Editing Polyploidy (section)

=== Classification ===

==== Autopolyploidy ====
'''Autopolyploids''' are polyploids with multiple chromosome sets derived from a single [[taxon]].

Two examples of natural autopolyploids are the piggyback plant, ''[[Tolmiea menziesii|Tolmiea menzisii]]''<ref>{{Cite journal| vauthors = Soltis DE |date=October 1984 |title=Autopolyploidy in ''Tolmiea menziesii'' (Saxifragaceae)|journal=American Journal of Botany|volume=71|issue=9|pages=1171–1174|doi=10.2307/2443640|jstor=2443640}}</ref> and the white sturgeon, ''[[White sturgeon|Acipenser transmontanum]]''.<ref>{{Cite journal| vauthors = Drauch Schreier A, Gille D, Mahardja B, May B |date= November 2011|title=Neutral markers confirm the octoploid origin and reveal spontaneous autopolyploidy in white sturgeon, ''Acipenser transmontanus''|journal=Journal of Applied Ichthyology|language=en|volume=27|pages=24–33|doi=10.1111/j.1439-0426.2011.01873.x|issn=1439-0426|doi-access=free|bibcode= 2011JApIc..27...24D}}</ref> Most instances of autopolyploidy result from the fusion of unreduced (2''n'') gametes, which results in either triploid (''n'' + 2''n'' = 3''n'') or tetraploid (2''n'' + 2''n'' = 4''n'') offspring.<ref name="Bretagnolle_1995">{{cite journal | vauthors = Bretagnolle F, Thompson JD | title = Gametes with the somatic chromosome number: mechanisms of their formation and role in the evolution of autopolyploid plants | journal = The New Phytologist | volume = 129 | issue = 1 | pages = 1–22 | date = January 1995 | pmid = 33874422 | doi = 10.1111/j.1469-8137.1995.tb03005.x | doi-access = free }}</ref> Triploid offspring are typically sterile (as in the phenomenon of [[triploid block]]), but in some cases they may produce high proportions of unreduced gametes and thus aid the formation of tetraploids. This pathway to tetraploidy is referred to as the ''triploid bridge''.<ref name="Bretagnolle_1995" /> Triploids may also persist through [[asexual reproduction]]. In fact, stable autotriploidy in plants is often associated with [[Apomixis|apomictic]] mating systems.<ref>{{Cite journal| vauthors = Müntzing A |date=March 1936|title=The Evolutionary Significance of Autopolyploidy|journal=Hereditas|language=en|volume=21|issue=2–3|pages=363–378|doi=10.1111/j.1601-5223.1936.tb03204.x|issn=1601-5223|doi-access=}}</ref> In agricultural systems, autotriploidy can result in seedlessness, as in [[watermelon]]s and [[banana]]s.<ref>{{cite journal | vauthors = Varoquaux F, Blanvillain R, Delseny M, Gallois P | title = Less is better: new approaches for seedless fruit production | journal = Trends in Biotechnology | volume = 18 | issue = 6 | pages = 233–242 | date = June 2000 | pmid = 10802558 | doi = 10.1016/s0167-7799(00)01448-7 }}</ref> Triploidy is also utilized in salmon and trout farming to induce sterility.<ref>{{Cite journal| vauthors = Cotter D, O'Donovan V, O'Maoiléidigh N, Rogan G, Roche N, Wilkins NP |date=June 2000|title=An evaluation of the use of triploid Atlantic salmon (''Salmo salar'' L.) in minimising the impact of escaped farmed salmon on wild populations|journal=Aquaculture|volume=186|issue=1–2|pages=61–75|doi=10.1016/S0044-8486(99)00367-1|bibcode=2000Aquac.186...61C }}</ref><ref>{{Cite journal| vauthors = Lincoln RF, Scott AP |year=1983|title=Production of all-female triploid rainbow trout|journal=Aquaculture|language=en|volume=30|issue=1–4|pages=375–380|doi=10.1016/0044-8486(83)90179-5|bibcode=1983Aquac..30..375L }}</ref>

Rarely, autopolyploids arise from spontaneous, somatic genome doubling, which has been observed in apple (''Malus domesticus'') [[Sport (botany)|bud sports]].<ref>{{Cite journal| vauthors = Dermen H |date=May 1951|title=Tetraploid and Diploid Adventitious Shoots: From a Giant Sport of McIntosh Apple|journal=Journal of Heredity|volume=42|issue=3|pages=145–149|doi=10.1093/oxfordjournals.jhered.a106189 }}</ref> This is also the most common pathway of artificially induced polyploidy, where methods such as [[Somatic fusion|protoplast fusion]] or treatment with [[colchicine]], [[oryzalin]] or [[mitotic inhibitor]]s are used to disrupt normal [[Mitosis|mitotic]] division, which results in the production of polyploid cells. This process can be useful in plant breeding, especially when attempting to introgress germplasm across ploidal levels.<ref>{{cite book |doi=10.1002/9780470380130.ch3 |chapter=Enhancing Crop Gene Pools with Beneficial Traits Using Wild Relatives |title=Plant Breeding Reviews |date=2007 |last1=Dwivedi |first1=Sangam L. |last2=Upadhyaya |first2=Hari D. |last3=Stalker |first3=H. Thomas |last4=Blair |first4=Matthew W. |last5=Bertioli |first5=David J. |last6=Nielen |first6=Stephan |last7=Ortiz |first7=Rodomiro |pages=179–230 |isbn=978-0-470-17152-3 |chapter-url=http://oar.icrisat.org/2546/1/Enhancing_Crop_Gene_Pools.pdf }}</ref>

Autopolyploids possess at least three [[homologous chromosome]] sets, which can lead to high rates of multivalent pairing during [[meiosis]] (particularly in recently formed autopolyploids, also known as neopolyploids) and an associated decrease in fertility due to the production of [[Aneuploidy|aneuploid]] gametes.<ref name="Justin_2002">{{Cite journal| vauthors = Justin R |date=January 2002|title=Neopolyploidy in Flowering Plants|journal=Annual Review of Ecology and Systematics|volume=33|issue=1|pages=589–639|doi=10.1146/annurev.ecolsys.33.010802.150437 }}</ref> Natural or artificial selection for fertility can quickly stabilize meiosis in autopolyploids by restoring bivalent pairing during meiosis. Rapid adaptive evolution of the meiotic machinery, resulting in reduced levels of multivalents (and therefore stable autopolyploid meiosis) has been documented in ''Arabidopsis arenosa''<ref>{{Cite journal |last1=Yant |first1=Levi |last2=Hollister |first2=Jesse D. |last3=Wright |first3=Kevin M. |last4=Arnold |first4=Brian J. |last5=Higgins |first5=James D. |last6=Franklin |first6=F. Chris H. |last7=Bomblies |first7=Kirsten |date=November 2013 |title=Meiotic Adaptation to Genome Duplication in Arabidopsis arenosa |url=|journal=Current Biology |volume=23 |issue=21 |pages=2151–2156 |doi=10.1016/j.cub.2013.08.059 |issn=0960-9822 |pmc=3859316 |pmid=24139735|bibcode=2013CBio...23.2151Y }}</ref> and ''Arabidopsis lyrata'',<ref>{{Cite journal |last1=Marburger |first1=Sarah |last2=Monnahan |first2=Patrick |last3=Seear |first3=Paul J. |last4=Martin |first4=Simon H. |last5=Koch |first5=Jordan |last6=Paajanen |first6=Pirita |last7=Bohutínská |first7=Magdalena |last8=Higgins |first8=James D. |last9=Schmickl |first9=Roswitha |last10=Yant |first10=Levi |date=2019-11-18 |title=Interspecific introgression mediates adaptation to whole genome duplication |journal=Nature Communications |language=en |volume=10 |issue=1 |pages=5218 |doi=10.1038/s41467-019-13159-5 |issn=2041-1723 |pmc=6861236 |pmid=31740675|bibcode=2019NatCo..10.5218M }}</ref> with specific adaptive alleles of these species shared between only the evolved polyploids.<ref>{{Cite journal |last1=Marburger |first1=Sarah |last2=Monnahan |first2=Patrick |last3=Seear |first3=Paul J. |last4=Martin |first4=Simon H. |last5=Koch |first5=Jordan |last6=Paajanen |first6=Pirita |last7=Bohutínská |first7=Magdalena |last8=Higgins |first8=James D. |last9=Schmickl |first9=Roswitha |last10=Yant |first10=Levi |date=2019-11-18 |title=Interspecific introgression mediates adaptation to whole genome duplication |journal=Nature Communications |language=en |volume=10 |issue=1 |pages=5218 |doi=10.1038/s41467-019-13159-5 |issn=2041-1723 |pmc=6861236 |pmid=31740675|bibcode=2019NatCo..10.5218M }}</ref><ref>{{Cite journal |last1=Seear |first1=Paul J. |last2=France |first2=Martin G. |last3=Gregory |first3=Catherine L. |last4=Heavens |first4=Darren |last5=Schmickl |first5=Roswitha |last6=Yant |first6=Levi |last7=Higgins |first7=James D. |date=2020-07-15 |editor-last=Grelon |editor-first=Mathilde |title=A novel allele of ASY3 is associated with greater meiotic stability in autotetraploid Arabidopsis lyrata |journal=PLOS Genetics |language=en |volume=16 |issue=7 |pages=e1008900 |doi=10.1371/journal.pgen.1008900 |doi-access=free |issn=1553-7404 |pmc=7392332 |pmid=32667955}}</ref> 

The high degree of [[Homology (biology)|homology]] among duplicated chromosomes causes autopolyploids to display [[polysomic inheritance]].<ref>{{cite journal | vauthors = Parisod C, Holderegger R, Brochmann C | title = Evolutionary consequences of autopolyploidy | journal = The New Phytologist | volume = 186 | issue = 1 | pages = 5–17 | date = April 2010 | pmid = 20070540 | doi = 10.1111/j.1469-8137.2009.03142.x | doi-access =  }}</ref> This trait is often used as a diagnostic criterion to distinguish autopolyploids from allopolyploids, which commonly display disomic inheritance after they progress past the neopolyploid stage.<ref name="Le Comber_2010">{{cite journal | vauthors = Le Comber SC, Ainouche ML, Kovarik A, Leitch AR | title = Making a functional diploid: from polysomic to disomic inheritance | journal = The New Phytologist | volume = 186 | issue = 1 | pages = 113–122 | date = April 2010 | pmid = 20028473 | doi = 10.1111/j.1469-8137.2009.03117.x | doi-access =  }}</ref> While most polyploid species are unambiguously characterized as either autopolyploid or allopolyploid, these categories represent the ends of a spectrum of divergence between parental subgenomes. Polyploids that fall between these two extremes, which are often referred to as segmental allopolyploids, may display intermediate levels of polysomic inheritance that vary by locus.<ref>{{Cite book| vauthors = Stebbins GL |title=Types of polyploids; their classification and significance|year=1947|isbn=9780120176014|series=Advances in Genetics|volume=1|pages=403–429|language=en|doi=10.1016/s0065-2660(08)60490-3|pmid=20259289}}</ref><ref>{{Cite book| vauthors = Stebbins GL |title=Variation and Evolution in Plants|publisher=Oxford University Press|year=1950}}{{page needed|date=March 2019}}</ref>

About half of all polyploids are thought to be the result of autopolyploidy,<ref>{{Cite journal| vauthors = Ramsey J, Schemske DW |date= January 1998 |title=Pathways, Mechanisms, and Rates of Polyploid Formation in Flowering Plants|journal=Annual Review of Ecology and Systematics|volume=29|issue=1|pages=467–501|doi=10.1146/annurev.ecolsys.29.1.467 }}</ref><ref>{{cite journal | vauthors = Barker MS, Arrigo N, Baniaga AE, Li Z, Levin DA | title = On the relative abundance of autopolyploids and allopolyploids | journal = The New Phytologist | volume = 210 | issue = 2 | pages = 391–398 | date = April 2016 | pmid = 26439879 | doi = 10.1111/nph.13698 | doi-access = free }}</ref> although many factors make this proportion hard to estimate.<ref>{{cite journal | vauthors = Doyle JJ, Sherman-Broyles S | title = Double trouble: taxonomy and definitions of polyploidy | journal = The New Phytologist | volume = 213 | issue = 2 | pages = 487–493 | date = January 2017 | pmid = 28000935 | doi = 10.1111/nph.14276 | doi-access = free }}</ref>

==== Allopolyploidy ====
'''Allopolyploids''' or '''amphipolyploids''' or '''heteropolyploids''' are polyploids with chromosomes derived from two or more diverged taxa.

As in autopolyploidy, this primarily occurs through the fusion of unreduced (2''n'') gametes, which can take place before or after [[Hybrid (biology)|hybridization]]. In the former case, unreduced gametes from each diploid taxon – or reduced gametes from two autotetraploid taxa – combine to form allopolyploid offspring. In the latter case, one or more diploid [[F1 hybrid|F<sub>1</sub> hybrids]] produce unreduced gametes that fuse to form allopolyploid progeny.<ref name="Ramsey_1998">{{Cite journal| vauthors = Ramsey J |date=January 1998|title=Pathways, Mechanisms, and Rates of Polyploid Formation in Flowering Plants|journal=Annual Review of Ecology and Systematics|volume=29|issue=1|pages=467–501|doi=10.1146/annurev.ecolsys.29.1.467 }}</ref> Hybridization followed by genome duplication may be a more common path to allopolyploidy because F<sub>1</sub> hybrids between taxa often have relatively high rates of unreduced gamete formation – divergence between the genomes of the two taxa result in abnormal pairing between [[homoeologous]] chromosomes or [[nondisjunction]] during meiosis.<ref name="Ramsey_1998" /> In this case, allopolyploidy can actually restore normal, [[Bivalent (genetics)|bivalent]] meiotic pairing by providing each homoeologous chromosome with its own homologue. If divergence between homoeologous chromosomes is even across the two subgenomes, this can theoretically result in rapid restoration of bivalent pairing and disomic inheritance following allopolyploidization. However multivalent pairing is common in many recently formed allopolyploids, so it is likely that the majority of meiotic stabilization occurs gradually through selection.<ref name="Justin_2002" /><ref name="Le Comber_2010" />

Because pairing between homoeologous chromosomes is rare in established allopolyploids, they may benefit from fixed [[heterozygosity]] of homoeologous alleles.<ref name="Comai_2005">{{cite journal | vauthors = Comai L | title = The advantages and disadvantages of being polyploid | journal = Nature Reviews. Genetics | volume = 6 | issue = 11 | pages = 836–846 | date = November 2005 | pmid = 16304599 | doi = 10.1038/nrg1711 }}</ref> In certain cases, such heterozygosity can have beneficial [[Heterosis|heterotic]] effects, either in terms of fitness in natural contexts or desirable traits in agricultural contexts. This could partially explain the prevalence of allopolyploidy among crop species. Both bread [[wheat]] and [[triticale]] are examples of an allopolyploids with six chromosome sets. [[Cotton]], [[peanut]], and [[quinoa]] are allotetraploids with multiple origins. In [[Brassicaceae|Brassicaceous]] crops, the [[Triangle of U]] describes the relationships between the three common diploid Brassicas (''[[Brassica oleracea|B. oleracea]], [[Brassica rapa|B. rapa]],'' and ''[[Brassica nigra|B. nigra]]'') and three allotetraploids (''[[Rapeseed|B. napus]], [[Brassica juncea|B. juncea]],'' and ''[[Brassica carinata|B. carinata]]'') derived from hybridization among the diploid species. A similar relationship exists between three diploid species of ''[[Tragopogon]]'' (''[[Tragopogon dubius|T. dubius]], [[Tragopogon pratensis|T. pratensis]],'' and ''[[Tragopogon porrifolius|T. porrifolius]]'') and two allotetraploid species (''[[Tragopogon mirus|T. mirus]]'' and ''[[Tragopogon miscellus|T. miscellus]]'').<ref>{{Cite journal| vauthors = Ownbey M |date=January 1950|title=Natural Hybridization and Amphiploidy in the Genus Tragopogon|journal=American Journal of Botany|volume=37|issue=7|pages=487–499|doi=10.2307/2438023|jstor=2438023}}</ref> Complex patterns of allopolyploid evolution have also been observed in animals, as in the frog genus ''[[Xenopus]].''<ref>{{cite journal | vauthors = Schmid M, Evans BJ, Bogart JP | title = Polyploidy in Amphibia | journal = Cytogenetic and Genome Research | volume = 145 | issue = 3–4 | pages = 315–330 | year = 2015 | pmid = 26112701 | doi = 10.1159/000431388 | doi-access = free }}</ref>

==== Aneuploid ====
{{main|Aneuploidy}}
Organisms in which a particular chromosome, or chromosome segment, is under- or over-represented are said to be [[Aneuploidy|aneuploid]] (from the Greek words meaning "not", "good", and "fold"). Aneuploidy refers to a numerical change in part of the chromosome set, whereas polyploidy refers to a numerical change in the whole set of chromosomes.<ref name="isbn0-7167-3520-2">{{cite book| vauthors = Griffiths AJ |title=An Introduction to genetic analysis|publisher=W.H. Freeman|year=1999|isbn=978-0-7167-3520-5|location=San Francisco, CA}}{{page needed|date=September 2013}}</ref>

==== Endopolyploidy ====
Polyploidy occurs in some tissues of animals that are otherwise diploid, such as human [[muscle]] tissues.<ref name="pmid19571289">{{cite journal | vauthors = Parmacek MS, Epstein JA | title = Cardiomyocyte renewal | journal = The New England Journal of Medicine | volume = 361 | issue = 1 | pages = 86–88 | date = July 2009 | pmid = 19571289 | pmc = 4111249 | doi = 10.1056/NEJMcibr0903347 }}</ref> This is known as '''endopolyploidy'''. Species whose cells do not have nuclei, that is, [[prokaryotes]], may be polyploid, as seen in the large [[bacterium]] ''[[Epulopiscium fishelsoni]]''.<ref>{{cite journal | vauthors = Mendell JE, Clements KD, Choat JH, Angert ER | title = Extreme polyploidy in a large bacterium | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 105 | issue = 18 | pages = 6730–6734 | date = May 2008 | pmid = 18445653 | pmc = 2373351 | doi = 10.1073/pnas.0707522105 | doi-access = free | bibcode = 2008PNAS..105.6730M }}</ref> Hence [[ploidy]] is defined with respect to a cell.

==== Monoploid ====
{{main|Monoploidy}}
A monoploid has only one set of chromosomes and the term is usually only applied to cells or organisms that are normally diploid. The more general term for such organisms is [[haploid]].