Fig. 1

The majority of the high-quality SNPs were heterozygous loci among all tested samples. a High-quality SNPs were selected in several steps. “gvcf” contains records for all sites (with or without mutation detection). DP, read depth; GQ, genotype quality; RGQ, GQ at reference sites; MQ, root mean square of the mapping quality of reads across all samples; N, no reads at the site; Ref ALT, loci determined to be homozygous alternative when a variant call was made for the short read used to create the reference genome; Other, loci that were not in the homozygous reference, heterozygous, or homozygous alternative category. GATK-4.2.3 HaplotypeCaller was used for variant calling, with the -ERC BP_RESOLUTION option. b, c High-quality SNPs were analyzed using UpSet plots. Many loci were heterozygous in all samples tested. These plots were created using the R package ComplexUpset. The top 20 combinations in terms of the number of loci were arranged in descending order. Combinations without at least one sample were excluded. The classification of five regions of China (East, Middle, West, South-A, and South-B) is the same as a previous report [14]. b Heterozygous sample combinations and the number of loci. HET, heterozygous. c Homozygous alternative sample combinations and the number of loci. ALT, homozygous alternative. d Loci where all tested samples were heterozygous in WGS analysis were not heterozygous in some of the seedlings of Moso bamboo obtained in 2022. Samples from 1 to 8 were seedlings from different seeds. JAPAN, Japanese Moso bamboo analyzed by WGS; M, pUC19 DNA/MspI (HpaII) Marker. We used dCAPs to detect polymorphisms. 228 bases around scaffold7:10,257,001 were amplified using PCR. After that, restriction enzyme treatment was performed with SmaI. The terminal 23 bases were cleaved by SmaI only in the case of the sequence where scaffold7:10,257,001 was an alternative. Electrophoresis was performed using DNA-500 with Multina. REF, homozygous reference; HET, heterozygous; ALT, homozygous alternative