Exploring candidate genes and rhizosphere microbiome in relation to iron cycling in Andean potatoes
| dc.contributor.author | Xiao, Hua | en |
| dc.contributor.committeechair | Williams, Mark A. | en |
| dc.contributor.committeechair | Veilleux, Richard E. | en |
| dc.contributor.committeemember | Zhang, Chenming | en |
| dc.contributor.committeemember | Zhao, Bingyu | en |
| dc.contributor.committeemember | Vinatzer, Boris A. | en |
| dc.contributor.department | Horticulture | en |
| dc.date.accessioned | 2017-06-06T08:01:01Z | en |
| dc.date.available | 2017-06-06T08:01:01Z | en |
| dc.date.issued | 2017-06-05 | en |
| dc.description.abstract | Fe biofortification of potato is a promising strategy to prevent Fe deficiency worldwide either through traditional breeding or biotechnological approaches. These approaches require the identification of candidate genes to uptake, transport and store Fe in potato tubers. We employed multiple approaches including SNP genotyping, QTL analysis, identifying genes orthologous to Arabidopsis ferrome, yeast complementation assay and genetic transformation to avoid the limitation from a single approach. We revealed several candidate genes potentially associated with potato plant Fe acquisition, PGSC0003DMG400024976 (metal transporter), PGSC0003DMG400013297 (oligopeptide transporter), PGSC0003DMG400021155 (IRT1) and IRTunannotated (an ortholog to the IRT gene that is not annotated in the potato genome). The microorganisms in the rhizosphere react intensely with the various metabolites released by plant roots in a variety of ways such as positive, negative, and neutral. These interactions can influence the uptake and transport of micronutrients in the plant roots. Therefore, the contribution of soil microorganisms in the rhizosphere to improve Fe supply of plants may play a key role in Fe biofortification, especially under real world field-based soil scenarios. We thus investigated rhizosphere microbial community diversity in Andean potato landraces to understand the role of plant-microbial interaction in potato Fe nutrient cycling. From the analysis of the high-throughput Illumina sequences of 16S and ITS region of ribosomal RNA gene, we found that both potato landraces with low and high Fe content in tubers and a landrace on which low or high Fe content fertilizer was applied to the leaf surface had large impacts on the rhizosphere fungal community composition. Indicator species analysis (ISA) indicated that Operational Taxonomic Units (OTUs) contributing most to these impacts were closely related to Eurotiomycetes and Leotiomycetes in the phylum Ascomycota, Glomeromycetes in the phylum Glomeromycota and Microbotryomycetes in the phylum Basidiomycota. Lots of species from these groups have been shown to regulate plant mineral nutrient cycling. Our research revealed potential candidate genes and fungal taxa involved in the potato plant Fe nutrient dynamics, which provides new insights into crop management and breeding strategies for sustainable Fe fortification in agricultural production. | en |
| dc.description.abstractgeneral | Sustainably enriching Fe nutrition and its bioavailability in the potato is a promising strategy to prevent Fe deficiency worldwide either through traditional breeding or biotechnological approaches. All of these approaches require the identification of candidate genes to uptake, transport and store Fe in potato tubers. In this study, we coupled plant molecular methods with analysis of soil microbial community in the rhizosphere (the region of soil within immediate vicinity of plant roots, and a hotspot of this plant-microbial interplay) to uncover relationships among Fe nutritional status in potato, potato genotype and soil microbes. We identified a number of genes that likely control the amount of Fe content in potato using multiple approaches. After functional analysis in yeasts and potato plants, we revealed several elite candidate genes potentially associated with potato plant Fe acquisition, <i>PGSC0003DMG400024976</i> (Metal Transporter), <i>PGSC0003DMG400013297</i> (Oligopeptide Transporter), <i>PGSC0003DMG400021155</i> (Iron-Regulated Transporter 1, IRT1) and <i>IRTunannotated</i> (an ortholog to the <i>IRT</i> gene that is not annotated in the potato genome). The microorganisms in the rhizosphere react intensely with the various metabolites released by plant roots in a variety of ways such as positive, negative, and neutral. These interactions can influence the uptake and transport of micronutrients in the plant roots. Therefore, the contribution of soil microorganisms in the rhizosphere to improve Fe supply of plants may play a key role in enriching Fe nutrition, especially under real world field-based scenarios, e.g., high-pH and calcareous soils that occupy one third of agriculture lands limit the Fe bioavailability to crops. We investigated rhizosphere microbial community diversity in Andean potato landraces to understand the role of plant-microbial interaction in potato Fe nutrient cycling using high-throughput Illumina sequencing method. We found that both potato landraces with low and high Fe content in tubers and a landrace on which low or high Fe content fertilizer was applied to the leaf surface had large impacts on the rhizosphere fungal community composition. These impacts were closely related to <i>Eurotiomycetes</i> and <i>Leotiomycetes</i> in the phylum <i>Ascomycota, Glomeromycetes</i> in the phylum <i>Glomeromycota</i> and <i>Microbotryomycetes</i> in the phylum <i>Basidiomycota</i>. Lots of species from these groups have been shown to regulate plant mineral nutrient cycling. Our research revealed potential candidate genes and fungal taxa involved in the potato plant Fe nutrient dynamics, which provides new insights into crop management and breeding strategies for sustainable Fe improvement in agricultural production. | en |
| dc.description.degree | Ph. D. | en |
| dc.format.medium | ETD | en |
| dc.identifier.other | vt_gsexam:10811 | en |
| dc.identifier.uri | http://hdl.handle.net/10919/77917 | en |
| dc.publisher | Virginia Tech | en |
| dc.rights | In Copyright | en |
| dc.rights.uri | http://rightsstatements.org/vocab/InC/1.0/ | en |
| dc.subject | Solanum tuberosum | en |
| dc.subject | Andean potato | en |
| dc.subject | Iron deficiency | en |
| dc.subject | Fe fortification | en |
| dc.subject | Micronutrients | en |
| dc.subject | Candidate genes | en |
| dc.subject | Iron cycling | en |
| dc.subject | Rhizosphere | en |
| dc.subject | Microbes | en |
| dc.title | Exploring candidate genes and rhizosphere microbiome in relation to iron cycling in Andean potatoes | en |
| dc.type | Dissertation | en |
| thesis.degree.discipline | Horticulture | en |
| thesis.degree.grantor | Virginia Polytechnic Institute and State University | en |
| thesis.degree.level | doctoral | en |
| thesis.degree.name | Ph. D. | en |