Unraveling the genetic and molecular bases of heterosis in a TGMS-based two-line rice derived F2 segregating population

Faraz Azeem^1,2Jauhar Ali^1*Tonette. P. Laude²Seyed Mahdi Hosseiniyan Khatibi¹Varunseelan Murugaiyan¹Neeraj Kumar^1,3Angelito Galang¹Madonna Dela Paz¹Erik Jon De Asis¹Atul Singh¹Christian John Robiso¹Carla Francesca Besa¹Pompe C. Sta. Cruz²Eureka Teresa Ocampo²Jose E. Hernandez²

• ¹International Rice Research Institute (IRRI), Los Baños, Philippines
• ²University of the Philippines Los Banos College of Agriculture and Food Science, Laguna, Philippines
• ³Indira Gandhi Krishi Vishwavidyalaya, Raipur, India

Heterosis has been critical for yield improvement in rice, and its genetic and molecular bases remain partially understood. The two-line thermosensitive genic male sterility (TGMS) system is a significant innovation in hybrid rice breeding, yet its heterotic architecture has not been thoroughly dissected. A segregating F₂ population comprising 392 lines, developed from the TGMS-based hybrid IR144693H (IRAC43S × IRV932), provides a strong framework for dissecting complex inheritance patterns. This population enables the concurrent estimation of additive, dominance, and epistatic genetic effects within a single segregating system, thereby enhancing the power and resolution of downstream quantitative genetic analyses. A highly heterotic high-yielding hybrid IR144693H was identified, and its F₂ population was studied using the 1K-RiCA SNPs panel and multi-trait phenotyping. It led to the detection of 24 QTL for yield-related traits, explaining between 4.1% and 67.5% of the variance. Detected QTLs were of large effect, like qNT3011 and qNT6011 on chromosome 11 that controlled tiller number, while qUFG7.2 and qUFG9 reduced unfilled grains, and qTGW12.1 influenced grain weight. In the absence of dedicated reference genomes and expression data for two-line hybrid systems, publicly available Nipponbare datasets were used to identify candidate genes, underscoring the need for hybrid-specific reference datasets. Within these regions, several functionally relevant genes were identified. These included SPP (sucrose-phosphate phosphatase), GW2 (grain width regulator), DEP1 (panicle architecture), and OsCCaMK (calcium/calmodulin-dependent kinase). These findings provide practical targets for marker-assisted selection and functional validation, which could accelerate the identification and development of rice hybrids exhibiting superior heterosis.