Reference "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"

Reference ID

11277

Title

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

Source

Genetics, 2005, vol. 169, pp. 1639-1647

Authors (4)

Semon-M	Nielsen-R
Jones-M-P	McCouch-S-R

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.