NDLI: Low linkage disequilibrium in wild Anopheles gambiae s.l. populations

Content Provider	Springer Nature : BioMed Central
Author	Harris, Caroline Rousset, François Morlais, Isabelle Fontenille, Didier Cohuet, Anna
Abstract	Background In the malaria vector Anopheles gambiae, 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 An. gambiae s.l. populations in 4 genes potentially involved in mosquito immune responses against pathogens (Gambicin, NOS, REL2 and FBN9) using previously published and newly generated sequences. Results The level of LD between SNP pairs in cloned sequences of each gene was determined for 7 species (or incipient species) of the An. gambiae complex. In all tested genes and species, LD between SNPs was low: even at short distances (< 200 bp), most SNP pairs gave an r2 < 0.3. Mean r2 ranged from 0.073 to 0.766. In most genes and species LD decayed very rapidly with increasing inter-marker distance. Conclusions 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.
Related Links	https://bmcgenomdata.biomedcentral.com/counter/pdf/10.1186/1471-2156-11-81.pdf
Ending Page	7
Page Count	7
Starting Page	1
File Format	HTM / HTML
ISSN	27306844
DOI	10.1186/1471-2156-11-81
Journal	BMC Genomic Data
Issue Number	1
Volume Number	11
Language	English
Publisher	BioMed Central
Publisher Date	2010-09-15
Access Restriction	Open
Subject Keyword	Life Sciences Animal Genetics and Genomics Microbial Genetics and Genomics Plant Genetics and Genomics Genetics and Population Dynamics Linkage Disequilibrium Linkage Disequilibrium Decay Chromosomal Inversion Gambiae Complex Incipient Species
Content Type	Text
Resource Type	Article
Subject	Health Informatics Genetics
Journal Impact Factor	1.9/2023
5-Year Journal Impact Factor	1.9/2023

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

Low linkage disequilibrium in wild Anopheles gambiae s.l. populations

Nucleotide variability and linkage disequilibrium patterns in the porcine MUC4 gene

Similar patterns of linkage disequilibrium and nucleotide diversity in native and introduced populations of the pea aphid, Acyrthosiphon pisum

Linkage disequilibrium compared between five populations of domestic sheep

Analysis of genetic variation in Ashkenazi Jews by high density SNP genotyping

Characterization of two MHC II genes (DOB, DRB) in white-tailed deer (Odocoileus virginianus)

Examining the effect of linkage disequilibrium on multipoint linkage analysis

Estimates of linkage disequilibrium and effective population size in rainbow trout

Volume measures for linkage disequilibrium

Low linkage disequilibrium in wild Anopheles gambiae s.l. populations

Similar Documents

Low linkage disequilibrium in wild Anopheles gambiae s.l. populations

Nucleotide variability and linkage disequilibrium patterns in the porcine MUC4 gene

Similar patterns of linkage disequilibrium and nucleotide diversity in native and introduced populations of the pea aphid, Acyrthosiphon pisum

Linkage disequilibrium compared between five populations of domestic sheep

Analysis of genetic variation in Ashkenazi Jews by high density SNP genotyping

Characterization of two MHC II genes (DOB, DRB) in white-tailed deer (Odocoileus virginianus)

Examining the effect of linkage disequilibrium on multipoint linkage analysis

Estimates of linkage disequilibrium and effective population size in rainbow trout

Volume measures for linkage disequilibrium

Low linkage disequilibrium in wild Anopheles gambiae s.l. populations