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

Mande Semon; Rasmus Nielsen; Monty P. Jones; Susan R. McCouch

doi:10.1534/genetics.104.033175

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

Mande Semon, Rasmus Nielsen, Monty P. Jones, Susan R. McCouch

Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

128 Citationer (Scopus)

Abstract

Udgivelsesdato: March 2005

Originalsprog	Engelsk
Tidsskrift	Genetics
Vol/bind	169
Udgave nummer	3
Sider (fra-til)	1639-1647
ISSN	0016-6731
DOI	https://doi.org/10.1534/genetics.104.033175
Status	Udgivet - 2005

Adgang til dokumentet

10.1534/genetics.104.033175

Citationsformater

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. et al.
I: Genetics, Bind 169, Nr. 3, 2005, s. 1639-1647.

Publikation: Bidrag til tidsskrift › Tidsskriftartikel › Forskning › peer review

@article{23e3fbb074c311dbbee902004c4f4f50,

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",

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. ",

author = "Mande Semon and Rasmus Nielsen and Jones, {Monty P.} and McCouch, {Susan R.}",

year = "2005",

doi = "10.1534/genetics.104.033175",

language = "English",

volume = "169",

pages = "1639--1647",

journal = "Genetics",

issn = "0016-6731",

publisher = "The Genetics Society of America (GSA)",

number = "3",

}

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

SN - 0016-6731

VL - 169

SP - 1639

EP - 1647

JO - Genetics

JF - Genetics

IS - 3

ER -