The crucial role of phosphate (Pi) for plant alongside the expected depletion of non-renewable phosphate rock have created an urgent need for phosphate-efficient rice varieties. In this study, 157 greenhouse-grown Vietnamese rice landraces were treated under Pi-deficient conditions to discover the genotypic variation among biochemical traits, including relative efficiency of phosphorus use (REP), relative root to shoot weight ratio (RRSR), relative physiological phosphate use efficiency (RPPUE), and relative phosphate uptake efficiency (RPUpE). Plants were grown in Yoshida nutrient media with either a full (320 lM) or a low Pi supply (10 lM) over six weeks. This genome-wide association study led to the discovery of 31 significant single nucleotide polymorphisms, 18 quantitative trait loci (QTLs), and 85 candidate genes. A common QTL named qRPUUE9.16 was found among the three investigated traits. Some interesting candidate genes, such as PLASMA MEMBRANE PROTEIN1 (OsPM1), CAL-MODULIN-RELATED CALCIUM SENSOR PROTEIN 15 (OsCML15), phosphatases 2C (PP2C), STRESS-ACTI-VATED PROTEIN KINASE (OsSAPK2), and GLYCER-OPHOSPHORYL DIESTER PHOSPHODIESTERASES (GDPD13), were found strongly correlated to the Pi starvation. RNA sequencing transcriptomes revealed that 45 out of 85 candidate genes were significantly regulated under Pi starvation. Furthermore, nearly two-thirds of genotypes did not possess the OsPsTOL1 gene; however, no significant difference was observed in response to Pi deficiency between genotypes with or without this gene, suggesting that other QTLs in rice may resist Pi starvation. These results provide new information on the genetics of nutrient use efficiency in rice and may potentially assist with developing more phosphate-efficient rice plants.
Phosphorus is an essential nutrient for plants that is often in short supply. In rice (Oryza sativa L.), phosphate (Pi) deficiency leads to various physiological disorders that consequently affect plant productivity. In this study, a large-scale phenotyping experiment of a set of 160 Vietnamese rice landraces was performed under greenhouse conditions by employing an alpha lattice design with three replicates to identify quantitative trait loci (QTLs) associated with plant growth inhibition by Pi deficiency. Rice plantlets were grown for six weeks in the PVC sand column (16 cm diameter x 80 cm height) supplied with Pi-deficient (10 uM P) medium or full Pi Yoshida (320 uM P) medium. The effects of Pi deficiency on the number of crown roots, root length, shoot length, root weight, shoot weight and total weight were studied. From 36 significant markers identified by using Genome-wide association study, a total of 21 QTLs associated with plant growth inhibition under Pi starvation conditions were defined. A list of 158 candidate genes co-located with defined QTLs was found. Interestingly, a QTL namely qRST9.14 were detected found common across three weight-traits. The co-located gene GLYCEROPHOSPHODIESTER PHOSPHODIESTERASE 13 was found potentially involved in Pi transport. Understanding the molecular mechanisms of Pi starvation responses, and identifying potential QTLs responsible for low-Pi stress tolerance will provide valuable information for developing new varieties tolerant to low-Pi conditions.
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