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<p>Anaerobic germination (also known as germination stage oxygen deficiency) tolerance is an important trait for tailoring direct-seeded rice varieties. In the present study, a meta-analysis of QTLs governing anaerobic germination we identified 21 Meta-QTLs with &lt; 1&#xa0;cM (~ 250&#xa0;kb) confidence interval, 10 with 1–4&#xa0;cM (~ 250–1000&#xa0;kb), and 15 with &gt; 4&#xa0;cM (&gt; 1000&#xa0;kb). Gene ontology (GO) analysis identified trehalose biosynthetic process (GO: 0005992), negative regulation of translation (GO: 0017148), protein and amino acid phosphorylation (GO: 0006468), cation transport activity (GO: 0006812), ATP binding (GO: 0005524), inorganic cation transmembrane transporter activity (GO: 0022890), protein serine/threonine kinase activity (GO: 0004674), rRNA N-glycosylase activity (GO: 0030598), and nucleoside-triphosphatase activity (GO: 0017111) as significant. We identified 56 differentially expressed genes (21 Meta-QTLs) and designated 13 candidates based on molecular functions and gene ontology. Genes <i>Os02g0304900</i>, <i>Os01g0568400</i>, and<i> Os01g0566500</i> encode proteins in abscisic acid (ABA) metabolism and signaling pathway which is essential in signaling-, response-, and management of hypoxic stress during anaerobic germination. Another candidate <i>Auxin-responsive SAUR protein</i> influences the auxin distribution within tissues to regulate the coleoptile elongation, possibly in coordination with another gene <i>OsNAC024</i> maintaining ROS activity in anaerobic germination response. Other probable genes act as a positive regulator of amylase (<i>Os03g0665200</i>), enhance proline content, lower hydrogen peroxide levels, and increase antioxidant enzyme activities (<i>Os01g0568400</i>), lipid transfer, metabolism, and storage (<i>Os04g0554800; Os08g0131300</i>), and in sugar signaling. These candidates can be validated in independent populations and targeted for haplotype-based genomic and marker-assisted breeding for direct-seeded rice.</p>

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QTL-Meta-analysis and Candidate Gene(s) for Anaerobic Germination Potential in Rice

  • 期刊论文

  • 发表日期：

    2025年1月3日

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  • Sanchika Snehi,
  • Pawan Kumar Singh,
  • R. Beena,
  • Suneetha Kota,
  • Satish Kumar Sanwal,
  • K. T. Ravi Kiran,
  • C. Anilkumar,
  • Krishnendu Chattopadhyay,
  • Nitish Ranjan Prakash,
  • Rameswar Prasad Sah

摘要

Anaerobic germination (also known as germination stage oxygen deficiency) tolerance is an important trait for tailoring direct-seeded rice varieties. In the present study, a meta-analysis of QTLs governing anaerobic germination we identified 21 Meta-QTLs with < 1 cM (~ 250 kb) confidence interval, 10 with 1–4 cM (~ 250–1000 kb), and 15 with > 4 cM (> 1000 kb). Gene ontology (GO) analysis identified trehalose biosynthetic process (GO: 0005992), negative regulation of translation (GO: 0017148), protein and amino acid phosphorylation (GO: 0006468), cation transport activity (GO: 0006812), ATP binding (GO: 0005524), inorganic cation transmembrane transporter activity (GO: 0022890), protein serine/threonine kinase activity (GO: 0004674), rRNA N-glycosylase activity (GO: 0030598), and nucleoside-triphosphatase activity (GO: 0017111) as significant. We identified 56 differentially expressed genes (21 Meta-QTLs) and designated 13 candidates based on molecular functions and gene ontology. Genes Os02g0304900, Os01g0568400, and Os01g0566500 encode proteins in abscisic acid (ABA) metabolism and signaling pathway which is essential in signaling-, response-, and management of hypoxic stress during anaerobic germination. Another candidate Auxin-responsive SAUR protein influences the auxin distribution within tissues to regulate the coleoptile elongation, possibly in coordination with another gene OsNAC024 maintaining ROS activity in anaerobic germination response. Other probable genes act as a positive regulator of amylase (Os03g0665200), enhance proline content, lower hydrogen peroxide levels, and increase antioxidant enzyme activities (Os01g0568400), lipid transfer, metabolism, and storage (Os04g0554800; Os08g0131300), and in sugar signaling. These candidates can be validated in independent populations and targeted for haplotype-based genomic and marker-assisted breeding for direct-seeded rice.