For outcrossing analyses, genotype data of progeny was recorded as homozygous genotypes (AA, BB, CC). or heterozygous genotypes (AB, AC, BC). and formatted according to the MLTR requirement to be used for outcrossing rates estimation under MLTR model [36].
In addition, such programs require genetic information to be integrated with phenotype data for progeny selection and crossing designs.
To assess the ability to predict breeding values of young bulls based on SNP data before progeny data were available, animals born before 1998 (N = 1,239) were included in the training set.
Genotypic data for progeny arrays from known mother plants were combined with known genotypes of all plants in each population for direct paternity analysis.
For most sires in our dataset, the amount of available data for progeny was not sufficient to accurately derive the QTL status.
Experimental data from progeny tests of forest trees indeed show that heritability values of phenologically-related traits can exceed 0.5, much larger than other phenotypic traits generally assessed in experimental plantations [ 43].
For 'Jonathan', the coverage levels were 2.13 (EcoRI) and 2.83 (HindIII), while they were 2.43 (EcoRI) and 2.38 (HindIII) for 'Golden Delicious' (Table 1).> -wrap-foot> Data of progeny were collected from all 318 individuals derived from 'Jonathan' × 'Golden Delicious'.
The low-quality data of progeny made that 61.3% of the Stacks marker were filtered and just right most of the markers in one arm of chromosome 9 were filtered.
The MADCE procedure for mapping studies is not directly applicable to pedigreed cultivars because of their higher genetic complexity (e.g., a greater number of alleles per locus) and the very limited availability of segregation data (few progeny per individual).
Without inbreeding, the expectation of these relationships is equal to 0.5, both based on pedigree and based on genomic data, because progeny receive half of their alleles from each parent.
