A typical allopolyploid species is derived from hybridizationfrom two or more diploid species and chromosome doublingfollowing the hybridization. Somatic chromosome doubling wasbelieved to be the mechanism. But now it is clear thatalloployploids are derived from fertilization between unreducedmale and female gametes. Most allopolyploid species aretetraploids. Hexaploids are less common. It is difficult toobtain ploidy level higher than octoploid experimentally. As agood example of allopolyploids, bread wheat (Triticum aestivum,AABBDD, 2n = 42) is a hexaploid and contains three genomes: A, Band D. The A genome is from a diploid wild wheat Triticumurartu (AA, 2n = 14); the B genome is from a wild goat grass Aegilopsspeltoides (BB, 2n = 14); the D genome is from another wildgoat grass Aegilops squarrosa (DD, 2n = 14). Chromosomes1A, 1B, and 1D from the three parental species contain a similarsets of genes in spite of their different sizes and bandingpatterns. These three chromosomes are called homoeologouschromosomes or homoeologous group 1 chromosomes.

Formation of 2n Gametes: The 2n gametesare gametes which have the sporophytic chromosome number.Formation of such gametes were reported from many plant species.The formation of 2n gametes have been extensively studied inpotato. There are five different mechanisms for 2n egg formationin potato and the most popular one is omission of the seconddivision. The 2n male gametes in potato is formed in a veryunique way. Normally, the first meiotic division is not followedby cytokinesis, and in the second division the two spindles areoriented such that their poles define a tetrahedron. Followingcytokinesis a tetrad of four, n microspores are formed. Duringthe formation of 2n gametes, the first meiotic division isnormal, but in some sporocytes the second division spindles wereparallel leading to the formation of two, 2n microspores (dyads)following cytokinesis. In an interspecific hybrid, such as AB(from a cross between AA and BB), fertilization between 2n maleand female gametes will result in an allotetraploid species AABB.

Genome Analysis

Genome Analysis is a method designed by H.Kihara at Kyoto University in 1930 to determine the diploidancestors of allopolyploid species. It was also Kihara whointroduced the terms auto- and allopolyploidy in order to betterdistinguish between these two important classes of ploidy. Themethod includes (1) select a possible diploid progenitor speciesbased on morphology, histology, anatomy, biochemistry, andgeographical distribution, etc.; (2) create hybrids between theallopolyploid species and the potential diploid progenitorspecies; (3) analyze the chromosome pairing of the hybrid. If thediploid contributed one of the genomes of the allopolyploidspecies, chromosome pairing should occur between two sets ofhomologous chromosomes in the hybrid. The test of the analysis isthe artificial resynthesis. When synthetic and naturalallopolyploid resemble each other closely and have a fertile F₁,it may be assumed that the analysis was correct. This method hassubsequently contributed to the knowledge of evolution of manycultivated and wild allopolyploid species.

Chromosome Pairing in Allopolyploid Species

There are only bivalent at metaphase I in meiosis for typicalallopolyploid species. In another word, there is only homologouspairing and no homoeologous pairing. For example, in wheatchromosome 1A does not pair with 1B or 1D. The fact thathomoeologous chromosomes do not have any tendency to pair wasformerly explained by assuming that structural differencesprevented pairing. When it appears that only exceptionally aclear structural differentiation could be observed, it wasassumed that cryptic structural differences were responsible forthe differentiation. However, in some allopolyploid species thisconcept was abandoned because it appeared that a rather simplegenetic system could sometimes regulate chromosome pairing. Inbread wheat, a single dominant gene Ph1 plays the majorrole in chromosome pairing. When this gene is present, there isonly homologous pairing. When this gene is absent, homoeologouspairing occurs. The Ph1 gene suppresses homoeologouspairing but not homologous pairing.

Allopolyploidization and Diploidization

In some respects the polysomic genetic system ofautopolyploids has disadvantages in comparison to the disomicgenetic system of allopolyploids, including lower fertility andstability. Homoeologous chromosome pairing may exist during theearly stage of an allopolyploid species. Such pairing isgradually replaced by strict homologous pairing because ofchromosome differentiation or introduction of a new geneticsystem controlling pairing. Such process is calledallopolyploidization. For example, chromosome 4A in wheat isinvolved in both inversion and translocation during evolution.This chromosome can no longer pair with 4B or 4D no matter thepresence or absence of the Ph1 gene.

Pairing differentiation often goes parallel with geneticdifferentiation. Corresponding loci on homoeologous chromosomesmay have different alleles, or even genes with differentfunction. How frequent this occurs depends on the differencebetween the parental species and increased continuously bymutation in the allopolyploid. For many genes duplication is notan advantage, and slightly modified function of part of the locimay result in an improvement of the fitness of the organism.Because by such modifications the duplication character ofpolyploids is gradually lost and converted into a situationresembling that in a diploid; the process is called diploidization.

Chromosomal Evolution of Polyploid Species

It is difficult to analyze the chromosome structuremodification in polyploid species by conventional cytogeneticmethods, such as karyotyping or chromosome pairing analysis.However, new technologies, such as chromosome painting andmolecular marker-assisted genetic mapping, can be used toprecisely determine translocation, duplication, deletion, andinversions. 

How to determine the genomic affinity of individualchromosomes in allopolyploid species

Application of aneuploid is the conventional method to assignindividual chromosomes to different genomes in allopolyploidspecies. For example, the monosomics of Nicotiana tabacum(2n = 24) were used to assign the 24 chromosomes to either S or Tgenome (see handouts for Monosomics). This aneuploid strategy canhardly be applied to most of the polyploid species because of thetime-consuming work of aneuploid isolation. Genome-specificrepetitive DNA sequences may be isolated from the diploidprogenitor species. In situ hybridization using such sequences orgenomic painting (see handouts for In Situ Hybridization) can beused to distinguish chromosomes from different genomes.

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