Genome-wide patterns of polymorphism in an inbred line of the African malaria mosquito Anopheles gambiae.
Bottom Line: We found that amenability to inbreeding varied between populations of A. gambiae.Although inbreeding dramatically reduced diversity across much of the genome, we discovered numerous, discrete genomic blocks that maintained high heterozygosity.Although creation of A. gambiae lines devoid of nearly all polymorphism may not be feasible, our results provide critical insights into how more fully isogenic lines can be created.
Affiliation: Department of Entomology, University of California, Riverside.Show MeSH
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Mentions: For the following analyses we only used SNPs genotyped in at least 16 individual mosquitoes from both the NGS and NGS INBRED groups leaving us with a total of 159,314 SNPs on the autosomes and 11,099 SNPs on the X. We observed a relatively even distribution of SNPs across the euchromatin of the autosomes, with a dip in SNP density at the heterochromatic centromeres (Sharakhova et al. 2010). Overall, the X chromosome exhibited a lower SNP frequency than the autosomes. The observed distribution of polymorphic sites is consistent with studies of nucleotide variation in natural populations (Lawniczak et al. 2010; White et al. 2010; Clarkson et al. 2014) suggesting that the ddRAD approach worked well in generating an unbiased, genome-wide panel of markers (fig. 1).Fig. 1.—
Affiliation: Department of Entomology, University of California, Riverside.