Patterns of genetic diversity and linkage disequilibrium in a highly structured Hordeum vulgare association-mapping population for the Mediterranean basin

J. Comodran, W.T.B. Thomas, F.A. van Eeuwijk, S. Ceccarelli, S. Grando, A.M. Stanca, N. Pecchioni, T. Akar, A. Al-Yassin, A. Benbelkacem, H. Ouabbou, J. Bort, I. Romagosa, C.A. Hackett, J.R. Russel

Research output: Contribution to journalArticleAcademicpeer-review

76 Citations (Scopus)

Abstract

Population structure and genome-wide linkage disequilibrium (LD) were investigated in 192 Hordeum vulgare accessions providing a comprehensive coverage of past and present barley breeding in the Mediterranean basin, using 50 nuclear microsatellite and 1,130 DArT® markers. Both clustering and principal coordinate analyses clearly sub-divided the sample into five distinct groups centred on key ancestors and regions of origin of the germplasm. For given genetic distances, large variation in LD values was observed, ranging from closely linked markers completely at equilibrium to marker pairs at 50 cM separation still showing significant LD. Mean LD values across the whole population sample decayed below r 2 of 0.15 after 3.2 cM. By assaying 1,130 genome-wide DArT® markers, we demonstrated that, after accounting for population substructure, current genome coverage of 1 marker per 1.5 cM except for chromosome 4H with 1 marker per 3.62 cM is sufficient for whole genome association scans. We show, by identifying associations with powdery mildew that map in genomic regions known to have resistance loci, that associations can be detected in strongly stratified samples provided population structure is effectively controlled in the analysis. The population we describe is, therefore, shown to be a valuable resource, which can be used in basic and applied research in barley
Original languageEnglish
Pages (from-to)175-187
JournalTheoretical and Applied Genetics
Volume119
Issue number1
DOIs
Publication statusPublished - 2009

Fingerprint

Genetic Linkage
Linkage Disequilibrium
Hordeum
linkage disequilibrium
Hordeum vulgare
chromosome mapping
basins
genetic variation
genome
Genome
Population
population structure
barley
powdery mildew
sampling
genetic distance
germplasm
ancestry
Microsatellite Repeats
Breeding

Keywords

  • multilocus genotype data
  • ssp-spontaneum
  • haplotype structure
  • powdery mildew
  • barley
  • genome
  • resistance
  • loci
  • polymorphism
  • cultivars

Cite this

Comodran, J. ; Thomas, W.T.B. ; van Eeuwijk, F.A. ; Ceccarelli, S. ; Grando, S. ; Stanca, A.M. ; Pecchioni, N. ; Akar, T. ; Al-Yassin, A. ; Benbelkacem, A. ; Ouabbou, H. ; Bort, J. ; Romagosa, I. ; Hackett, C.A. ; Russel, J.R. / Patterns of genetic diversity and linkage disequilibrium in a highly structured Hordeum vulgare association-mapping population for the Mediterranean basin. In: Theoretical and Applied Genetics. 2009 ; Vol. 119, No. 1. pp. 175-187.
@article{ce09b8ed3bb94ee583b55692a4c4f244,
title = "Patterns of genetic diversity and linkage disequilibrium in a highly structured Hordeum vulgare association-mapping population for the Mediterranean basin",
abstract = "Population structure and genome-wide linkage disequilibrium (LD) were investigated in 192 Hordeum vulgare accessions providing a comprehensive coverage of past and present barley breeding in the Mediterranean basin, using 50 nuclear microsatellite and 1,130 DArT{\circledR} markers. Both clustering and principal coordinate analyses clearly sub-divided the sample into five distinct groups centred on key ancestors and regions of origin of the germplasm. For given genetic distances, large variation in LD values was observed, ranging from closely linked markers completely at equilibrium to marker pairs at 50 cM separation still showing significant LD. Mean LD values across the whole population sample decayed below r 2 of 0.15 after 3.2 cM. By assaying 1,130 genome-wide DArT{\circledR} markers, we demonstrated that, after accounting for population substructure, current genome coverage of 1 marker per 1.5 cM except for chromosome 4H with 1 marker per 3.62 cM is sufficient for whole genome association scans. We show, by identifying associations with powdery mildew that map in genomic regions known to have resistance loci, that associations can be detected in strongly stratified samples provided population structure is effectively controlled in the analysis. The population we describe is, therefore, shown to be a valuable resource, which can be used in basic and applied research in barley",
keywords = "multilocus genotype data, ssp-spontaneum, haplotype structure, powdery mildew, barley, genome, resistance, loci, polymorphism, cultivars",
author = "J. Comodran and W.T.B. Thomas and {van Eeuwijk}, F.A. and S. Ceccarelli and S. Grando and A.M. Stanca and N. Pecchioni and T. Akar and A. Al-Yassin and A. Benbelkacem and H. Ouabbou and J. Bort and I. Romagosa and C.A. Hackett and J.R. Russel",
year = "2009",
doi = "10.1007/s00122-009-1027-0",
language = "English",
volume = "119",
pages = "175--187",
journal = "Theoretical and Applied Genetics",
issn = "0040-5752",
publisher = "Springer Verlag",
number = "1",

}

Comodran, J, Thomas, WTB, van Eeuwijk, FA, Ceccarelli, S, Grando, S, Stanca, AM, Pecchioni, N, Akar, T, Al-Yassin, A, Benbelkacem, A, Ouabbou, H, Bort, J, Romagosa, I, Hackett, CA & Russel, JR 2009, 'Patterns of genetic diversity and linkage disequilibrium in a highly structured Hordeum vulgare association-mapping population for the Mediterranean basin' Theoretical and Applied Genetics, vol. 119, no. 1, pp. 175-187. https://doi.org/10.1007/s00122-009-1027-0

Patterns of genetic diversity and linkage disequilibrium in a highly structured Hordeum vulgare association-mapping population for the Mediterranean basin. / Comodran, J.; Thomas, W.T.B.; van Eeuwijk, F.A.; Ceccarelli, S.; Grando, S.; Stanca, A.M.; Pecchioni, N.; Akar, T.; Al-Yassin, A.; Benbelkacem, A.; Ouabbou, H.; Bort, J.; Romagosa, I.; Hackett, C.A.; Russel, J.R.

In: Theoretical and Applied Genetics, Vol. 119, No. 1, 2009, p. 175-187.

Research output: Contribution to journalArticleAcademicpeer-review

TY - JOUR

T1 - Patterns of genetic diversity and linkage disequilibrium in a highly structured Hordeum vulgare association-mapping population for the Mediterranean basin

AU - Comodran, J.

AU - Thomas, W.T.B.

AU - van Eeuwijk, F.A.

AU - Ceccarelli, S.

AU - Grando, S.

AU - Stanca, A.M.

AU - Pecchioni, N.

AU - Akar, T.

AU - Al-Yassin, A.

AU - Benbelkacem, A.

AU - Ouabbou, H.

AU - Bort, J.

AU - Romagosa, I.

AU - Hackett, C.A.

AU - Russel, J.R.

PY - 2009

Y1 - 2009

N2 - Population structure and genome-wide linkage disequilibrium (LD) were investigated in 192 Hordeum vulgare accessions providing a comprehensive coverage of past and present barley breeding in the Mediterranean basin, using 50 nuclear microsatellite and 1,130 DArT® markers. Both clustering and principal coordinate analyses clearly sub-divided the sample into five distinct groups centred on key ancestors and regions of origin of the germplasm. For given genetic distances, large variation in LD values was observed, ranging from closely linked markers completely at equilibrium to marker pairs at 50 cM separation still showing significant LD. Mean LD values across the whole population sample decayed below r 2 of 0.15 after 3.2 cM. By assaying 1,130 genome-wide DArT® markers, we demonstrated that, after accounting for population substructure, current genome coverage of 1 marker per 1.5 cM except for chromosome 4H with 1 marker per 3.62 cM is sufficient for whole genome association scans. We show, by identifying associations with powdery mildew that map in genomic regions known to have resistance loci, that associations can be detected in strongly stratified samples provided population structure is effectively controlled in the analysis. The population we describe is, therefore, shown to be a valuable resource, which can be used in basic and applied research in barley

AB - Population structure and genome-wide linkage disequilibrium (LD) were investigated in 192 Hordeum vulgare accessions providing a comprehensive coverage of past and present barley breeding in the Mediterranean basin, using 50 nuclear microsatellite and 1,130 DArT® markers. Both clustering and principal coordinate analyses clearly sub-divided the sample into five distinct groups centred on key ancestors and regions of origin of the germplasm. For given genetic distances, large variation in LD values was observed, ranging from closely linked markers completely at equilibrium to marker pairs at 50 cM separation still showing significant LD. Mean LD values across the whole population sample decayed below r 2 of 0.15 after 3.2 cM. By assaying 1,130 genome-wide DArT® markers, we demonstrated that, after accounting for population substructure, current genome coverage of 1 marker per 1.5 cM except for chromosome 4H with 1 marker per 3.62 cM is sufficient for whole genome association scans. We show, by identifying associations with powdery mildew that map in genomic regions known to have resistance loci, that associations can be detected in strongly stratified samples provided population structure is effectively controlled in the analysis. The population we describe is, therefore, shown to be a valuable resource, which can be used in basic and applied research in barley

KW - multilocus genotype data

KW - ssp-spontaneum

KW - haplotype structure

KW - powdery mildew

KW - barley

KW - genome

KW - resistance

KW - loci

KW - polymorphism

KW - cultivars

U2 - 10.1007/s00122-009-1027-0

DO - 10.1007/s00122-009-1027-0

M3 - Article

VL - 119

SP - 175

EP - 187

JO - Theoretical and Applied Genetics

JF - Theoretical and Applied Genetics

SN - 0040-5752

IS - 1

ER -