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<p>Plants establish a complex signalling network to acquire nitrogen (NO<sub>2</sub>⁻/NH<sub>4</sub>⁺) and phosphate (Pi) from the soil. In rice, <i>OsSPX-MFS3</i> (LOC_Os06g0129400) has been characterized as a vacuolar low-affinity Pi transporter gene, which plays a crucial role under phosphorus-deficient conditions. This study aimed to identify genetic variants and favourable haplotypes of the <i>OsSPX-MFS3</i> gene (Chr06: 1554861-1561163) associated with seedling traits under combined low N and low P conditions. A total of 99 genetic variants of <i>OsSPX-MFS3</i> were identified across 223 <i>indica</i> rice accessions, and their association with eight seedling traits was analysed under low N and low P conditions at 28 and 42 days after sowing (DAS) in Kharif and Rabi seasons. Among the eight major <i>OsSPX-MFS3</i> haplotypes, significant differences were observed for three traits (shoot length (0.01*), shoot area (0.05*), and root area (0.02*)) in kharif and six traits (Root length (0.03*), shoot area (0.003**), root area (0.02*), shoot dry weight (0.002**), root dry weight (0.01*), and SPAD (0.005**,0.03*) in kharif and rabi seasons. Further, Hap_5 was identified as a favourable haplotype at the seedling stage under combined N and P deficiency. Promoter cis-regulatory analysis of Hap_5 identified unique cis-regulatory elements (ERE, MYC, O<sub>2</sub>-site, MYM, and ABRE) relative to other haplotypes. Besides, three tolerant <i>indica</i>accessions (IRGC 131940, IRGC 126966, and IRGC 122165) were identified for better shoot and root growth under nutrient-deficient conditions. These findings highlight the potential application of <i>OsSPX-MFS3</i> haplotypes in haplotype-based breeding programs aimed at developing rice cultivars with improved tolerance to low nitrogen and phosphorus conditions.</p>

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Haplotype characterization of phosphorus homeostasis gene, SPX-MFS3 under combination of low nitrogen and phosphorus conditions in indica rice at seedling stage

  • 期刊论文

  • 发表日期：

    2025年5月26日

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  • Baishnab Charan Muduli,
  • Sabarinathan Selvaraj,
  • Shivraj Sahu,
  • Subhadarshani Dhall,
  • Nibedita Swain,
  • Parameswaran Chidambaranathan,
  • Jitendriya Meher,
  • Chinmay Pradhan,
  • Dibyendu Chatterjee,
  • Sangita Mohanty,
  • Sanghamitra Samantaray

摘要

Plants establish a complex signalling network to acquire nitrogen (NO2⁻/NH4⁺) and phosphate (Pi) from the soil. In rice, OsSPX-MFS3 (LOC_Os06g0129400) has been characterized as a vacuolar low-affinity Pi transporter gene, which plays a crucial role under phosphorus-deficient conditions. This study aimed to identify genetic variants and favourable haplotypes of the OsSPX-MFS3 gene (Chr06: 1554861-1561163) associated with seedling traits under combined low N and low P conditions. A total of 99 genetic variants of OsSPX-MFS3 were identified across 223 indica rice accessions, and their association with eight seedling traits was analysed under low N and low P conditions at 28 and 42 days after sowing (DAS) in Kharif and Rabi seasons. Among the eight major OsSPX-MFS3 haplotypes, significant differences were observed for three traits (shoot length (0.01*), shoot area (0.05*), and root area (0.02*)) in kharif and six traits (Root length (0.03*), shoot area (0.003**), root area (0.02*), shoot dry weight (0.002**), root dry weight (0.01*), and SPAD (0.005**,0.03*) in kharif and rabi seasons. Further, Hap_5 was identified as a favourable haplotype at the seedling stage under combined N and P deficiency. Promoter cis-regulatory analysis of Hap_5 identified unique cis-regulatory elements (ERE, MYC, O2-site, MYM, and ABRE) relative to other haplotypes. Besides, three tolerant indicaaccessions (IRGC 131940, IRGC 126966, and IRGC 122165) were identified for better shoot and root growth under nutrient-deficient conditions. These findings highlight the potential application of OsSPX-MFS3 haplotypes in haplotype-based breeding programs aimed at developing rice cultivars with improved tolerance to low nitrogen and phosphorus conditions.