Identification of Quantitative Trait Loci and Candidate Genes Involved in Rice Seedling Growth under Hypoxic Stress

Progress in developing rice cultivars that thrive under flooding and low oxygen (hypoxic) conditions has been limited over the past two decades due to a lack of tolerant plant varieties and a limited understanding of genetic mechanisms. This study evaluated hypoxia tolerance in the Cheongcheong Nagdong Double Haploid (CNDH) rice population, along with their parent lines, for hypoxia tolerance. Significant phenotypic differences were identified, with the Cheongcheong and CNDH lines CNDH13, CNDH35, and CNDH91 showing strong hypoxia tolerance, while Nagdong and CNDH lines CNDH14-2, CNDH43, and CNDH50-1 were susceptible to hypoxia. Root length was unaffected by hypoxia, while shoot length and fresh weight were key tolerance indicators. Comprehensive quantitative trait loci (QTL) analysis based on logarithm of the odds (LOD) scores above 3.0 identified three QTLs associated with hypoxia tolerance, indicating significant genetic control: qSL-8 and qSL-10 (shoot length) and qFW-2 (fresh weight). The gene expression analysis performed under hypoxic conditions highlighted that 35 candidate genes within these QTL regions exhibited differential regulation: Os02g0184200, Os08g0430200, Os08g0431900, and Os08g0432500 were upregulated, whereas Os08g0439100, Os10g0343400, Os10g0395400, and Os10g0405600 were downregulated in both resistant and susceptible lines. Os08g0431900 displayed significant expression changes correlating with hypoxia resistance. Phylogenetic and protein–protein interaction analyses revealed that Os08g0431900 is highly conserved and interacts with proteins involved in stress responses, suggesting that these proteins are crucial in hypoxia tolerance. These findings provide valuable insights into the genetic basis of hypoxia tolerance and identify key genes for future breeding programs to develop hypoxia-resistant rice varieties.