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Exact(60)
= number of accessions carrying the haplotype among the 91 sequenced; Myanmar = number of accessions from Myanmar carrying the haplotype among the 60 sequenced.
The numbers in the brackets of middle table indicated the number of accessions.
A larger number of accessions from each geographical location should be tested to confirm patterns.
All surveyed O. sativa varieties contain SUB1B and SUB1C, whereas SUB1A is present only in a limited number of accessions.
There was a significant positive correlation between the resolving power (Rp) of each primer and the number of accessions identified (r = 0.96, **P < 0.01).
Despite these chloroplast-related studies, a large number of accessions must be applied to extend these studies from limited collections and specific varieties.
It may be because of less number of accessions grouping in many haplotypes resulting in low minor allele frequencies (<2 %), and synonymous or noncoding nature of the SNPs.
Fig. 3 Provinces of Sri Lanka colour coded by herbicide score with pie graphs indicating group of landraces by province (area proportional to number of accessions).
For analyses involving the HDRA datasets, the number of accessions was 20%and13%3% lower than for the GBS data for the indica and japonica panels, respectively.
This illustrates the trade-off in power between the number of SNPs and the number of accessions.
The highest number of K tested, 20, was an arbitrary and relatively low number given the high number of accessions and geographical locations sampled.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com