Many important ornamental, vegetable and field crops are polyploids. Genetic analysis of these crop is still challenging due to their complex nature.
Bottleneck in genetic analysis of polyploid crops
- multiple alleles at marker loci and at loci for traits of interest
- different possibilities of allele dosages across the homologous chromosomes (nulliplex, simplex, duplex, triplex, quadruplex for a tetraploid)
- dominant markers, based on presence/absence, hide the underlying dosage of the marker allele, and because of the larger number of possibilities in polyploids this leads to large amounts of ‘unobserved’ or incomplete marker data.
- occurrence of both bivalent and multivalent pairing during meiosis in autopolyploids
- possibility of preferential pairing of different homologs
- possibility of different recombination frequencies for different pairs of homologs
- the higher number of possibilities for the linkage phases between markers
- no clear distinction between cosegregation due to linkage on the same homologous chromosome or cosegregation due to the presence of alleles on two different homologs that end up in the same progeny individual
- existence of meiotic phenomena such as double reduction giving rise to progeny genotypes that would otherwise be impossible (AAAa x AAAa can result in aaaa progeny).
- many polyploid crops are cross pollinators and do not allow selfing (rose, potato) and homozygous parents are usually not available.
- good quality sequence information for many polyploids is often not (yet) available