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We selected unique sequences that represented the primary haplotype groups, and we used 16 sequences that originated from individuals sampled in 11 European countries (Austria, France, Germany, Holland, Hungary, Italy, Poland, Serbia, Spain, Sweden, and the UK).
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The mutations (different SNPs) between haplotypes and the primary haplotype in each group were less than five.
Three haplotype groups (japonica-haplotypes I, II and indica/aus-haplotype) represented the largest proportion of DPRK germplasm and contained both landraces and improved varieties.
Excluding W1 and admixed individuals, there was good correspondence between chloroplast haplotype groups and subpopulations.
Two distinct haplotype groups were identified that may both be associated with Pi33 resistance (Additional file 6: Table S4).
We find three closely related haplotype groups.
Some of these haplotype groups have been associated with ARHI.
For the assignment of haplotype groups, homoplasious substitutions were ignored.
cpHG = cpDNA diversity measured by the number of haplotype groups.
There are two main haplotypes that explain 25% of variation: low-dose haplotype group (A) and a high-dose haplotype group (B).
The other four accessions belonged to the haplotype group VII.
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