Open access peer-reviewed chapter

The North American Plums (Prunus Spp.): A Review of the Taxonomic and Phylogenetic Relationships

Written By

Dario J. Chavez and José X. Chaparro

Submitted: October 29th, 2019 Reviewed: February 6th, 2020 Published: March 9th, 2020

DOI: 10.5772/intechopen.91638

From the Edited Volume

Prunus

Edited by Ayzin Küden and Ali

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Abstract

North America is a center of diversity for Prunus species. Tree architecture, chilling requirement, heat requirement, fruit development period, fruit size, fruit texture, disease resistance, and adaptive changes to multiple environmental conditions are a few examples of the traits of which tremendous genetic variability is available in the native plum species. Wild native Prunus species constitute an important potential source of genetic diversity for stone fruit breeding and selection. A review of the North American plum taxonomic treatment and phylogenetic studies is described. Various studies have been done with three major groups being identified: Americana series, Chickasaw series, and Beach series.

Keywords

  • plums
  • phylogeny
  • taxonomy
  • Prunus
  • Prunocerasus

1. Introduction

The genus PrunusL. belongs to the subfamily Amygdaloideae (=Prunoideae) of the Rosaceae. It has a worldwide distribution with approximately 200 species. Edible species are mostly distributed in the northern hemisphere [1, 2, 3, 4, 5]. The genus contains species that are important in the production of fruit, nuts, and lumber. Plums, cherries, almonds, apricots, and peaches are the most commonly known fruit and nuts in this genus. The world’s net production of almonds, apricots, cherries, peaches, nectarines, plums, and sloes in 2010 was approximately 40.8 million tons. Peach and nectarine production was the largest in the world with 20.5 million tons. US peach and nectarine production was approximately 1.3 million tons, with a farm gate value of ∼683 million dollars [6].

North America is an important center of diversity for plum species adapted (native) to widely divergent climates and soils representing an important potential source of genes for plant breeding. In [7], Layne and Bassi reported high levels of variation in the Prunusgermplasm for tree size, growth habit, flower size and color, chill hour requirement, fruit size, flesh texture, flesh color, resistance to diseases, and adaptability to diverse climatic and geographic regions. Plums are the stone fruit with the greatest diversity of flavor, aroma, texture, color, form, and size [2, 8].

Stone fruit breeders have used this tremendous genetic variability through interspecific hybridizations (in particular with species in the subgenus Prunusor Prunophora) for the improvement of Prunusscion and rootstock cultivars [9]. Among those, native North American plum species have been identified as a source of resistance to blossom blight and brown rot (Monilinia fructicola), bacterial spot (Xanthomonas campestrispv. pruni), bacterial canker (Pseudomonas syringaepv. syringae), plum leaf scald (Xylella fastidiosa), peach tree short life (PTSL), root-knot nematode (Meloidogynespp.), lesion nematode (Pratylenchusspp.), clitocybe root rot (Armillaria tabescens), and others [9, 10, 11, 12].

Resistance to bacterial leaf spot and bacterial canker was identified in a cultivar derived from P. salicinaLindl., P. cerasiferaEhrh., P. angustifoliaMarshall, P. americanaMarshall, and P. munsonianaW. Wight & Hedrick. Prunus hortulanaL.H. Bailey was found resistant to root-knot nematode and has been recommended as a rootstock for European plums. Improved tolerance for PTSL was found in hybrids from P. americana, P. hortulana, P. angustifolia, and/or P. umbellataElliot. Potential uses of the native North American plum species as breeding parents, scions, and/or rootstocks were summarized by [10, 12].

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2. Taxonomic treatment

In [8], Waugh described the genus Prunusas trees or shrubs, mostly with edible fruit and flowers, white or pink, with spreading petals. Stamens 15–30, distinct, with filiform filaments. Style, terminal; stigma, usually truncate. The fruit has a fleshy exterior, is glabrous, and contains a hard bony pit, which contains the seed.

Inconsistencies in the taxonomy of Prunuswere recognized by Waugh [8] and Hedrick [2]. Bortiri et al. [1] summarized the classification discrepancies in Prunusas follows: (1) four different genera (Amygdalus, Cerasus, Prunus, and Padus[13]) and later two (Amygdalusand Prunus) [14]; (2) five genera (Amygdalus, Persica, Prunus, Armeniaca, and Cerasus(including Padusand Laurocerasus)) [15]; (3) Prunusas a single genus divided in seven sections (Amygdalus, Armeniaca, Prunus, Cerasus, Laurocerasus, Ceraseidos, and Amygdalopsis) [16]; (4) Prunuswith previous seven sections as subgenera [17]; (5) Prunusclassified into five subgenera (Prunophora(Prunus), Amygdalus, Cerasus, Padus, and Laurocerasus) and with subgenus Prunusdivided in three sections (Euprunus, Prunocerasus, and Armeniaca) [3]; and (6) Prunusdivided into three genera (Padus, Laurocerasus, and Prunus) [18].

Recently, the concept of Prunusas single genus has become widely accepted, but subgenera classification is still undistinguished as new phylogenetic relationships within Prunuscome to light. The USDA-GRIN [19] germplasm collection organizes the genus Prunusinto subgenus Amygdalus, Cerasus, Emplectocladus, and Prunus. Subgenus Cerasuswas divided into sections Cerasusand Laurocerasusand subgenus Prunusinto sections Armeniaca, Microcerasus(including some plums), Penarmeniaca, Prunocerasus(the North American plums), and Prunus.

Waugh [8] recognized the difficulty in classifying the North American plums and stated “plums grow pretty much as they please, and the botanist has to take them as he finds them.” The distribution, cultivation, hybridization, and breeding value of native plums have been extensively studied [2, 4, 5, 8, 20, 21].

Waugh [8] classified the cultivated and indigenous Prunusof North America into groups. These groups were clustered into seven series: Americana, Chickasaw, Hortulana, Maritima, Sand Cherry, Choke Cherry, and Black Cherry [22] (Table 1). The Americana series included the Americana group (including P. americanavar. lanata) and the Nigra group (Prunus nigraAiton). The Chickasaw series included the Chickasaw and the Sand plum groups. The Hortulana series, categorized as “hybrids,” included the Wildgoose group, the Wayland group, and the Miner group. The Maritima series the Beach plum group, the Southern sloe group [including P. umbellataElliot var. injuncunda(Small) Sarg.], the Oklahoma plum group, and P. glandulosaThunb. (ungrouped). The Sand Cherry series were equivalent to the Dwarf cherries group. The Choke Cherry and the Black Cherry series conserved their name as groups [8, 22] (Table 1).

GroupSpeciesOriginCultivation
CultivatedDomestica plumsPrunus domesticaEastern Europe and west-central AsiaNova Scotia, central New England, New York, southern Ontario and Michigan, and the Pacific coast states
DamsonsPrunus domesticaEurope
Myrobalan plumsPrunus cerasiferaEurope and US used as rootstock
Simon plumsPrunus simoniiChinaNew York, California
Japanese plumsPrunus trifloraChina, JapanMaine, Vermont, Ontario, and southern Iowa
IndigenousAmericana groupPrunus americanaUSA (Ohio, Texas, northward to Minnesota and Montana)Prince Edward Island, Manitoba, and Vancouver, to Florida, Louisiana, and Texas
Nigra groupPrunus americana nigraCAN (Newfoundland west to Rainy and Assiniboine rivers), USA (New England states)Prince Edward Island, Manitoba, and Vancouver, to Florida, Louisiana, and Texas
Miner GroupPrunus hortulana mineriUSA (standing between P. americanaand the Wildgoose group)Not cultivated
Wayland groupPrunus rivularisz
Prunus hortulanay
USA (Colorado, Guadalupe, and the Leona)North of Burlington, Vermont, and Iowa
Wildgoose groupPrunus hortulanaUSA (the Mississippi valley)From Texas to Massachusetts
ChickasawsPrunus angustifoliaUSA (Southern range to Delaware and Kentucky, including southern Atlantic and Gulf states)Iowa, Vermont, New York, and Massachusetts
Sand plumPrunus angustifolia watsoniiUSA (South and southeast Nebraska and central and western Kansas)Cultivated by settlers in Kansas and Maryland
Beach plumPrunus maritimaUSA (sea beaches, New Brunswick to Virginia, Georgia, Alabama, and Connecticut)Not cultivated
Pacific plumPrunus subcordataUSA (Pacific coast)Sierra regions of California and southern Oregon
Oklahoma plumPrunus gracilisUSA (Southern Kansas to Texas and Tennessee)Not cultivated
Alleghany plumPrunus alleghaniensisUSA (Alleghany mountains in Pennsylvania)Not cultivated
Southern sloePrunus umbellataUSA (seashore from South Carolina to Florida and westward to Mississippi, Louisiana, and Arkansas)Not cultivated
Dwarf cherriesPrunus pumila
Prunus pumila besseyi
Prunus cuneata
P. pumilain USA (coasts of northern states), P. pumilabesseyi (from Manitoba to Kansas, westward to California and Utah), and P. cuneatain USA (New Hampshire to Minnesota and southward to North Carolina)Nebraska eastward
Choke CherryPrunus virginianaCAN (Newfoundland to Manitoba and British Columbia) to USA (Georgia, Texas, and Colorado)Not cultivated
Black CherryPrunus serotinaCAN (Quebec) to USA (Kansas and southward, New Mexico, and Mexico)Not cultivated

Table 1.

Cultivated and indigenous plums in North America by group, area of origin, and cultivation [8].

Classified as Prunus rivularisbut with doubts.


Prunus hortulanaconsider as part of the Wayland and the Wildgoose group.


Wight [5] separated the genus Prunusin plums, cherries, and dwarf cherries. Waugh’s [8, 22] taxonomic treatment included cherries as part of plums. Wight’s [5] groups/series were Americana, Subcordata, Hortulana, Angustifolia, Maritima, and Gracilis. The Angustifolia group agreed with Waugh’s [22] Chickasaw series. Waugh [22] did not include P. mexicana S. Watson(Americana group), P. munsoniana(Angustifolia group), P. subcordataBenth. (Subcordata group), P. alleghaniensisPorter (Maritima group), and P. umbellata(Maritima group), as part of his groups/series.

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3. Prunusphylogenetic studies

Phylogeny and systematics in the genus Prunuswas reported by [23]. They employed isozymes to study the phylogenetic relationships in Prunus. Section Prunocerasuswas found to be polyphyletic, with a clade formed by P. americana, P. munsoniana, P. hortulana, P. subcordata, and P. angustifolia, and a clade formed by P. maritimaMarshall and P. umbellata.

Chloroplast DNA is an alternative source of genetic variation and is maternally inherited in Prunus. Chloroplast DNA is highly conserved and in relative abundance in the cell as compared with the nuclear DNA. Kaneko et al. [24] and Uematsu et al. [25] used cpDNA to classify cherries, apricots, and wild and cultivated peaches in Japan. In [26], Badenes and Parfitt reported a phylogeny similar to Mowrey and Werner [23]. All the Prunusspecies were grouped as in conventional subgenus classifications [3]. Prunus persicaL.-P. dulcis(Mill.) D.A. Webb, P. domesticaL.-P. salicinaLindl., and P. cerasusL.-P. fruticosaPall were monophyletic.

Lee and Wen’s [27] phylogenetic analysis of the genus Prunususing ITS sequences recognized two major groups: the Amygdalus-Prunusgroup, and the Cerasus-Laurocerasus-Padusgroup. The results were not congruent with Rehder’s [3] taxonomic treatment.

In Bortiri et al. [1] the phylogeny and systematics of Prunusbased on ITS and chloroplast trnL-trnFspacer DNA sequences identified two major clades: subgenera Padus-Laurocerasus-Cerasusand subgenera Prunus-Amygdalus-Emplectocladus-Cerasus(sect. Microcerasus)-sect. Penarmeniaca(similar to Mowrey and Werner [23], Lee and Wen [27], and Bortiri et al. [1]). Their results indicated that plums of northeastern North America were closely related and that P. mexicanabelonged to a sister clade.

Bortiri et al. [28] used the nuclear gene s6pdh, which encodes NADP+-dependent sorbitol-6-phosphate dehydrogenase, to assess the lack of support for deep nodes in the clade subgenera Prunus-Amygdalus-Emplectocladus(as reported in previous data). The phylogenies based on ITS, cpDNA trnL-trnF, and s6pdhsequences were compared and combined. Phylogenetic analysis of the combined data supported two major clades: subgenera Cerasus-Laurocerasus-Padusand subgenera Amygdalus-Emplectocladus-Prunus. Section Microcerasus(subgenera Cerasus) was reported nested within subgenus Prunus.

Prunussubg. Prunussect. Prunocerasuswas reported to be monophyletic by Shaw and Small [29]. The phylogenetic analysis was based on seven cpDNA regions: rpS16, rpL16, trnL, trnG, trnL-trnF, trnS-trnG, and trnH-psbA. Three clades were strongly supported in sect. Prunocerasus: the “American Clade,” the “Chickasaw Clade,” and the “Beach Clade” (names based on Waugh’s (1901) classification). The American clade included P. americanaMarshall var. americanaSudw., P. americanaMarshall var. lanata, P. mexicana, P. rivularisScheele, P. hortulana, and P. umbellatavar. injucunda; the Chickasaw clade included P. angustifolia, P. munsoniana, P. gracilisEngelm. & A. Gray, P. nigra, P. umbellataElliot var. umbellata, P. alleghaniensisPorter var. alleghaniensis, and P. alleghaniensisPorter var. davisii(W. Wight) Sarg.; and the Beach clade included P. geniculataHarper, P. maritimaMarshall var. maritima, and P. maritimaMarshall var. gravesii(Small) G.J. Anderson.

Similarly, a survey of cpDNA haplotypes available within section Prunocerasuswas reported by Shaw and Small [30]. The cpDNA rpL16 region was sequenced for 207 accession representatives of 17 North American plums, including P. texanaD. Dietr. (as described before). More than one of the three primary cpDNA haplotypes was found in many of the taxa.

Bortiri et al. [31] studied the evolution of vegetative and morphological characters of 37 species of Prunusand other genera of Rosaceae. Morphological characters were combined with ITS, trnL-trnF, and trnS-trnG data from previous studies [1, 28]. The addition of the morphological data with trnS-trnG supported some nodes that were found in ITS and trnL-trnF studies. Three clades were reported: “Clade A” with subgenera Padusand Laurocerasus; “Clade B” with subgenera Amygdalus, Emplectocladus, and Prunus; and “Clade C” with subgenera Cerasus. “Clade B” was characterized by the production of three axillary buds. Padusand Laurocerasuswere not supported as monophyletic (high homoplasy).

Genetic diversity within Prunus cerasifera(cherry plum) was studied using morphological characters, cytometry, cpDNA, and SSR markers [32]. Morphological characters showed differences between clones. Analysis of cpDNA reported 15 haplotypes clustered in 3 groups. Considerable diversity among accessions was reported based on these studies.

Endocarp and leaf morphometrics combined with AFLP markers were used to study the morphological and genetic variation of five European members of section Prunus: P. cerasifera, P. cocomiliaTen., P. domestica, P. insititiaL., P. spinosaL., and P.× fruticans[33]. Three clusters were reported: a first cluster P. cerasifera-P. cocomilia, a second P. domestica-P. insititia, and a third P. spinosaand P.× fruticans.

Phylogenetic analysis based on four single-copy cpDNA regions (atpB-rbcL, matK, rpl16, and trnL-trnF) of Eurasian plums, Prunussection Prunus, confirmed this section to be monophyletic. Four well supported clades were reported: “Clade A” with P. salicina, P. sogdiana, and P. ussuriensis; “Clade B” with P. cocomilia; “Clade C” with P. brigantina, P. ramburii, and P. spinosa; and “Clade D” with subclade D1 P. domestica-P. insititia-P. divaricata-P. ursineand subclade D2 P. cerasifera[34].

Chavez et al. [39] identified genomic regions that provided the greatest number of characters and variability and improved the phylogenetic signal at the low level in Prunussection Prunocerasusrelationships. The American and the Chickasaw clades were identified. An outgroup clade was comprised by P. persicaand P. fasciculata. The results reported were similar to those reported by Mowrey and Werner [23].

Previous studies demonstrated the value of morphology, cytometry, nuclear DNA, and cpDNA as data for phylogenetic studies in Prunus.Most of the previous phylogenetic research used Mason’s [21] and Rehder’s [3] taxonomic classification. A complete summary of Prunusphylogenetic research is summarized in Table 2.

PaperzKaneko et al. [24]Mowrey and Werner [23]
Phylogenetic analysisMolecularMolecular
Analytical methodsPhenetics—percent differential restriction fragments and Engel’s genetic distancePhenetics—principal components
Metrics (analysis)cpDNA using BamHI, HindIII, and SmaIIsozyme
Taxa (no.)/subgenus (sect.) genus11 species/3 subgenus: Cerasus, Padus, Armeniaca[3]/genus Prunus34 species/4 subgenus: Prunus(sect.: Prunus, Prunocerasus, Armeniaca), Amygdalus, Cerasus(sect.: Sargentiella, Microcalymma, Magniculpula, Phyllomahaleb), and Lithocerasus(sect.: Microcerasus, Armeniacocerasus) [35]
Outgroups
Trees (no.)22 (average 30 principal components)
Characters or bp (no.)
Informative characters (no.)
Indels (no.)
Substitutions (no.)
Inversions (no.)
PIC
Percent variability
Phylogeny in classificationSupport for subgenus Prunus.Subgenus Lithocerasuswas identified as an artificial grouping of species
NotesLithocerasusformed part of Cerasusin Rehder’s [3] classification
PaperBadenes and Parfitt [26]Lee and Wen [27]
Phylogenetic analysisMolecularMolecular
Analytical methodsMPMP, NJ, ML
Metrics (analysis)cpDNA cutting with 21 3.2 kb and 10 2.1 kb endonucleasesITS nuclear ribosomal DNA
Taxa (no.)/subgenus (sect.)9 species/5 subgenus: Prunus, Amygdalus, and Cerasus.40 species (represented by 52 accessions)/5 subgenus: Prunus(sect.: Prunus, Prunocerasus, Armeniaca), Amygdalus, Cerasus(sect.: Microcerasus, Pseudocerasus, Mahaleb, Phyllomahaleb), Padus, and Laurocerasus[3]
OutgroupsFragaria vescaExochorda giraldii, Maddenia hypoleuca, Oemleria cerasiformis, Prinsepia sinensis, Prinsepia uniflora, Lyonothamnus floribundus
Trees (no.)10MP = 15,000 MPT (L = 630, CI = 0.632, RC = 0.510). Consensus tree 16,383 MPTs (L = 630, CI = 0.632, RI = 0.808). ML tree log likelihood = −3641.3155
Characters (no.)23662 bp aligned (ITS1 = 223–242 bp, 5.8 s = 154 bp, and ITS2 = 201–219 bp)
Informative characters (no.)218 bp aligned (ITS1 = 114 bp, 5.8 s = 12 bp, and ITS2 = 92 bp)
Indels (no.)29 indels (>3 bp) aligned (ITS1 = 13 bp, ITS2 = 16 bp)
Substitutions (no.)
Inversions (no.)
PIC218 bp aligned (ITS1 = 114 bp, 5.8 s = 12 bp, ITS2 = 92 bp) (not including indels)
Percent variability32.9% aligned (ITS1 = 47.1%, 5.8 s = 7.79%, ITS2 = 42.0%)
Phylogeny in classificationSupport for subgenus Prunus, Cerasus, and Amygdalus. Relative small number of taxa used in the study. Subgenus Cerasussuggested to be more extensively evolved than either Prunusor AmygdalusGenus Prunuswas monophyletic. Support for Maddenianested within genus Prunus. Within genus Prunus, two major groups were recognizable: Amygdalus-Prunusgroup and Cerasus-Laurocerasus-Padusgroup
NotesNumber of parsimony informative characters included outgroups. The % variability cannot be directly compared with studies that excluded the outgroups for the number of PICs
PaperBortiri et al. [1]Bortiri et al. [28]
Phylogenetic analysisMolecularMolecular
Analytical methodsMPMP, ML
Metrics (analysis)ITS nuclear ribosomal DNA and chloroplast trnL-trnF spacer DNANuclear gene sorbitol 6-phosphate dehydrogenase (s6pdh) and data from previous study ITS and trnL-trnF [1]
Taxa (no.)/subgenus (sect.)48 species/5 subgenus: Prunus(sect.: Prunus, Prunocerasus, Armeniaca), Amygdalus, Cerasus(sect.: Microcerasus, Pseudocerasus, Mahaleb, Phyllomahaleb), Padus, and Laurocerasus[3]22 species (representing all the major clades found in previous study)/5 subgenus: Prunus(sect.: Prunus, Prunocerasus, Armeniaca), Amygdalus, Cerasus(sect.: Microcerasus, Pseudocerasus, Mahaleb, Phyllomahaleb), Padus, and Laurocerasus[3]
OutgroupsExochorda racemosa, Oemleria cerasiformis, Prinsepia sinensis, Physocarpus capitatus, Sorbaria sorbifolia,and Spiraea cantoniensisExochorda racemosa, Oemleria cerasiformis, Sorbaria sorbifolia, Spiraea cantoniensi, Holodiscus microphyllus, Chamaebatiaria millefolium, Kageneckia oblonga, Vauquelinia californica, Gillenia stipulata, Pyrus caucasica, Sorbussp., Amelanchier alnifolia, Aruncus dioicus, Neilla sinensis, and Spiraea betulifolia
Trees (no.)trnL-trnFsequence—MP = 76 MPT (L = 187, CI = 0.733, RI = 0.834). ITS sequence—MP = stopped at 30000 MPT (L = 678, CI = 0.567, RI = 0.714). Combined data set—consensus tree 8318 MPT (L = 876, CI = 0.695, RI = 0.727)s6pdhsequence—MP = 273 MPT (L = 1198, CI = 0.58, RI = 0.81). s6pdh sequence—ML tree log likelihood = −7720.96. For combined data set—MP = 9 MPT (L = 1592, CI = 0.58, RI = 0.61). For combined data set—ML tree log likelihood = −12056.56
Characters (no.)trnL-trnF = 563 bp, ITS = 759 bps6pdh = 1387 bp. Combined data set = 2760 bp (s6pdh, trnL-trnF, and ITS)
Informative characters (no.)trnL-trnF = 26 bp (excluding outgroups), ITS = 76 bp (excluding outgroups = among Prunusspecies)s6pdh = 234 bp (excluding outgroups = among Prunusspecies). Combined data set = 226 bp (s6pdh = 148, trnL-trnF = 18, and ITS = 60)
Indels (no.)trnL-trnF = 9 indels (>2 bp), ITS = 2 indels (>2 bp)
Substitutions (no.)
Inversions (no.)
PICtrnL-trnF = 26 bp (excluding outgroups), ITS = 76 bp (excluding outgroups = among Prunusspecies) (not including indels)s6pdh = 234 bp (excluding outgroups = among Prunusspecies). Combined data set = 226 bp (s6pdh = 148, trnL-trnF = 18, and ITS = 60)
Percent variabilitytrnL-trnF = 4.62%, ITS = 10.01%s6pdh = 16.87%. For combined data set = 8.18% (s6pdh = 10.67%, trnL-trnF = 3.19%, and ITS = 7.9% = calculated with characters from Bortiri et al. [1])
Phylogeny in classificationGenus Prunuswas monophyletic. Exochorda, Oemleria, and Prinsepiawere not supported as sister groups with Prunus. Genus Prunuswas divided in two clades: subgenera Amygdalus-Prunus-Cerasus(sect. Microcerasus)-Emplectocladusgroup and subgenera Cerasus-Laurocerasus-Padusgroup. Subgenus Prunussect. Prunuswas monophyleticGenus Prunuswas monophyletic. In the combined data set, the genus Prunuswas formed by two groups: subgenera Cerasus-Laurocerasus-Padusand subgenera Amygdalus-Emplectocladus-Prunus-Cerasus(sect. Microcerasus)
NotesFirst time that P. fasciculata(sect. Emplectocladus) was used in a studyIncludes P. fasciculatasect. Emplectocladus
PaperShaw and Small [29]
Phylogenetic analysisMolecular
Analytical methodsMP, BI
Metrics (analysis)Seven noncoding chloroplast DNA regions: trnLUAA, rpS16, rpL16, and trnGUUC introns; trnSGCU-trnGUUC; trnLUUA-trnFGAA; and trnHGUG-psbAintergeneric spacers
Taxa (no.)/subgenus (sect.)43 species/5 subgenus: Prunus[sect.: Prunus, Prunocerasus(17 taxa), Armeniaca], Amygdalus, Cerasus(sect.: Microcerasus, Pseudocerasus, Mahaleb, Phyllomahaleb), Padus, and Laurocerasus[3]
OutgroupsPhysocarpus opulifolius
Trees (no.)Combined data set—MP = 25,171 MPT (L = 422, CI = 0.92, RI = 0.94)
Characters or bp (no.)Prunocerasusanalysis introns: trnLUAA = 522 bp, rpS16 = 683 bp, rpL16 = 996 bp, and trnGUUC = 711 bp. Intergeneric spacers: trnSGCU-trnGUUC = 703 bp, trnLUUA-trnFGAA = 397 bp, and trnHGUG-psbA = 363 bp. Combined data = 4375 bp. Prunusanalysis trnHGUG-psbA = 516 bp, rpL16 = 1105 bp, trnSGCU-trnGUUC = 903 bp, and trnGUUC = 746 bp. Combined data = 3270 bp
Informative characters (no.)
Indels (no.)Prunocerasusanalysis introns: trnLUAA = 0 bp, rpS16 = 2 bp, rpL16 = 7 bp, and trnGUUC = 0 bp. Intergeneric spacers: trnSGCU-trnGUUC = 2 bp, trnLUUA-trnFGAA = 0 bp, and trnHGUG-psbA = 3 bp. Combined data = 14 bp. Prunusanalysis trnHGUG-psbA = 13 bp, rpL16 = 10 bp, trnSGCU-trnGUUC = 14 bp, trnGUUC = 4 bp. Combined data = 41 bp
Substitutions (no.)Prunocerasusanalysis introns: trnLUAA = 1 bp, rpS16 = 4 bp, rpL16 = 6 bp, and trnGUUC = 4 bp. Intergeneric spacers: trnSGCU-trnGUUC = 4 bp, trnLUUA-trnFGAA = 3 bp, and trnHGUG-psbA = 1 bp. Combined data = 23 bp. Prunusanalysis trnHGUG-psbA = 11 bp, rpL16 = 21 bp, trnSGCU-trnGUUC = 28 bp, and trnGUUC = 32 bp. Combined data = 92 bp
Inversions (no.)Prunocerasusanalysis introns: trnLUAA = 0 bp, rpS16 = 0 bp, rpL16 = 0 bp, and trnGUUC = 0 bp. Intergeneric spacers: trnSGCU-trnGUUC = 0 bp, trnLUUA-trnFGAA = 0 bp, and trnHGUG-psbA = 0 bp. Combined data = 0 bp. Prunusanalysis trnHGUG-psbA = 0 bp, rpL16 = 0 bp, trnSGCU-trnGUUC = 1 bp, and trnGUUC = 0 bp. Combined data = 1 bp
PICPrunocerasusanalysis introns: trnLUAA = 1 bp, rpS16 = 6 bp, rpL16 = 13 bp, and trnGUUC = 4 bp. Intergeneric spacers: trnSGCU-trnGUUC = 6 bp, trnLUUA-trnFGAA = 3 bp, and trnHGUG-psbA = 4 bp. Combined data = 37 bp. Prunusanalysis trnHGUG-psbA = 24 bp, rpL16 = 31 bp, trnSGCU-trnGUUC = 43 bp, and trnGUUC = 36 bp. Combined data = 134 bp
Percent variabilityPrunocerasusanalysis introns: trnLUAA = 0.19%, rpS16 = 0.88%, rpL16 = 1.31%, and trnGUUC = 0.56%. Intergeneric spacers: trnSGCU-trnGUUC = 0.85%, trnLUUA-trnFGAA = 0.76%, and trnHGUG-psbA = 1.10%. Combined data = 37 bp. Prunusanalysis trnHGUG-psbA = 4.65%, rpL16 = 2.80%, trnSGCU-trnGUUC = 4.76%, and trnGUUC = 4.80%. Combined data = 4.09%.
Phylogeny in classificationGenus Prunuswas monophyletic. Subgenus Prunussect. Prunocerasusand sect. Prunuswere monophyletic. The genus Prunuswas formed by two groups: subgenera Laurocerasus-Padusand subgenera Amygdalus-Emplectocladus-Prunus-Cerasus(sect. Microcerasus). Prunus texanaand P. subcordatawere included in sect. Prunocerasus. Within sect. Prunocerasusthree groups were identified: the American, the Chickasaw, and the Beach clades
NotesPrunus texanawas first used in this study. Prunus texanaand P. fasciculatawere not recognized by Waugh [8], Wight [5], and Rehder [3]
PaperRohrer et al. [36]Shaw and Small [30]Katayama and Uematsu [37]
Phylogenetic analysisMolecularMolecularMolecular
Analytical methodsUPGMAMPUPGMA
Metrics (analysis)Fifteen microsatellites primer pairsrpL16 intronCpDNA analysis based on five restriction enzymes (SalI, XhoI, BamHI, SacI, and PstI) by RFLP
Taxa (no.)/subgenus (sect.)/genus18 species/subgenus Prunussect. Prunocerasus(13 and 3 undetermined hybrids), subgenus Prunus(P. cerasifera), and subgenus Armeniaca(P. armeniaca).A total of 207 accessions = 18 species (subgenus Prunussect. Prunocerasus)A total of 18 accessions = 14 Prunusspecies and 1 interspecific hybrid
OutgroupsPyrus ussuriensisvar. hondoensis
Trees (no.)Strict consensus = 3 MPT (L = 34, CI = 0.97, RI = 0.99)Strict consensus = 8 MPT (L = 68, CI = 0.93, RI = 0.64)
Characters or bp (no.)A total of 186 putative alleles with a mean value of 12.4 per locusrpL16 intron = 797 bp
Informative characters (no.)rpL16 intron = 23 bp
Indels (no.)
Substitutions (no.)
Inversions (no.)
PICrpL16 intron = 23 bp
Percent variabilityrpL16 intron = 2.88%
Phylogeny in classificationNo clear phylogenetic relationships were determined. The microsatellites are evolving too rapidly in North American plums to be truly useful at resolving species relationshipsTwenty-two unique haplotypes were identified in sect. Prunocerasus. Ten different haplotypes were associated with the American clade, two haplotypes with the Beach clade, and seven haplotypes with the Chickasaw clade. Additionally, one Texana haplotype, one Subcordata haplotype, and one peculiar UmbellatahaplotypeEleven genome types. The UPGMA tree consisted of two major groups: genome types A-I (subgenus Amygdalus, Prunus, and Cerasussect. Microcerasus) and other with genomes J-K (subgenus Laurocerasusand Padus).
NotesThe congeneric relationship of plums to peach and cherry allowed the successful use of these primers in section Prunocerasus. Microsatellites are evolving too rapidly to be truly useful at resolving species phylogenyThe common practice of choosing one specimen to represent a taxon can be misleading in closely related groups. Choosing different genotypes could have resulted in a different result than previous studiesThe 9.1 kb region between psbA and atpA genes would be useful tool to study the cpDNA evolution in Prunus
PaperBortiri et al. [31]Wen et al. [38]
Phylogenetic analysisMorphology and molecularMolecular
Analytical methodsMP, ML, and BIMP and BI
Metrics (analysis)ITS nuclear ribosomal gene, trnL-trnF spacer, trnS-trnG spacer, trnG intron, and 25 morphological characters.Chloroplast ndhF region and ITS nuclear ribosomal gene.
Taxa (no.)/subgenus (sect.)/genus37 species/5 subgenus: Prunus(sect.: Prunus, Prunocerasus, Armeniaca), Amygdalus, Cerasus(sect.: Microcerasus, Pseudocerasus, Mahaleb, Phyllomahaleb), Padus, and Laurocerasus[3]A total of 59 (ndhF) or 51 (ITS) accessions of Prunus/5 subgenus: Prunus(sect.: Prunus, Prunocerasus, Armeniaca), Amygdalus, Cerasus(sect.: Microcerasus, Pseudocerasus, Mahaleb, Phyllomahaleb), Padus, and Laurocerasus[3]. In addition, Madenia hypoleucaand the Pygeumgroup
OutgroupsOemleria cerasiformis, Sorbaria sorbifolia, Spiraea cantoniensi, Gillenia stipulata, Lyonothamnus floribundus, Maddenia hypoleuca, Physocarpus capitatus, Physocarpus opulifolius, and Rhodotypos scandensOemleria cerasiformis, Prinsepia uniflora, Physocarpus monogynus, Lyonothamnus floribundus, and Holodiscus discolor
Trees (no.)Morphological data set—MP = 50,000 MPT (L = 110, CI = 0.36, RI = 0.73). Molecular data results from Bortiri et al. [1] and Bortiri et al. [28]. Combined data set—MP = 20 MPT (L = 1741, CI = 0.49, RI = 0.65). Combined data set—ML tree log likelihood = 12499.63ndhF sequence—MP = 196,200 MPT (L = 815, CI = 0.71, COI = 056, RI = 0.86). ITS sequence—MP = 49,200 MPT (L = 791, CI = 0.56, COI = 0.45, RI = 0.70)
Characters or bp (no.)Combined data set = 771 bp
Informative characters (no.)ITS = 178 bp, trnL-trnF = 50 bp, and trnS-trnG = 142 bp
Indels (no.)Combined data set = 3
Substitutions (no.)
Inversions (no.)
PICITS = 178 bp, trnL-trnF = 50 bp, and trnS-trnG = 142 bp
Percent variability
Phylogeny in classificationThree clades were reported: “Clade A” with subgenera Padusand Laurocerasus; “Clade B” with subgenera Amygdalus, Emplectocladus, and Prunus; and “Clade C” with subgenera Cerasus. “Clade B” was characterized by the production of three axillary buds. Padusand Laurocerasuswere not supported as monophyletic (highly homoplasy)Both data set identified genus Prunusas a monophyletic group. Both data sets were incongruent at the species level in Prunus. The ndhF data supported two major groups: subgenera Laurocerasus(including Pygeum) and Padus, and subgenera Amygdalus, Cerasus, and Prunus. The ITS data supported a clade composed of subgenera Amygdalus, Prunus,and Cerasussect. Microcerasus, and the paraphyletic clade of Padusand Laurocerasus
PaperDepypere et al. [33]Chavez et al. [39]
Phylogenetic analysisMorphology and molecularMolecular
Analytical methodsUPGMA, PCo, and BIMP and ML
Metrics (analysis)Leaf and endocarp morphometrics and AFLP primersSSRs (41), cpDNA (seven regions), nuclear genes (33 vernalization response genes, 16 tree architecture, and 3 isozymes), and ITS
Taxa (no.)/subgenus (sect.)/genusA total of 82 accessions/5 species: P. cerasifera, P. domestica, P. insititia, P. spinosa,and P.× fruticans,A total of 8 species: P. americana, P. angustifolia, P. hortulana, P. mexicana, P. munsoniana, P. geniculata, P. maritima, P. umbellata
OutgroupsP. fasciculata, P. persica, and P. pumila
Trees (no.)cpDNA sequences—MP = 13 MPT (L = 623, CI = 0.92, RI = 0.81, RC = 0.74) – ML = −lnL = 5414.74. Nuclear genes – MP = 1 MPT (L = 2535, CI = 0.88, RI = 0.88, RC = 0.78) – ML = −lnL = 41509.34. Combined nuclear + cpDNA + ITS – MP = 2 MPT (L = 2732, CI = 0.88, RI = 0.88, RC = 0.77) – ML = −lnL = 48496.34.
Characters or bp (no.)Combined data set = 27,623 bp
Informative characters (no.)1594
Indels (no.)
Substitutions (no.)
Inversions (no.)
PIC
Percent variability
Phylogeny in classificationPCoA and AFLP of three distinct clusters. A first cluster consists of all P. cerasiferasamples and the sole P. cocomilia. A second cluster includes all individuals of P. domesticaand P. insititia. A third cluster comprises all P. spinosaand P.× fruticanssamplesThe American and the Chickasaw clades were identified. An outgroup clade was comprised by P. persicaand P. fasciculata
NotesLow number of Prunusspecies for samplingIdentified multiple gene regions that provided the greatest number of characters, variability, and improved phylogenetic signal at the species level in Prunussection Prunocerasus

Table 2.

Summary of Prunusphylogenetic studies.

PIC = total indels + nucleotide substitutions + inversions. Percent variability = PIC/characters or bp. PIC = potentially informative character.


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4. Final remark

The subgenus Prunussection Prunocerasus(the North American plums) constitutes important genetic resources (gene pool) of unique traits such as tree architecture, chilling requirement, heat requirement, fruit development period, fruit size, fruit texture, disease and insect resistance, and adaptive changes to multiple environmental conditions, among others. These species could be used in the breeding of improved stone fruit cultivars in the future. The summary of the taxonomic and phylogenetic relationships presented in this chapter provides a base to understand the species relationships. In addition, it will help for the conservation and maintenance of a broader germplasm base within Prunus.

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Written By

Dario J. Chavez and José X. Chaparro

Submitted: October 29th, 2019 Reviewed: February 6th, 2020 Published: March 9th, 2020