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A glutinous texture of endosperm is one of the important traits of rice ( Oyza sativa 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 Granule bound starch synthase I ( Wx ). INDEL markers revealed a high frequency of recombinant genotypes between indica and japonica . Principal component analysis using SSR genotypes of Wx flanking region revealed that glutinous indica landraces were scattered between non-glutinous indica and glutinous- japonica types. High ratios of heterozygosity were found especially in glutinous indica . Haplotype analysis using SNP markers around Wx locus revealed that glutinous indica landraces would have a few chromosome segments of glutinous japonica . Frequent recombinations were confirmed outside of this region in glutinous indica . This intricate genetic structure of landraces suggested that glutinous indica landraces in Laos were generated through repeated natural crossing with glutinous- japonica landraces and severe selection by local farmers.

Genetic diversity of the <i>wx</i> flanking region in rice landraces in northern Laos