Population genetic analysis of genomic variation in rice
In the total sample containing 92 YYT and 216 worldwide rice accessions,
population subdivision was assessed without considering a prioriinformation about the name, rice type or location of origin of rice
samples with FastStructure, by varying the number of clusters
(K) from 2 to 10 (Raj,
Stephens, & Pritchard, 2014), using BED and BIM files generated with
PLINK (Purcell et al.,
2017). Genetic clustering was also inferred for the 46 rice accessions
paired with corresponding P. oryzae isolates using sNMF analyses
by generating GenLight object in R-statistical environment, and running
the analyses by varying the number of clusters (K) from 2 to 10. We
inferred the genealogical relationships between these 46 accessions with
RAxML (Stamatakis,
2014), based on pseudo-assembled genomic sequences (i.e. genomic
sequences generated from the table of SNPs and reference sequences). We
used the General Time-Reversible model of nucleotide substitution with
the Γ model of rate heterogeneity, and performed 100 bootstrap
replicates to estimate branch support.