Population structural analysis of an <i>in-situ</i> conservation site for wild rice in Laos

Abstract

An in-situ conservation site in Laos for a mixture of annual and perennial wild rice, LV27, which is a single swamp with an observation pier has been developed. In order to develop a strategy for evaluation of natural resources, systematic leaf sampling has been conducted and their genetic characteristics measured with 16 SSR loci. In order to determine population structure, a small number of individuals localized together were regarded as sub-populations belonging to a single mother population. Annual individuals were clustered at particular peripheral areas of the pond. Perennial individuals were close by and growing within deeper pond water. Scores of observed heterozygosity (Ho) were not significantly different between annual and perennial sub-populations, but relatively lower in annual ones. Genetic distance among annual and perennial sub-populations in close juxtaposition at peripheral sites showed that annuals were clustered against perennials. In addition, comparison of perennial sub-populations peripheral areas and inside the swamp, found they clustered together and were some distance from annual ones. When the genetic components were compared in detail, private alleles were frequently found in annual plants, suggesting there might be restriction of gene flow between annual and perennial types. Partitions of deep water perennial sub-populations identified private alleles in particular areas, suggesting there were some areas with unique polymorphisms. Combining peripheral perennial sub-populations led to the disappearance of most private alleles which implied there is frequent gene flow among perennial sub-populations. This in-situ conservation site allowed us to observe the succession of populations and also to research detailed population structure of a typical wild population and this found wild rice genetic structure in this single swamp is complex. The data obtained will provide valuable insight about how to evaluate wild populations genetically and how to deal with such populations as field collections.

Diverse genetic variation in maternal lineages with high heterogeneity among <i>in situ</i>-conserved wild rice (<i>Oryza rufipogon</i> Griff.) developed in Thailand

“…Eight SSR primer pairs were used to genotype wild rice in order to characterize the wild populations (Table 1). The PCR conditions employed were the same as those reported by Wang et al (2012). In addition to the SSR markers, three SSR loci were developed and applied.…”

“…Laos is another country where an in situ -conserved population has been developed through collaboration between local and Japanese researchers (Kuroda et al 2007). The site in Laos has been examined for its genetic structure at the molecular level (Wang et al 2012). Annual and perennial rice plants grow together in a shallow area, and only perennial plants are present in the deep water area at the center.…”

Evaluation of genetic variation among wild rice populations in Cambodia

“…Several studies have evaluated genetic variation among wild natural populations in China, Laos, Myanmar, Vietnam and Thailand ( Gao 2004 , Ishii et al 2011 , Kuroda et al 2007 , Pusadee et al 2013 , Wang et al 2012 , Zhou et al 2003 ). They estimated observed and expected heterozygosity values, gene diversity values and genetic distances based on the allelic variation at SSR loci.…”

Genetic diversity among perennial wild rice Oryza rufipogon Griff., in the Mekong Delta

“…Molecular markers have provided a powerful tool for studies of genetic diversity among crop species (Gao, 2004;Olsen & Schaal, 2001;Song, Xu, Wang, Chen, & Lu, 2003), clarifying details of population structure and genetics, and having a significant impact on in situ conservation management (Barbier, 1989;Cai et al, 2004;Ishii et al, 2011;Kaewcheenchai et al, 2018;Wang et al, 2012). In fact, such data can be sampled efficiently from natural populations to monitor the transition of population structures in nature (Gao, 2004;Gao, Shaal, Zang, Jia, & Dong, 2002;Orn et al, 2015;Qian, Tianhua, Song, & Lu, 2005;Wang et al, 2012).…”

“…Molecular markers have provided a powerful tool for studies of genetic diversity among crop species (Gao, 2004;Olsen & Schaal, 2001;Song, Xu, Wang, Chen, & Lu, 2003), clarifying details of population structure and genetics, and having a significant impact on in situ conservation management (Barbier, 1989;Cai et al, 2004;Ishii et al, 2011;Kaewcheenchai et al, 2018;Wang et al, 2012). In fact, such data can be sampled efficiently from natural populations to monitor the transition of population structures in nature (Gao, 2004;Gao, Shaal, Zang, Jia, & Dong, 2002;Orn et al, 2015;Qian, Tianhua, Song, & Lu, 2005;Wang et al, 2012). Since the complete chloroplast (cp) genome became available, cytoplasmic molecular tools have also been developed to clarify evolutionary processes (Chen, Nakamura, Sato, & Nakai, 1993;Kano, Watanabe, Nakamura, & Hirai, 1993;Kim et al., 2015;Masood et al, 2004;Sotowa et al, 2013;Takahashi, Sato, & Nakamura, 2008 (Wambugu, Brozynska, Furtado, Waters, & Henry, 2015;Waters, Nock, Ishikawa, Rice, & Henry, 2012).…”