Academic journal article Genetics

The Population Structure of African Cultivated Rice Oryza Glaberrima (Steud.): Evidence for Elevated Levels of Linkage Disequilibrium Caused by Admixture with O. Sativa and Ecological Adaptation

Academic journal article Genetics

The Population Structure of African Cultivated Rice Oryza Glaberrima (Steud.): Evidence for Elevated Levels of Linkage Disequilibrium Caused by Admixture with O. Sativa and Ecological Adaptation

Article excerpt

ABSTRACT

Genome-wide linkage disequilibrium (LD) was investigated for 198 accessions of Oryza glaberrima using 93 nuclear microsatellite markers. Significantly elevated levels of LD were detected, even among distantly located markers. Free recombination among loci at the population genetic level was shown (1) by a lack of decay in LD among markers on the same chromosome and (2) by a strictly increasing composite likelihood function for the recombination parameter. This suggested that the elevation in LD was due not to physical linkage but to other factors, such as population structure. A Bayesian clustering analysis confirmed this hypothesis, indicating that the sample of O. glaberrima in this study was subdivided into at least five cryptic subpopulations. Two of these subpopulations clustered with control samples of O. sativa, subspecies indica and japonica, indicating that some O. glaberrima accessions represent admixtures. The remaining three O. glaberrima subpopulations were significantly associated with specific combinations of phenotypic traits-possibly reflecting ecological adaptation to different growing environments.

ORYZA glaberrima (Steud.) is a form of cultivated rice that was domesticated in the Niger River delta ~3500 years ago (VIGUIER 1939) and is widely grown in West Africa today. Germplasm collections of O. glaberrima at the West Africa Rice Development Association (WARDA), the International Institute for Tropical Agriculture and the International Rice Research Institute (IRRI) include ~2800 accessions. Estimates of genetic diversity in O. glaberrima based on RFLP and isozyme markers are significantly lower than those in cultivated Asian rice, O. sativa (secOND 1982, 1986; WANG et al. 1992). Despite this fact and the smaller number of accessions available for study, O. glaberrima harbors a rich reservoir of genes that have allowed the species to survive and prosper in West Africa with minimal human intervention (JONES et al. 1997). Recently, new, highyielding varieties suitable for cultivation in the West African region (NERICA varieties) have been developed from interspecific crosses between O. glaberrima and O. sativa (http://www.warda.org).

There are believed to be three centers of domestication for O. glaberrima, in Mali, the Sene-Gambia, and Guinea (PORTERES 1970), and this may have contributed to the broad ecological adaptation of African rice cultivars today. While genetic evidence points to a common ancestral gene pool ( O. barthii) for all O. glaberrima domesticates, the recent nature of rice domestication in West Africa offers a view into the early stages of genetic differentiation among subpopulations. As a selfpollinating species that has undergone a founder effect, the degree of variation between populations is expected to exceed the variability observed within a field or population, and thus O. glaberrima offers an unusual opportunity to detect and characterize the nature of emerging population structure.

In domesticated species, levels of gene flow among subpopulations are determined by both human-mediated movement of germplasm along major trade routes and natural gene flow resulting from cross-pollination. Between the 15th and 17th centuries, O. sativavfus introduced to West Africa by Arab traders and Portuguese navigators and rapidly spread throughout West Africa. Today, both O. glaberrima and O. sativa are commonly grown in mixtures by farmers in upland and rainfed lowland environments. Natural intermediates between the two species have been reported, but the outcrossing rate is estimated to be low (between 2 and 5%). While O. glaberrima can be crossed with O. sativa, the FI offspring are male sterile and can survive only if pollinated by the mother species. When this occurs, interspecific hybrid progeny can be very productive, as demonstrated by the new, high-yielding varieties for the West Africa region (JONES et al. 1997; http://www.warda.org).

It is of interest to understand the structure and evolution of O. …

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