Location: Floral and Nursery Plants Research
Title: Comparative Transcriptomics of Arabidopsis, Brachypodium, Medicago and Setaria species Pinpoints Conserved and Specific Transcriptional Responses to Phosphorus LimitationAuthor
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Pant, Pooja |
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Duan, Hui |
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KROM, NICK - Noble Research Institute |
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WOLF-RUDIGER, SCHEIBLE - Noble Research Institute |
Submitted to: Journal of Experimental Botany
Publication Type: Peer Reviewed Journal Publication Acceptance Date: 11/4/2024 Publication Date: 1/10/2025 Citation: Pant, P.P., Duan, H., Krom, N., Wolf-Rudiger, S. 2025. Comparative Transcriptomics of Arabidopsis, Brachypodium, Medicago and Setaria species Pinpoints Conserved and Specific Transcriptional Responses to Phosphorus Limitation. Journal of Experimental Botany. https://doi.org/10.1093/jxb/erae434. DOI: https://doi.org/10.1093/jxb/erae434 Interpretive Summary: Phosphorus (P) is often in short supply in agricultural soils, and its low availability limits crop production. Since P-limitation leads to considerable changes in gene expression in plants, gene expression studies have been used to identify important P-limitation responsive genes and potential target genes for improving plant P-use efficiency. However, these studies were mostly carried out in model plants, or the experimental variation was too large to compare the results from different studies, especially from different species. Scientists at the Noble Research Institute performed a comparative transcriptome analysis of P-responsive genes in shoots and roots of four different plant species by growing them side-by-side in the same conditions. In collaboration with ARS scientists, the comparative transcriptomics study was successfully used to pinpoint the functional orthologs in ornamental cherry (Prunus) species. The study provides new insight into conserved and species-specific P-limitation responses and a method for translating knowledge from model species to other evolutionarily close and distant species to eventually improve plant growth under P-limitation conditions. Technical Abstract: Translating biological knowledge from Arabidopsis to legume and grass crop species is important to advance agriculture and secure food production in the face of dwindling fertilizer resources, climate change, biotic and abiotic stresses. However, it is often not trivial to identify functional homologs (orthologs) of Arabidopsis genes in crop species. Combining sequence and expression data can improve the correct prediction of orthologs. Here, we conducted a large RNA-Seq transcriptomics study of Arabidopsis, Medicago, Brachypodium and Setaria grown side-by-side in P-limited and P-sufficient conditions to gain insights into orthologous relationships of phosphorus (P) status-responsive genes. Known, conserved, and novel P-responsive genes were identified in the four species. Comparison of the top 200 P starvation-inducible genes in Arabidopsis revealed that ~80% of these genes have identifiable close homologs in the other three species but only ~50% retain their P-limitation response in the legume and grasses. Most of the hallmark genes of the phosphate starvation response were found conserved in all four species. The results show the usefulness of comparative transcriptomics for pinpointing orthologous genes across species and reveal considerable species-specific regulation of the transcriptional P-starvation response. Identification and experimental verification of expressologs by independent RT-qPCR for P-limitation marker genes in Prunus showed the usefulness of comparative transcriptomics in pinpointing the functional orthologs in diverse crop species. The study provides an unprecedented insight into conserved and species-specific P-limitation responses and a resource for functional genomics, applied and translational research for Arabidopsis, legumes, grasses, and tree species. |