A Haplotype-Based Method for QTL Mapping of F1 Populations in Outbred Plant Species

نویسندگان

  • Cuauhtemoc Cervantes-Martinez
  • Steven Brown
چکیده

detection. Luo (1993), Soller and Genizi (1978), and Weller et al. (1990) have confirmed that very large progeny The integration of quantitative trait loci (QTL) analysis into breedsizes are needed to detect QTL with good statistical ing strategies rather than being seen as separated processes has been proposed to increase the power and accuracy of QTL detection and power in outbred populations for different designs. to allow the two activities to be joined. The main objective of this However, extremely large progeny sizes and designs research is to develop a specific scheme for mapping QTL in actual requiring two or more generations are not generally feabreeding F1 populations of outbred plant species with a high degree sible in practice for trees and some other outbred plant of accuracy. The proposed method groups populations by common species. For example, the most recent QTL maps for founders and statistically associates founder-origin probabilities that yield components, vigor, resistance to Phytophthora paltrace the common founder haplotypes in a given region of the progeny mivora (E.J. Butler) E.J. Butler, beans traits, and ovule genome with the phenotypic expression, using a linear model with a number in T. cacao were estimated from F1 populations structured covariance matrix. The method was applied to computer ranging from 88 to 125 individuals. These were obtained simulated data sets, corresponding to five F1 populations of 100 indifrom the cross of a highly homozygous clone (Catongo) viduals each obtained from the crosses of a common founder with several other founders. We are currently using this scheme with cocoa with other heterozygous clones (DR1, S52, and IMC78) (Theobroma cacao L.) crosses, using selected clones resistant to spe(Clement et al., 2003a, 2003b). Therefore, alternative cific diseases to widen the genetic base of disease resistance. The accurate methods must be developed for mapping QTL results indicate that the position and effect of QTLs in the common given the conditions and genetic structure of outbred founder, that explain each at least 14% of the phenotypic variance, plant species. Beavis (1998) first proposed the integracan be estimated with good precision and accuracy. The theoretical astion of QTL analysis into cultivar development to insumptions on which this approach was developed render the method crease the resolution of QTL detection, by integrating appropriate for outbred plant species that are highly heterozygous, mapping analyses across the numerous and large popuwhich is often the case in tropical tree crops like cocoa, and have phelations typically used by maize (Zea mays L.) breeders. notypic traits that show few interlocus interaction effects. A haplotypic method for QTL analysis in trees species using founder-origin probabilities that trace specific segments of the chromosomes in individual offspring as inA QTL analyses have been developed in redependent variables with phenotypic values as the decent years to detect and estimate the effects of pendent variable in a simple regression analysis has been quantitative trait loci in plant populations with different proposed for one population using the granddaughter genetic structures. While high resolution QTL maps can design (Reyes-Valdés and Williams, 2002). Their results be obtained from large populations of annual plant spewere similar to those obtained by Haley et al. (1994) cies developed from crossing inbred lines followed by that used all marker information. This method requires, self-fertilization for two or more generations, the analyhowever, the information from three generations for sis of quantitative trait loci is more difficult in outbred QTL detection. In contrast, we suggest an approach that plant species. Some of the difficulties arise when heterouses founder-origin probabilities in several F1 populazygous heterogeneous parents are crossed to develop a tions obtained in a full-sib mating design and combines mapping population, in which parents are differentially the F1 populations with a selected common founder in informative at different loci. To be informative, a parent a regression-based analysis, using a linear model with a must be heterozygous both at marker loci and a linked structured covariance matrix (Searle, 1971; Littell et al., QTL. Complications arise if parents have alleles in com1996). Jannink and Jansen (2001) and Jansen et al. (2003), mon at the QTL or marker loci, or if the parents share assuming additive effects, showed that combining reQTL alleles in different linkage phases with the marker lated breeding populations for QTL analysis increases loci (Jansen et al., 1998; Lynch and Walsh, 1998). In adthe power and accuracy of detection, associated mainly dition, the biological properties of some outbred species, with the increased progeny numbers in the combined like fruit trees and forest trees, impose limiting factors analysis. for mapping QTL. The number of generations per time QTL mapping analyses based on linear regression modunit and the progeny size per space unit are usually fewer els (Haley and Knott, 1992), such as the one we propose than in annual species, resulting in lower power for QTL in this study, are approximate methods that generally give results similar to maximum likelihood methods (Lander C. Cervantes-Martinez, University of Florida, C/O USDA-ARS, SHRS, and Botstein, 1989); however, they are computationally 13601 Old Cutler Road, Miami, FL 33158, USA; S. Brown, USDAmuch less demanding and have greater flexibility to imARS, SHRS, 13601 Old Cutler Road, Miami, FL 33158, USA. Received 6 Nov. 2003. *Corresponding author ([email protected]). plement complex linear models (Piepho, 2000). The obPublished in Crop Sci. 44:1572–1583 (2004).  Crop Science Society of America Abbreviations: QTL, quantitative trait loci; REML, restricted maximum likelihood. 677 S. Segoe Rd., Madison, WI 53711 USA

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تاریخ انتشار 2004