Fig. 4.

Haplotype analyses for the GCC and nucleotide diversity of the LOC_Os05g33300 candidate gene at qCC-5.1. a Haplotype analyses and comparisons of the mean GCC vs LOC_Os05g33300 haplotypes in five rice subgroups. Each red point around each boxplot indicates the GCC of one accession with the relative haplotype in its subgroup. Haplotypes in fewer than 10 accessions are not shown. b Ratio of the nucleotide diversity between modern varieties and landraces for the 600-kb genomic region flanking LOC_Os05g33300. Red and blue lines represent XI and GJ subgroups, respectively. The translucent green rectangle represents the LOC_Os05g33300 genomic region. c Frequencies of different haplotypes of LOC_Os05g33300 in XI and GJ landraces and modern varieties