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Maxime Bastien, Chiheb Boudhrioua, Gabrielle Fortin, François Belzile
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 (5,824 data points in diploid mode and 3,243 data points in tetraploid mode) and found the match rates between genotype calls was 90...
April 24, 2018: Genome Génome / Conseil National de Recherches Canada
Benjamin Stich, Delphine Van Inghelandt
Genomic prediction is a routine tool in breeding programs of most major animal and plant species. However, its usefulness for potato breeding has not yet been evaluated in detail. The objectives of this study were to (i) examine the prospects of genomic prediction of key performance traits in a diversity panel of tetraploid potato modeling additive, dominance, and epistatic effects, (ii) investigate the effects of size and make up of training set, number of test environments and molecular markers on prediction accuracy, and (iii) assess the effect of including markers from candidate genes on the prediction accuracy...
2018: Frontiers in Plant Science
Sapinder Bali, Bruce R Robinson, Vidyasagar Sathuvalli, John Bamberg, Aymeric Goyer
Micronutrient deficiency, also known as the hidden hunger, affects over two billion people worldwide. Potato is the third most consumed food crops in the world, and is therefore a fundamental element of food security for millions of people. Increasing the amount of micronutrients in food crop could help alleviate worldwide micronutrient malnutrition. In the present study, we report on the identification of single nucleotide polymorphism (SNP) markers associated with folate, an essential micronutrient in the human diet...
2018: PloS One
Molla F Mengist, Sheila Alves, Denis Griffin, Joanne Creedon, Mike J McLaughlin, Peter W Jones, Dan Milbourne
Cd is a toxic metal, whilst Zn is an essential for plant and human health. Both can accumulate in potato tubers. We examine the genetic control of this process. The aim of this study was to map quantitative trait loci (QTLs) influencing tuber concentrations of cadmium (Cd) and zinc (Zn). We developed a segregating population comprising 188 F1 progeny derived from crossing two tetraploid cultivars exhibiting divergent tuber-Cd-accumulation phenotypes. These progeny were genotyped using the SolCap 8303 SNP array, and evaluated for Cd, Zn, and maturity-related traits...
April 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
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
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
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
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
Bichseam Kim, Nahui Kim, Jun Young Kim, Byung Sup Kim, Hee-Jeong Jung, Indoek Hwang, Ill-Sup Noua, Sung-Chur Sim, Younghoon Park
Fusarium crown and root rot is a severe fungal disease of tomato caused by Fusarium oxysporum f. sp. radicis-lycopersici (FORL). In this study, the genomic location of the FORL-resistance locus was determined using a set of molecular markers on chromosome 9 and an F2 population derived from FORL-resistant inbred 'AV107-4' (Solanum lycopersicum) × susceptible 'L3708' (Solanum pimpinellifolium). Bioassay performed using Korean FORL strain KACC 40031 showed single dominant inheritance of FORL resistance in the F2 population...
March 2016: Genome Génome / Conseil National de Recherches Canada
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
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
M J Asins, V Raga, D Roca, A Belver, E A Carbonell
Rootstock HKT1 genotype affected fruit [Na(+)] and non-commercial fruit yield; QTL analysis of rootstock-mediated scion nutrition is a powerful forward genetic approach to identify wild genes for rootstock breeding. The present study approaches the QTL dissection of rootstock effects on a commercial hybrid variety grafted on a population of RILs derived from Solanum pimpinellifolium, genotyped for 4370 segregating SNPs from the SolCAP tomato panel and grown under moderate salinity. Results are compared to those previously obtained under high salinity...
April 2015: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
Valentino Ruggieri, Gianluca Francese, Adriana Sacco, Antonietta D'Alessandro, Maria Manuela Rigano, Mario Parisi, Marco Milone, Teodoro Cardi, Giuseppe Mennella, Amalia Barone
BACKGROUND: Genome Wide Association Studies (GWAS) have been recently used to dissect complex quantitative traits and identify candidate genes affecting phenotype variation of polygenic traits. In order to map loci controlling variation in tomato marketable and nutritional fruit traits, we used a collection of 96 cultivated genotypes, including Italian, Latin American, and other worldwide-spread landraces and varieties. Phenotyping was carried out by measuring ten quality traits and metabolites in red ripe fruits...
2014: BMC Plant Biology
Norma C Manrique-Carpintero, James G Tokuhisa, Idit Ginzberg, Jason A Holliday, Richard E Veilleux
Natural variation in five candidate genes of the steroidal glycoalkaloid (SGA) metabolic pathway and whole-genome single nucleotide polymorphism (SNP) genotyping were studied in six wild [Solanum chacoense (chc 80-1), S. commersonii, S. demissum, S. sparsipilum, S. spegazzinii, S. stoloniferum] and cultivated S. tuberosum Group Phureja (phu DH) potato species with contrasting levels of SGAs. Amplicons were sequenced for five candidate genes: 3-hydroxy-3-methylglutaryl coenzyme A reductase 1 and 2 (HMG1, HMG2) and 2...
September 4, 2013: G3: Genes—Genomes—Genetics
Marcela Víquez-Zamora, Ben Vosman, Henri van de Geest, Arnaud Bovy, Richard G F Visser, Richard Finkers, Adriaan W van Heusden
BACKGROUND: The major bottle neck in genetic and linkage studies in tomato has been the lack of a sufficient number of molecular markers. This has radically changed with the application of next generation sequencing and high throughput genotyping. A set of 6000 SNPs was identified and 5528 of them were used to evaluate tomato germplasm at the level of species, varieties and segregating populations. RESULTS: From the 5528 SNPs, 1980 originated from 454-sequencing, 3495 from Illumina Solexa sequencing and 53 were additional known markers...
2013: BMC Genomics
G R Rodríguez, H J Kim, E van der Knaap
Tomato fruit shape varies significantly in the cultivated germplasm. To a large extent, this variation can be explained by four genes including OVATE. While most varieties with the OVATE mutation bear elongated fruits, some accessions carry round fruit, suggesting the existence of suppressors of OVATE in the germplasm. We developed three intraspecific F2 populations with parents that carried the OVATE mutation but differed in fruit shape. We used a bulk segregant analysis approach and genotyped the extreme classes using a high-throughput genotyping platform, the SolCAP Infinium Assay...
September 2013: Heredity
Jose Blanca, Joaquín Cañizares, Laura Cordero, Laura Pascual, María José Diez, Fernando Nuez
Tomato, Solanum lycopersicum, is divided into two widely distributed varieties: the cultivated S. lycopersicum var. lycopersicum, and the weedy S. lycopersicum var. cerasiforme. Solanum pimpinellifolium is the most closely related wild species of tomato.The roles of S. pimpinellifolium and S. l. cerasiforme during the domestication of tomato are still under debate. Some authors consider S. l. cerasiforme to be the ancestor, whereas others think that S. l. cerasiforme is an admixture of S. pimpinellifolium and the cultivated S...
2012: PloS One
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