tailieunhanh - Báo cáo sinh học: "Estimating genetic diversity across the neutral genome with the use of dense marker maps"

Tuyển tập các báo cáo nghiên cứu về sinh học được đăng trên tạp chí sinh học quốc tế đề tài: Estimating genetic diversity across the neutral genome with the use of dense marker maps | Engelsma et al. Genetics Selection Evolution 2010 42 12 http content 42 1 12 GSE Ge n et i cs Selection Evolution RESEARCH Open Access Estimating genetic diversity across the neutral genome with the use of dense marker maps Krista A Engelsma 1 2 Mario PL Calus1 Piter Bijma2 and Jack J Windig1 3 Abstract Background With the advent of high throughput DNA typing dense marker maps have become available to investigate genetic diversity on specific regions of the genome. The aim of this paper was to compare two marker based estimates of the genetic diversity in specific genomic regions lying in between markers IBD-based genetic diversity and heterozygosity. Methods A computer simulated population was set up with individuals containing a single 1-Morgan chromosome and 1665 SNP markers and from this one an additional population was produced with a lower marker density . 166 SNP markers. For each marker interval based on adjacent markers the genetic diversity was estimated either by IBD probabilities or heterozygosity. Estimates were compared to each other and to the true genetic diversity. The latter was calculated for a marker in the middle of each marker interval that was not used to estimate genetic diversity. Results The simulated population had an average minor allele frequency of and an LD r2 of comparable to those of real livestock populations. Genetic diversities estimated by IBD probabilities and by heterozygosity were positively correlated and correlations with the true genetic diversity were quite similar for the simulated population with a high marker density both for specific regions r and large regions r over the genome. For the population with a lower marker density the correlation with the true genetic diversity turned out to be higher for the IBD-based genetic diversity. Conclusions Genetic diversities of ungenotyped regions of the genome . between markers estimated by IBD-based methods and .

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