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

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


  • Breeding Science

    Breeding Science 66(4), 580-590, 2016

    Japanese Society of Breeding


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