An integrated analysis of mRNA and sRNA transcriptional profiles in Coffea arabica L. roots: insights on nitrogen starvation responses

Abstract

Coffea arabica L. is an important agricultural commodity, accounting for 60% of traded coffee worldwide. Nitrogen (N) is a macronutrient that is usually limiting to plant yield; however, molecular mechanisms of plant acclimation to N limitation remain largely unknown in tropical woody crops. In this study, we investigated the transcriptome of coffee roots under N starvation, analyzing poly-A+ libraries and small RNAs. We also evaluated the concentration of selected amino acids and N-source preferences in roots. Ammonium was preferentially taken up over nitrate, and asparagine and glutamate were the most abundant amino acids observed in coffee roots. We obtained 34,654 assembled contigs by mRNA sequencing, and validated the transcriptional profile of 12 genes by RT-qPCR. Illumina small RNA sequencing yielded 8,524,332 non-redundant reads, resulting in the identification of 86 microRNA families targeting 253 genes. The transcriptional pattern of eight miRNA families was also validated. To our knowledge, this is the first catalog of differentially regulated amino acids, N sources, mRNAs, and sRNAs in Arabica coffee roots.

A Small RNA-Mediated Regulatory Network in Arabidopsis thaliana Demonstrates Connectivity Between phasiRNA Regulatory Modules and Extensive Co-Regulation of Transcription by miRNAs and phasiRNAs

“…It became apparent that to identify changes in the plant sRNA response to virus (or any other biotic or abiotic stress), a global meta-network of interactions between sRNAs and transcribed RNA targets was required that could serve as reference for mapping changes. Changes in crop plant sRNA responses are being studied to improve crop productivity and better understand responses to drought (Zheng et al, 2019), nutritional stress (dos Santos et al, 2019), cold (Ghildiyal and Zamore, 2009;Bustamante et al, 2018;Zhu et al, 2019), and metal toxicity (Wang et al, 2019). Plant sRNAs regulate innate immunity to pathogens (Deng et al, 2018) and cross-kingdom RNA trafficking is being exploited as a crop protection strategy (Cai et al, 2018); the mechanism underlying these latter processes is sRNA-mediated RNA interference.…”

Biochemical parameters of an Oxisol submitted to high doses of gypsum in the coffee culture

“…Coffee is one of the most important agricultural commodities in the world, representing one of the main plants grown in tropical and subtropical countries. Currently, Brazil is the largest coffee producer, accounting for 32.4% of world production, estimated at about 158.93 million bags for the 2017 -18 crops, the species cultivated being Coffea arabica and Coffea canephora (Couto et al, 2019;Santos et al, 2019).…”

MicroRNAs in Woody Plants

“…The expression of miR159 increased after 10 days of nitrogen starvation; its target MYB and TCP genes play important roles in regulating root activity. These findings indicate that this miRNA responds to nitrogen starvation by regulating different biological pathways at different time points ( Zhao M. et al, 2012 ; dos Santos et al, 2019 ). Similarly, nitrogen deficiency increases the expression of miR159, miR160, miR166, miR167, miR169, miR171, miR172, miR390, and miR475 but decreases the expression of miR393 and miR395 in P. tomentosa ( Ren et al, 2015 ).…”