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United States Department of Agriculture

Agricultural Research Service

Research Project: FUNCTIONAL GENOMICS FOR IMPROVING NUTRIENTS AND QUALITY IN ALFALFA AND SOYBEAN Title: An RNA-seq transcriptome analysis of orthophosphate-deficient white lupin reveals novel insights into phosphorus acclimation in plants

Authors
item O'Rourke, Jamie
item Yang, Suk
item Miller, Susan
item Bucciarelli, Bruna
item Liu, Junqi -
item Rydeen, Ariel -
item Uhde-Stone, Claudia -
item Tu, Zheng Jin -
item Allan, Deborah -
item Gronwald, John
item Vance, Carroll

Submitted to: Plant Physiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: November 21, 2012
Publication Date: November 29, 2012
Citation: O'Rourke, J.A., Yang, S.H., Miller, S.S., Bucciarelli, B., Liu, J., Rydeen, A., Uhde-Stone, C., Tu, Z., Allan, D., Gronwald, J.W., Vance, C.P. 2012. An RNA-seq transcriptome analysis of orthophosphate-deficient white lupin reveals novel insights into phosphorus acclimation in plants. Plant Physiology. 161(1):705-724.

Interpretive Summary: Phosphorus (Pi) fertilizer additions are generally required for maximum yield and seed quality. However, inexpensive supplies of Pi fertilizer are predicted to become limiting by 2050. In addition, when Pi fertilizer is added to fields its use by crop plants is inefficient. Only about 25% of the added Pi is used by the crop. The remaining Pi is either complexed to the soil to become unavailable or runs off in surface water. White lupin plants are very efficient at obtaining Pi and have served as a model crop to evaluate how plants acclimate to insufficient Pi. The work presented in this paper was undertaken to identify the genes in white lupin that contribute to the efficient use of Pi by this crop species. White lupin plants were grown in Pi-sufficient or Pi-deficient soil. Roots and shoots from plants were collected after 14 days of growth, and expression of all of the genes in these tissues was evaluated through a technique called RNA-seq. The RNA-seq technology provides a quantitative measure of the abundance of RNA for each gene. We found that 48,852 gene transcripts were expressed and this represents approximately 7.8% of the white lupin genome. We identified a total of 17,986 differentially expressed genes in four pair-wise comparisons with a greater than or equal to 2-fold change and a p-value less than or equal to 0.05. Of these differentially expressed genes, 2,246 were differentially expressed specifically due to Pi concentration. Because white lupin roots show unique adaptations to Pi deficiency, we focused on the root genes that are responsive to Pi-deficiency stress. Several novel genes involved in regulating root development and nutrient uptake were identified. These genes will be useful for marker-assisted selection to plant geneticists and breeders working on improvement of crop plant nutrient acquisition and utilization.

Technical Abstract: Phosphorus (P) is one of the most limiting macronutrients in soils for plant growth and development. However, the whole genome molecular mechanisms contributing to plant acclimation to Pi-deficiency remains largely unknown. White lupin (Lupinus albus L.) has evolved unique adaptation systems for growth in Pi-deficient soils including the development of cluster roots to increase root surface area. In this study, we utilized RNA-seq technology to assess global gene expression in white lupin cluster roots, normal roots, and leaves in response to Pi supply. We de novo assembled 277,224,180 Illumina reads from 12 cDNA libraries to build the first white lupin gene index (LAGI 1.0). LAGI 1.0 contains a total of 125,821 unique sequences with an average length of 1,155 bp. Of these sequences, 48,852 were transcriptionally active (RPKM=3), representing approximately 7.8% of the Lupinus albus genome. We identified a total of 17,986 differentially expressed genes in four pair-wise comparisons with a greater than or equal to 2-fold change and a p-value less than or equal to 0.05. Of these differentially expressed genes, 2,246 were differentially expressed specifically due to Pi concentration. Eleven sequences were found to consistently be differentially expressed due to Pi stress in three species, making them ideal candidates for use in marker-assisted selection. Additionally, classical physiological experiments were coupled to RNAseq data to examine the role of selected plant hormones in Pi-deficiency induced cluster root development. This global gene expression analysis provides new insights into the biochemical and molecular mechanisms involved in acclimation to Pi-deficiency.

Last Modified: 10/20/2014
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