Codominant scoring of AFLP in association panels

A study on the codominant scoring of AFLP markers in association panels without prior knowledge on genotype probabilities is described. Bands are scored codominantly by fitting normal mixture models to band intensities, illustrating and optimizing existing methodology, which employs the EM-algorithm. We study features that improve the performance of the algorithm, and the unmixing in general, like parameter initialization, restrictions on parameters, data transformation, and outlier removal. Parameter restrictions include equal component variances, equal or nearly equal distances between component means, and mixing probabilities according to Hardy–Weinberg Equilibrium. Histogram visualization of band intensities with superimposed normal densities, and optional classification scores and other grouping information, assists further in the codominant scoring. We find empirical evidence favoring the square root transformation of the band intensity, as was found in segregating populations. Our approach provides posterior genotype probabilities for marker loci. These probabilities can form the basis for association mapping and are more useful than the standard scoring categories A, H, B, C, D. They can also be used to calculate predictors for additive and dominance effects. Diagnostics for data quality of AFLP markers are described: preference for three-component mixture model, good separation between component means, and lack of singletons for the component with highest mean. Software has been developed in R, containing the models for normal mixtures with facilitating features, and visualizations. The methods are applied to an association panel in tomato, comprising 1,175 polymorphic markers on 94 tomato hybrids, as part of a larger study within the Dutch Centre for BioSystems Genomics

Identification of QTLs for sex expression in dioecious and monoecious hemp (Cannabis sativa L.)

Hemp (Cannabis sativa L.) is a diploid species including both dioecious and monoecious cultivars with hetero- and homomorphic sex chromosomes, respectively. It displays a high plasticity of sex expression, i.e., the ratio of female and male flowers. In this study, we investigated the role of sex chromosomes in the genetic determinism of sex expression in dioecious and monoecious hemp. The experimental materials were three F1 segregating populations, two dioecious (C1 and C2: ‘Carmagnola’ ♀ × ‘Carmagnola’ ♂), and one monoecious (UF: ‘Uso 31’ × ‘Fedora 17’). A ‘sex’ phenotypic marker was mapped in C1 and C2. In total, 23, 42, and 26 AFLP markers (71 markers in total) were mapped to three, nine, and three co-segregation groups putatively located on sex chromosomes in C1, C2, and UF, respectively. Recombination rates with sex ranged from 0 to 0.5. Five sex-linked markers were detected in UF, revealing homologies between the X chromosomes of monoecious hemp and the X and Y chromosomes of dioecious hemp. Five QTLs associated with quantitative variations in sex expression were identified in each map. Four markers associated with variations in sex expression in UF segregated with sex or accounted for a putative QTL in C1 or C2. Two QTLs and three of these markers were mapped in UF in a region homologous to the sex-locus region of the dioecious maps. Given these results, conducting further research on the genetic determinism of sex expression in hemp using a quantitative approach appears relevant