Development of a mapping population in polyploid plant species
Some crop species are polyploid, i.e. they contain more than two copies per chromosome. Tetraploids have four homologues of every chromosome, hexaplois have six, octoploids eight. This situation presents a problem during genotyping and genetic analysis, since, per locus, different types of heterozygotes are possible, which are hard and sometimes impossible to distinguish (AAAa:AAaa:Aaaa). Recently, software has been developed for so-called dosage scoring of SNP markers, so that, e.g. for a tetraploid crop, all five possible dosage classes (nulliplex, simplex, duplex, triplex, quadruplex, for aaaa, Aaaa, AAaa, AAAa and AAAA, respectively) may be distinguished. Often, not all five classes are present and fewer classes need to be distinguished. Still, it may happen that for individual SNPs, the classification is very difficult.
Moreover, during the mapping of a polyploid species, there can be uncertainty about whether a certain allele originated from the father or from the mother (if both parents are heterozygous). Also, during meiosis, preferential pairing may have occurred: homologues from one parent might pair together more frequently than with homologues from the other parent. At meiosis, complex chromosome pairing patterns may occur, involving more than two chromosomes. These are called trivalents, quadrivalents, etc., according to the number of chromosomes participating in the pairing complex. Such multivalents may recombine chromosome fragments between more than two chromosomes, and are therefore more complex to study than recombination in diploid parents, where only bivalents occur.
A solution to overcome these problems is the mapping of only simplex X nulliplex markers that are in coupling phase with each other, these are all from the same homologue (simplex = recessive at all alleles of a gene except one; nulliplex = recessive in all alleles of a gene; e.g. in tetraploids: Aaaa X aaaa). This situation is similar (with respect to recombination frequency estimation, ordering and distance determination) to a backcross in diploids (Aa x aa), though not identical.
It may also be possible to map simplex X simplex (=Aaaa x Aaaa) or duplex X nulliplex markers (AAaa x aaaa or aaaa x AAaa). More complex situations are not treated here.
Another option is to construct a linkage map using diploid relatives of the polyploid crop species. However, these do not always exist, but may be developed in the same way as haploids are induced in diploid species and even if they do,
it is still far from straightforward to translate results back to the polyploid level at which research and/or breeding is usually done.
Summary
→ In autogamous plant species, a linkage map can be created, based on a population (F2, backcross, RIL or doubled haploids) derived from homozygous inbred parents
→ In allogamous plant species, a linkage map can be created, based on an F1 population derived from a cross between heterozygous parents or on a progeny from selfing of one single heterozygous plant.
→ Mapping of polyploid plant species is often performed on simplex X nulliplex markers
→ Sometimes, mapping of polyploid plant species can be aided using diploid relatives