Development of DNA markers related to grain size in F5 seed population of a cross between KDML 105 photoperiod-insensitive, semi-dwarf rice line (KDML 105-9351(57D)) and Basmati rice
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Abstract
The size of rice grains is a critical trait that impacts both yield and quality. Considered by length, width, and thickness, it is controlled by polygene. This research aimed to develop grain size-related DNA markers in the F5 seed population of a cross between KDML 105 photoperiod-insensitive, semi-dwarf rice line (KDML 105-9351(57D)) and Basmati rice. In this research, the whole genome sequence of the female parent, KDML 105-9351(57D), and the male parent, Basmati variety, were examined. A comparative analysis of the DNA sequences of the parents was conducted to identify the differences in genes that involved in controlling the size of rice grains at 83 loci. A set of 29 gene markers was discovered and developed, allowing for the discrimination between homozygous alleles of the female parent or male parent and heterozygous alleles between the female and male parent alleles. The analysis of the correlation between genotype and phenotype by Simple regression method was performed. The genotypes of 7 DNA markers of GL7, qGL7-2, GS7, SMG1, TGW6, GS5 and GW6a genes, were found to be significantly relationship with grain length, with the R2 values of 55.51, 54.50, 52.61, 13.59, 4.37, 3.79 and 2.93% respectively. The genotypes of 5 DNA markers of qGL7-2, GL7, GS7, GW10 and TGW6 genes, were significantly relationship with grain width, with the R2 values of 50.62, 50.54, 46.31, 4.16 and 3.26%, respectively. The genotypes of 8 DNA markers of GL7, qGL7-2, GS7, TGW6, GW6a, GW10, GL4 and qGL10 genes, were significantly relationship with grain thickness, with the R2 values of 17.13, 16.27, 14.52, 13.17, 7.44, 6.06, 3.73 and 2.92%, respectively. Analyzed by Multiple regression method, genotypes of DNA markers of GL7, SMG1 and TGW6 genes model were related with grain length, with the R2 value of 64.15%.
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