moléculaires (ADN nucléaire et plastidique). La variabilité observée au sein de l’ADNmt s’avère également importante pour mieux caractériser les ressources génétiques disponibles pour la sélection chez la pomme de terre. [ABSTRACT FROM AUTHOR]

Over 3500 accessions of Andean landraces have been known in potato, classified into 7 cultivated species ranging from 2x to 5x (Hawkes 1990). Chloroplast DNA (ctDNA), distinguished into T, W, C, S, and A types, showed extensive overlaps in their frequencies among cultivated species and between cultivated and putative ancestral wild species. In this study, 76 accessions of cultivated and 19 accessions of wild species were evaluated for ctDNA types and examined by ctDNA high-resolution markers (ctDNA microsatellites and H3 marker) and nuclear DNA restriction fragment length polymorphisms (RFLPs). ctDNA high-resolution markers identified 25 different ctDNA haplotypes. The S- and A-type ctDNAs were discriminated as unique haplotypes from 12 haplotypes having C-type ctDNA and T type ctDNA from 10 haplotypes having W-type ctDNA. Differences among ctDNA types were strongly correlated with those of ctDNA high-resolution markers (r = 0.822). Differentiation between W-type ctDNA and C-, S-, and A-type ctDNAs was supported by nDNA RFLPs in most species except for those of recent or immediate hybrid origin. However, differentiation among C-, S-, and A-type ctDNAs was not clearly supported by nDNA RFLPs, suggesting that frequent genetic exchange occurred among them and (or) they shared the same gene pool owing to common ancestry. [ABSTRACT FROM AUTHOR]

In this study, the use of inter-simple sequence repeats (ISSR) to assess genetic diversity between cultivated potatoes (Solanum tuberosum subsp. tuberosum) is reported. ISSR technology rapidly reveals high polymorphic fingerprints and thus determines the genetic diversity among potato cultivars. Nine primers were selected according to the number of amplified markers and the level of polymorphism detected. Three primers (GAG(CAA)[sub 5] , CTG(AG)[sub 8] , and (AG)[sub 8] ) were used to cluster the 28 potato accessions and 77 polymorphic markers were sufficient to identify all of the accessions. Among the 15 simple sequence repeat (SSR) motifs tested, the most abundant were CAA and AG. Argentinian- and European-grown potatoes were easily distinguished, with a higher level of genetic diversity among potatoes from Argentina. An ISSR study using a limited number of cultivars and very few primers clearly differentiated between all cultivars, thus ISSR was revealed to be a good tool for the genetic identification of potato and for future germplasm-management programs.Key words: Solanum tuberosum subsp. tuberosum, potato, ISSR, genetic diversity.L'emploi des ISSR est rapporté dans cet article en vue de déterminer la diversité génétique entre différents cultivars de pommes de terre (Solanum tuberosum subsp. tuberosum). La technique ISSR a rapidement permis de révéler des empreintes génétiques fortement polymorphes et d'étudier la diversité génétique chez cette espèce. Neuf amorces ont été sélectionnées selon le nombre de marqueurs amplifiés et le niveau de polymorphisme détecté. Seulement trois ont servi pour le regroupement des 28 cultivars étudiés. Les trois amorces (GAG(CAA)[sub 5] , CTG(AG)[sub 8] et (AG)[sub 8] ) ont permis d'obtenir 77 marqueurs polymorphes et ont suffi à l'identification de tous les cultivars. CAA et AG représentent les deux motifs SSR les plus abondants parmi les 15 testés. Les pommes de terre d'Argentine et d'Europe ont été facilement différenciées et une plus grande diversité génétique est observée parmi celles d'Argentine. L'analyse effectuée avec les marqueurs ISSR, sur un nombre limité de cultivars et avec un petit nombre d'amorces, permet cependant de différencier clairement tous les cultivars. Les ISSR se révèlent donc être de bons outils pour l'identification génétique des pommes de terre et pour de futurs programmes de gestion des ressources.Mots clés : Solanum tuberosum subsp. tuberosum, pomme de terre, ISSR, diversité génétique. [ABSTRACT FROM AUTHOR]

Clones with 24 or 25 chromosomes were obtained by pollinating an Andean cultivated tetraploid potato (Solanum tuberosum subsp. andigena clone 94H94, 2n = 4x = 48) with the Solanum phureja haploid-inducer clone 1.22. Their genetic composition was analyzed in an RAPD assay using 135 decamer primers and in an RFLP assay using 45 single-copy DNA probes. In total, 22 RAPD and 20 RFLP markers were found to be specific to S. phureja. None of these markers were found in the 24- and 25-chromosome clones. RFLP genotypes for the 45 RFLP loci were further determined for each clone. Genotypes of the 24-chromosome clones were characterized using two alleles randomly selected from four alleles of the parental tetraploid clone for almost all RFLP loci. Five 25-chromosome clones had extra alleles for all of the RFLP loci of chromosomes 4, 8, 10, 11, and 12, respectively, suggesting primary trisomy for one of these chromosomes. Clones with genotypes showing double reduction were also identified. Therefore, the obtained clones likely originated from random samples of female gametes, and hence are euhaploids or aneuhaploids of S. tuberosum subsp. andigena, strongly supporting parthenogenesis to be a primary mechanism for haploid induction in potato.Key words: Solanum tuberosum subsp. andigena, RFLP, RAPD, haploid, trisomic.Des clones à 24 ou 25 chromosomes ont été obtenus en fécondant une pomme de terre tétraploïde cultivée dans les Andes (Solanum tuberosum ssp. andigena clone 94H94, 2n = 4x = 48) avec le clone 1.22 inducteur d'haploïdie du S. phureja. Leur composition génétique a été analysée à l'aide de 135 amorces RAPD et à l'aide de 45 sondes RFLP à simple copie. Au total, 22 marqueurs RAPD et 20 marqueurs RFLP étaient spécifiques du S. phureja, mais aucun de ces marqueurs n'était présent chez les clones à 24 ou à 25 chromosomes. Les génotypes à 45 locus RFLP ont été examinés plus en détail chez chaque clone. Les génotypes des clones à 24 chromosomes étaient composés de deux allèles choisis aléatoirement parmi les quatre allèles du clone tétraploïde parental pour presque tous les locus RFLP. Cinq clones à 25 chromosomes possédaient des allèles additionnels pour tous les locus RFLP des chromosomes 4, 8, 10, 11 et 12, respectivement, suggérant ainsi une trisomie primaire pour l'un de ces chromosomes. Des clones dont les génotypes indiquaient une double réduction ont également été identifiés. Conséquemment, les clones obtenus provenaient vraisemblablement d'un échantillonnage aléatoire des gamètes femelles du S. tuberosum ssp. andigena, lesquels étaient ainsi euhaploïdes ou encore aneuhaploïdes. Ces observations supportent fortement l'hypothèse de la parthénogenèse comme mécanisme primaire pour l'induction haploïde chez la pomme de terre.Mots clés : Solanum tuberosum subsp. andigena, RFLP, RAPD, haploïde, trisomique.[Traduit par la Rédaction] [ABSTRACT FROM AUTHOR]

Genomic in situ hybridization (GISH) is one of the most popular and effective techniques for detecting alien chromatin introgressed into breeding lines; however, GISH analysis alone does not reveal the genetic identity of the alien chromosomes. We previously isolated a set of bacterial artificial chromosomes (BACs) specific to each of the 12 potato chromosomes. These BAC clones can be used as chromosome-specific cytogenetic DNA markers (CSCDMs) for potato chromosome identification. Here we demonstrate that GISH and fluorescence in situ hybridization (FISH), using CSCDMs, can be performed sequentially on the same chromosome preparations. Somatic metaphase chromosomes prepared using an enzymatic digestion and "flame-drying" procedure allows repeated probing up to five times without significant damage to chromosome morphology. The sequential GISH and FISH analyses reveal the genomic origin and genetic identity of the alien chromosomes in a single experiment and also determine whether an alien chromosome has been added to the genetic background of potato or is substituting for a homoeologous potato chromosome. The sequential GISH and FISH procedures should be widely applicable for germplasm characterization, especially in plant species with small-sized chromosomes.Key words: FISH, GISH, chromosome indentification, molecular cytogenetics, potato.L'hybridation génomique in situ (GISH) est l'une des techniques les plus populaires et les plus efficaces pour détecter la présence de chromatine étrangère dans des lignées d'amélioration. Cependant, l'analyse GISH à elle seule ne permet pas d'identifier l'origine génétique du segment étranger. Les auteurs ont précédemment isolé un ensemble de clones BAC (chromosomes bactériens artificiels) spécifiques de chacun des 12 chromosomes de la pomme de terre. Ces clones BAC peuvent servir de marqueurs cytogénétiques spécifiques de chaque chromosome (CSCDM, « chromosome-specific cytogenetic DNA marker ») en vue de l'identification chromosomique chez la pomme de terre. Dans le présent travail, les auteurs montrent que les techniques GISH et FISH (utilisant les CSCDM) peuvent être utilisées l'une à la suite de l'autre sur une même préparation chromosomique. Des chromosomes en métaphase somatique, préparés par digestion enzymatique et séchage à la flamme, ont pu être utilisés jusqu'à cinq fois sans altération à la morphologie des chromosomes. Les analyses GISH et FISH séquentielles révèlent l'origine génomique et l'identité génétique des segments étrangers en une seule expérience. Ces analyses permettent également de déterminer si un chromosome étranger s'est ajouté au bagage génétique de la pomme de terre ou s'il s'est substitué à un chromosome homéologue de la pomme de terre. Cette procédure d'analyses GISH et FISH séquentielles devrait être applicable largement dans le cadre de travaux de caractérisation des ressources génétiques et ce surtout chez les espèces végétales ayant de petits chromosomes.Mots clés : FIGH, GISH, indentification chromosomique, cytogénétique moléculaire, pomme de terre.[Traduit par la Rédaction] [ABSTRACT FROM AUTHOR]

A 4x potato (+) tomato fusion hybrid (2n = 4x = 48) was successfully backcrossed with a diploid Lycopersicon pennellii (2n = 2x = 24). Genomic in situ hybridization (GISH) on somatic and meiotic chromosomes confirmed that the progenies were triploids (2n = 3x = 36) and possessed three different genomes: potato, tomato, and L. pennellii. Therefore, they have been called trigenomic hybrids. Total genomic probes of both Lycopersicon species were found to hybridize mutually, whereas the potato genome was clearly differentiated. During metaphase I, bivalents were formed predominantly between tomato and L. pennellii chromosomes and the univalents of potato chromosomes were most common. Trivalents in all cases included homoeologous chromosomes of potato, tomato, and L. pennellii. However, the triploids were totally sterile as determined from extensive crossing. On chromosome doubling of triploids by shoot regeneration from callus, hexaploids (2n = 6x = 72) were obtained. Despite exhibiting clear allohexaploid behaviour by forming 36 bivalents at meiosis, these were also completely sterile like their triploid counterparts. In spite of this drawback, the prospects of chromosome pairing between potato L. pennellii and Solanum genomes does open the possibilities for bringing the two genera close.Key words: trigenomic triploids, GISH, bridge species, potato (+) tomato fusion hybrids.Un hybride de fusion 4x (2n = 4x = 48) pomme de terre (+) tomate a été rétrocroisé au Lycopersicon pennellii diploïde (2n = 2x = 24). Une analyse GISH sur les chromosomes somatiques et méiotiques a confirmé que les progénitures étaient triploïdes (2n = 3x = 36) et qu'elles possédaient trois génomes différents : celui de la pomme de terre, de la tomate et du L. pennellii. C'est pourquoi ces hybrides ont été appelés des hybrides trigénomiques. Des sondes d'ADN génomique total des deux espèces du genre Lycopersicon hybridaient mutuellement tandis que le génome de la pomme de terre se distinguait nettement. Lors de la métaphase I, des bivalents se sont formés de façon prédominante entre les chromosomes de la tomate et ceux du L. pennellii tandis que les chromosomes de la pomme de terre se présentaient habituellement sous forme d'univalents. Dans tous les cas de trivalents observés, ceux-ci impliquaient des chromosomes homéologues des trois espèces. Cependant les triploïdes ayant fait l'objet de cette étude étaient totalement stériles en dépit de très nombreuses tentatives de croisement. Suite au doublement chromosomique des triploïdes induit par la régénération de tiges à partir de cals, des hexaploïdes (2n = 6x = 72) ont été obtenus. Malgré le fait que ceux-ci montraient un comportement très clair d'allohexaploïdes (la formation de 36 bivalents à la méiose), ceux-ci étaient également complètement stériles tout comme les triploïdes dont ils sont dérivés. En dépit de cet obstacle, les perspectives d'appariement chromosomique entre les génomes de la pomme de terre, du L. pennellii et de la tomate ouvrent la voie au rapprochement des génomes des genres Solanum et Lycopersicon.Mots clés : triploïdes trigénomiques, GISH, espèce-pont, hybrides de fusion pomme de terre (+) tomate.[Traduit par la Rédaction] [ABSTRACT FROM AUTHOR]