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<p>Anaerobic germination tolerance in direct-seeded rice (DSR) is regarded as an important characteristic for the uniform establishment of seedlings where areas are often affected by&#xa0;a flash flood&#xa0;and under waterlogged conditions. The uniqueness of this study is we explored the range of variation in anaerobic germination tolerance traits and genome-wide association mapping in rice in the BAAP panel.&#xa0;This helped in identification of 30 QTLs across the chromosomes with specific candidate genes for the targeted traits. Genes such as BRI 1 (LOC_Os11g38920) involved in the longitudinal growth of internodes, <i>SKIPa29/SIP29</i> (Ski-interacting protein 29) (LOC Os04g07830) with a crucial role in higher shoot growth, <i>CYP51G3</i> (Cytochrome P450 51G3) (LOC Os05g12040) involved in development of higher root lengths, <i>MYB4P</i> (Myeloblastosis) (LOC Os11g35390) and <i>YUCCA7</i> (LOC Os04g03980) involved in higher shoot and root biomass, respectively, were identified as putative candidate genes contributing towards anaerobic germination tolerance. The haplotype grouping based on SNP variation across the traits has led to the identification of the superior haplotype which may be used for haplotype-based breeding programmes. ARC 14950 was identified as a potential donor that could be exploited in upcoming breeding programmes of DSR. The tolerant genotype has a long shoot length and good germination percentage (55.56%), along with a high internode length (8.13&#xa0;cm) and modest root length (10.9&#xa0;cm).</p>

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Insights into the genetic architecture of anaerobic germination in rice through haplotype analysis of candidate genes

  • 期刊论文

  • 发表日期：

    2025年8月6日

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  • Vijay Kumar Reddy Challa,
  • Siddharth Panda,
  • Anthony J. Travis,
  • Gareth J. Norton,
  • Sanjay Kumar,
  • Anandan Annamalai,
  • Manasi Dash,
  • Adam H. Price

摘要

Anaerobic germination tolerance in direct-seeded rice (DSR) is regarded as an important characteristic for the uniform establishment of seedlings where areas are often affected by a flash flood and under waterlogged conditions. The uniqueness of this study is we explored the range of variation in anaerobic germination tolerance traits and genome-wide association mapping in rice in the BAAP panel. This helped in identification of 30 QTLs across the chromosomes with specific candidate genes for the targeted traits. Genes such as BRI 1 (LOC_Os11g38920) involved in the longitudinal growth of internodes, SKIPa29/SIP29 (Ski-interacting protein 29) (LOC Os04g07830) with a crucial role in higher shoot growth, CYP51G3 (Cytochrome P450 51G3) (LOC Os05g12040) involved in development of higher root lengths, MYB4P (Myeloblastosis) (LOC Os11g35390) and YUCCA7 (LOC Os04g03980) involved in higher shoot and root biomass, respectively, were identified as putative candidate genes contributing towards anaerobic germination tolerance. The haplotype grouping based on SNP variation across the traits has led to the identification of the superior haplotype which may be used for haplotype-based breeding programmes. ARC 14950 was identified as a potential donor that could be exploited in upcoming breeding programmes of DSR. The tolerant genotype has a long shoot length and good germination percentage (55.56%), along with a high internode length (8.13 cm) and modest root length (10.9 cm).