Article

Fractioned DNA pooling: a new cost-effective strategy for fine mapping of quantitative trait loci.

Institute of Evolution, University of Haifa, Mount Carmel, Haifa 31905, Israel.
Genetics (Impact Factor: 4.39). 09/2007; 176(4):2611-23. DOI: 10.1534/genetics.106.070011
Source: PubMed

ABSTRACT Selective DNA pooling (SDP) is a cost-effective means for an initial scan for linkage between marker and quantitative trait loci (QTL) in suitable populations. The method is based on scoring marker allele frequencies in DNA pools from the tails of the population trait distribution. Various analytical approaches have been proposed for QTL detection using data on multiple families with SDP analysis. This article presents a new experimental procedure, fractioned-pool design (FPD), aimed to increase the reliability of SDP mapping results, by "fractioning" the tails of the population distribution into independent subpools. FPD is a conceptual and structural modification of SDP that allows for the first time the use of permutation tests for QTL detection rather than relying on presumed asymptotic distributions of the test statistics. For situations of family and cross mapping design we propose a spectrum of new tools for QTL mapping in FPD that were previously possible only with individual genotyping. These include: joint analysis of multiple families and multiple markers across a chromosome, even when the marker loci are only partly shared among families; detection of families segregating (heterozygous) for the QTL; estimation of confidence intervals for the QTL position; and analysis of multiple-linked QTL. These new advantages are of special importance for pooling analysis with SNP chips. Combining SNP microarray analysis with DNA pooling can dramatically reduce the cost of screening large numbers of SNPs on large samples, making chip technology readily applicable for genomewide association mapping in humans and farm animals. This extension, however, will require additional, nontrivial, development of FPD analytical tools.

0 Bookmarks
 · 
233 Views
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Abstract 17 Ovarioles are the functional unit of the female insect reproductive organs and the number,of ovarioles per 18 ovary strongly influences egg-laying rate and fecundity. Social evolution in the honey bee (Apis 19 mellifera) has resulted in queens with typically 200-360 total ovarioles and workers with usually 20 or 20 less. In addition, variation in ovariole number among workers relates to a broad array of worker traits, 21 including sensory tuning, foraging behavior, and the ability to lay unfertilized male-destined eggs in the 22 event of queen death. In order to study the genetic architecture of worker ovariole number, we performed 23 a series of crosses between Africanized and European bees that differ in worker ovariole number. 24 Unexpectedly, these crosses produced transgressive worker phenotypes with extreme ovariole numbers 25 that were sensitive to the social environment. Alleles causing this ovary phenotype are derived from and 26 segregate in the Africanized population. We used a new selective pooled DNA interval mapping,approach 27 with two parallel Africanized backcrosses to identify the genomic,location of quantitative trait loci (QTL) 28 that are responsible for the observed extreme worker ovariole numbers. We identified one QTL on 29 chromosome,11 and found some evidence for another QTL on chromosome,2. Both QTL regions contain 30 plausible functional candidate genes. The ovariole number,of foragers was weakly correlated with the 31
  • Source
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Advances in next-generation sequencing technology have facilitated the discovery of single nucleotide polymorphisms (SNPs). Sequenom-based SNP-typing assays were developed for 1359 maize SNPs identified via comparative next-generation transcriptomic sequencing. Approximately 75% of these SNPs were successfully converted into genetic markers that can be scored reliably and used to generate a SNP-based genetic map by genotyping recombinant inbred lines from the intermated B73 × Mo17 population. The quantitative nature of Sequenom-based SNP assays led to the development of a time- and cost-efficient strategy to genetically map mutants via quantitative bulked segregant analysis. This strategy was used to rapidly map the loci associated with several dozen recessive mutants. Because a mutant can be mapped using as few as eight multiplexed sets of SNP assays on a bulk of as few as 20 mutant F2 individuals, this strategy is expected to be widely adopted for mapping in many species.
    Genetics 08/2010; 184(1):19-26. · 4.39 Impact Factor

Full-text (2 Sources)

Download
29 Downloads
Available from
May 30, 2014