Global Identification of White Lupin lncRNAs Reveals Their Role in Cluster Roots under Phosphorus Deficiency

Abstract

Phosphorus (P) deficiency heterogeneously affected plant nutritional status and physiological performance, ultimately leading to a severe yield reduction. A few putative long non-coding RNAs (lncRNAs) responding to P-starvation in the model crops Arabidopsis thaliana and Oryza sativa have been characterized. White lupin (Lupinus albus) is of prime importance, and is a legume with increasing agronomic value as a protein crop as it exhibits extreme tolerance to nutrient deficiency, particularly P deficiency. Despite its adapted nature to P deficiency, nothing is known about low P-induced lncRNAs in white lupin roots. To address this issue, we identified 39,840 mRNA and 2028 lncRNAs in the eight developmental stages of white lupin root (S0–S7 and lateral root, LR) grown under P deficiency. From these 2028 lncRNAs, 1564 were intergenic and 464 natural antisense intergenic transcript (NAT) lncRNAs. We further predicted six potential targets of miRNAs with twelve lncRNAs, which may regulate P-deficiency-related processes. Moreover, the weighted gene co-expression network analysis (WGCNA) revealed seven modules that were correlated with the expression pattern of lncRNAs. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed 606 GO terms and 27 different pathways including signal transduction, energy synthesis, detoxification, and Pi transport. In addition, we screened 13 putative lncRNAs that showed a distinct expression pattern in each root, indicating their role in the P deficiency regulatory network. Therefore, white lupin may be a reference legume to characterize P-deficiency-responsive novel lncRNAs, which would highlight the role of lncRNAs in the regulation of plant responses to P deficiency.

Changes in Soil Phosphorus Availability and Microbial Community Structures in Rhizospheres of Oilseed Rapes Induced by Intercropping with White Lupins

“…Previous studies confirmed that white lupin is a genotype crop with high phosphorus utilization [ 47 , 48 , 49 ], and that white lupin can be used for activating phosphorus in the soil by means of its implementation in RL with other crops [ 6 , 50 , 51 ].…”

Analysis of lncRNAs in Lupinus mutabilis (Tarwi) and Their Potential Role in Drought Response

“…The L. mutabilis data allowed the identification of 625 lncRNAs. In contrast, Aslam et al [18] found 2028 lncRNAs in L. albus roots under P deficit and Khemka et al [15] found 2248 lincRNAs in C. arietinum using the same algorithm. The higher number count for lncRNA in these studies, in contrast to the 625 L. mutabilis, might be due to the inclusion of more developmental stages.…”

“…In other legumes, the genetic control of the flowering process has been studied by Hidalgo et al [17], demonstrating that the lncRNA EL0144 is involved in floral development and abiotic responses in Lupinus angustifolius. Likewise, Aslam et al [18] analyzed lncRNAs in L. albus grown under phosphorous deficiency and found 1564 intergenic lncRNAs and 464 natural antisense intergenic transcripts (NAT) that participate in the regulation network under P-deficiency stress. Similarly, different lncRNAs regulate drought response by forming potential subtle regulatory networks that control multiple genes to determine the overall response of plants [19].…”

Editorial: Salinity and drought stress in plants: understanding physiological, biochemical and molecular responses

“…Non-coding RNAs (ncRNAs) are emerging regulators of various biological processes, including stress tolerance ( Waseem et al, 2021 ; Waseem et al, 2022 ; Aslam et., 2022 ). Zou et al.…”