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Tetraploid potatoes

Mariette Andersson, Helle Turesson, Alessandro Nicolia, Ann-Sofie Fält, Mathias Samuelsson, Per Hofvander
Altered starch quality with full knockout of GBSS gene function in potato was achieved using CRISPR-Cas9 technology, through transient transfection and regeneration from isolated protoplasts. Site-directed mutagenesis (SDM) has shown great progress in introducing precisely targeted mutations. Engineered CRISPR-Cas9 has received increased focus compared to other SDM techniques, since the method is easily adapted to different targets. Here, we demonstrate that transient application of CRISPR-Cas9-mediated genome editing in protoplasts of tetraploid potato (Solanum tuberosum) yielded mutations in all four alleles in a single transfection, in up to 2 % of regenerated lines...
October 3, 2016: Plant Cell Reports
Peter G Vos, M João Paulo, Roeland E Voorrips, Richard G F Visser, Herman J van Eck, Fred A van Eeuwijk
The number of SNPs required for QTL discovery is justified by the distance at which linkage disequilibrium has decayed. Simulations and real potato SNP data showed how to estimate and interpret LD decay. The magnitude of linkage disequilibrium (LD) and its decay with genetic distance determine the resolution of association mapping, and are useful for assessing the desired numbers of SNPs on arrays. To study LD and LD decay in tetraploid potato, we simulated autotetraploid genotypes and used it to explore the dependence on: (1) the number of haplotypes in the population (the amount of genetic variation) and (2) the percentage of haplotype specific SNPs (hs-SNPs)...
October 3, 2016: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
Peter M Bourke, Roeland E Voorrips, Twan Kranenburg, Johannes Jansen, Richard G F Visser, Chris Maliepaard
Linkage mapping can help unravel the complexities of polyploid genomes. Here, we integrate haplotype-specific linkage maps in autotetraploid potato and explore the possibilities for mapping in other polyploid species. High-density linkage mapping in autopolyploid species has become possible in recent years given the increasing number of molecular markers now available through modern genotyping platforms. Such maps along with larger experimental populations are needed before we can obtain sufficient accuracy to make marker-trait association studies useful in practice...
August 25, 2016: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
Xianzhou Nie, Darcy Sutherland, Virginia Dickison, Mathuresh Singh, Agnes M Murphy, David De Koeyer
Sequence analysis of the chromosome region harboring the sequence-tagged site (STS) markers YES3-3A and YES3-3B for Rysto, a gene responsible for extreme resistance to Potato virus Y (PVY) in potato, was performed in tetraploid potato 'Barbara' (Rrrr) and 'AC Chaleur' (rrrr) as well as their progeny selections. Three and two sequence variants were identified in Barbara resistant (R) selections and AC Chaleur susceptible (S) selections, respectively. Further analysis indicates that the variant with a 21-nucleotide (nt) deletion is likely the chromosome copy harboring the STS markers...
November 2016: Phytopathology
Teresa Mosquera, Maria Fernanda Alvarez, José M Jiménez-Gómez, Meki Shehabu Muktar, Maria João Paulo, Sebastian Steinemann, Jinquan Li, Astrid Draffehn, Andrea Hofmann, Jens Lübeck, Josef Strahwald, Eckhard Tacke, Hans-Reinhardt Hofferbert, Birgit Walkemeier, Christiane Gebhardt
The oomycete Phytophthora infestans causes late blight of potato, which can completely destroy the crop. Therefore, for the past 160 years, late blight has been the most important potato disease worldwide. The identification of cultivars with high and durable field resistance to P. infestans is an objective of most potato breeding programs. This type of resistance is polygenic and therefore quantitative. Its evaluation requires multi-year and location trials. Furthermore, quantitative resistance to late blight correlates with late plant maturity, a negative agricultural trait...
2016: PloS One
Chaozhi Zheng, Roeland E Voorrips, Johannes Jansen, Christine A Hackett, Julie Ho, Marco C A M Bink
For both plant (e.g., potato) and animal (e.g., salmon) species, unveiling the genetic architecture of complex traits is key to the genetic improvement of polyploids in agriculture. F1 progenies of a biparental cross are often used for quantitative trait loci (QTL) mapping in outcrossing polyploids, where haplotype reconstruction by identifying the parental origins of marker alleles is necessary. In this paper, we build a novel and integrated statistical framework for multilocus haplotype reconstruction in a full-sib tetraploid family from biallelic marker dosage data collected from single-nucleotide polymorphism (SNP) arrays or next-generation sequencing technology given a genetic linkage map...
May 2016: Genetics
Nathaniel M Butler, Paul A Atkins, Daniel F Voytas, David S Douches
Genome editing using sequence-specific nucleases (SSNs) offers an alternative approach to conventional genetic engineering and an opportunity to extend the benefits of genetic engineering in agriculture. Currently available SSN platforms, such as zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and CRISPR/Cas (clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated systems (Cas)) have been used in a range of plant species for targeted mutagenesis via non-homologous end joining (NHEJ) are just beginning to be explored in crops such as potato (Solanum tuberosum Group Tuberosum L...
2015: PloS One
Meki S Muktar, Jens Lübeck, Josef Strahwald, Christiane Gebhardt
Late blight of potato (Solanum tuberosum L.) caused by the oomycete Phytophthora infestans (Mont.) de Bary, is one of the most important bottlenecks of potato production worldwide. Cultivars with high levels of durable, race unspecific, quantitative resistance are part of a solution to this problem. However, breeding for quantitative resistance is hampered by the correlation between resistance and late plant maturity, which is an undesirable agricultural attribute. The objectives of our research are (i) the identification of genes that condition quantitative resistance to P...
2015: Frontiers in Genetics
Peter M Bourke, Roeland E Voorrips, Richard G F Visser, Chris Maliepaard
The creation of genetic linkage maps in polyploid species has been a long-standing problem for which various approaches have been proposed. In the case of autopolyploids, a commonly used simplification is that random bivalents form during meiosis. This leads to relatively straightforward estimation of recombination frequencies using maximum likelihood, from which a genetic map can be derived. However, autopolyploids such as tetraploid potato (Solanum tuberosum L.) may exhibit additional features, such as double reduction, not normally encountered in diploid or allopolyploid species...
November 2015: Genetics
Alicia N Massa, Norma C Manrique-Carpintero, Joseph J Coombs, Daniel G Zarka, Anne E Boone, William W Kirk, Christine A Hackett, Glenn J Bryan, David S Douches
The objective of this study was to construct a single nucleotide polymorphism (SNP)-based genetic map at the cultivated tetraploid level to locate quantitative trait loci (QTL) contributing to economically important traits in potato (Solanum tuberosum L.). The 156 F1 progeny and parents of a cross (MSL603) between "Jacqueline Lee" and "MSG227-2" were genotyped using the Infinium 8303 Potato Array. Furthermore, the progeny and parents were evaluated for foliar late blight reaction to isolates of the US-8 genotype of Phytophthora infestans (Mont...
November 2015: G3: Genes—Genomes—Genetics
Peter G Vos, Jan G A M L Uitdewilligen, Roeland E Voorrips, Richard G F Visser, Herman J van Eck
A 20K SNP array was developed and a comprehensive set of tetraploid cultivar was genotyped. This allowed us to identify footprints of the breeding history in contemporary breeding material such as identification of introgression segments, selection and founder signatures. A non-redundant subset of 15,138 previously identified SNPs and 4454 SNPs originating from the SolCAP project were combined into a 20k Infinium SNP array for genotyping a total of 569 potato genotypes. In this study we describe how this SNP array (encoded SolSTW array) was designed and analysed with fitTetra, software designed for autotetraploids...
December 2015: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
Yuhui Liu, Kui Lin-Wang, Cecilia Deng, Ben Warran, Li Wang, Bin Yu, Hongyu Yang, Jing Wang, Richard V Espley, Junlian Zhang, Di Wang, Andrew C Allan
INTRODUCTION: The potato (Solanum tuberosum) cultivar 'Xin Daping' is tetraploid with white skin and white flesh, while the cultivar 'Hei Meiren' is also tetraploid with purple skin and purple flesh. Comparative transcriptome analysis of white and purple cultivars was carried out using high-throughput RNA sequencing in order to further understand the mechanism of anthocyanin biosynthesis in potato. METHODS AND RESULTS: By aligning transcript reads to the recently published diploid potato genome and de novo assembly, 209 million paired-end Illumina RNA-seq reads from these tetraploid cultivars were assembled on to 60,930 transcripts, of which 27,754 (45...
2015: PloS One
Kazuo Watanabe
Potato has a variety of reproductive uniquenesses besides its clonal propagation by tubers. These traits are controlled by a different kind of genetic control. The reproductive information has been applied to enable interspecific hybridization to enhance valuable traits, such as disease and pest resistances, from the tuber-bearing Solanum gene pool. While progress has been made in potato breeding, many resources have been invested due to the requirements of large populations and long time frame. This is not only due to the general pitfalls in plant breeding, but also due to the complexity of polyploid genetics...
March 2015: Breeding Science
Jude Eijkeme Obidiegwu, Rena Sanetomo, Kerstin Flath, Eckhard Tacke, Hans-Reinhard Hofferbert, Andrea Hofmann, Birgit Walkemeier, Christiane Gebhardt
BACKGROUND: The soil borne, obligate biotrophic fungus Synchytrium endobioticum causes tumor-like tissue proliferation (wart) in potato tubers and thereby considerable crop damage. Chemical control is not effective and unfriendly to the environment. S. endobioticum is therefore a quarantined pathogen. The emergence of new pathotypes of the fungus aggravate this agricultural problem. The best control of wart disease is the cultivation of resistant varieties. Phenotypic screening for resistant cultivars is however time, labor and material intensive...
2015: BMC Genetics
Alessandro Nicolia, Estelle Proux-Wéra, Inger Åhman, Nawaporn Onkokesung, Mariette Andersson, Erik Andreasson, Li-Hua Zhu
Potato is the third largest food crop in the world, however, the high degree of heterozygosity, the tetrasomic inheritance and severe inbreeding depression are major difficulties for conventional potato breeding. The rapid development of modern breeding methods offers new possibilities to enhance breeding efficiency and precise improvement of desirable traits. New site-directed mutagenesis techniques that can directly edit the target genes without any integration of recombinant DNA are especially favorable...
June 20, 2015: Journal of Biotechnology
Iga Tomczyńska, Florian Jupe, Ingo Hein, Waldemar Marczewski, Jadwiga Sliwka
Potato virus Y (PVY, Potyvirus) is the fifth most important plant virus worldwide in terms of economic and scientific impact. It infects members of the family Solanaceae and causes losses in potato, tomato, tobacco, pepper and petunia production. In potato and its wild relatives, two types of resistance genes against PVY have been identified. While Ry genes confer symptomless extreme resistance, Ny genes cause a hypersensitive response visible as local necrosis that may also be able to prevent the virus from spreading under certain environmental conditions...
2014: Molecular Breeding: New Strategies in Plant Improvement
Jun Zhou, Hui Fang, Jianwei Shan, Xiaoxi Gao, Lin Chen, Conghua Xie, Tingting Xie, Jun Liu
The cultivated potato (Solanum tuberosum L.) is an autotetraploid species. The complexity of tetrasomic inheritance and the lack of pure lines increase the difficulty of genetic analysis of the inherited characteristics. Tuberization is the determinant step for economic yield of potato. To understand the complex genetic basis of tuberization of the cultivated potato, we developed linkage maps for a tetraploid population (F1) of 237 genotypes and mapped QTLs for the percent of in vitro tuberized plantlets (% IVT)...
August 2014: Molecular Genetics and Genomics: MGG
Rahim Ahmadvand, Péter Poczai, Ramin Hajianfar, Balázs Kolics, Ahmad Mousapour Gorji, Zsolt Polgár, János Taller
Intron-targeting (IT) markers were developed from next generation sequencing (NGS) derived transcript sequencing data from the potato cultivar White Lady. The applicability of the IT markers was analyzed in other potato genotypes, and their transferability was studied in other Solanum species: section Archaesolanum (5 species), sect. Solanum (6 species) and a Solanum nigrum population (11 genotypes). Out of 250 randomly chosen transcript sequences, 144 intron harboring loci could be identified for which primer pairs were designed on exons flanking the putative introns...
April 25, 2014: Gene
Niels O Frandsen
The average number of plastids in ten pairs of guard cells is a very useful aid for screening haploids among tetraploid plants fromS. tuberosum x S. phureja.In individual seedlings the stomatal plastid number decreases from the cotyledons to the first leaves. From the lower to the upper part of stems there exists a decreasing gradient for plastid number and an increasing gradient for the number of stomata per leaf area unit, whereas the stomatal length does not show a consistent trend.In the stomata, plastid number and stomatal length are positively correlated...
April 1968: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
D W Mok, S J Peloquin
The relative breeding value of first division restitution (FDR) and second division restitution (SDR) 2n male gametes from diploids, and n (2x) gametes from tetraploids were compared. This was done by measuring tuber yield of 105 4x families obtained from 4x x 2x (FDR), 4x x 2x (SDR), and 4x x 4x crosses at two locations. All tetraploid families obtained from 4x x 2x (FDR) matings exhibitedheterosis (the mean of the F1 exceeded that of the higher yielding parent), and outyielded other tetraploid families and 4x cultivars at both locations...
January 1975: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
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