Abstract
BackgroundPhosphorus is often present naturally in the soil as inorganic phosphate, Pi, which bio-availability is limited in many ecosystems due to low soil solubility and mobility. Plants respond to low Pi with a Pi Starvation Response, involving Pi sensing and long-distance signalling. There is extensive cross-talk between Pi homeostasis mechanisms and the homeostasis mechanism for other anions in response to Pi availability.ResultsRecombinant Inbred Line (RIL) and Genome Wide Association (GWA) mapping populations, derived from or composed of natural accessions of Arabidopsis thaliana, were grown under sufficient and deficient Pi supply. Significant treatment effects were found for all traits and significant genotype x treatment interactions for the leaf Pi and sulphate concentrations. Using the RIL/QTL population, we identified 24 QTLs for leaf concentrations of Pi and other anions, including a major QTL for leaf sulphate concentration (SUL2) mapped to the bottom of chromosome (Chr) 1. GWA mapping found 188 SNPs to be associated with the measured traits, corresponding to 152 genes. One of these SNPs, associated with leaf Pi concentration, mapped to PP2A-1, a gene encoding an isoform of the catalytic subunit of a protein phosphatase 2A. Of two additional SNPs, associated with phosphate use efficiency (PUE), one mapped to AT5G49780, encoding a leucine-rich repeat protein kinase involved in signal transduction, and the other to SIZ1, a gene encoding a SUMO E3 ligase, and a known regulator of P starvation-dependent responses. One SNP associated with leaf sulphate concentration was found in SULTR2;1, encoding a sulphate transporter, known to enhance sulphate translocation from root to shoot under P deficiency. Finally, one SNP was mapped to FMO GS-OX4, a gene encoding glucosinolate S-oxygenase involved in glucosinolate biosynthesis, which located within the confidence interval of the SUL2 locus.ConclusionWe identified several candidate genes with known functions related to anion homeostasis in response to Pi availability. Further molecular studies are needed to confirm and validate these candidate genes and understand their roles in examined traits. Such knowledge will contribute to future breeding for improved crop PUE .
Highlights
Phosphorus is often present naturally in the soil as inorganic phosphate, Inorganic phosphate (Pi), which bio-availability is limited in many ecosystems due to low soil solubility and mobility
Phenotyping the mapping populations Upon growing the F6 Recombinant Inbred Line (RIL)/quantitative trait locus (QTL) population, composed of 164 lines and derived from crossing the Shahdara (Sha) and Columbia (Col) accessions [76], under both sufficient (+Pi) and deficient phosphate (−Pi) supply, significant effects of the -Pi treatment were observed for all traits as well as significant genotype x treatment interactions for the leaf Pi, phytate and sulphate concentrations
The associations presented here between the studied traits and several genes with known functions related to anion cross-talks and homeostasis in response to Pi availability confirms the suitability of the followed HapMap/Genome-Wide Association Studies (GWAS) approach to identify candidate genes without the need for additional fine-mapping, as will be needed to resolve the QTLs identified in the RIL population
Summary
Phosphorus is often present naturally in the soil as inorganic phosphate, Pi, which bio-availability is limited in many ecosystems due to low soil solubility and mobility. Present intensive field crop cultivation practices lead to land degradation, lowering soil fertility and productivity, while depending heavily on the extensive use of fertilizers. Pi is taken up by roots at a relatively low efficiency due to its low solubility and mobility in soils [8,9,10], making Pi availability one of the most limiting factors for plant growth and productivity worldwide. Despite the excessive amounts of Pi fertilizers currently applied, on average only 10–20% of applied Pi may be used by crops, while the remainder will be lost by leaching into the groundwater or by long-term immobilization in soil, both leading to substantial socioeconomic and environmental costs [12]
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