Author
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CERVANTES-MARTINEZ, CUAUHTEMOC - UNIV OF FLORIDA |
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Brown, James |
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Submitted to: Crop Science
Publication Type: Peer Reviewed Journal Publication Acceptance Date: 1/28/2004 Publication Date: 9/1/2004 Citation: Cervantes-Martinez, C., Brown, J.S. 2004. A haplotype-based method for QTL mapping of F1 populations in outbred plant species. Crop Science. 44:1572-1583. Interpretive Summary: The localization of Quantitative Trait Loci (QTL) within the genomes of economically important crops has become very important since the advent of molecular markers, which gave plant breeders for the first time, the ability to make an entire genomic map from genetic recombination data. Such "QTL mapping" has been done extensively in annual crops, in animals, and in many perennial crops and fruit and forest tree species, however it has remained an expensive and laborious proposition. In crops like maize or soybeans with a large critical mass of researchers, extensive mapping can be done easily along with the other genetic/breeding work that must be done. However in minor crops, especially tree crops with long generation times and large space requirements, this becomes a strain on the breeding project as well as the budget. Hence the ability to combine the two activities seemed attractive, and a breeding plant and analysis were derived for accomplishing this. This scheme, though computationally involved, increased the accuracy and precision of QTL mapping, as well. As would be expected, there are trade-offs: in order to be able to combine the two activities, one can only analyze crosses of highly heterozygous clones with other clones, and the higher the heterozygousity of all parents, the better. Fortunately, most, but not all, cacao clones have relatively high levels of heterozygousity, and most crosses of cacao made for clonal improvement consist of one highly heterozygous clone with another clone, usually a less heterozygous clone. Therefore this breeding system/QTL mapping system should work quite well with real data, as with simulated data, as was shown in this research. Technical Abstract: The integration of QTL identification into breeding strategies, as sopposed to separate processes, has been proposed both to increase the power and accuracy of QTL detection and to allow the two activities to be merged for increased efficiency. The main objective of this research is to develop a specific scheme for mapping quantitative trait loci (QQTL) in actual F1 breeding populations of outbred plant species with an acceptable degree of accuracy and precision. The proposed method groups populations by common founders, and statistically associates founder-origin probabilities of the common founder haplotypes in a given region of the progeny genome with the phenotype expression using a covariance linear model with a structured covariance matrix to accommodate heterogeneous residual variance among populations. The method was applied to computer simulated data sets, corresponding to five F1 populations of 100 individuals each obtained from the cross of a common founder with five other founders. We are currently using this scheme in cocoa (Theobroma cacao L.) improvement, using selected clones resistant to specific diseases to widen the genetic base of disease resistance. The results indicate that the position and effect of QTLs in a common founder, that explain each at least approximately 14% of the phenotypic variance, can be estimated with good precision and accuracy. The theoretical restrictions on which this approach was developed render the method appropriate for outbred plant species that are highly heterozygous, which is often the case in cocoa, and have phenotypic traits that show few interlocus interaction effects. |
