Analysis of molecular diversity, population structure and linkage disequilibrium in a worldwide survey of cultivated barley germplasm (Hordeum vulgare L.).
Identifieur interne : 003E71 ( Main/Exploration ); précédent : 003E70; suivant : 003E72Analysis of molecular diversity, population structure and linkage disequilibrium in a worldwide survey of cultivated barley germplasm (Hordeum vulgare L.).
Auteurs : Lyudmyla V. Malysheva-Otto [Allemagne] ; Martin W. Ganal ; Marion S. RöderSource :
- BMC genetics [ 1471-2156 ] ; 2006.
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Abstract
BACKGROUND
The goal of our study was a systematic survey of the molecular diversity in barley genetic resources. To this end 953 cultivated barley accessions originating from all inhabited continents except Australia were genotyped with 48 SSR markers. Molecular diversity was evaluated with routine statistics (allelic richness, gene diversity, allele frequency, heterozygosity and unique alleles), Principal Coordinate Analysis (PCoA), and analysis of genome-wide linkage disequilibrium.
RESULTS
A genotyping database for 953 cultivated barley accessions profiled with 48 SSR markers was established. The PCoA revealed structuring of the barley population with regard to (i) geographical regions and (ii) agronomic traits. Geographic origin contributed most to the observed molecular diversity. Genome-wide linkage disequilibrium (LD) was estimated as squared correlation of allele frequencies (r2). The values of LD for barley were comparable to other plant species (conifers, poplar, maize). The pattern of intrachromosomal LD with distances between the genomic loci ranging from 1 to 150 cM revealed that in barley LD extended up to distances as long as 50 cM with r2 > 0.05, or up to 10 cM with r2 > 0.2. Few loci mapping to different chromosomes showed significant LD with r2 > 0.05. The number of loci in significant LD as well as the pattern of LD were clearly dependent on the population structure. The LD in the homogenous group of 207 European 2-rowed spring barleys compared to the highly structured worldwide barley population was increased in the number of loci pairs with r2 > 0.05 and had higher values of r2, although the percentage of intrachromosomal loci pairs in significant LD based on P < 0.001 was 100% in the whole set of varieties, but only 45% in the subgroup of European 2-rowed spring barleys. The value of LD also varied depending on the polymorphism of the loci selected for genotyping. The 17 most polymorphic loci (PIC > 0.80) provided higher LD values as compared to 19 low polymorphic loci (PIC < 0.73) in both structured (all accessions) and non-structured (European 2-rowed spring varieties) barley populations.
CONCLUSION
A global population of cultivated barley accessions was highly structured. Clustering highlighted the accessions with the same geographic origin, as well as accessions possessing similar agronomic characters. LD in barley extended up to 50 cM, and was strongly dependent on the population structure. The data on LD were summarized as a genome-wide LD map for barley.
DOI: 10.1186/1471-2156-7-6
PubMed: 16433922
PubMed Central: PMC1408084
Affiliations:
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Malysheva-Otto</name><affiliation wicri:level="1"><nlm:affiliation>Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Gatersleben, Germany. malysh@ipk-gatersleben.de</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Gatersleben</wicri:regionArea><wicri:noRegion>06466 Gatersleben</wicri:noRegion><wicri:noRegion>06466 Gatersleben</wicri:noRegion><wicri:noRegion>06466 Gatersleben</wicri:noRegion></affiliation></author><author><name sortKey="Ganal, Martin W" sort="Ganal, Martin W" uniqKey="Ganal M" first="Martin W" last="Ganal">Martin W. Ganal</name></author><author><name sortKey="Roder, Marion S" sort="Roder, Marion S" uniqKey="Roder M" first="Marion S" last="Röder">Marion S. 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Malysheva-Otto</name><affiliation wicri:level="1"><nlm:affiliation>Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Gatersleben, Germany. malysh@ipk-gatersleben.de</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Gatersleben</wicri:regionArea><wicri:noRegion>06466 Gatersleben</wicri:noRegion><wicri:noRegion>06466 Gatersleben</wicri:noRegion><wicri:noRegion>06466 Gatersleben</wicri:noRegion></affiliation></author><author><name sortKey="Ganal, Martin W" sort="Ganal, Martin W" uniqKey="Ganal M" first="Martin W" last="Ganal">Martin W. Ganal</name></author><author><name sortKey="Roder, Marion S" sort="Roder, Marion S" uniqKey="Roder M" first="Marion S" last="Röder">Marion S. Röder</name></author></analytic><series><title level="j">BMC genetics</title><idno type="eISSN">1471-2156</idno><imprint><date when="2006" type="published">2006</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Chromosome Mapping (MeSH)</term><term>Genetic Variation (MeSH)</term><term>Genome, Plant (MeSH)</term><term>Geography (MeSH)</term><term>Hordeum (genetics)</term><term>Linkage Disequilibrium (MeSH)</term><term>Repetitive Sequences, Nucleic Acid (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Cartographie chromosomique (MeSH)</term><term>Déséquilibre de liaison (MeSH)</term><term>Génome végétal (MeSH)</term><term>Géographie (MeSH)</term><term>Hordeum (génétique)</term><term>Séquences répétées d'acides nucléiques (MeSH)</term><term>Variation génétique (MeSH)</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Hordeum</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Hordeum</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Chromosome Mapping</term><term>Genetic Variation</term><term>Genome, Plant</term><term>Geography</term><term>Linkage Disequilibrium</term><term>Repetitive Sequences, Nucleic Acid</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Cartographie chromosomique</term><term>Déséquilibre de liaison</term><term>Génome végétal</term><term>Géographie</term><term>Séquences répétées d'acides nucléiques</term><term>Variation génétique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><b>BACKGROUND</b></p><p>The goal of our study was a systematic survey of the molecular diversity in barley genetic resources. To this end 953 cultivated barley accessions originating from all inhabited continents except Australia were genotyped with 48 SSR markers. Molecular diversity was evaluated with routine statistics (allelic richness, gene diversity, allele frequency, heterozygosity and unique alleles), Principal Coordinate Analysis (PCoA), and analysis of genome-wide linkage disequilibrium.</p></div><div type="abstract" xml:lang="en"><p><b>RESULTS</b></p><p>A genotyping database for 953 cultivated barley accessions profiled with 48 SSR markers was established. The PCoA revealed structuring of the barley population with regard to (i) geographical regions and (ii) agronomic traits. Geographic origin contributed most to the observed molecular diversity. Genome-wide linkage disequilibrium (LD) was estimated as squared correlation of allele frequencies (r2). The values of LD for barley were comparable to other plant species (conifers, poplar, maize). The pattern of intrachromosomal LD with distances between the genomic loci ranging from 1 to 150 cM revealed that in barley LD extended up to distances as long as 50 cM with r2 > 0.05, or up to 10 cM with r2 > 0.2. Few loci mapping to different chromosomes showed significant LD with r2 > 0.05. The number of loci in significant LD as well as the pattern of LD were clearly dependent on the population structure. The LD in the homogenous group of 207 European 2-rowed spring barleys compared to the highly structured worldwide barley population was increased in the number of loci pairs with r2 > 0.05 and had higher values of r2, although the percentage of intrachromosomal loci pairs in significant LD based on P < 0.001 was 100% in the whole set of varieties, but only 45% in the subgroup of European 2-rowed spring barleys. The value of LD also varied depending on the polymorphism of the loci selected for genotyping. The 17 most polymorphic loci (PIC > 0.80) provided higher LD values as compared to 19 low polymorphic loci (PIC < 0.73) in both structured (all accessions) and non-structured (European 2-rowed spring varieties) barley populations.</p></div><div type="abstract" xml:lang="en"><p><b>CONCLUSION</b></p><p>A global population of cultivated barley accessions was highly structured. Clustering highlighted the accessions with the same geographic origin, as well as accessions possessing similar agronomic characters. LD in barley extended up to 50 cM, and was strongly dependent on the population structure. The data on LD were summarized as a genome-wide LD map for barley.</p></div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">16433922</PMID><DateCompleted><Year>2006</Year><Month>04</Month><Day>24</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2156</ISSN><JournalIssue CitedMedium="Internet"><Volume>7</Volume><PubDate><Year>2006</Year><Month>Jan</Month><Day>24</Day></PubDate></JournalIssue><Title>BMC genetics</Title><ISOAbbreviation>BMC Genet</ISOAbbreviation></Journal><ArticleTitle>Analysis of molecular diversity, population structure and linkage disequilibrium in a worldwide survey of cultivated barley germplasm (Hordeum vulgare L.).</ArticleTitle><Pagination><MedlinePgn>6</MedlinePgn></Pagination><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">The goal of our study was a systematic survey of the molecular diversity in barley genetic resources. To this end 953 cultivated barley accessions originating from all inhabited continents except Australia were genotyped with 48 SSR markers. Molecular diversity was evaluated with routine statistics (allelic richness, gene diversity, allele frequency, heterozygosity and unique alleles), Principal Coordinate Analysis (PCoA), and analysis of genome-wide linkage disequilibrium.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">A genotyping database for 953 cultivated barley accessions profiled with 48 SSR markers was established. The PCoA revealed structuring of the barley population with regard to (i) geographical regions and (ii) agronomic traits. Geographic origin contributed most to the observed molecular diversity. Genome-wide linkage disequilibrium (LD) was estimated as squared correlation of allele frequencies (r2). The values of LD for barley were comparable to other plant species (conifers, poplar, maize). The pattern of intrachromosomal LD with distances between the genomic loci ranging from 1 to 150 cM revealed that in barley LD extended up to distances as long as 50 cM with r2 > 0.05, or up to 10 cM with r2 > 0.2. Few loci mapping to different chromosomes showed significant LD with r2 > 0.05. The number of loci in significant LD as well as the pattern of LD were clearly dependent on the population structure. The LD in the homogenous group of 207 European 2-rowed spring barleys compared to the highly structured worldwide barley population was increased in the number of loci pairs with r2 > 0.05 and had higher values of r2, although the percentage of intrachromosomal loci pairs in significant LD based on P < 0.001 was 100% in the whole set of varieties, but only 45% in the subgroup of European 2-rowed spring barleys. The value of LD also varied depending on the polymorphism of the loci selected for genotyping. The 17 most polymorphic loci (PIC > 0.80) provided higher LD values as compared to 19 low polymorphic loci (PIC < 0.73) in both structured (all accessions) and non-structured (European 2-rowed spring varieties) barley populations.</AbstractText><AbstractText Label="CONCLUSION" NlmCategory="CONCLUSIONS">A global population of cultivated barley accessions was highly structured. Clustering highlighted the accessions with the same geographic origin, as well as accessions possessing similar agronomic characters. LD in barley extended up to 50 cM, and was strongly dependent on the population structure. 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Ganal</name><name sortKey="Roder, Marion S" sort="Roder, Marion S" uniqKey="Roder M" first="Marion S" last="Röder">Marion S. Röder</name></noCountry><country name="Allemagne"><noRegion><name sortKey="Malysheva Otto, Lyudmyla V" sort="Malysheva Otto, Lyudmyla V" uniqKey="Malysheva Otto L" first="Lyudmyla V" last="Malysheva-Otto">Lyudmyla V. Malysheva-Otto</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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