Genetic diversity of the flanking region in rice landraces in northern Laos.

A glutinous texture of endosperm is one of the important traits of rice ( L.). Northern Laos is known as a center of glutinous rice diversity. We genotyped INDEL, SSR and SNP markers in a sample of 297 rice landraces collected in northern Laos. These glutinous varieties were confirmed to share a loss-of-function mutation in (). INDEL markers revealed a high frequency of recombinant genotypes between and . Principal component analysis using SSR genotypes of flanking region revealed that glutinous landraces were scattered between non-glutinous and glutinous- types. High ratios of heterozygosity were found especially in glutinous . Haplotype analysis using SNP markers around locus revealed that glutinous landraces would have a few chromosome segments of glutinous . Frequent recombinations were confirmed outside of this region in glutinous . This intricate genetic structure of landraces suggested that glutinous landraces in Laos were generated through repeated natural crossing with glutinous- landraces and severe selection by local farmers.