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Browsing by Author "Bonierbale, Merideth"

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    Construction of Reference Chromosome-Scale Pseudomolecules for Potato: Integrating the Potato Genome with Genetic and Physical Maps
    Sharma, Sanjeev Kumar; Bolser, Daniel; de Boer, Jan; Sonderkaer, Mads; Amoros, Walter; Carboni, Martin Federico; D'Ambrosio, Juan Martin; de la Cruz, German; Di Genova, Alex; Douches, David S.; Eguiluz, Maria; Guo, Xiao; Guzman, Frank; Hackett, Christine A.; Hamilton, John P.; Li, Guangcun; Li, Ying; Lozano, Roberto; Maass, Alejandro; Marshall, David; Martinez, Diana; McLean, Karen; Mejia, Nilo; Milne, Linda; Munive, Susan; Nagy, Istvan; Ponce, Olga; Ramirez, Manuel; Simon, Reinhard; Thomson, Susan J.; Torres, Yerisf; Waugh, Robbie; Zhang, Zhonghua; Huang, Sanwen; Visser, Richard G. F.; Bachem, Christian W. B.; Sagredo, Boris; Feingold, Sergio E.; Orjeda, Gisella; Veilleux, Richard E.; Bonierbale, Merideth; Jacobs, Jeanne M. E.; Milbourne, Dan; Martin, David Michael Alan; Bryan, Glenn J. (Genetics Society of America, 2013-11)
    The genome of potato, a major global food crop, was recently sequenced. The work presented here details the integration of the potato reference genome (DM) with a new sequence-tagged site marker-based linkage map and other physical and genetic maps of potato and the closely related species tomato. Primary anchoring of the DM genome assembly was accomplished by the use of a diploid segregating population, which was genotyped with several types of molecular genetic markers to construct a new similar to 936 cM linkage map comprising 2469 marker loci. In silico anchoring approaches used genetic and physical maps from the diploid potato genotype RH89-039-16 (RH) and tomato. This combined approach has allowed 951 superscaffolds to be ordered into pseudomolecules corresponding to the 12 potato chromosomes. These pseudomolecules represent 674 Mb (similar to 93%) of the 723 Mb genome assembly and 37,482 (similar to 96%) of the 39,031 predicted genes. The superscaffold order and orientation within the pseudomolecules are closely collinear with independently constructed high density linkage maps. Comparisons between marker distribution and physical location reveal regions of greater and lesser recombination, as well as regions exhibiting significant segregation distortion. The work presented here has led to a greatly improved ordering of the potato reference genome superscaffolds into chromosomal pseudomolecules.
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    Foliar application of Fe resonates to the belowground rhizosphere microbiome in Andean landrace potatoes
    Xiao, Hua; Rodrigues, Richard R.; Bonierbale, Merideth; Veilleux, Richard E.; Williams, Mark A. (2018-10)
    Iron (Fe) is a crucial nutrient for plant growth (e.g. chlorophyll production), and though it is one of the most abundant elements in soil, very low bioavailability can limit plant growth. Studies indicate that many soil bacteria and fungi (e.g. mycorrhizal) play a role in Fe nutrient cycling and plant production, but the evidence for fungal support of plant growth is overwhelmingly correlative and in need of experimental corroboration. An Andean native potato landrace was grown in a greenhouse under Fe limitation and using three levels (Low, Medium, High) of foliar fertilization (FeEDDHA). Application occurred at 45, 60 and 70 days of growth corresponding to periods where Fe limitation is expected to be greatest. The rhizosphere soils were sampled at the flowering stage (80 days). Soil bacterial and fungal communities were examined using high-throughput sequencing of 16S and ITS regions of ribosomal RNA gene, respectively, followed by analysis using Quantitative Insights Into Microbial Ecology (QIIME v1.8). Multivariate data analyses showed that Fe fertilization of leaves significantly (p < 0.05) influenced the beta diversity of fungi but not bacterial communities in the rhizosphere. Using our novel approach, it was expected and confirmed that fungal communities would shift and mycorrhizal genera (Glomus) would be altered, however, the degree to which community change was observed was more than expected. Glomeromycota (-16.3%) related to the family Gigasporaceae accounted for 2.8% of OTU and were 2-3 times greater in the rhizosphere of high relative to medium and low Fe conditions. Overall, the results indicate that foliar addition of Fe influences plant Fe and resonates into the root system to affect rhizosphere fungal communities. Potato Fe status thus appears to impact potato root-fungal interactions potentially mediated through mycorrhizal fungi.