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440 results for “Potato”
Data from: Equivalence analysis to support environmental safety assessment: using nontarget organism count data from field trials with cisgenically modified potato
This paper considers the statistical analysis of entomological count data from field experiments with genetically modified (GM) plants. Such trials are carried out to assess environmental safety. Potential effects on nontarget organisms (NTOs), as indicators of biodiversity, are investigated. The European Food Safety Authority (EFSA) gives broad guidance on the environmental risk assessment (ERA) of GM plants. Field experiments must contain suitable comparator crops as a benchmark for the assessment of designated endpoints. In this paper, a detailed protocol is proposed to perform data analysis for the purpose of assessing environmental safety. The protocol includes the specification of a list of endpoints and their hierarchical relations, the specification of intended levels of data analysis, and the specification of provisional limits of concern to decide on the need for further investigation. The protocol emphasizes a graphical representation of estimates and confidence intervals for the ratio of mean abundances for the GM plant and its comparator crop. Interpretation relies mainly on equivalence testing in which confidence intervals are compared with the limits of concern. The proposed methodology is illustrated with entomological count data resulting from multiyear, multilocation field trials. A cisgenically modified potato line (with enhanced resistance to late blight disease) was compared to the original conventional potato variety in the Netherlands and Ireland in two successive years (2013, 2014). It is shown that the protocol encompasses alternative schemes for safety assessment resulting from different research questions and/or expert choices. Graphical displays of equivalence testing at several hierarchical levels and their interpretation are presented for one of these schemes. The proposed approaches should be of help in the ERA of GM or other novel plants.
Data from: The coexistence of generalist and specialist clonal lineages in natural populations of the Irish Famine pathogen Phytophthora infestans explains local adaptation to potato and tomato
Phytophthora infestans, causing late blight on Solanaceae, is a serious threat to potato and tomato crops worldwide. P. infestans populations sampled on either potato or tomato differ in genotypes and pathogenicity, suggesting niche exclusion in the field. We hypothesized that such niche separation can reflect differential host exploitation by different P. infestans genotypes. We thus compared genotypes and phenotypes in 21 isolates sampled on potato (n = 11) or tomato (n = 10). Typing at 12 microsatellite loci assigned potato isolates to the 13_A2, 6_A1 and 1_A1 lineages, and tomato isolates to the 23_A1, 2_A1 and unclassified multi-locus genotypes. Cross-inoculations on potato and tomato leaflets showed that all isolates were pathogenic on both hosts. However: tomato isolates performed much better on tomato than did potato isolates, which performed better on potato than did tomato isolates, thus revealing a clear pattern of local adaptation. Potato isolates were significantly fitter on potato than on tomato, and are best described as potato-specialists; tomato isolates appear to be generalists, with similar pathogenicity on both hosts. Niche separation in the field may thus result mainly from the large fitness gap on tomato between generalists and unadapted potato-specialists, while the small, but significant fitness difference on potato between both types of isolates may prevent population invasion by generalists. Extreme specialization to potato seems very costly relative to performance loss on the alternative host. This study therefore shows that local adaptation and niche separation, commonly expected to involve and generate specialists, can occur with generalists.
Data from: The Solanum commersonii genome sequence provides insights into adaptation to stress conditions and genome evolution of wild potato relatives
Here, we report the draft genome sequence of Solanum commersonii, which consists of ∼830 megabases with an N50 of 44,303 bp anchored to 12 chromosomes, using the potato (Solanum tuberosum) genome sequence as a reference. Compared with potato, S. commersonii shows a striking reduction in heterozygosity (1.5% versus 53 to 59%), and differences in genome sizes were mainly due to variations in intergenic sequence length. Gene annotation by ab initio prediction supported by RNA-seq data produced a catalog of 1703 predicted microRNAs, 18,882 long noncoding RNAs of which 20% are shown to target cold-responsive genes, and 39,290 protein-coding genes with a significant repertoire of nonredundant nucleotide binding site-encoding genes and 126 cold-related genes that are lacking in S. tuberosum. Phylogenetic analyses indicate that domesticated potato and S. commersonii lineages diverged ∼2.3 million years ago. Three duplication periods corresponding to genome enrichment for particular gene families related to response to salt stress, water transport, growth, and defense response were discovered. The draft genome sequence of S. commersonii substantially increases our understanding of the domesticated germplasm, facilitating translation of acquired knowledge into advances in crop stability in light of global climate and environmental changes.
FIGURE 11 in A new species of Longitarsus (Coleoptera: Chrysomelidae) feeding on Chinese potato, Plectranthus rotundifolius (Lamiaceae) in southern India
FIGURE 11. Longitarsus serrulatus sp. nov. 11. spermatheca; 12. vaginal palpi; 13. tignum.
FIGURE 1 in A new species of Longitarsus (Coleoptera: Chrysomelidae) feeding on Chinese potato, Plectranthus rotundifolius (Lamiaceae) in southern India
FIGURE 1. Longitarsus serrulatus sp. nov., dorsal habitus
Data from: Investigating human repeatability of a computer vision based task to identify meristems on a potato plant (Solanum tuberosum)
<p>Labelled training data in artificial intelligence (AI) is used to teach so-called 'supervised learning models'. However, such data may contain error or bias, which can impact model prediction accuracy. Thus, obtaining accurate training data is of high importance. In applications of AI, such as in classification and detection problems, raw training data is not always made available in published research. Likewise, the process of obtaining labelled data is not always documented well enough to enable reproducibility. This training data set captures a repeatability exercise in AI training data collection for a task that is difficult for humans to perform, delineating a bounding box in a two-dimensional image of a growing apical meristem in potato plants.</p>
Phased, chromosome-scale genome assemblies of tetraploid potato reveals a complex genome, transcriptome, and predicted proteome landscape underpinning genetic diversity
<p>Hoopes G., Meng X., Hamilton J.P., Achakkagari S.R., de Alves Freitas Guesdes F., Bolger M.E., Coombs J.J., Esselink D., Kaiser N.R., Kodde L., Kyriakidou M., Lavrijssen B., van Lieshout N., Shereda R., Tuttle H.K., Vaillancourt B., Wood J.C., de Boer J.M., Bornowski N., Bourke P., Douches D., van Eck H.J., Ellis D., Feldman M.J., Gardner K.M., Hopman J.C.P., Jiang J., De Jong W.S., Kuhl J.C., Novy R.G., Oome S., Sathuvalli V., Tan E.H., Ursum R.A., Vales M.I., Vining K., Visser R.G.F., Vossen J., Yencho G.C., Anglin N.L., Bachem C.W.B., Endelman J.B., Shannon L.M., Strömvik M.V., Tai H.H., Usadel B., Buell C.R., and Finkers R. (2022). Phased, chromosome-scale genome assemblies of tetraploid potato reveals a complex genome, transcriptome, and predicted proteome landscape underpinning genetic diversity. Mol. Plant. doi: https://doi.org/10.1016/j.molp.2022.01.003.</p> <p>Cultivated potato is a clonally propagated autotetraploid species with a highly heterogeneous genome. Phased assemblies of six cultivars including two chromosome-scale phased genome assemblies revealed extensive allelic diversity including altered coding and transcript sequences, preferential allele expression, and structural variation that collectively result in a highly complex transcriptome and predicted proteome which are distributed across the homologous chromosomes. Wild species contribute to the extensive allelic diversity in tetraploid cultivars, demonstrating ancestral introgressions predating modern breeding efforts. As a clonally propagated autotetraploid that undergoes limited meiosis, dysfunctional and deleterious alleles are not purged in tetraploid potato. Nearly a quarter of the loci bore mutations predicted to have a high negative impact on protein function, complicating breeder's efforts to reduce genetic load. The <em>StCDF1</em> locus controls maturity and analysis of six tetraploid genomes revealed 12 allelic variants correlated with maturity in a dosage dependent manner. Knowledge of the complexity of the tetraploid potato genome with its rampant structural variation and embedded deleterious and dysfunctional alleles will be key not only to implementing precision breeding of tetraploid cultivars but also to the construction of homozygous, diploid potato germplasm containing favorable alleles to capitalize on heterosis in F1 hybrids.</p>
Figs. 3 A-E in Copper and zinc interactions: morphophysiological responses in sweet potato plants (Ipomoea batatas L.)
Figs. 3 A-E. Effects of treatments with different Cu and Zn concentrations on antioxidant metabolism in sweet potato plants (Ipomoea batatas L.). A. Superoxide dismutase (SOD); B. Ascorbate peroxidase (APX); C. Catalase (CAT); D. Lipid peroxidation (MDA); E. Hydrogen peroxide (H2O2) content. Means followed by the same lowercase letters, associated with either leaf or root tissues, do not differ significantly from one another based on Tukey's test (p <0.05).
Figs. 1 A-G in Copper and zinc interactions: morphophysiological responses in sweet potato plants (Ipomoea batatas L.)
Figs. 1 A-G. Effects treatments with Cu and Zn concentrations on morphological parameters of sweet potato plants (Ipomoea batatas L.). A. Shoot length (cm); B. Leaf number; C. Leaf area (cm2 plant-1); D. Shoot-fresh weight (mg); E. Shoot-dry weight (mg); F. Root-fresh weight (mg); G. Root-dry weight (mg). Means followed by the same letter among treatments do not differ significantly according to Tukey's test (p<0.05).
Fig. 2 in The effect of food source on survival and development of Lilioceris cheni (Coleoptera: Chrysomelidae), a biological control agent of air potato (Dioscoreales: Dioscoreaceae)
Fig. 2. Development time (mean ± SE) of Lilioceris cheni from 3rd instar to adult when reared on leaves or brown bulbils of air potato.
Figure 1 in Exploring the efficacy of RNAi-mediated gene knock-down via oral delivery of dsRNA in the Colorado potato beetle (Leptinotarsa decemlineata Say)
Figure 1.Phylogenetic relationship of the Vacuolar ATPase proteolipid subunits of several insect species. The phylogenetic tree was constructed using the neighbor-joining approach.
THE PROBLEM OF MECHANIZATION OF EARLY POTATO CULTIVATION
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Data from: Genome-wide inference of somatic translocation events during potato dihaploid production
Potato (Solanum tuberosum L.) breeders often use dihaploids, which are 2× progeny derived from 4× autotetraploid parents. Dihaploids can be used in diploid crosses to introduce new genetic material into breeding germplasm that can be integrated into tetraploid breeding through the use of unreduced gametes in 4× by 2× crosses. Dihaploid potatoes are usually produced via pollination by haploid inducer lines known as in vitro pollinators (IVP). In vitro pollinator chromosomes are selectively degraded from initially full hybrid embryos, resulting in 2× seed. During this process, somatic translocation of IVP DNA may occur. In this study, a genome-wide approach was used to identify such events and other chromosome-scale abnormalities in a population of 95 dihaploids derived from a cross between potato cultivar Superior and the haploid inducing line IVP101. Most Superior dihaploids showed translocation rates of <1% at 16,947,718 assayable sites, yet two dihaploids showed translocation rates of 1.86 and 1.60%. Allelic ratios at translocation sites suggested that most translocations occurred in individual cell lineages and were thus not present in all cells of the adult plants. Translocations were enriched in sites associated with high gene expression and H3K4 dimethylation and H4K5 acetylation, suggesting that they tend to occur in regions of open chromatin. The translocations likely result as a consequence of double-stranded break repair in the dihaploid genomes via homologous recombination during which IVP chromosomes are used as templates. Additionally, primary trisomy was observed in eight individuals. As the trisomic chromosomes were derived from Superior, meiotic nondisjunction may be common in potato.
Figure 4 from: Petrović-Obradović O (2013) Monitoring of aphid flight activities in seed potato crops in Serbia. ZooKeys 319: 333-346. https://doi.org/10.3897/zookeys.319.4315
Figure 4 - Dendrogram shows similarity between the sites, constructed on the basis of Morisita–Horn similarity index.
Figure 1 from: Petrović-Obradović O (2013) Monitoring of aphid flight activities in seed potato crops in Serbia. ZooKeys 319: 333-346. https://doi.org/10.3897/zookeys.319.4315
Figure 1 - Map of Serbia with monitored aphid flight activities sites. Coordinates of localities: Begeč 2007 (45°13'26"N, 19°36'53"E), Begeč 2008 (45°13'34"N, 19°37'23"E), Glumač 2008 (43°52'27"N, 20°1'1"E), Golija 1 2007 (43°27'45"N, 20°20'58"E), Golija 2 2007 (43°21'58"N, 20°32'12"E), Golija 1 2008 (43°26'25"N, 20°14'56"E), Golija 2 2008 (43°23'36"N, 20°24'53"E), Golija 1 2009 (43°24'6"N, 20°29'38"E), Golija 2 2009 (43°23'48"N, 20°18'31"E), Kotraža 2007 (43°42'7"N, 20°13'49"E), Kotraža 2008 (43°42'17"N, 20°13'34"E), Kotraža 2010 (43°41'49"N, 20°13'9"E), Kupusina 2008 (45°44'24"N, 19°0'6"E), Kupusina 2009 (45°43'49"N, 18°59'58"E), Stanišić 2008 (45°56'48"N, 19°10'51"E), Stanišić 2009 (45°57'7"N, 19°9'10"E), Stanišić 2010 (45°57'46"N, 19°11'6"E), Prijevor (43°54'49"N, 20°16'2"E), Zablaće 2 2009 (43°50'51"N, 20°26'51"E), Zablaće 1 2010 (43°50'27"N, 20°27'25"E).
Figure 2 from: Petrović-Obradović O (2013) Monitoring of aphid flight activities in seed potato crops in Serbia. ZooKeys 319: 333-346. https://doi.org/10.3897/zookeys.319.4315
Figure 2 - Maximum of Shannon–Weaver index per locality (number in brackets - number of weeks of monitoring aphid flight activities, number without brackets - week with maximum value of Shannon–Weaver index).
Impact of Consumption of Orange-fleshed Sweet Potatoes on the Vitamin A Status of Bangladeshi Women of Reproductive Age
ClinicalTrials.gov study NCT00453648. IPD Sharing: Not stated. Countries: 0. Publications: 1.
Consumption of Potatoes, Avocados and Chickpeas and Cognitive Function in Older Adults
ClinicalTrials.gov study NCT01620567. IPD Sharing: NO. Countries: 1. Publications: 0.
Effects of White Potato Consumption on Measures of Cardiometabolic Health in Individuals With Type 2 Diabetes Mellitus
ClinicalTrials.gov study NCT04511325. IPD Sharing: YES. Countries: 1. Publications: 0.
How a Mediterranean Diet With Potatoes Impacts Heart and Metabolic Health in Adults With Pre-Diabetes
ClinicalTrials.gov study NCT06817252. IPD Sharing: NO. Countries: 1. Publications: 0.
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