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<p>In rice, <i>NCED2</i>, <i>NAM</i>, <i>DEC</i> genes have been characterized for their role in yield under aerobic conditions and reproductive stage drought stress tolerance. Initial linkage disequilibrium (LD) analysis identified a relatively higher LD across a genomic region spanning ~ 800&#xa0;kb among the three genes, based on different pairs of SNPs. As combination of both the vegetative and reproductive stage stress tolerance is preferable, this study hypothesized that the genetic variations in these three genes would also affect the vegetative stage drought stress responses in rice. Marker trait associations using 253 SNPs within the three genes identified 24 significant associations for different vegetative stage drought stress related traits. Among the four major haplotypes identified between the three genes, HapD showed ~ 26% lesser leaf drying score and 7.5% higher relative water content under stress conditions. Mendelian randomization analysis identified a SNP in the exon of the <i>NAM</i> (Chr12: 17391783) having significant positive effect between the tiller number and leaf rolling under stress conditions. Thus, in addition to the reproductive stage tolerance, three genes also associated with the vegetative drought stress in rice and the favorable haplotype identified could be employed in trait improvement for developing drought resilient rice cultivars.</p> Graphical Abstract <p></p>

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OsNCED2, OsNAM, and OsDEC genes association with vegetative stage drought stress in rice validated through mendelian randomization

  • 期刊论文

  • 发表日期：

    2025年10月23日

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  • Parameswaran Chidambaranathan,
  • Gyanisha Nayak,
  • Kishor Pundlik Jeughale,
  • Sabarinathan Selvaraj,
  • Cayalvizhi Balasubramania Sai,
  • Sushma Awaji,
  • Devanna Basavantraya Navadagi,
  • Jawahar Lal Katara,
  • Sanghamitra Samantaray

摘要

In rice, NCED2, NAM, DEC genes have been characterized for their role in yield under aerobic conditions and reproductive stage drought stress tolerance. Initial linkage disequilibrium (LD) analysis identified a relatively higher LD across a genomic region spanning ~ 800 kb among the three genes, based on different pairs of SNPs. As combination of both the vegetative and reproductive stage stress tolerance is preferable, this study hypothesized that the genetic variations in these three genes would also affect the vegetative stage drought stress responses in rice. Marker trait associations using 253 SNPs within the three genes identified 24 significant associations for different vegetative stage drought stress related traits. Among the four major haplotypes identified between the three genes, HapD showed ~ 26% lesser leaf drying score and 7.5% higher relative water content under stress conditions. Mendelian randomization analysis identified a SNP in the exon of the NAM (Chr12: 17391783) having significant positive effect between the tiller number and leaf rolling under stress conditions. Thus, in addition to the reproductive stage tolerance, three genes also associated with the vegetative drought stress in rice and the favorable haplotype identified could be employed in trait improvement for developing drought resilient rice cultivars.

Graphical Abstract