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<p>Haplotype-based breeding approaches hold promise for enhancing crop improvement strategies, allowing for targeted selection of superior genetic combinations to develop high-yielding and resilient varieties. This study aimed to identify <i>NRT1.1</i> nitrate transporter haplotypes in rice that could serve as "donors" in haplotype-based breeding. We phenotyped 272 rice accessions in hydroponics with sufficient and low nitrogen (N). The accessions were grouped into N-efficient, N-intermediate, and N-inefficient clusters through principal component and hierarchical cluster analysis. Haplotype analysis revealed the presence of two haplogroups for <i>OsNRT1.1A</i>, three for <i>OsNRT1.1B</i>, and five for <i>OsNRT1.1C</i>. Through haplo-pheno association, the comparison of mean trait values showed H2 and H3 as the superior haplotypes (SH) for <i>OsNRT1.1A</i> and <i>OsNRT1.1B</i>, respectively. In the case of <i>OsNRT1.1C</i>, H3 and H1 emerged as the SH within the N-efficient cluster. Conversely, the inferior haplotypes (IH) consisted of H1 in <i>OsNRT1.1A</i>, H3 in <i>OsNRT1.1B</i>, and H3 and H2 in <i>OsNRT1.1C</i> within the N-inefficient cluster. However, the relative expression of <i>OsNRT1.1</i> (with specific paralogs) in contrasting rice accessions revealed that some inferior accessions exhibited higher expression levels in the roots but lower in shoot, and might have contributed to their N-inefficiency. Furthermore, amino acid change at position 403 (Valine to Isoleucine) in inferior accessions might affect the active site of OsNRT1.1C protein causing N-inefficiency. This is the first report on haplotype analysis of the <i>OsNRT1.1</i> paralogs demonstrating its genetic diversity and association with phenotype, and could have potential implications for improving nitrate uptake.</p>

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Haplo-pheno association for OsNRT1.1 paralog in rice reveals superior haplogroup with high nitrate uptake

  • 期刊论文

  • 发表日期：

    2026年3月30日

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  • Dharani Elangovan,
  • Sandeep Sharma,
  • Balaji Balamurugan,
  • Neha Anand,
  • Adhip Das,
  • Tarun Kumar,
  • Ranjith Kumar Ellur,
  • Sanjay Kalia,
  • Jagadish Rane,
  • Renu Pandey

摘要

Haplotype-based breeding approaches hold promise for enhancing crop improvement strategies, allowing for targeted selection of superior genetic combinations to develop high-yielding and resilient varieties. This study aimed to identify NRT1.1 nitrate transporter haplotypes in rice that could serve as "donors" in haplotype-based breeding. We phenotyped 272 rice accessions in hydroponics with sufficient and low nitrogen (N). The accessions were grouped into N-efficient, N-intermediate, and N-inefficient clusters through principal component and hierarchical cluster analysis. Haplotype analysis revealed the presence of two haplogroups for OsNRT1.1A, three for OsNRT1.1B, and five for OsNRT1.1C. Through haplo-pheno association, the comparison of mean trait values showed H2 and H3 as the superior haplotypes (SH) for OsNRT1.1A and OsNRT1.1B, respectively. In the case of OsNRT1.1C, H3 and H1 emerged as the SH within the N-efficient cluster. Conversely, the inferior haplotypes (IH) consisted of H1 in OsNRT1.1A, H3 in OsNRT1.1B, and H3 and H2 in OsNRT1.1C within the N-inefficient cluster. However, the relative expression of OsNRT1.1 (with specific paralogs) in contrasting rice accessions revealed that some inferior accessions exhibited higher expression levels in the roots but lower in shoot, and might have contributed to their N-inefficiency. Furthermore, amino acid change at position 403 (Valine to Isoleucine) in inferior accessions might affect the active site of OsNRT1.1C protein causing N-inefficiency. This is the first report on haplotype analysis of the OsNRT1.1 paralogs demonstrating its genetic diversity and association with phenotype, and could have potential implications for improving nitrate uptake.