keyword
MENU ▼
Read by QxMD icon Read
search

Tetraploid potatoes

keyword
https://www.readbyqxmd.com/read/28898255/molecular-and-biochemical-characterization-of-a-potato-collection-with-contrasting-tuber-carotenoid-content
#1
Maria Sulli, Giuseppe Mandolino, Monica Sturaro, Chiara Onofri, Gianfranco Diretto, Bruno Parisi, Giovanni Giuliano
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...
2017: PloS One
https://www.readbyqxmd.com/read/28869794/extensive-genome-heterogeneity-leads-to-preferential-allele-expression-and-copy-number-dependent-expression-in-cultivated-potato
#2
Gina M Pham, Linsey Newton, Krystle Wiegert-Rininger, Brieanne Vaillancourt, David S Douches, C Robin Buell
Relative to homozygous diploids, the presence of multiple homologs or homeologs in polyploids affords greater tolerance to mutations that can impact genome evolution. In this study, we describe sequence and structural variation in the genomes of six accessions of cultivated potato (Solanum tuberosum L.), a vegetatively propagated autotetraploid and their impact on the transcriptome. Sequence diversity was high with a mean single nucleotide polymorphisms (SNP) rate of approximately 1 per 50 bases suggestive of high levels of allelic diversity...
September 4, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28830357/physical-mapping-of-qtl-for-tuber-yield-starch-content-and-starch-yield-in-tetraploid-potato-solanum-tuberosum-l-by-means-of-genome-wide-genotyping-by-sequencing-and-the-8-3%C3%A2-k-solcap-snp-array
#3
Elske Maria Schönhals, Jia Ding, Enrique Ritter, Maria João Paulo, Nicolás Cara, Ekhard Tacke, Hans-Reinhard Hofferbert, Jens Lübeck, Josef Strahwald, Christiane Gebhardt
BACKGROUND: Tuber yield and starch content of the cultivated potato are complex traits of decisive importance for breeding improved varieties. Natural variation of tuber yield and starch content depends on the environment and on multiple, mostly unknown genetic factors. Dissection and molecular identification of the genes and their natural allelic variants controlling these complex traits will lead to the development of diagnostic DNA-based markers, by which precision and efficiency of selection can be increased (precision breeding)...
August 22, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28712501/gene-editing-in-polyploid-crops-wheat-camelina-canola-potato-cotton-peanut-sugar-cane-and-citrus
#4
Donald P Weeks
Polyploid crops make up a significant portion of the major food and fiber crops of the world and include wheat, potato, cotton, apple, peanut, citrus, and brassica oilseeds such as rape, canola, and Camelina. The presence of three sets of chromosomes in triploids, four sets in tetraploids, and six sets in hexaploids present significant challenges to conventional plant breeding and, potentially, to efficient use of rapidly emerging gene and genome-editing systems such as zinc finger nucleases, single-stranded oligonucleotides, TALE effector nucleases, and clustered regularly interspaced short palindromic repeats (CRISPR/Cas9)...
2017: Progress in Molecular Biology and Translational Science
https://www.readbyqxmd.com/read/28707250/genomic-prediction-of-starch-content-and-chipping-quality-in-tetraploid-potato-using-genotyping-by-sequencing
#5
Elsa Sverrisdóttir, Stephen Byrne, Ea Høegh Riis Sundmark, Heidi Øllegaard Johnsen, Hanne Grethe Kirk, Torben Asp, Luc Janss, Kåre L Nielsen
Genomic prediction models for starch content and chipping quality show promising results, suggesting that genomic selection is a feasible breeding strategy in tetraploid potato. Genomic selection uses genome-wide molecular markers to predict performance of individuals and allows selections in the absence of direct phenotyping. It is regarded as a useful tool to accelerate genetic gain in breeding programs, and is becoming increasingly viable for crops as genotyping costs continue to fall. In this study, we have generated genomic prediction models for starch content and chipping quality in tetraploid potato to facilitate varietal development...
October 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28674545/identification-of-novel-associations-of-candidate-genes-with-resistance-to-late-blight-in-solanum-tuberosum-group-phureja
#6
María F Álvarez, Myrian Angarita, María C Delgado, Celsa García, José Jiménez-Gomez, Christiane Gebhardt, Teresa Mosquera
The genetic basis of quantitative disease resistance has been studied in crops for several decades as an alternative to R gene mediated resistance. The most important disease in the potato crop is late blight, caused by the oomycete Phytophthora infestans. Quantitative disease resistance (QDR), as any other quantitative trait in plants, can be genetically mapped to understand the genetic architecture. Association mapping using DNA-based markers has been implemented in many crops to dissect quantitative traits...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28653150/linkage-map-construction-and-qtl-analysis-for-internal-heat-necrosis-in-autotetraploid-potato
#7
Mitchell J Schumann, Zhao-Bang Zeng, Mark E Clough, G Craig Yencho
A tetraploid potato population was mapped for internal heat necrosis (IHN) using the Infinium (®) 8303 potato SNP array, and QTL for IHN were identified on chromosomes 1, 5, 9 and 12 that explained 28.21% of the variation for incidence and 25.3% of the variation for severity. This research represents a significant step forward in our understanding of IHN, and sets the stage for future research focused on testing the utility of these markers in additional breeding populations. Internal heat necrosis (IHN) is a significant non-pathogenic disorder of potato tubers and previous studies have identified AFLP markers linked to IHN susceptibility in the tetraploid, B2721 potato mapping population...
October 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28279167/novel-snp-markers-in-invge-and-sssi-genes-are-associated-with-natural-variation-of-sugar-contents-and-frying-color-in-solanum-tuberosum-group-phureja
#8
Diana Duarte-Delgado, Deissy Juyó, Christiane Gebhardt, Felipe Sarmiento, Teresa Mosquera-Vásquez
BACKGROUND: Potato frying color is an agronomic trait influenced by the sugar content of tubers. The candidate gene approach was employed to elucidate the molecular basis of this trait in Solanum tuberosum Group Phureja, which is mainly diploid and represents an important genetic resource for potato breeding. The objective of this research was to identify novel genetic variants related with frying quality in loci with key functions in carbohydrate metabolism, with the purpose of discovering genetic variability useful in breeding programs...
March 9, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28257509/genetic-diversity-and-association-mapping-in-the-colombian-central-collection-of-solanum-tuberosum-l-andigenum-group-using-snps-markers
#9
Jhon Berdugo-Cely, Raúl Iván Valbuena, Erika Sánchez-Betancourt, Luz Stella Barrero, Roxana Yockteng
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...
2017: PloS One
https://www.readbyqxmd.com/read/28070610/automated-tetraploid-genotype-calling-by-hierarchical-clustering
#10
Cari A Schmitz Carley, Joseph J Coombs, David S Douches, Paul C Bethke, Jiwan P Palta, Richard G Novy, Jeffrey B Endelman
New software to make tetraploid genotype calls from SNP array data was developed, which uses hierarchical clustering and multiple F1 populations to calibrate the relationship between signal intensity and allele dosage. SNP arrays are transforming breeding and genetics research for autotetraploids. To fully utilize these arrays, the relationship between signal intensity and allele dosage must be calibrated for each marker. We developed an improved computational method to automate this process, which is provided as the R package ClusterCall...
April 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28065918/exploiting-next-generation-sequencing-to-solve-the-haplotyping-puzzle-in-polyploids-a-simulation-study
#11
Ehsan Motazedi, Richard Finkers, Chris Maliepaard, Dick de Ridder
Haplotypes are the units of inheritance in an organism, and many genetic analyses depend on their precise determination. Methods for haplotyping single individuals use the phasing information available in next-generation sequencing reads, by matching overlapping single-nucleotide polymorphisms while penalizing post hoc nucleotide corrections made. Haplotyping diploids is relatively easy, but the complexity of the problem increases drastically for polyploid genomes, which are found in both model organisms and in economically relevant plant and animal species...
January 8, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/27898814/software-for-genome-wide-association-studies-in-autopolyploids-and-its-application-to-potato
#12
Umesh R Rosyara, Walter S De Jong, David S Douches, Jeffrey B Endelman
Genome-wide association studies (GWAS) are widely used in diploid species to study complex traits in diversity and breeding populations, but GWAS software tailored to autopolyploids is lacking. The objectives of this research were to (i) develop an R package for autopolyploids based on the + mixed model, (ii) validate the software with simulated data, and (iii) analyze a diversity panel of tetraploid potatoes. A unique feature of the R package, called GWASpoly, is its ability to model different types of polyploid gene action, including additive, simplex dominant, and duplex dominant...
July 2016: Plant Genome
https://www.readbyqxmd.com/read/27872942/graphical-genotyping-as-a-method-to-map-ny-o-n-sto-and-gpa5-using-a-reference-panel-of-tetraploid-potato-cultivars
#13
Herman J van Eck, Peter G Vos, Jari P T Valkonen, Jan G A M L Uitdewilligen, Hellen Lensing, Nick de Vetten, Richard G F Visser
The method of graphical genotyping is applied to a panel of tetraploid potato cultivars to visualize haplotype sharing. The method allowed to map genes involved in virus and nematode resistance. The physical coordinates of the amount of linkage drag surrounding these genes are easily interpretable. Graphical genotyping is a visually attractive and easily interpretable method to represent genetic marker data. In this paper, the method is extended from diploids to a panel of tetraploid potato cultivars. Application of filters to select a subset of SNPs allows one to visualize haplotype sharing between individuals that also share a specific locus...
March 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/27699473/efficient-targeted-multiallelic-mutagenesis-in-tetraploid-potato-solanum-tuberosum-by-transient-crispr-cas9-expression-in-protoplasts
#14
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...
January 2017: Plant Cell Reports
https://www.readbyqxmd.com/read/27699464/evaluation-of-ld-decay-and-various-ld-decay-estimators-in-simulated-and-snp-array-data-of-tetraploid-potato
#15
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)...
January 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/27561740/integrating-haplotype-specific-linkage-maps-in-tetraploid-species-using-snp-markers
#16
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...
November 2016: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/27442536/development-and-validation-of-high-resolution-melting-markers-derived-from-rysto-sts-markers-for-high-throughput-marker-assisted-selection-of-potato-carrying-rysto
#17
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
https://www.readbyqxmd.com/read/27281327/targeted-and-untargeted-approaches-unravel-novel-candidate-genes-and-diagnostic-snps-for-quantitative-resistance-of-the-potato-solanum-tuberosum-l-to-phytophthora-infestans-causing-the-late-blight-disease
#18
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
https://www.readbyqxmd.com/read/26920758/probabilistic-multilocus-haplotype-reconstruction-in-outcrossing-tetraploids
#19
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
https://www.readbyqxmd.com/read/26657719/generation-and-inheritance-of-targeted-mutations-in-potato-solanum-tuberosum-l-using-the-crispr-cas-system
#20
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
keyword
keyword
42554
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"