Genetic and Physiological Insights into Salt Resistance in Rice through Analysis of Germination, Seedling Traits, and QTL Identification

Understanding the genetic basis of salt resistance in crops is crucial for agricultural productivity. This study investigates the phenotypic and genetic basis of salt stress response in rice (<i>Oryza sativa</i> L.), focusing on germination and seedling traits. Under salt stress conditions, significant differences were observed in seed germination and seedling traits between parental LH99 (Indica rice LuHui 99) and SN265 (japonica rice ShenNong 265). Transgressive segregation was evident within the RIL population, indicating complex genetic interactions. Nine QTLs were detected at germination and seedling stages under salt stress, namely <i>qSGE5</i> and <i>qSGE7</i> for seed germination energy (SGE); <i>qSGP7</i> for seed germination percentage (SGP); <i>qSSH7</i>, <i>qSSH9-1</i>, and <i>qSSH9-2</i> for seeding height (SSH); <i>qSRN6</i> for root number (SRN); and <i>qSDW6</i> and <i>qSDW9</i> for dry weight (SDW). Among them, <i>qSSH9-1</i> and <i>qSDW9</i> were localized in the same interval, derived from the salt-resistant parent SN265. PCA revealed distinct trait patterns under salt stress, captured by six PCs explaining 81.12% of the total variance. PC composite scores were used to localize a QTL associated with early salt resistance in rice <i>qESC9</i>, which was located in the same interval as <i>qSSH9-1</i> and <i>qSDW9,</i> and was subsequently unified under the name <i>qESC9</i>, an important QTL for early-growth salt tolerance in rice. Correlation analysis also confirmed a relationship between alleles of <i>qESC9</i> and the resistance to salt, underscoring the critical role this locus plays in the determination of overall salt tolerance in rice. Physiological analyses of extreme phenotype lines highlighted the importance of ion exclusion mechanisms in salt-resistant lines, while salt-susceptible lines exhibited elevated oxidative stress and impaired antioxidant defense, contributing to cellular damage. This comprehensive analysis sheds light on the genetic and physiological mechanisms underlying salt stress response in rice, providing valuable insights for breeding programs aimed at enhancing salt resistance in rice.