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: 5.96). 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.

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Available from: Abraham B. Korol, Sep 28, 2015
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    • "There are several economic traits in tilapia such as growth [10] and sex-ratio [11] that need improvement and require genetic markers for their selection. Likewise, identification of QTLs (Quantitative Trait Loci) for other economic traits are being performed in tilapia [12] as well as for immune responses [13]. Two Nile tilapia genetic maps were constructed, for QTL mapping and for selection purposes, of which the latest contains 538 microsatellites and 21 gene markers [14,15]. "
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    ABSTRACT: The Nile tilapia (Oreochromis niloticus) is the second most farmed fish species worldwide. It is also an important model for studies of fish physiology, particularly because of its broad tolerance to an array of environments. It is a good model to study evolutionary mechanisms in vertebrates, because of its close relationship to haplochromine cichlids, which have undergone rapid speciation in East Africa. The existing genomic resources for Nile tilapia include a genetic map, BAC end sequences and ESTs, but comparative genome analysis and maps of quantitative trait loci (QTL) are still limited. We have constructed a high-resolution radiation hybrid (RH) panel for the Nile tilapia and genotyped 1358 markers consisting of 850 genes, 82 markers corresponding to BAC end sequences, 154 microsatellites and 272 single nucleotide polymorphisms (SNPs). From these, 1296 markers could be associated in 81 RH groups, while 62 were not linked. The total size of the RH map is 34,084 cR3500 and 937,310 kb. It covers 88% of the entire genome with an estimated inter-marker distance of 742 Kb. Mapping of microsatellites enabled integration to the genetic map. We have merged LG8 and LG24 into a single linkage group, and confirmed that LG16-LG21 are also merged. The orientation and association of RH groups to each chromosome and LG was confirmed by chromosomal in situ hybridizations (FISH) of 55 BACs. Fifty RH groups were localized on the 22 chromosomes while 31 remained small orphan groups. Synteny relationships were determined between Nile tilapia, stickleback, medaka and pufferfish. The RH map and associated FISH map provide a valuable gene-ordered resource for gene mapping and QTL studies. All genetic linkage groups with their corresponding RH groups now have a corresponding chromosome which can be identified in the karyotype. Placement of conserved segments indicated that multiple inter-chromosomal rearrangements have occurred between Nile tilapia and the other model fishes. These maps represent a valuable resource for organizing the forthcoming genome sequence of Nile tilapia, and provide a foundation for evolutionary studies of East African cichlid fishes.
    BMC Genomics 06/2012; 13(1):222. DOI:10.1186/1471-2164-13-222 · 3.99 Impact Factor
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    • "This approach has also been used to detect significant changes in marker allele frequency through two cycles of recurrent selection (Moreau et al. 2004). A fractioned DNA pooling approach has also been used in which the tails of the population distribution are randomly allocated among a number of independent sub-pools (Sham et al. 2002; Brohede et al. 2005; Korol et al. 2007; Shifman et al. 2008). Selective genotyping and pooled DNA analysis have been shown to have significant advantages in terms of cost savings, compared to entire population analysis, with negligible practical disadvantages in terms of power of detection in medical genomics research (Knight and Sham 2006; Macgregor et al. 2008). "
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    ABSTRACT: Selective genotyping of individuals from the two tails of the phenotypic distribution of a population provides a cost efficient alternative to analysis of the entire population for genetic mapping. Past applications of this approach have been confounded by the small size of entire and tail populations, and insufficient marker density, which result in a high probability of false positives in the detection of quantitative trait loci (QTL). We studied the effect of these factors on the power of QTL detection by simulation of mapping experiments using population sizes of up to 3,000 individuals and tail population sizes of various proportions, and marker densities up to one marker per centiMorgan using complex genetic models including QTL linkage and epistasis. The results indicate that QTL mapping based on selective genotyping is more powerful than simple interval mapping but less powerful than inclusive composite interval mapping. Selective genotyping can be used, along with pooled DNA analysis, to replace genotyping the entire population, for mapping QTL with relatively small effects, as well as linked and interacting QTL. Using diverse germplasm including all available genetics and breeding materials, it is theoretically possible to develop an “all-in-one plate” approach where one 384-well plate could be designed to map almost all agronomic traits of importance in a crop species. Selective genotyping can also be used for genomewide association mapping where it can be integrated with selective phenotyping approaches. We also propose a breeding-to-genetics approach, which starts with identification of extreme phenotypes from segregating populations generated from multiple parental lines and is followed by rapid discovery of individual genes and combinations of gene effects together with simultaneous manipulation in breeding programs. KeywordsSelective genotyping-Pooled DNA analysis-Genetic mapping-Inclusive composite interval mapping-Marker-assisted selection
    Molecular Breeding 10/2010; 26(3):493-511. DOI:10.1007/s11032-010-9390-8 · 2.25 Impact Factor
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    • "Since copy-number variations (CNVs) are common in maize (Springer et al. 2009), we hypothesize that this SNP marker might exhibit a CNV in the Mo17 haplotype. SNP-based BSA of maize mutants in a mixed B73- and Mo17-derived genetic background: The quantitative nature of the Sequenom platform provides the potential to map mutants via BSA (Michelmore et al. 1991; Korol et al. 2007; Lambreghts et al. 2009). A series of 40 recessive mutants (Table S7 and Figure S3) generated via EMS mutagenesis (Till et al. 2004) of B73 was used to demonstrate the utility of combining Sequenom-based quantitative SNP detection with BSA. "
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    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 x 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 F(2) individuals, this strategy is expected to be widely adopted for mapping in many species.
    Genetics 11/2009; 184(1):19-26. DOI:10.1534/genetics.109.107557 · 5.96 Impact Factor
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