Abstract
Large nitrogen, phosphorus and potassium fertilizer inputs are used in many crop systems. Identifying genetic loci controlling nutrient accumulation may be useful in crop breeding strategies to increase fertilizer use efficiency and reduce financial and environmental costs. Here, variation in leaf nitrate concentration across a diversity population of 383 genotypes of Brassica napus was characterized. Genetic loci controlling variation in leaf nitrate, phosphorus and potassium concentration were then identified through Associative Transcriptomics using single nucleotide polymorphism (SNP) markers and gene expression markers (GEMs). Leaf nitrate concentration varied over 8-fold across the diversity population. A total of 455 SNP markers were associated with leaf nitrate concentration after false-discovery-rate (FDR) correction. In linkage disequilibrium of highly associated markers are a number of known nitrate transporters and sensors, including a gene thought to mediate expression of the major nitrate transporter NRT1.1. Several genes influencing root and root-hair development co-localize with chromosomal regions associated with leaf P concentration. Orthologs of three ABC-transporters involved in suberin synthesis in roots also co-localize with association peaks for both leaf nitrate and phosphorus. Allelic variation at nearby, highly associated SNPs confers large variation in leaf nitrate and phosphorus concentration. A total of five GEMs associated with leaf K concentration after FDR correction including a GEM that corresponds to an auxin-response family protein. Candidate loci, genes and favorable alleles identified here may prove useful in marker-assisted selection strategies to improve fertilizer use efficiency in B. napus.
Highlights
The plant macronutrients nitrogen (N), phosphorus (P) and potassium (K) are required in large amounts by higher plants, which typically contain approximately 1.5% N, 0.2% P, and 1% K on a dry weight (DW) basis (Hawkesford et al, 2012)
That all three of these genes were identified close to single nucleotide polymorphism (SNP) highly associated with leaf NO−3 and P concentration in this study provides further evidence for the role of suberin in the control of nutrient uptake in B. napus
Characterizing variation in traits related to suberin synthesis and root hair development across genotypes of the Renewable Industrial Products from Rapeseed (RIPR) diversity population would likely add to the understanding of their function and how they can be applied in crop breeding strategies
Summary
The plant macronutrients nitrogen (N), phosphorus (P) and potassium (K) are required in large amounts by higher plants, which typically contain approximately 1.5% N, 0.2% P, and 1% K on a dry weight (DW) basis (Hawkesford et al, 2012). Whilst largely unavailable to plants directly (Dechorgnat et al, 2011), there is evidence to suggest that plants can acquire organic N through root uptake of free amino acids (Näsholm et al, 2009) These can be made available through the breakdown of peptides and proteins by soil micro-organisms, and may be the dominant form of N in some high latitude ecosystems (Miller and Cramer, 2004). Total soil P content is generally considered to be relatively high, bioavailable P is present at much lower concentrations (White and Hammond, 2008) This is largely due to the ability of P to form insoluble complexes with cations including calcium (Ca), magnesium (Mg), iron (Fe), and aluminum (Al; Hinsinger, 2001). Whilst further sources of K from exchangeable and non-exchangeable fractions of the soil are generally available to replenish soil solution K, typically 90–98% of total soil K remains effectively inaccessible to crop plants
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