The DNA sequences of each cultivar were analysed by an Illumina HiSeq 2000/2500 system (Illumina Co, Ltd.)38 (link),39 (link) and mapped to Os-Nipponbare-Reference-IRGSP-1.040 (link),41 (link). We identified a total of 670,069 single nucleotide polymorphisms (SNPs) and InDels after removing nucleotide variations with missing rates > 0.10 and a minor allele frequency < 0.025. To illustrate the population structure from genotype data, we performed principal component analysis using the R function “prcomp”.
Chigira K., Kojima N., Yamasaki M., Yano K., Adachi S., Nomura T., Jiang M., Katsura K, & Ookawa T. (2020). Landraces of temperate japonica rice have superior alleles for improving culm strength associated with lodging resistance. Scientific Reports, 10, 19855.
Dna sequencesGenotype Indels Nucleotide Single nucleotide polymorphisms
Corresponding Organization :
Other organizations :
Tokyo University of Agriculture and Technology, Kobe University, RIKEN Center for Advanced Intelligence Project, Ibaraki University, Guizhou Academy of Agricultural Sciences, Rice Research Institute
Single nucleotide polymorphisms (SNPs) and InDels identified after removing nucleotide variations with missing rates > 0.10 and a minor allele frequency < 0.025
Population structure from genotype data
control variables
Os-Nipponbare-Reference-IRGSP-1.0 genome used for mapping
controls
Positive control: Not specified
Negative control: Not specified
Annotations
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