Physiology and genetics of nitrogen use efficiency under saline conditions in rice (Oryza sativa L.)
(2023)
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- Approximately 75% of the total area of harvested rice in the world is cultivated in the South and South-East Asian countries. However, these regions are facing both over-use of N fertilizers and salt intrusion from the sea into coastal area and river deltas. Therefore, improvement of nitrogen use efficiency (NUE) under saline conditions is crucial for both food security and sustainable agriculture. To evaluate the physiology of NUE under saline condition, hydroponic and soil pot experiments were carried out under four N concentrations and three NaCl levels. In hydroponics, four N concentrations were 2.86 mM N [1N – standard N concentration in the solution of Yoshida et al. (1976)], 1.43 (1/2N), 0.72 (1/4N), and 0.36 mM N (1/8N) as NH4NO3. These four N concentrations were crossed with three NaCl concentrations: 0, 56 mM (11.5 – 12 dS m-1), and 113 mM (11.5 – 12 dS m-1). In soil pot experiments, the four N levels were 1.0, 0.5, 0.25 and 0.125 gN pot-1 (6.3 dm3 containing 4 kg of soil) as urea and the three NaCl treatments applied were no NaCl added, NaCl applied corresponding to EC of 4.0 – 4.5 dS m-1, and 8.0 – 8.5 dS m-1 in the water surface layer. The effects of N on NUE were observed at active tillering stage, whereas those at heading and maturity stages were not clear. Reducing N levels resulted in increasing agronomical NUE (agNUE) and its components – absorption NUE (aNUE) and physiological NUE (pNUE) but the increase differed depending on NUE components and salinity level. By increasing NaCl, the positive effect of lowering N applied on both aNUE and agNUE was stronger than in non-saline condition; however, the effect on pNUE dismissed and had no influence under the highest NaCl concentration. Under saline-conditions, rice showed the highest growth under reduced N levels (1/2 - 1/4N) with the highest values of number of tillers, number of crown roots, shoot dry weight, and shoot N content. These parameters reached a peak at 1N level under non-saline condition. Thus, reducing N level is beneficial for rice under saline conditions. The four cultivars used in this study showed different responses to NaCl and aNUE – but not pNUE – with differences between the salt-tolerant and salt- sensitive cultivars. aNUE markedly decreased with NaCl concentration in the most salt-sensitive cultivar, whereas it was the highest at the intermediate NaCl concentration in the most salt-tolerant cultivar, especially under low N levels. We also highlighted a positive and significant correlation between shoot nitrogen content in the one hand and tiller number, shoot dry weight, effective panicle number and grain yield on the other hand. Therefore, reducing N level and improvement of N uptake at active tillering should be searched for to enhance NUE and grain yield of rice under saline conditions. In order to study the genetics of NUE of rice under saline conditions, hydroponic experiments were conducted with 2,391 accessions from 75 countries from the 3,000 Rice Genomes Project under two N concentrations [2.86 mM – standard N (SN), and 0.36 mM – low N (LN)] crossed with two NaCl concentrations [0 (0Na) and 60 mM (60Na)] at the seedling stage. A genome-wide association study was carried out for shoot dry weight (SDW), root dry weight (RDW), whole plant dry weight (PDW), the ratio SDW/RDW (SRR), and relative PDW between treatments on the whole panel of 2,391 accessions and on subpanels of 1,418 and 652 accessions of indica and japonica types, respectively. Another experiment was conducted with 1,332 accessions selected from the 2,391 accessions based on low relatedness to confirm the results. The GWAS analysis was performed using a Factored Spectrally Transformed Linear Mixed Model (FaST-LMM) by FaST-LMM software using 235,210 SNPs. This software and number of SNPs were retained after comparisons of different program softwares, number of accessions, and number of SNPs in the analysis from our preliminary researches. A total of 55 QTLs including 32 in the whole panel, 16 in the indica panel and 7 in the japonica panel associated with one of the tested traits were identified by GWAS in both experiments repeatedly. Among these, 24, 8, 11, and 4 QTLs were detected in SN-0Na, LN-0Na, SN-60Na, and LN-60Na, respectively, and the remaining 8 QTLs were for the relative PDW between treatments. No QTL was detected in all four treatments simultaneously; however, one QTL was detected under both SN-0Na and LN-0Na, and three ones were detected under both SN-0Na and SN-60Na. Among the 55 QTLs, 27 QTLs co-localized with previously identified QTLs for DW-related traits while the other 28 were newly detected. Some QTLs identified under saline but not under non-saline treatment have been identified to co-localize with QTLs previously identified for salt tolerance in rice. Combining gene-based association study plus functional annotation and haplotype analyses let us shortlist 10 candidate genes for eight important QTLs affecting SDW, RDW, and PDW under three experimental conditions: SN-0Na, SN-60Na, and LN-60Na. Only 1 of the 10 candidate genes was detected in both SN-0Na and SN-60Na, while 5, 0, 2, and 2 candidate genes were identified only once under SN-0Na, LN-0Na, SN-60Na, and LN-60Na, respectively. The identified QTLs and genes provide useful materials and genetic information for future functional characterization and genetic improvement of NUE in rice, especially under salt conditions.
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Phan Thi Hong, N. (2023). Physiology and genetics of nitrogen use efficiency under saline conditions in rice (Oryza sativa L.). https://hdl.handle.net/2078.5/233639