Genetic diversity and population structure of ‘Khao Kai Noi’, a Lao rice (<i>Oryza sativa</i> L.) landrace, revealed by microsatellite DNA markers

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  • Vilayheuang Koukham
    Graduate School of Life and Environmental Sciences, University of Tsukuba Agriculture Research Center, National Agriculture and Forestry Research Institute (NAFRI)
  • Machida-Hirano Ryoko
    Gene Research Center, University of Tsukuba
  • Bounphanousay Chay
    Agriculture Research Center, National Agriculture and Forestry Research Institute (NAFRI)
  • Watanabe Kazuo N.
    Gene Research Center, University of Tsukuba Faculty of Life and Environmental Sciences, University of Tsukuba

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  • Genetic diversity and population structure of 'Khao Kai Noi', a Lao rice (Oryza sativa L.) landrace, revealed by microsatellite DNA markers
  • Breeding, genetics, and genomics of fruit trees

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Abstract

Rice (Oryza sativa L.) is the main food for people in Laos, where it has been grown and eaten since prehistory. Diverse landraces are grown in Laos. ‘Khao Kai Noi’, a landrace favored for its eating quality, is held in the nationwide collection of traditional landraces in the Lao national genebank. Genetic diversity is crucial for sustainable use of genetic resources and conservation. To investigate the genetic diversity of ‘Khao Kai Noi’ for conservation, we genotyped 70 accessions by using 23 polymorphic simple sequence repeat markers. The markers generated 2 to 17 alleles (132 in total), with an average of 5.7 per locus. The total expected heterozygosity over all ‘Khao Kai Noi’ accessions was 0.271. Genetic variation was largest among accessions and smallest within accessions. Khao Kai Noi accessions were classified into three different genetic backgrounds, but there was unclear association between the three inferred population and name subgroups and geographical distribution. Most of the accessions were clustered with temperate japonica and showed genetic relatedness to rice from neighboring provinces of Vietnam, suggesting a Vietnamese origin. The results of this study will contribute to the conservation, core collection and future breeding of the Khao Kai Noi population.

Journal

  • Breeding Science

    Breeding Science 66 (2), 204-212, 2016

    Japanese Society of Breeding

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