Low linkage disequilibrium in wild <it>Anopheles gambiae s.l</it>. populations
<p>Abstract</p> <p>Background</p> <p>In the malaria vector <it>Anopheles gambiae</it>, understanding diversity in natural populations and genetic components of important phenotypes such as resistance to malaria infection is crucial for developing new malaria...
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BMC
2010-09-01
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| Series: | BMC Genetics |
| Online Access: | http://www.biomedcentral.com/1471-2156/11/81 |
| _version_ | 1811234316087197696 |
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| author | Harris Caroline Rousset François Morlais Isabelle Fontenille Didier Cohuet Anna |
| author_facet | Harris Caroline Rousset François Morlais Isabelle Fontenille Didier Cohuet Anna |
| author_sort | Harris Caroline |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>In the malaria vector <it>Anopheles gambiae</it>, understanding diversity in natural populations and genetic components of important phenotypes such as resistance to malaria infection is crucial for developing new malaria transmission blocking strategies. The design and interpretation of many studies here depends critically on Linkage disequilibrium (LD). For example in association studies, LD determines the density of Single Nucleotide Polymorphisms (SNPs) to be genotyped to represent the majority of the genomic information. Here, we aim to determine LD in wild <it>An. gambiae s.l</it>. populations in 4 genes potentially involved in mosquito immune responses against pathogens (<it>Gambicin</it>, <it>NOS</it>, <it>REL2 </it>and <it>FBN9</it>) using previously published and newly generated sequences.</p> <p>Results</p> <p>The level of LD between SNP pairs in cloned sequences of each gene was determined for 7 species (or incipient species) of the <it>An. gambiae </it>complex. In all tested genes and species, LD between SNPs was low: even at short distances (< 200 bp), most SNP pairs gave an r<sup>2 </sup>< 0.3. Mean r<sup>2 </sup>ranged from 0.073 to 0.766. In most genes and species LD decayed very rapidly with increasing inter-marker distance.</p> <p>Conclusions</p> <p>These results are of great interest for the development of large scale polymorphism studies, as LD generally falls below any useful limit. It indicates that very fine scale SNP detection will be required to give an overall view of genome-wide polymorphism. Perhaps a more feasible approach to genome wide association studies is to use targeted approaches using candidate gene selection to detect association to phenotypes of interest.</p> |
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| format | Article |
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| institution | Directory Open Access Journal |
| issn | 1471-2156 |
| language | English |
| last_indexed | 2024-04-12T11:34:32Z |
| publishDate | 2010-09-01 |
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| series | BMC Genetics |
| spelling | doaj.art-a076f4082575483ab93fd87122a2d4982022-12-22T03:34:53ZengBMCBMC Genetics1471-21562010-09-011118110.1186/1471-2156-11-81Low linkage disequilibrium in wild <it>Anopheles gambiae s.l</it>. populationsHarris CarolineRousset FrançoisMorlais IsabelleFontenille DidierCohuet Anna<p>Abstract</p> <p>Background</p> <p>In the malaria vector <it>Anopheles gambiae</it>, understanding diversity in natural populations and genetic components of important phenotypes such as resistance to malaria infection is crucial for developing new malaria transmission blocking strategies. The design and interpretation of many studies here depends critically on Linkage disequilibrium (LD). For example in association studies, LD determines the density of Single Nucleotide Polymorphisms (SNPs) to be genotyped to represent the majority of the genomic information. Here, we aim to determine LD in wild <it>An. gambiae s.l</it>. populations in 4 genes potentially involved in mosquito immune responses against pathogens (<it>Gambicin</it>, <it>NOS</it>, <it>REL2 </it>and <it>FBN9</it>) using previously published and newly generated sequences.</p> <p>Results</p> <p>The level of LD between SNP pairs in cloned sequences of each gene was determined for 7 species (or incipient species) of the <it>An. gambiae </it>complex. In all tested genes and species, LD between SNPs was low: even at short distances (< 200 bp), most SNP pairs gave an r<sup>2 </sup>< 0.3. Mean r<sup>2 </sup>ranged from 0.073 to 0.766. In most genes and species LD decayed very rapidly with increasing inter-marker distance.</p> <p>Conclusions</p> <p>These results are of great interest for the development of large scale polymorphism studies, as LD generally falls below any useful limit. It indicates that very fine scale SNP detection will be required to give an overall view of genome-wide polymorphism. Perhaps a more feasible approach to genome wide association studies is to use targeted approaches using candidate gene selection to detect association to phenotypes of interest.</p>http://www.biomedcentral.com/1471-2156/11/81 |
| spellingShingle | Harris Caroline Rousset François Morlais Isabelle Fontenille Didier Cohuet Anna Low linkage disequilibrium in wild <it>Anopheles gambiae s.l</it>. populations BMC Genetics |
| title | Low linkage disequilibrium in wild <it>Anopheles gambiae s.l</it>. populations |
| title_full | Low linkage disequilibrium in wild <it>Anopheles gambiae s.l</it>. populations |
| title_fullStr | Low linkage disequilibrium in wild <it>Anopheles gambiae s.l</it>. populations |
| title_full_unstemmed | Low linkage disequilibrium in wild <it>Anopheles gambiae s.l</it>. populations |
| title_short | Low linkage disequilibrium in wild <it>Anopheles gambiae s.l</it>. populations |
| title_sort | low linkage disequilibrium in wild it anopheles gambiae s l it populations |
| url | http://www.biomedcentral.com/1471-2156/11/81 |
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