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Haplotype analysis revealed that significant differences for LVN were between different haplotypes at the gene in japonica accessions.
Highly significant differences in LVN were detected between different haplotypes at the candidate gene (Os06g0685700) in japonica, though there was no significant difference for LVN between different haplotypes in indica accessions (Fig. 3c d).
However, no significant difference in SVA and SVXA was detected between different haplotypes at the two candidate genes in indica subpopulation, and only one prevalent haplotype of each gene was detected in japonica subpopulation (Additional file 5: Table S2).
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Significant differences for LVN between different haplotypes were observed at Os06g0685700 in whole population (Fig. 3c d).In this study, haplotype was separately analyzed for indica and japonica varieties owing to the significant differentiation in LVN between the two subspecies.
Highly significant differences for qLVA4.1 and qLVPA4.1 between different haplotypes were observed at the two genes (Os04g0613000 and Os04g0615000) in whole population (Fig. 4c d).
We detected no differences in T1D manifestation age between different haplotypes.
It is interesting that the logic applied by Bandelt and Salas means that any single somatic mutation occurring at a nucleotide that is polymorphic between different haplotypes can simply be explained by sample mixing.
Platten et al. (2013) observed comparatively lower nucleotide diversity and haplotypic diversity in cultivated rice and identified relationship between different haplotypes and salt tolerance for HKT1 5 gene.
T1D onset age, residual serum C-peptide level, and insulin requirement were comparable between different haplotypes.
To assess the level of variation in the COI sequences, uncorrected (p) pairwise genetic distances between different haplotypes were estimated with PAUP* v4.0b10 (Swofford, 2002).
The model is flexible to be extended to model a complex network of genetic regulation that includes the interactions between different haplotypes and between haplotypes and environments.
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