Development of molecular markers associated with early heading date in F2 populations of RD79 rice variety and RD43 fragrant glutinous rice line

Abstract

The heading date of rice is a significant agricultural characteristic affecting its adaptation to the environment, with direct implications for both quantity and quality of rice yield. The heading date is a quantitative trait controlled by multiple gene pairs and is influenced by the environment, especially the length of the photoperiod. The purpose of this research was to develop molecular markers associated with an early heading date in the F₂ population resulting from the cross between the RD79 rice variety (female parent) and the RD43 fragrant glutinous rice line with an early heading date (male parent), studying both in natural long-day (NLD) and natural short-day (NSD) conditions. The female and male parent rice cultivars were analyzed using whole genome sequencing (WGS) to analyze and identify variations in single nucleotide polymorphisms (SNPs) and insertion/deletion (InDel) positions within the exons of genes controlling the early heading date. Subsequently, molecular markers were developed, which are associated with specific gene regions and enabling clear distinction between the female and male parents. Molecular markers were subsequently employed to establish a correlation with the early heading date of the F₂ population under NLD and NSD. Through simple regression analysis, it was observed that the genotypes of molecular markers located at the Hd5 gene exhibited the highest relationship with the early heading date, achieving the coefficient of determination (R-squared; R²) value of 50.94% in NLD and 54.81% in NSD. Furthermore, a multiple regression analysis was conducted to examine the relationship between molecular markers and the early heading date, it was found that the model incorporated the use of molecular markers located within specific gene regions of Hd5 and RFT1 genes. The combined model exhibited the most substantial association with the early heading date, yielding R² values of 76.51% in NLD and 68.25% in NSD.