12 research outputs found
Bayesian QTL analyses using pedigreed families of an outcrossing species, with application to fruit firmness in apple
Bayesian QTL linkage mapping approaches
offer the flexibility to study multiple full sib families with
known pedigrees simultaneously. Such a joint analysis
increases the probability of detecting these quantitative trait
loci (QTL) and provide insight of the magnitude of QTL
across different genetic backgrounds. Here, we present an
improved Bayesian multi-QTL pedigree-based approach on
an outcrossing species using progenies with different (complex)
genetic relationships. Different modeling assumptions
were studied in the QTL analyses, i.e., the a priori
expected number of QTL varied and polygenic effects were
considered. The inferences include number of QTL, additive
QTL effect sizes and supporting credible intervals,
posterior probabilities of QTL genotypes for all individuals
in the dataset, and QTL-based as well as genome-wide
breeding values. All these features have been implemented
in the FlexQTL\u2122 software. We analyzed fruit firmness in a
large apple dataset that comprised 1,347 individuals forming
27 full sib families and their known ancestral pedigrees,
with genotypes for 87 SSR markers on 17 chromosomes.
We report strong or positive evidence for 14 QTL for fruit
firmness on eight chromosomes, validating our approach
as several of these QTL were reported previously, though
dispersed over a series of studies based on single mapping
populations. Interpretation of linked QTL was possible via
individuals\u2019 QTL genotypes. The correlation between the
genomic breeding values and phenotypes was on average
90 %, but varied with the number of detected QTL in a
family. The detailed posterior knowledge on QTL of potential
parents is critical for the efficiency of marker-assisted
breeding