Dynamic Development of White Lupin Rootlets Along a Cluster Root.
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ABSTRACT:
SUBMITTER: Le Thanh T
PROVIDER: S-EPMC8452988 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BACKGROUND: Highly adapted plant species are able to alter their root architecture to improve nutrient uptake and thrive in environments with limited nutrient supply. Cluster roots (CRs) are specialised structures of dense lateral roots formed by several plant species for the effective mining of nutrient rich soil patches through a combination of increased surface area and exudation of carboxylates. White lupin is becoming a model-species allowing for the discovery of gene networks involved in CR development. A greater understanding of the underlying molecular mechanisms driving these developmental processes is important for the generation of smarter plants for a world with diminishing resources to improve food security. RESULTS: RNA-seq analyses for three developmental stages of the CR formed under phosphorus-limited conditions and two of non-cluster roots have been performed for white lupin. In total 133,045,174 high-quality paired-end reads were used for a de novo assembly of the root transcriptome and merged with LAGI01 (Lupinus albus gene index) to generate an improved LAGI02 with 65,097 functionally annotated contigs. This was followed by comparative gene expression analysis. We show marked differences in the transcriptional response across the various cluster root stages to adjust to phosphate limitation by increasing uptake capacity and adjusting metabolic pathways. Several transcription factors such as PLT, SCR, PHB, PHV or AUX/IAA with a known role in the control of meristem activity and developmental processes show an increased expression in the tip of the CR. Genes involved in hormonal responses (PIN, LAX, YUC) and cell cycle control (CYCA/B, CDK) are also differentially expressed. In addition, we identify primary transcripts of miRNAs with established function in the root meristem. CONCLUSIONS: Our gene expression analysis shows an intricate network of transcription factors and plant hormones controlling CR initiation and formation. In addition, functional differences between the different CR developmental stages in the acclimation to phosphorus starvation have been identified.
| S-EPMC4028058 | biostudies-literature
Project description:The formation of cluster roots by plants represents a highly efficient strategy for acquisition of sparingly available phosphate. This particular root type is characterized by a densely branched structure and high exudation of organic acids and protons, which are likely to influence the resident bacterial community. Until now, the identity of the bacterial populations living in cluster roots has not been investigated. We applied cultivation-dependent and cultivation-independent methods to characterize the dominant bacterial genera inhabiting the growing cluster roots of white lupin. We observed a high relative abundance of Burkholderia species (up to 58% of all isolated strains and 44% of all retrieved 16S rRNA sequences) and a significant enrichment with increasing cluster root age. Most of the sequences retrieved clustered together with known plant- or fungus-associated Burkholderia species, while only one of 98 sequences was affiliated with the Burkholderia cepacia complex. In vitro assays revealed that Burkholderia strains were much more tolerant to low pH than non-Burkholderia strains. Moreover, many strains produced large amounts of siderophores and were able to utilize citrate and oxalate as carbon sources. These features seem to represent important traits for the successful colonization and maintenance of Burkholderia species in white lupin cluster roots.
| S-EPMC3209158 | biostudies-literature
Project description:The Scarecrow (SCR) transcription factor plays a crucial role in root cell radial patterning and is required for maintenance of the quiescent centre and differentiation of the endodermis. In response to phosphorus (P) deficiency, white lupin (Lupinus albus L.) root surface area increases some 50-fold to 70-fold due to the development of cluster (proteoid) roots. Previously it was reported that SCR-like expressed sequence tags (ESTs) were expressed during early cluster root development. Here the cloning of two white lupin SCR genes, LaSCR1 and LaSCR2, is reported. The predicted amino acid sequences of both LaSCR gene products are highly similar to AtSCR and contain C-terminal conserved GRAS family domains. LaSCR1 and LaSCR2 transcript accumulation localized to the endodermis of both normal and cluster roots as shown by in situ hybridization and gene promoter::reporter staining. Transcript analysis as evaluated by quantitative real-time-PCR (qRT-PCR) and RNA gel hybridization indicated that the two LaSCR genes are expressed predominantly in roots. Expression of LaSCR genes was not directly responsive to the P status of the plant but was a function of cluster root development. Suppression of LaSCR1 in transformed roots of lupin and Medicago via RNAi (RNA interference) delivered through Agrobacterium rhizogenes resulted in decreased root numbers, reflecting the potential role of LaSCR1 in maintaining root growth in these species. The results suggest that the functional orthologues of AtSCR have been characterized.
| S-EPMC2837254 | biostudies-literature
Project description:Root morphological/physiological modifications are important for phosphorus (P) acquisition of plants under P deficiency, but strategies differ among plant species. Detailed studies on the response of maize roots to P deficiency are limited. Nitrogen (N) form influences root morphology/physiology, and thus may influence root responses to P deficiency. This work investigated adaptive mechanisms of maize roots to low P by comparison with white lupin and faba bean supplied with two N forms. Plants were grown for 7-16 days in hydroponics with sufficient (250 µmol L(-1)) and deficient P supply (1 µmol L(-1)) under supply of NH4NO3 or Ca(NO3)2 Plant growth and P uptake were measured, and release of protons and organic acid anions, and acid phosphatase activity in the root were monitored. The results showed that P deficiency significantly decreased shoot growth while increased root growth and total root length of maize and faba bean, but not white lupin. It enhanced the release of protons and organic acid anions, and acid phosphatase activity, from the roots of both legumes but not maize. Compared with Ca(NO3)2, NH4NO3 dramatically increased proton release by roots but did not alter root morphology or physiology of the three species in response to low P. It is concluded that the N form did not fundamentally change root morphological/physiological responses of the three species to P deficiency. Morphological variation in maize and morpho-physiological modifications in white lupin and faba bean were the main adaptive strategies to P deficiency.
| S-EPMC5018397 | biostudies-literature
Project description:White lupin (Lupinus albus L.) is a legume grain crop cultivated since ancient Greece and Egypt. Modern white lupin cultivars are appreciated as a source of protein with positive nutraceutical impact. However, white lupins produce anti-nutritional compounds, quinolizidine alkaloids, which provide bitter taste and have a negative influence on human health. During domestication of this species, several recessive alleles at unlinked loci controlling low alkaloid content were selected. One of these loci, pauper, was exploited worldwide providing numerous low-alkaloid cultivars. However, molecular tracking of pauper has been hampered due to the lack of diagnostic markers. In the present study, the synteny-based approach was harnessed to target pauper locus. Single-nucleotide polymorphisms flanking pauper locus on white lupin linkage map as well as candidate gene sequences elucidated from the narrow-leafed lupin (L. angustifolius L.) chromosome segment syntenic to the pauper linkage group region were transformed to PCR-based molecular markers. These markers were analyzed both in the mapping population and world germplasm collection. From fourteen markers screened, eleven were localized at a distance below 1.5 cM from this locus, including five co-segregating with pauper. The linkage of these markers was confirmed by high LOD values (up to 58.4). Validation performed in the set of 127 bitter and 23 sweet accessions evidenced high applicability of one marker, LAGI01_35805_F1_R1, for pauper locus selection, highlighted by the low ratio of false-positive scores (2.5%). LAGI01_35805 represents a homolog of L. angustifolius acyltransferase-like (LaAT) gene which might hypothetically participate in the alkaloid biosynthesis process in lupins.
| S-EPMC6803572 | biostudies-literature
Project description:Iron (Fe) and phosphorus (P) are essential nutrients for plants growth. Despite their abundance in soils, they are barely available for plants. In order to overcome these nutritional stresses, plants have evolved strategies including physiological, biochemical and morphological adaptations. Biosynthesis and release of low molecular weight compounds from the roots play a crucial role in P and Fe mobilization. White lupin (Lupinus albus L.) is considered a model plant for studying root exudates and for P-deficient adaptation. White lupin is able to markedly modify its root architecture by forming special structures called cluster roots, and modifies the rhizospheric soil characteristics by biosynthesising and releasing great amounts of exudates. These phenomena are quite well described in response to P deficiency, but there is few information on the adaptation of a cluster-root producing plant species to Fe deficiency. This prompted this work, aimed to characterize the physiological and transcriptomic responses of white lupin plants to Fe deficiency. Occurrence of Strategy I components and interactions with P nutrition has been also investigated in this work. Results showed a physiological and transcriptional link between the responses to Fe and P deficiency in white lupin roots. Phosphorus-deficient plants activated the Strategy I Fe acquisition mechanisms that lead to an enhanced Fe mobilization and translocation and that might help the P acquisition process. On the other hand, also the Fe deficiency enhanced the phosphate acquisition and some P-deficient-responsive genes were overexpressed.
2019-03-22 | GSE112220 | GEO
Project description:White lupin (Lupinus albus) is a legume crop that develops cluster roots and has high phosphorus (P)-use efficiency (PUE) in low-P soils. Here, we assemble the genome of white lupin and find that it has evolved from a whole-genome triplication (WGT) event. We then decipher its diploid ancestral genome and reconstruct the three sub-genomes. Based on the results, we further reveal the sub-genome dominance and the genic expression of the different sub-genomes varying in relation to their transposable element (TE) density. The PUE genes in white lupin have been expanded through WGT as well as tandem and dispersed duplications. Furthermore, we characterize four main pathways for high PUE, which include carbon fixation, cluster root formation, soil-P remobilization, and cellular-P reuse. Among these, auxin modulation may be important for cluster root formation through involvement of potential genes LaABCG36s and LaABCG37s. These findings provide insights into the genome evolution and low-P adaptation of white lupin.
| S-EPMC7044338 | biostudies-literature
Project description:BACKGROUND AND AIMS: Formation of cluster roots is one of the most specific root adaptations to nutrient deficiency. In white lupin (Lupinus albus), cluster roots can be induced by phosphorus (P) or iron (Fe) deficiency. The aim of the present work was to investigate the potential shared signalling pathway in P- and Fe-deficiency-induced cluster root formation. METHODS: Measurements were made of the internal concentration of nutrients, levels of nitric oxide (NO), citrate exudation and expression of some specific genes under four P × Fe combinations, namely (1) 50 µm P and 10 µm Fe (+P + Fe); (2) 0 P and 10 µm Fe (-P + Fe); (3) 50 µm P and 0 Fe (+P-Fe); and (4) 0 P and 0 Fe (-P-Fe), and these were examined in relation to the formation of cluster roots. KEY RESULTS: The deficiency of P, Fe or both increased the cluster root number and cluster zones. It also enhanced NO accumulation in pericycle cells and rootlet primordia at various stages of cluster root development. The formation of cluster roots and rootlet primordia, together with the expression of LaSCR1 and LaSCR2 which is crucial in cluster root formation, were induced by the exogenous NO donor S-nitrosoglutathione (GSNO) under the +P + Fe condition, but were inhibited by the NO-specific endogenous scavenger 2-(4-carboxyphenyl)-4, 4, 5, 5-tetramethylimidazoline-1-oxyl- 3-oxide (cPTIO) under -P + Fe, +P-Fe and -P-Fe conditions. However, cluster roots induced by an exogenous supply of the NO donor did not secrete citrate, unlike those formed under -P or -Fe conditions. CONCLUSIONS: NO plays an important role in the shared signalling pathway of the P- and Fe-deficiency-induced formation of cluster roots in white lupin.
| S-EPMC3336943 | biostudies-literature
Project description:White lupin (Lupinus albus L.) is a high-protein grain legume crop, grown since ancient Greece and Rome. Despite long domestication history, its cultivation remains limited, partly because of susceptibility to anthracnose. Only some late-flowering, bitter, low-yielding landraces from Ethiopian mountains displayed resistance to this devastating disease. The resistance is controlled by various genes, thereby complicating the breeding efforts. The objective of this study was developing tools for molecular tracking of Ethiopian resistance genes based on genotyping-by-sequencing (GBS) data, envisaging linkage mapping and genomic selection approaches. Twenty GBS markers from two major quantitative trait loci (QTLs), antr04_1/antr05_1 and antr04_2/antr05_2, were converted to PCR-based markers using assigned transcriptome sequences. Newly developed markers improved mapping resolution around both anthracnose resistance loci, providing more precise QTL estimation. PCR-based screening of diversified domesticated and primitive germplasm revealed the high specificity of two markers for the antr04_1/antr05_1 locus (TP222136 and TP47110) and one for the antr04_2/antr05_2 locus (TP338761), highlighted by simple matching coefficients of 0.96 and 0.89, respectively. Moreover, a genomic selection approach based on GBS data of a recombinant inbred line mapping population was assessed, providing an average predictive ability of 0.56. These tools can be used for preselection of candidate white lupin germplasm for anthracnose resistance assays.
| S-EPMC7652745 | biostudies-literature
Project description:BACKGROUND: Members of the legume genus Lupinus exude phloem 'spontaneously' from incisions made to the vasculature. This feature was exploited to document macromolecules present in exudate of white lupin (Lupinus albus [L.] cv Kiev mutant), in particular to identify proteins and RNA molecules, including microRNA (miRNA). RESULTS: Proteomic analysis tentatively identified 86 proteins from 130 spots collected from 2D gels analysed by partial amino acid sequence determination using MS/MS. Analysis of a cDNA library constructed from exudate identified 609 unique transcripts. Both proteins and transcripts were classified into functional groups. The largest group of proteins comprised those involved in metabolism (24%), followed by protein modification/turnover (9%), redox regulation (8%), cell structural components (6%), stress and defence response (6%) with fewer in other groups. More prominent proteins were cyclophilin, ubiquitin, a glycine-rich RNA-binding protein, a group of proteins that comprise a glutathione/ascorbate-based mechanism to scavenge oxygen radicals, enzymes of glycolysis and other metabolism including methionine and ethylene synthesis. Potential signalling macromolecules such as transcripts encoding proteins mediating calcium level and the Flowering locus T (FT) protein were also identified. From around 330 small RNA clones (18-25 nt) 12 were identified as probable miRNAs by homology with those from other species. miRNA composition of exudate varied with site of collection (e.g. upward versus downward translocation streams) and nutrition (e.g. phosphorus level). CONCLUSIONS: This is the first inventory of macromolecule composition of phloem exudate from a species in the Fabaceae, providing a basis to identify systemic signalling macromolecules with potential roles in regulating development, growth and stress response of legumes.
| S-EPMC3055823 | biostudies-literature