Development of DNA markers associated with early heading date in F2 populations of RD41 rice variety and KDML 105 photoperiod-insensitive, semi-dwarf rice line. (KDML 105-PISD)
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Abstract
The heading date of rice is a key trait affecting its adaptation and growing season. It is regulated by multiple genetic loci and influenced by environmental factors, especially photoperiod length. This study aimed to develop DNA markers associated with an early heading date in an F2 population derived from a cross between the RD41 rice variety and the photoperiod-insensitive, semi-dwarf KDML 105-PISD rice line. Whole genome sequencing (WGS) was performed on the female and male parent rice cultivars to analyze and identify variations in single nucleotide polymorphisms (SNPs) and insertion/deletion (InDel) positions within the exons of genes involved in controlling heading date at 56 loci. A set of 20 gene markers was identified and developed, enabling a clear distinction between the homozygous alleles of either the female or male parent and the heterozygous alleles combining alleles from both parents. DNA markers were subsequently used to establish a correlation with the early heading date of the F2 population under both NLD and NSD conditions. Through the simple regression analysis, it was observed that the genotypes of DNA markers located at the RFT1 gene exhibited the highest relationship with the early heading date, achieving the coefficient of determination (R-squared; R2) value of 36.52% in NLD and
17.88% in NSD. Analyzed by the multiple regression method, between DNA markers and early heading date, it was found that the genotypes of DNA markers of the RFT1, Hd2, OsDof12 and OsCOL9 genes model were related with early heading date, the R2 value was 61.06% in NLD. While the genotypes of DNA markers of RFT1, Hd6, OsCOL9 and OsDof12 genes model were related to early heading date, the R2 value was 44.54% in NSD. The identified DNA markers can improve breeding efficiency for early heading rice when combined with conventional methods.
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References
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