Rebaï A, Goffinet B.. More about quantitative trait locus mapping with diallel designs. Genet Res 75: 243-247

INRA Centre de Toulouse, Unit of Biometry and Artificial Intelligence, Castanet-Tolosan, France.
Genetics Research (Impact Factor: 1.47). 05/2000; 75(2):243-7. DOI: 10.1017/S0016672399004358
Source: PubMed


We present a general regression-based method for mapping quantitative trait loci (QTL) by combining different populations derived from diallel designs. The model expresses, at any map position, the phenotypic value of each individual as a function of the specific-mean of the population to which the individual belongs, the additive and dominance effects of the alleles carried by the parents of that population and the probabilities of QTL genotypes conditional on those of neighbouring markers. Standard linear model procedures (ordinary or iteratively reweighted least-squares) are used for estimation and test of the parameters.

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    • "On the other hand, association mapping, which relies on both wider genetic diversity and cumulated historical recombinations, may suffer from inferential problems caused by residual hidden population structure (Flint-Garcia et al., 2003). Mapping of QTL in multiparental populations is expected to combine the advantages of the two approaches: high number of informative crossovers, possibility to interrogate multiple alleles, limited population structure effects (Rebai and Goffinet, 2000). So far, only a few balanced multiparental populations have been developed in Arabidopsis thaliana (Huang et al., 2011; Kover et al., 2009), tomato (Pascual et al., 2014), bread wheat (Huang et al., 2012; Mackay et al., 2014; Rebetzke et al., 2014; Th epot et al., 2015) and rice (Bandillo et al., 2013). "
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    ABSTRACT: Multiparental cross designs for mapping quantitative trait loci (QTL) provide an efficient alternative to biparental populations because of their broader genetic basis and potentially higher mapping resolution. We describe the development and deployment of a recombinant inbred line (RIL) population in durum wheat (Triticum turgidum ssp. durum) obtained by crossing four elite cultivars. A linkage map spanning 2664 cM and including 7594 single nucleotide polymorphisms (SNPs) was produced by genotyping 338 RILs. QTL analysis was carried out by both interval mapping on founder haplotype probabilities and SNP bi-allelic tests for heading date and maturity date, plant height and grain yield from four field experiments. Sixteen QTL were identified across environments and detection methods, including two yield QTL on chromosomes 2BL and 7AS, with the former mapped independently from the photoperiod response gene Ppd-B1, while the latter overlapped with the vernalization locus VRN-A3. Additionally, 21 QTL with environment-specific effects were found. Our results indicated a prevalence of environment-specific QTL with relatively small effect on the control of grain yield. For all traits, functionally different QTL alleles in terms of direction and size of genetic effect were distributed among parents. We showed that QTL results based on founder haplotypes closely matched functional alleles at known heading date loci. Despite the four founders, only 2.1 different functional haplotypes were estimated per QTL, on average. This durum wheat population provides a mapping resource for detailed genetic dissection of agronomic traits in an elite background typical of breeding programmes. © 2015 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.
    Plant Biotechnology Journal 07/2015; DOI:10.1111/pbi.12424 · 5.75 Impact Factor
    • "Therefore, QTL mapping in complex population designs has been proposed as a more efficient and relevant approach for plant breeding and MAS (Beavis 1994; Muranty 1996; Xu 1998). Additional to the possibility of exploring a larger genetic base, simulation studies (Rebai and Goffinet 2000; Jannink and Jansen 2001; Jansen et al. 2003) have shown that these complex populations may increase the statistical power of QTL detection and the accuracy of their location and allelic effect estimates, especially when some inbred lines are used as parents for different segregating populations. In this situation, it creates connections between the segregating populations that may lead to reduction in the number of allelic effects to be estimated, under the hypothesis of additivity. "
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    ABSTRACT: Advancements in genotyping are rapidly decreasing marker costs and increasing marker density. This opens new possibilities for mapping quantitative trait loci (QTL), in particular by combining linkage disequilibrium information and linkage analysis (LDLA). In this study, we compared different approaches to detect QTL for four traits of agronomical importance in two large multi-parental datasets of maize (Zea mays L.) of 895 and 928 testcross progenies composed of 7 and 21 biparental families, respectively, and genotyped with 491 markers. We compared to traditional linkage-based methods two LDLA models relying on the dense genotyping of parental lines with 17,728 SNP: one based on a clustering approach of parental line segments into ancestral alleles and one based on single marker information. The two LDLA models generally identified more QTL (60 and 52 QTL in total) than classical linkage models (49 and 44 QTL in total). However, they performed inconsistently over datasets and traits suggesting that a compromise must be found between the reduction of allele number for increasing statistical power and the adequacy of the model to potentially complex allelic variation. For some QTL, the model exclusively based on linkage analysis, which assumed that each parental line carried a different QTL allele, was able to capture remaining variation not explained by LDLA models. These complementarities between models clearly suggest that the different QTL mapping approaches must be considered to capture the different levels of allelic variation at QTL involved in complex traits.
    Theoretical and Applied Genetics 08/2013; 126(11). DOI:10.1007/s00122-013-2167-9 · 3.79 Impact Factor
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    • "This was conducted first mainly in a context of biparental populations derived from the cross between two inbred lines. By addressing a broader diversity, multiparental designs 1) increase the power and the accuracy of QTL detection; 2) enable to estimate simultaneously the different parental allele effects and to identify the most favorable ones for selection (Rebaï and Goffinet 2000; Blanc et al. 2006, 2008). Recently, two main types of multiparental designs have received specific interest in the plant breeding community to increase the resolution of QTL mapping by the joint use of dense genotyping of parental lines and linkage analysis in the progenies: the Nested Association Mapping design (NAM; Yu et al. 2008) and the Multiparent Advanced Inter-Cross design (MAGIC; Cavanagh et al. 2008). "
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    ABSTRACT: Current advances in plant genotyping lead to major progress in the knowledge of genetic architecture of traits of interest. It is increasingly important to develop decision support tools to help breeders and geneticists to conduct marker-assisted selection methods to assemble favorable alleles that are discovered. Algorithms have been implemented, within an interactive graphical interface, to 1) trace parental alleles throughout generations, 2) propose strategies to select the best plants based on estimated molecular scores, and 3) efficiently intermate them depending on the expected value of their progenies. With the possibility to consider a multi-allelic context, OptiMAS opens new prospects to assemble favorable alleles issued from diverse parents and further accelerate genetic gain.
    The Journal of heredity 04/2013; 104(4). DOI:10.1093/jhered/est020 · 2.09 Impact Factor
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