Citrus taxonomy

Various citrus types in cross section. Some of them are hybrids between two or more original species.
The investigation of this matter and the botanical classification of the species, varieties and cultivars belonging to the genus Citrus, is called "citrus taxonomy".

Citrus taxonomy refers to the botanical classification of the species, varieties, cultivars, and graft hybrids within the genus Citrus, subgenus Papeda, and related genera, found in cultivation and in the wild.

Citrus taxonomy is complex.[1][2] Cultivated citrus are derived from various forms of old citrus species found in the wild. Some are only selections of the original wild types, while others are hybrids between two or more ancestors. Citrus plants hybridize easily between species with completely different morphologies, and similar-looking citrus fruits may have quite different ancestries.[3][4][5]

Most hybrids express different ancestral traits when planted from seeds (F2 hybrids) and can continue a stable lineage only through vegetative propagation. Others do reproduce true to type via nucellar seeds in a process called apomixis.[5] Many different-looking varieties are nearly genetically identical, and differ only by a bud mutation. Some differ only in disease resistance.[6]

Clear genetic lineages are very important for breeding improved cultivars.[7]

Genetic history

Citrus fruits clustered by genetic similarity (PCA of SNP diversity). Citrus micrantha (top right) is a papeda.
Hybrids are expected to plot between their parents. ML: 'Mexican' lime; A: 'Alemow'; V: 'Volkamer' lemon; M: 'Meyer' lemon; L: Regular and 'Sweet' lemons; B: Bergamot; H: Haploid clementine; C: Clementines; S: Sour oranges; O: Sweet oranges; G: Grapefruits.

Interbreeding seems possible between all citrus plants, and between citrus plants and some plants which may or may not be categorized as citrus. The ability of citrus hybrids to self-pollinate and to reproduce sexually also helps create new varieties.

The four core ancestral citrus taxa are citron (C. medica), pummelo (C. maxima), mandarine (C. reticulata), and papeda (C. micrantha).[8]

These taxa all interbreed freely, despite being quite genetically distinct. They probably arose through allopatric speciation, with citrons evolving in northern Indochina, pummelos in the Malay Archipelago, and mandarines in Vietnam, southern China, and Japan.[8]

The hybrids of these four taxa include familiar citrus fruits like oranges, grapefruit, lemons, limes, and some tangerines.[1][9][10] In many cases, these crops are propagated asexually, and lose their characteristic traits if bred. However, some of these hybrids have interbred with one another and with the original taxa, making the citrus family tree a complicated network.

There are also groups that interbreed with the four core taxa, but which have not historically been categorized as citrus. The trifoliate orange and kumquats do not naturally interbreed with the four undisputed citrus taxa due to different flowering times,[11] but hybrids (such as the citrange and calamondin) exist. Australian limes and Clymenia are native to Australia and Papua New Guinea, so they did not naturally interbreed with the four core taxa; but they have been crossbred with mandarins and calamondins by modern breeders.

Humans have deliberately bred new citrus fruits by propagating wild-found seedlings (e.g. clementines), creating or selecting mutations of hybrids, (e.g. Meyer lemon), and crossing different varieties (e.g. 'Australian Sunrise', a finger lime and calamondin cross).

Genetic analysis is starting to make sense of this complex phylogeny.[12] Two citrus fruits have had their full genomes sequenced (sweet orange and clementines). Many different phylogenies for the non-hybrid citrus have been proposed,[12][13][13] and taxonomic terminology is not yet settled.

Citrus naming systems

See also: Botanical name

Because citrus taxonomy is still understudied, there are many systems of classification that very often contradict each other. There are two main complete systems, that of Tanaka and that of Swingle; however, many citrus types were identified and named by individual taxonomists.

The basis of the "Tanaka system" is to provide a separate name for each cultivar, regardless of whether it is pure or a hybrid of two or more species or varieties. The "Swingle system" works differently, in that it first divides the genus Citrus into species, secondly divides it further into varieties, and lastly divides it again into cultivars or hybrids. The Swingle system is generally followed today with much modification; however, there are still huge differences in nomenclature between countries and even individual scientists.[14][15]

Common name confusions

See also: Folk taxonomy

Most commercial varieties are descended from one or more of citrons, mandarins, and pommelos.

The same common names may be given to different citrus hybrids or mutations. Fruit with similar ancestry may be quite different in name and traits (e.g. grapefruit, common oranges, and ponkans, all pommelo-mandarin hybrids).


The common oranges as well as the grapefruits are hybrids between the mandarin and the pummelo.
Mandarin orange is a true species, it is one of the progenitors of most cultivated citrus.
Trifoliate orange belongs to the genus poncirus, according to Swingle.

Not all the fruits that are called by the name "orange" share much genetic affiliation.

The common sweet orange and sour orange genetics are like those of the grapefruit, a cross between a pommelo and a mandarin orange. They are all intermediate between the two ancestors in size, flavor and shape. The above-mentioned oranges have the orange color of the mandarin orange in their outer peels and segments, and are easier to peel than the grapefruits,.[5][16]

Grapefruits are more akin to the pommelo ancestor[17] and so probably a cross between the sweet orange and the pommelo.[18]

Mandarins are one of the basic species. Even pure-bred ones are genetically diverse. Many varieties commercially called mandarins are actually hybrids.[5][19] Most are hybrids with sweet oranges, but some are hybrids with lemons. Some are hybrids with pomelos (and thus like sweet oranges).

The trifoliate orange is a cold hardy plant distinguishable by its leaves with three leaflets. It is the only member of the Poncirus genus (disputed[20]), but is close enough to the Citrus genus to be used as a rootstock.[21] The Indian wild orange is, according to some research, one of the ancestors of today's cultivated citrus fruits.[22] The bergamot orange is likely to be a hybrid of Citrus limetta and Citrus aurantium.[23]

Lemons and limes

The Lumia

Most lemons are from one common ancestor, and diverged by mutation. The ancestor was a hybrid with citron, pummelo and mandarin ancestry; citrons contribute the largest share of the genome.[24]

Sweet lemons and sweet limes

Sweet lemons, sweet limes, and rough lemons are hybrids similar to non-sweet lemons and limes, but with less citron parentage.[24]

Genetically, one study showed that the Persian sweet lemon clusters with the pummelo, mandarin orange and common orange groups, and not with the citrons, limes and lemons group.[18]

Sweet lemons and sweet limes are less acid than regular lemons and limes. The name is applied to:

  1. The lumia from the Mediterranean basin, probably Italy, is a big dry citron-like citrus that is pear shaped and not necessarily sweet.
  2. The Persian sweet lime, also known as the limetta, is small and round like a common lime, with sweet juice.
  3. The Palestinian sweet lime from India is mainly used as a rootstock.[25]

Sweet limes and lemons are not sharply separated:

The sweet lime, Citrus limettioides Tan. (syn. C. lumia Risso et Poit.), is often confused with the sweet lemon, C. limetta Tan., (q.v. under LEMON) which, in certain areas, is referred to as "sweet lime". In some of the literature, it is impossible to tell which fruit is under discussion.[26][27]

The same plant may also be known by different names:

The Indian sweet lime is the mitha nimbu (numerous modifications and other local names) of India, the limûn helou or succari of Egypt, and the Palestine sweet lime (to distinguish it from the Millsweet and Tunisian limettas, commonly called sweet limes).[28][29]


Two varieties of citron, etrog and fingered, are both citrons but are extremely distinct-looking.
3 more varieties of Citrus medica that are all true non-hybrid citrons.

Citron has many true varieties that are extremely distinct looking. Some of the fingered varieties are used in a buddhist offering and some of the common varieties are used for the Jewish ritual etrog, and there is also a variety of citron called etrog.

While in Modern Hebrew etrog is the name for citron of any variety or form, whether kosher for the ritual or not, its English usage applies only to those varieties and specimens used as one of the Four Species. The various Jewish rites utilize different varieties, according to their tradition or the decision of their respective Posek.[30] The Mountain citron, however, has no relation to the true citron and belongs to the citrus subg. Papeda.

Many citrons are not hybrids but pure ancestral species. Citrons are usually fertilized by self-pollination, and is therefore generally a male parent of any citrus hybrid, rather than a female one. Many citron varieties were proven to be pure-bred despite their morphological differences;[31][32][33][34][35][36] however, the florentine citron is probably of hybrid origin.

Lemons are a citron hybrid.[24]


Kumquats are a separate species, with few hybrids, none of which is commonly called "kumquat".

Australian and New Guinean species

Australian and New Guinean citrus species are genetically separate, although some commercial varieties are hybrids with mandarins, lemons, and/or sweet oranges.

Citrus relatives

Another issue of controversy is whether the citrus-related genera are to be included in the genus or not.


Swingle coined the Citrus subg. Papeda to separate its members from the more edible citrus. Papedas also differ from regular citrus in that its stamens grow separately, not united at the base.[37]

Fortunella & Citrofortunella

Carl Peter Thunberg originally classified the kumquats as Citrus japonica in his 1784 book, Flora Japonica. In 1915, Walter T. Swingle reclassified them in a segregate genus, Fortunella, named in honor of Robert Fortune. Seven species of Fortunella have generally been recognized—F. japonica, F. margarita, F. crassifolia, F. hindsii, F. obovata and F. polyandra, as well as the recently described F. bawangica. Since the kumquat is a cold hardy species, there are many hybrids between common citrus members and the kumquat (most popularly the calamondin that occurred naturally). Those hybrids are not citrus hybrids, according to Swingle, but reside in a separate hybrid genus which he called × Citrofortunella.

Subsequent study of the many commercial lineages revealed such complexity that the genera could not be separated.[38] Consequently, in accordance with the International Code of Nomenclature for algae, fungi, and plants, the correct genus name reverted to Citrus. The Flora of China returns the kumquat to Citrus and combines the species into the single species as Citrus japonica,[39] and today the Fortunella and Citrofortunella are nothing else but regular citrus.[40]

Poncirus and Citrocirus

According to the Swingle system, the trifoliate orange, a cold hardy plant that is commonly used as a citrus rootstock, is not included in the genus Citrus, but in a related genus, Poncirus. Therefore, the citrange, which is a hybrid between the trifoliate and the sweet orange, is placed into a hybrid genus called Citrocirus (not a valid botanical name). However, molecular investigation suggests Poncirus should be equivocally included in the genus Citrus.[41]

Reclassification of Microcitrus and Eremocitrus

The desert lime, formerly Eremocitrus, but now Citrus glauca, hangs from a branch.

The edible Australian limes are starting to be domesticated and commercially grown. Recent molecular research suggests that although Swingle placed them in the separate genera Microcitrus and Eremocitrus, they should also be included in the genus Citrus.[41]

Australian limes
former Eremocitrus

Citrus glauca

former Microcitrus

Citrus warburgiana

Citrus inodora

Citrus maideniana

Citrus garrawayi

Citrus australasica

Citrus australis


Triphasia and Clymenia

Two additional genera, Triphasia and Clymenia, are likewise very closely related to the Citrus genus and bear hesperidium fruits, but they are not usually considered part of it. At least one, Clymenia, will hybridize with kumquats and some limes.

Wild lime

The wild lime—native to southern Florida and Texas in the United States, Mexico, Central America, the Caribbean, and South America as far south as Paraguay—does not belong in the Citrus genus. It is part of another genus in the Rutaceae family, Zanthoxylum (which also includes Sichuan pepper), and was classified as Zanthoxylum fagara by Charles Sprague Sargent.[43]

International taxonomy

The International Association for Plant Taxonomy was founded in 1950 to resolve the taxonomic problem of all the plants. They hold meetings every five years to review the updated information and try to reach consensus. The current president is David Mabberley.[44]

See also


  1. 1 2 G. A. Moore. "Oranges and lemons: clues to the taxonomy of Citrus from molecular markers". PMID 11525837.
  2. What is an Orange
  3. A genealogy of the citrus family
  4. An Introduction to Citrus
  5. 1 2 3 4 G Albert Wu; et al. "Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication". Nature.
  6. Xiaomeng Li. "The Origin of Cultivated Citrus as Inferred from Internal Transcribed Spacer and Chloroplast DNA Sequence and Amplified Fragment Length Polymorphism Fingerprints".
  7. "Genetic Diversity Assessment of Acid Lime (Citrus aurantifolia Swingle) Landraces in Nepal, Using SSR Markers - Open Access Library".
  8. 1 2 "BMC Genetics - Full text - Next generation haplotyping to decipher nuclear genomic interspecific admixture in Citrus species: analysis of chromosome 2".
  9. Phylogenetic Relationships of Citrus and Its Relatives Based on matK Gene Sequences
  10. Citrus limon (L.) Burm. f. (pro. sp.) — Classifications: Lemon and more
  11. "New universal mitochondrial PCR markers reveal new information on maternal citrus phylogeny". doi:10.1007/s11295-010-0314-x.
  12. 1 2 Andrés García Lor (2013). Organización de la diversidad genética de los cítricos (PDF) (Thesis). p. 79.(Spanish)
  13. 1 2 "Assessing genetic diversity and population structure in a citrus germplasm collection utilizing simple sequence repeat markers (SSRs)". doi:10.1007/s00122-006-0255-9.
  14. Iqrar A. Khan, Citrus Genetics, Breeding and Biotechnology p. 49.
  15. Classification of Citrus
  16. The draft genome of sweet orange (Citrus sinensis)
  17. "Assessment of genetic variability in grapefruits (Citrus paradisi Macf.) and pummelos (C. maxima (Burm.) Merr.) using RAPD and SSR markers".
  18. 1 2 Genetic Diversity of Citrus
  19. Genetic similarity of citrus fresh fruit market cultivars
  20. See below Citrus taxonomy#Poncirus, Microcitrus & Eremocitrus
  21. "Genetic Transformation of Poncirus trifoliata (Trifoliate Orange)".
  22. Malik, S. K., R. Chaudhury, O. P. Dhariwal and R. K. Kalia. (2006). Collection and characterization of Citrus indica Tanaka and C. macroptera Montr.: wild endangered species of northeastern India.
  23. "RFLP Analysis of the Origin of Citrus Bergamia, Citrus Jambhiri, and Citrus Limonia".
  24. 1 2 3 Lemons: Diversity and Relationships with Selected Citrus Genotypes as Measured with Nuclear Genome Markers
  25. See respective pages for sources.
  26. Purdue University
  27. Please note that this author also confused the lumia and the Palestinian sweet lime. Those two are quite distinguishable, and definitely not the same, whereas the Palestinian sweet lime and the limetta can possibly be similar or even identical. See following citation of The Citrus Industry (book) and adjacent photos.
  28. The Citrus Industry Volume I Palestine at Citrus Variety Collection Website
  29. Volume I See heading: Indian (Palestine)
  30. "ethrog". University of California, Riverside.
  31. Citrus phylogeny and genetic origin of important species as investigated by molecular markers. 2000
  32. Assessing genetic diversity and population structure in a Citrus germplasm collection utilizing simple sequence repeat markers (SSRs) by: Noelle A. Barkley, Mikeal L. Roose, Robert R. Krueger and Claire T. Federici
  33. Phylogenetic relationships in the "true citrus fruit trees" revealed by PCR-RFLP analysis of cpDNA. 2004
  34. "The Search for the Authentic Citron: Historic and Genetic Analysis"; HortScience 40(7):1963–1968. 2005 Archived September 21, 2008, at the Wayback Machine.
  35. Chromosome Numbers in the Subfamily Aurantioideae with Special Reference to the Genus Citrus; C. A. Krug. Botanical Gazette, Vol. 104, No. 4 (Jun., 1943), pp. 602–611
  36. The relationships among lemons, limes and citron: a chromosomal comparison. by R. Carvalhoa, W.S. Soares Filhob, A.C. Brasileiro-Vidala, M. Guerraa.
  37. A classification for edible Citrus (Rutaceae) by David Mabberley
  38. Mabberley (Blumea 49: 481–498. 2004) Citrus (Rutaceae): A Review of Recent Advances in Etymology, Systematics and Medical Applications
  39. Zhang Dianxiang, Thomas G. Hartley, David J. Mabberley, Rutaceae in Flora of China 11: 51-97 (2008)
  40. Jorma Koskinen and Sylvain Jousse. "Citrus Pages / Kumquats".
  41. 1 2 Nicolosi et al. (2000), de Araújo et al. (2003)
  42. Jorma Koskinen and Sylvain Jousse. "Citrus Pages / Native Australian varieties".
  43. "Zanthoxylum fagara (L.) Sarg.". Germplasm Resources Information Network. United States Department of Agriculture. 2007-02-15. Retrieved 2009-11-27.
  44. Citrus Pages - a comprehensive article on citrus taxonomy


Molecular classification

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