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
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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. / Semon, Mande; Nielsen, Rasmus; Jones, Monty P.; McCouch, Susan R.
I: Genetics, Bind 169, Nr. 3, 2005, s. 1639-1647.Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › fagfællebedømt
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TY - JOUR
T1 - The Population Structure of African Cultivated Rice Oryza glaberrima (Steud.)
T2 - Evidence for Elevated Levels of Linkage Disequilibrium Caused by Admixture with O. sativa and Ecological Adaptation
AU - Semon, Mande
AU - Nielsen, Rasmus
AU - Jones, Monty P.
AU - McCouch, Susan R.
PY - 2005
Y1 - 2005
N2 - 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.
AB - 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.
U2 - 10.1534/genetics.104.033175
DO - 10.1534/genetics.104.033175
M3 - Journal article
C2 - 15545652
VL - 169
SP - 1639
EP - 1647
JO - Genetics
JF - Genetics
SN - 1943-2631
IS - 3
ER -
ID: 87249