A Numerical Taxonomic Study of Affinity Relationships in Cultivated Citrus and Its Close Relatives

Barrett, H. C.; Rhodes, A. M.

doi:10.2307/2418763

Cited by 352 publications

(324 citation statements)

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“…The first two principal coordinates in the multidimensional scaling (Fig. 1a) separate three ancestral (sometimes called 'fundamental') Citrus species associated with commercially important types 8,9 citrons (C. medica), mandarins (C. reticulata) and pummelos (Citrus maxima)-and display lemons, limes, oranges and grapefruits as hybrids involving these three species. The nucleotide diversity distributions (Fig.…”

Section: Article Researchmentioning

confidence: 99%

Genomics of the origin and evolution of Citrus

Terol

Ibáñez

et al. 2018

Nature

632

604

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Genomics of the origin and evolution of CitrusGuohong albert Wu 1 , Javier Terol 2 , Victoria ibanez 2 , antonio López-García 2 , estela Pérez-román 2 , carles borredá 2 , concha Domingo 2 , francisco r. Tadeo 2 , Jose carbonell-caballero 3 , roberto alonso 3 , franck curk 4 , Dongliang Du 5 , Patrick Ollitrault 6 , Mikeal L. roose 7 , Joaquin Dopazo 3,8 , frederick G. Gmitter Jr 5 , Daniel S. rokhsar 1,9,10 & Manuel Talon 2The genus Citrus and related genera (Fortunella, Poncirus, Eremocitrus and Microcitrus) belong to the angiosperm subfamily Aurantioideae of the Rutaceae family, which is widely distributed across the monsoon region from west Pakistan to north-central China and south through the East Indian Archipelago to New Guinea and the Bismarck Archipelago, northeastern Australia, New Caledonia, Melanesia and the western Polynesian islands 1 . Native habitats of citrus and related genera roughly extend throughout this broad area (Extended Data Fig. 1a and Supplementary Table 1), although the geogra phical origin, timing and dispersal of citrus species across southeast Asia remain unclear. A major obstacle to resolving these uncertainties is our poor understanding of the genealogy of complex admixture in cultivated citrus, as has recently been shown 2 . Some citrus are clonally propagated apomictically 3 through nucellar embryony, that is, the development of non-sexual embryos originating in the maternal nucellar tissue of the ovule, and this natural process may have been co-opted during domestication; grafting is a relatively recent phenomenon 4 . Both modes of clonal propagation have led to the domestication of fixed (desirable) genotypes, including interspecific hybrids, such as oranges, limes, lemons, grapefruits and other types.Under this scenario, it is not surprising that the current chaotic citrus taxonomy-based on long-standing, conflicting proposals 5,6 -requires a solid reformulation consistent with a full understanding of the hybrid and/or admixture nature of cultivated citrus species. Here we analyse genome sequences of diverse citrus to characterize the diversity and evolution of citrus at the species level and identify citrus admixtures and interspecific hybrids. We further examine the network of relatedness among mandarins and sweet orange, as well as the pattern of the introgression of pummelos among mandarins for clues to the early stages of citrus domestication. Diversity and evolution of the genus CitrusTo investigate the genetic diversity and evolutionary history of citrus, we analysed the genomes of 58 citrus accessions and two outgroup genera (Poncirus and Severinia) that were sequenced to high coverage, including recently published sequences 2,3,7 as well as 30 new genome sequences described here. For our purpose, we do not include accessions related by somatic mutations. These sequences represent a diverse sampling of citrus species, their admixtures and hybrids (Supplementary Tables 2, 3 and Supplementary Notes 1, 2). Our collection includes accessions from eight previously unsequ...

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Section: Article Researchmentioning

confidence: 99%

Genomics of the origin and evolution of Citrus

Terol

Ibáñez

et al. 2018

Nature

632

604

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“…Many commercial Citrus varieties have a hybrid origin (Scora, 1975;Barrett and Rhodes, 1976;Nicolosi et al, 2000;Moore, 2001). Hybrids derived from citron display intense purple pigmentation in young, developing leaves and flowers, where anthocyanins can provide protection for vulnerable tissues undergoing new growth.…”

Section: Ruby In Citrus Hybridsmentioning

confidence: 99%

“…Sexual promiscuity and thousands of years of human cultivation have generated many hybrids whose origin cannot be inferred solely on the basis of morphological and geographical data. However, a growing body of evidence supports the view that there are three basic or primary species: mandarin (Citrus reticulata), pummelo (Citrus maxima), and citron (Citrus medica; Scora, 1975;Barrett and Rhodes, 1976). All the other so-called species are hybrids derived from these three primary species (Moore, 2001).…”

mentioning

confidence: 99%

Changes in Anthocyanin Production during Domestication of Citrus

et al. 2017

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Mandarin (Citrus reticulata), citron (Citrus medica), and pummelo (Citrus maxima) are important species of the genus Citrus and parents of the interspecific hybrids that constitute the most familiar commercial varieties of Citrus: sweet orange, sour orange, clementine, lemon, lime, and grapefruit. Citron produces anthocyanins in its young leaves and flowers, as do species in genera closely related to Citrus, but mandarins do not, and pummelo varieties that produce anthocyanins have not been reported. We investigated the activity of the Ruby gene, which encodes a MYB transcription factor controlling anthocyanin biosynthesis, in different accessions of a range of Citrus species and in domesticated cultivars. A white mutant of lemon lacks functional alleles of Ruby, demonstrating that Ruby plays an essential role in anthocyanin production in Citrus. Almost all the natural variation in pigmentation by anthocyanins in Citrus species can be explained by differences in activity of the Ruby gene, caused by point mutations and deletions and insertions of transposable elements. Comparison of the allelic constitution of Ruby in different species and cultivars also helps to clarify many of the taxonomic relationships in different species of Citrus, confirms the derivation of commercial varieties during domestication, elucidates the relationships within the subgenus Papeda, and allows a new genetic classification of mandarins.

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“…The difficulty in classifying Citrus taxa is mainly due to repeated crosspollination and to adventitious nucellar embryony, which stabilizes and perpetuates hybrid taxa (Scora 1975). Scora (1975) and Barrett and Rhodes (1976) suggested that there are only three ''basic'' true species of Citrus within the subgenus Citrus as defined by Swingle: citron (C. medica L.), mandarin (C. reticulata Blanco), and pummelo (C. maxima L. Osbeck). Nearly all Citrus species freely hybridize with one another, and thus, Mabberley (1997) suggests that taxonomic rank has been inflated due to the commercial importance of this crop and that only three species (C. medica, C. maxima, and C. reticulata) should be recognized for the subgenus Citrus.…”

Section: Allele and Taxa Selectionmentioning

confidence: 99%

What phylogeny and gene genealogy analyses reveal about homoplasy in citrus microsatellite alleles

et al. 2009

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Sixty-five microsatellite alleles amplified from ancestral citrus accessions classified in three separate genera were evaluated for sequence polymorphism to establish the basis of inter-and intra-allelic genetic variation, evaluate the extent of size homoplasy, and determine an appropriate model (stepwise or infinite allele) for analysis of citrus microsatellite alleles. Sequences for each locus were aligned and subsequently used to determine relationships between alleles of different taxa via parsimony. Interallelic size variation at each SSR locus examined was due to changes in repeat copy number with one exception. Sequencing these alleles uncovered new distinct point mutations in the microsatellite region and the region flanking the microsatellite. Several of the point mutations were found to be genus, species, or allele specific, and some mutations were informative about the inferred evolutionary relationships among alleles. Overall, homoplasy was observed in alleles from all three loci, where the core microsatellite repeat was changed causing alleles of the same size class to be identical in state but not identical by descent. Because nearly all changes in allele size (with one exception) were due to expansion or contraction of the repeat motif, this suggests that a stepwise mutation model, which assumes homoplasy may occur, would be the most appropriate for analyzing Citrus SSR data. The collected data indicate that microsatellites can be a useful tool for evaluating Citrus species and two related genera since repeat motifs were reasonably well retained. However, this work also demonstrated that the number of microsatellite alleles is clearly an underestimate of the number of sequence variants present.

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A Numerical Taxonomic Study of Affinity Relationships in Cultivated Citrus and Its Close Relatives

Cited by 352 publications

References 10 publications

Genomics of the origin and evolution of Citrus

Genomics of the origin and evolution of Citrus

Changes in Anthocyanin Production during Domestication of Citrus

What phylogeny and gene genealogy analyses reveal about homoplasy in citrus microsatellite alleles

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