Genetic diversity in the northernmost Oryza rufipogon populations estimated by SSR markers

Abstract

To estimate genetic diversity of the residual northern populations of Oryza rufipogon, a total of 232 individuals from six populations were analyzed using microsatellites (SSRs). The O. rufipogon populations with different status included three from Dongxiang (Jiangxi Province) and three from Chaling (Hunan Province) in China. The 23 rice SSR primer pairs selected from the RiceGenes Database detected a total of 115 alleles, indicating that all the SSR loci were polymorphic in this study. The total gene diversity was 0.919 in the six O. rufipogon populations, and the Donxiang populations showed higher diversity than the Chaling populations. More significant genetic differentiation and less gene flow were found among the Dongxiang populations than those from Chaling. The two putative introgressed populations showed relatively high genetic variation. One in situ conserved population from Dongxiang had the lowest level of genetic diversity. The re-introduced population from Chaling restored about 90% of the genetic variation, compared with the original source population. It is concluded from these results that a relatively high level of genetic variation resided in the northern O. rufipogon populations and continued efforts of conservation of these populations are needed; and that the conservation of some Chaling and Dongxiang populations has been effective in preventing gene flow from cultivated rice. Introgression of cultivated rice demonstrated significant impacts on genetic variability of the O. rufipogon populations, and should be carefully considered in conserving this wild rice. This study also suggested that re-introduction to its original habitats is an effective approach to restore O. rufipogon populations.

Microsatellite Analysis of Genetic Variation and Population Genetic Differentiation in Autotetraploid and Diploid Rice

“…The 50 accessions included 36 three-line parents of autotetraploid rice and 14 original diploid rices. The observed level of genetic diversity from the SSRs and its distributive pattern in our diploid rices were generally consistent with those of most previous studies based on much larger samples (Song et al 2003); this, however, is the first study of diversity in autotetraploid rices. The UPGMA tree presented in Fig.…”

“…Consequently, the codominant SSR banding patterns were scored as AA or BB (for homozygote) and AB (for heterozygote) genotypes, corresponding to the alleles identified in the Gramene Database (Song et al 2003). SSR genotypes were determined based on their migration relative to the DNA marker and four varieties (Minghui63, Gang46B, IR36, and CDR22) loaded in each gel as references (Yu et al 2003).…”

“…The 36 SSR loci produced a total of 303 alleles among the 50 accessions assayed. The A e , H e , PIC, and I were used to demonstrate the population level of genetic diversity (Table 2) (Song et al 2003;Hovmalm et al 2004). In general, the populations included in this study showed a relatively high level of genetic diversity, with A e of 3.028, ranging from 2 to 6; H e of 0.366, ranging from 0.039 to 0.762; PIC of 0.339, ranging from 0.027 (RM125 on chromosome 8) to 0.734 (RM102 on chromosome 11); and I of 0.649, ranging from 0.098 to 1.613.…”

Genetic Diversity of Isolated Populations of Indonesian Landraces of Rice (Oryza sativa L.) Collected in East Kalimantan on the Island of Borneo

“…Natural populations tend to be more stable than cultivars in their geographic distributions because the forces of natural selection generally lead to gradual changes over evolutionary time. Several studies carried out on wild rice populations in China have characterized the local diversity of Oryza rufipogon and found varying degrees of differentiation within and between local populations (Song et al 2003;Xu et al 2006;Zhou et al 2003). In contrast, the accelerated evolution provided by intense artificial selection and seed exchanges among local farmers has led to dramatic changes in the genetics of cultivated crops in a relatively short time frame (<10,000 years).…”

Evaluation of Genetic Variation Among Wild Populations and Local Varieties of Rice

“…They usually used seed/plant materials derived from wild rice accessions maintained in germplasm institutes or seed banks, but these accessions do not represent the features of natural wild rice. Wild natural populations in southern China were investigated by several research groups (Song et al 2003;Zhou et al 2003;Gao 2004); however, those in the major distribution area of O. rufipogon have never been analyzed in detail. In this study, a large-scale survey on wild rice was carried out using 976 individuals from six natural populations in Myanmar and Vietnam, and genetic variation among wild rice populations was evaluated.…”