Dissection of the Control of Anion Homeostasis by Associative Transcriptomics in Brassica napus

Abstract

To assess the variation in nutrient homeostasis in oilseed rape and to identify the genes responsible for this variation, we determined foliar anion levels in a diversity panel of Brassica napus accessions, 84 of which had been genotyped previously using messenger RNA sequencing. We applied associative transcriptomics to identify sequence polymorphisms linked to variation in nitrate, phosphate, or sulfate in these accessions. The analysis identified several hundred significant associations for each anion. Using functional annotation of Arabidopsis (Arabidopsis thaliana) homologs and available microarray data, we identified 60 candidate genes for controlling variation in the anion contents. To verify that these genes function in the control of nutrient homeostasis, we obtained Arabidopsis transfer DNA insertion lines for these candidates and tested them for the accumulation of nitrate, phosphate, and sulfate. Fourteen lines differed significantly in levels of the corresponding anions. Several of these genes have been shown previously to affect the accumulation of the corresponding anions in Arabidopsis mutants. These results thus confirm the power of associative transcriptomics in dissection of the genetic control of complex traits and present a set of candidate genes for use in the improvement of efficiency of B. napus mineral nutrition.

Root morphology and seed and leaf ionomic traits in a Brassica napus L. diversity panel show wide phenotypic variation and are characteristic of crop habit

“…For example, using associative transcriptomics (AT) with a panel of 84 B. napus genotypes from within the same panel used here, Harper et al [ 37 ] showed that seed contents of both erucic acid and glucosinolates (GS) were associated with specific genes known to be involved in their biosynthetic pathways, whilst identifying additional new target loci of potential use in breeding. Similarly, Koprivova et al [ 78 ] used a subset of this study’s population to identify novel loci linked to shoot anion accumulation. The AT technique is based on transcriptome-sequencing, combined with association mapping.…”

Root nodule symbiosis in Lotus japonicus drives the establishment of distinctive rhizosphere, root, and nodule bacterial communities

“…Root nitrate contents were determined by the ion chromatography method as previously described (72). Proteins were extracted in 10 mM Tris·HCl buffer (pH 8) and determined with a Bio-Rad Protein Assay Kit using BSA as the standard.…”

Molecular mechanisms of regulation of sulfate assimilation: first steps on a long road

“…It is, however, possible to speculate that at least for Sha and the Swedish accessions, growth might be restricted due to harsh conditions and the reduction of sulfate assimilation would prevent accumulation of reduced sulfur compound and increasingly reducing cellular environment. The analysis is not limited to Arabidopsis , similar approaches have been made directly with crops and similar haplotypes have been identified ( Harper et al, 2012 ; Koprivova et al, 2014b ). Thus, modulation of, e.g., sulfate levels, seems to be possible without knowing the regulatory networks, transcription factors, cis elements, or signals controlling sulfate homeostasis.…”