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Summary: Kiwifruit (Actinidia spp) is a woody, perennial and deciduous vine. In this genus, there are multiple ploidy levels but the main cultivated cultivars are polyploid. Despite the availability of many genomic resources in kiwifruit, SNP genotyping is still a challenge given these different levels of polyploidy. Recent advances in SNP array technologies have offered a high‐throughput genotyping platform for genome‐wide DNA polymorphisms. In this study, we developed a high‐density SNP genotyping array to facilitate genetic studies and breeding applications in kiwifruit. SNP discovery was performed by genome‐wide DNA sequencing of 40 kiwifruit genotypes. The identified SNPs were stringently filtered for sequence quality, predicted conversion performance and distribution over the available Actinidia chinensis genome. A total of 134 729 unique SNPs were put on the array. The array was evaluated by genotyping 400 kiwifruit individuals. We performed a multidimensional scaling analysis to assess the diversity of kiwifruit germplasm, showing that the array was effective to distinguish kiwifruit accessions. Using a tetraploid F1 population, we constructed an integrated linkage map covering 3060.9 cM across 29 linkage groups and performed QTL analysis for the sex locus that has been identified on Linkage Group 3 (LG3) in Actinidia arguta. Finally, our dataset presented evidence of tetrasomic inheritance with partial preferential pairing in A. arguta. In conclusion, we developed and evaluated a 135K SNP genotyping array for kiwifruit. It has the advantage of a comprehensive design that can be an effective tool in genetic studies and breeding applications in this high‐value crop. [ABSTRACT FROM AUTHOR]

Potato (Solatium tuberosum L.) originates from the Andes and evolved short-day-dependent tuber formation as a vegetative propagation strategy. Here we describe the identification of a central regulator underlying a major-effect quantitative trait locus for plant maturity and initiation of tuber development. We show that this gene belongs to the family of DOF (DNA-binding with one finger) transcription factors (1) and regulates tuberization and plant life cycle length, by acting as a mediator between the circadian clock and the StSP6A mobile tuberization signal (2). We also show that natural allelic variants evade post-translational light regulation, allowing cultivation outside the geographical centre of origin of potato. Potato is a member of the Solanaceae family and is one of the world's most important food crops. This annual plant originates from the Andean regions of South America (3). Potato develops tubers from underground stems called stolons. Its equatorial origin makes potato essentially short-day dependent for tuberization and potato will not make tubers in the long-day conditions of spring and summer in the northern latitudes. When introduced in temperate zones, wild material will form tubers in the course of the autumnal shortening of day-length. Thus, one of the first selected traits in potato leading to a European potato type (4) is likely to have been long-day acclimation for tuberization. Potato breeders can exploit the naturally occurring variation in tuberization onset and life cycle length, allowing varietal breeding for different latitudes, harvest times and markets., The timing of reproductive development is determined by environmental cues (5). In Arabidopsis thaliana, flowering is initiated by the expression and transport of a peptide hormone or 'florigen' called FLOWERING [...]

A Brassica rapa collection of 239 accessions, based on two core collections representing different morphotypes from different geographical origins, is presented and its use for association mapping is illustrated for flowering time. We analyzed phenotypic variation of leaf and seed pod traits, plant architecture, and flowering time using data collected from three field experiments and evaluated the genetic diversity with a set of SSR markers. The Wageningen University and Research Centre (WUR) and the Vavilov Research Institute of Plant Industry (VIR) core collections had similar representations of most morphotypes, as illustrated by the phenotypic and genetic variation within these groups. The analysis of population structure revealed five subgroups in the collection, whereas previous studies of the WUR core collection indicated four subgroups; the fifth group identified consisted mainly of oil accessions from the VIR core collection, winter oils from Pakistan, and a number of other types. A very small group of summer oils is described, that is not related to other oil accessions. A candidate gene approach was chosen for association mapping of flowering time with a BrFLC1 biallelic CAPS marker and a BrFLC2 multiallelic SSR marker. The two markers were significantly associated with flowering time, but their effects were confined to certain morphotypes and (or) alleles. Based on these results, we discuss the optimal design for an association mapping population and the need to fix the heterogeneous accessions to facilitate phenotyping and genotyping. Key words: Brassica rapa, morphotypes, structure, alleles, association mapping, doubled haploids. Une collection de 239 accessions du Brassica rapa composee de deux collections nuckeaires representant les differents types morphologiques de diverses origines geographiques est deecrite et son utilisation en analyse d'association est illustree avec la date de floraison. Les auteurs ont analyse; la variation pheenotypique pour des caracteres de la feuille et de la silique, la forme de la plante et la date de floraison en utilisant les donneees recueillies lors de trois experiences au champ et evaluee la diversite genetique avec un jeu de marqueurs SSR. Les collections nuckeaires de Wageningen (WUR) et de Vavilov (VIR) comptaient des nombres comparables de la plupart des types morphologiques, tel qu'illustre par la variation pheenotypique et genetique au sein de ces groupes. L'analyse de la structure de la population a reveke l'existence de cinq sous-groupes au sein de la collection, tandis que les etudes anterieures de la collection WUR avaient suggere la presencedequatresous-groupes. Lecinquieme groupe identifie etait compose principalement d'accessions oleagineuses de la collection VIR, d'oleagineux d'automne du Pakistan et de quelques autres types. Un tres petit groupe d'oleagineux de printemps, sans lien avec les autres accessions d'oleagineux, est deecrit. Une approche faisant appel a des genes candidats a ete choisie pour l'analyse d'association avec la date de floraison. Un marqueur CAPS biallelique pour le gene BrFLC1 et un marqueur SSR multiallelique pour le gene BrFLC2 ont ete employes. Les deux marqueurs etaient significativement assockesa la date de floraison, mais leurs effets etaient limitesa certains types morphologiques ou alleles. Surla basedeces resultats, les auteurs discutent de la composition optimale d'une population pour l'analyse d'association et de la necessite de fixer les accessions heterogenes pour faciliter le phenotypage et le geenotypage. Mots-cles : Brassica rapa, types morphologiques, structure, alleles, analyse d'association, haploides doubles. [Traduit par la Redaction], Introduction The genus Brassica has a long history of world wide cultivation, and cultivated Brassica species comprises a large and diverse group of important vegetable, oil, fodder, and condiment crops. [...]

Chromosomal recombination maps were constructed for three genomes of lily (Lilium) using GISH analyses. For this purpose, the backcross (BC) progenies of two diploid (2n = 2x = 24) interspecific hybrids of lily, viz. Longiflorum x Asiatic (LA) and Oriental x Asiatic (OA), were used. Mostly the BC progenies of LA hybrids consisted of both triploid (2n = 3x = 36) and diploid (2n = 2x = 24) with some aneuploid genotypes and those of OA hybrids consisted of triploid (2n = 3x = 36) and some aneuploid genotypes. In all cases, it was possible to identify the homoeologous recombinant chromosomes as well as accurately count the number of crossover points, which are called 'recombination sites'. Recombination sites were estimated in the BC progeny of 71 LA and 41 OA genotypes. In the case of BC progenies of LA hybrids, 248 recombination sites were cytologically localized on 12 different chromosomes of each genome (i.e., L and A). Similarly, 116 recombinant sites were localized on the 12 chromosomes each from the BC progenies of OA hybrids (O and A genomes). Cytological maps were constructed on the basis of the percentages of distances (micrometres) of the recombination sites from the centromeres. Since an Asiatic parent was involved in both hybrids, viz. LA and OA, two maps were constructed for the A genome that were indicated as Asiatic (L) and Asiatic (O). The other two maps were Longiflorum (A) and Oriental (A). Remarkably, the recombination sites were highly unevenly distributed among the different chromosomes of all four maps. Because the recombination sites can be unequivocally identified through GISH, they serve as reliable landmarks and pave the way for assigning molecular markers or desirable genes to chromosomes of Lilium and also monitor introgression of alien segments. Key words: cytological maps, 2n gametes, genomic in situ hybridization (GISH), interspecific hybrids, Lilium, recombination sites. Des cartes de recombinaison chromosomique ont ete produites pour les trois genomes du lys (Lilium) au moyen d'analyses GISH. Pour y arriver, les progenitures retrocroisees (BC) de deux hybrides interspecifiques du lys (2n = 2x = 24), i.e. Longiflorum x Asiatic (LA) et Oriental x Asiatic (OA) ont ete employees. Pour la plupart les descendants BC des hybrides LA etaient triploides (2n = 3x = 36) ou diploides (2n = 2x = 24) en plus des quelques genotypes aneuploides alors que ceux des hybrides OA etaient triploides (2n = 3x = 36) avec quelques genotypes aneuploides. Dans tous les cas, il a ete possible d'identifier les chromosomes homeologues recombinants et de compter precisement le nombre d'enjambements, lesquels sont appeles des sites de recombinaison. Le nombre de sites de recombinaison a ete estime chez les progenitures BC des 71 genotypes LA et des 41 genotypes OA. En ce qui a trait aux progenitures BC des hybrides LA, 248 sites de recombinaison ont ete localises par examen cytologique sur les 12 chromosomes de chacun des genomes (L et A). De maniere semblable, 116 sites de recombinaison ont ete situes sur les 12 chromosomes de chaque genome (O et A) au sein des progenitures BC des hybrides OA. Des cartes cytologiques ont ete produites sur la base du pourcentage des distances (micrometres) separant les sites de recombinaison et les centromeres. Puisqu'un parent Asiatic etait implique dans les deux hybrides, LA et OA, deux cartes ont ete construites pour le genome A et celles-ci ont ete nommees Asiatic (L) et Asiatic (O). Les deux autres cartes ont ete nommees Longiflorum (A) et Oriental (A). Remarquablement, les sites de recombinaison etaient repartis tres inegalement sur les differents chromosomes sur les quatre cartes. Comme les sites de recombinaison sont identifiables sans equivoque par analyse GISH, ils peuvent servir de reperes et ouvrent la voie a l'assignation de marqueurs moleculaires ou de genes a des chromosomes chez le genre Lilium ainsi qu'au suivi de l'introgression de segments etrangers. Mots-cles : cartes cytologiques, gametes 2n, hybridation genomique in situ (GISH), hybrides interspecifiques, Lilium, sites de recombinaison., Introduction Cytological maps represent the location and order of markers along the chromosomes in relation to structures such as centromeres, telomeres, secondary constrictions (if any), and knobs among others. Such [...]

Ongoing genomics projects of tomato (Solanum lyropersicum) and potato (S. tuberosum) are providing unique tools for comparative mapping studies in Solanaceae. At the chromosomal level, bacterial artificial chromosomes (BACs) can be positioned on pachytene complements by fluorescence in situ hybridization (FISH) on homologous chromosomes of related species. Here we present results of such a cross-species multicolor cytogenetic mapping of tomato BACs on potato chromosomes 6 and vice versa. The experiments were performed under low hybridization stringency, while blocking with Cot-100 was essential in suppressing excessive hybridization of repeat signals in both within-species FISH and cross-species FISH of tomato BACs. In the short arm we detected a large paracentric inversion that covers the whole euchromatin part with breakpoints close to the telomeric heterochromatin and at the border of the short arm pericentromere. The long arm BACs revealed no deviation in the colinearity between tomato and potato. Further comparison between tomato cultivars Cherry VFNT and Heinz 1706 revealed colinearity of tile tested tomato BACs, whereas one of the six potato clones (RH98-856-18) showed minor putative rearrangements within the inversion. Our results present cross-species multicolor BAC-FISH as a unique tool for comparative genetic studies across Solanum species.

From biological and genetic standpoints, centromeres play an important role in the delivery of the chromosome complement to the daughter cells at cell division. The positions of the centromeres of potato were determined by half-tetrad analysis in a 4x-2x population where the male parent produced 2n pollen by first-division restitution (FDR). The genetic linkage groups and locations of 95 male parent-derived amplified fragment length polymorphism markers could be determined by comparing their position on a 2x-2x highly saturated linkage map of potato. Ten centromere positions were identified by 100% heterozygosity transmitted from the 2n heterozygous gametes of the paternal parent into the tetraploid offspring. The position of these centromeric marker loci was in accordance with those predicted by the saturated 2x-2x map using the level of marker clustering as a criterion. Two remaining centromere positions could be determined by extrapolation. The frequent observation of transmission of 100% heterozygosity proves that the meiotic restitution mechanism is exclusively based on FDR. Additional investigations on the position of recombination events of three chromosomes with sufficient numbers of markers showed that only one crossover occurred per chromosome arm, proving strong interference of recombination between centromere and telomere.

An ultradense genetic linkage map with > 10,000 AFLP loci was constructed from a heterozygous diploid potato population. To our knowledge, this is the densest meiotic recombination map ever constructed. A fast marker-ordering algorithm was used, based on the minimization of the total number of recombination events within a given marker order in combination with genotyping error-detection software. This resulted in 'skeleton bin maps,' which can be viewed as the most parsimonious marker order. The unit of distance is not expressed in centimorgans but in 'bins.' A bin is a position on the genetic map with a unique segregation pattern that is separated from adjacent bins by a single recombination event. Putative centromeres were identified by a strong clustering of markers, probably due to cold spots for recombination. Conversely, recombination hot spots resulted in large intervals of up to 15 cM without markers. The current level of marker saturation suggests that marker density is proportional to physical distance and independent of recombination frequency. Most chromatids (92%) recombined once or never, suggesting strong chiasma interference. Absolute chiasma interference within a chromosome arm could not be demonstrated. Two examples of contig construction and map-based cloning have demonstrated that the marker spacing was in accordance with the expected physical distance: approximately one marker per BAC length. Currently, the markers are used for genetic anchoring of a physical map of potato to deliver a sequence-ready minimal tiling path of BAC contigs of specific chromosomal regions for the potato genome sequencing consortium (http://www.potatogenome.net).