Genetic structure and diversity in YYT rice accessions
The SNP dataset combining GBS data from 92 YYT accessions and full-genome data from 216 worldwide accessions (Supplementary Information SI1) contained 44,855 SNPs having less than 30% missing calls. Analysis of population subdivision using FastStructure (Fig. 1) showed that YYT rice accessions formed two main groups that differentiated at K=3, i.e., most of the YYT rice lines were closely related to the indica worldwide ecotype, while a part of YYT lines were related to the japonica worldwide ecotype (Fig. 1). This was confirmed by the genealogical relationships among accessions inferred using RAxML (Fig. SI1.1). The FastStructure analysis also showed that from K=7 YYT genotypes clustered according to landrace names used by farmers, indicating that these landraces are ‘population’ varieties composed of distinct, closely related genotypes. Altogether, these analyses showed that, for both indica and japonicatypes, the YYT landraces formed a genetic pool that is related to, but distant from, the worldwide representatives.