Table 1.
Details of the 10 molecular markers for 7 grain size regulating genes used in the present studied.
Table 2.
Descriptive statistics for grain size traits in 89 rice germplasm.
Table 3.
Correlation coefficients analysis among the four traits for grain size.
Fig 1.
Profiling of GS3-PstI functional CAPS marker in representative rice germplasm.
The digested PCR fragments were separated in 1.2% agarose gel. Lane: M—100 bp DNA ladder, 1–36 represents rice germplasm. The size of the DNA fragments is indicated on the side of the figure.
Fig 2.
Representatives of PCR amplified fragments of linked/functional markers of 7 genes.
Lane: M1–100 bp DNA ladder, M2 – 1Kb DNA ladder, 1–24 represents rice germplasm. The size of the DNA fragments is indicated on the right side of the figure.
Table 4.
Analysis of allelic variation of 7 grain regulating genes in 89 germplasm.
Fig 3.
Frequency distribution of favourable alleles of six genes related to grain size in 89 rice germplasm.
Table 5.
Pyramiding of favourable alleles of six genes for GL and GLWR.
Table 6.
Estimation of major allele frequency, allele per locus, gene diversity, expected heterozygosity, PIC in 89 rice germplasm.
Fig 4.
Cluster analysis of 89 germplasm based on 7 grain size regulating genes.
Table 7.
Genetic association of 7 genes for rice grain size traits.
Fig 5.
Population structure of 89 germplasm based on 10 markers (K = 3) and graph of estimated membership fraction for K = 3.
The maximum of adhoc measure ΔK determined by structure harvester was found to be K = 3, which indicated that the entire population can be grouped into three subgroups. Different color within group indicates the proportion of shared ancestry with other group which has the same color with the admixture.
Fig 6.
Analysis of molecular variance (AMOVA) and Principal Coordinate Analysis (PCoA) of 89 rice germplasm based on 10 linked/functional markers.
Two dimensional PCoA display of 89 germplasm based on 10 markers. Coord-1 and Coord-2 represent first and second coordinates, respectively. The two PCA axes accounted for 32.89% and 20.98% % of the genetic variation among populations.
Table 8.
Results of analysis of molecular variance (AMOVA).
Table 9.
Pair-wise FST estimates among three populations of germplasm.