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426 Forum TRENDS in Genetics Vol.18 No.

8 August 2002

Science Chronicle

Genetic clues to the origin of the apple


Stephen A. Harris, Julian P. Robinson and Barrie E. Juniper
Molecular genetic markers complement
Box 1. Taxonomic hierarchy and apple classification
archaeological, breeding and geographical
investigations of the origins, history and Species are arranged according to a taxonomic and M. sieversii to refer to the Central Asian
domestication of plants. With increasing hierarchy, in which they are placed into larger ‘wild apple’. However, the term ‘wild apple’
access to wild apples from Central Asia, groups or divided into smaller groups to has been applied to all Malus spp. other than
account for observed variation. Each of these the domesticated apple. For example, in
along with the use of molecular genetic groups is given a particular name. Thus, the Europe, the common name ‘wild apple’ refers
markers capable of distinguishing between family Rosaceae includes the genus Malus to M. sylvestris Miller, whilst in North America
species, and explicit methods of phylogeny (apples) with its ~55 species, which are grouped the term has been applied to species including
into infrageneric groups (section, series), and M. angustifolia (Ait.) Michx. and M. coronaria
reconstruction, it is now possible to test
each species can be divided into intraspecific (L.) Miller. The situation is further complicated
hypotheses about the origin of the groups (cultivar). Malus spp. are arranged by the application of the name ‘wild apple’ to
domesticated apple. Analyses of nuclear according to Phipps et al.’s classification [a]. hybrids between domesticated apple and
rDNA and chloroplast DNA (cpDNA) The genus Malus comprises some other members of the genus Malus.
55 species [a], although between eight and The taxonomic hierarchy for the
sequences indicate that the domesticated 79 species have been recognized. Part of the domesticated apple ‘Bramley’s Seedling’
apple is most closely related to series problem of Malus taxonomy is the intimate would be:
Malus species. Moreover, the occurrence of association that humans have with apples, • Family: Rosaceae
a shared 18-bp duplication in the cpDNAs of where the distinction between wild and • Subfamily: Maloideae
cultivated species could become blurred and • Genus: Malus
wild and cultivated apple supports the close hence the recognition of distinct categories • Section: Malus
relationship between them. Hypotheses difficult. Furthermore, the scientific names • Series: Malus
about the hybridization and the origin of the that have been applied to the domesticated • Species: domestica
apple are legion, and include Malus pumila • Variety/cultivar: ‘Bramley’s seedling’
domesticated apple cannot be rejected
Miller, M. communis Desf., M. sylvestris (L.)
completely until more variable, Miller and M. domestica Borkh. Recently, it References
phylogenetically informative markers has been argued that M. pumila is the correct a Phipps, J.B. et al. (1990) A checklist of the
name for the domesticated apple and that this subfamily Maloideae (Rosaceae). Can. J. Bot.
are found.
also includes the presumed wild relative, 68, 2209–2269
M. sieversii (Ledeb.) M. Roem [b]. We use b Mabberley, D.J. et al. (2001) The name of the
The domesticated apple is one of the most M. domestica to refer to ‘domesticated apple’ apple. Telopea 9, 421–430
important fruit crops of the colder and
temperate parts of the world [1]. Vavilov
suggested that the wild apple of Turkestan found in four widely distributed up to ten million years, mammals, such as
(Kazakstan, Kyrgystan, Uzbekistan, NorthAmerican wild apples [8,9]. bears, acted as distribution vehicles by
Turkmenistan and Tajikistan) and its close The Central Asian wild apple is closely selecting the largest and juiciest fruits;
relatives were the progenitors of the related to a group of apples that have a small, bird-distributed, cherry-like
domesticated apple*; the whole process of different-sized fruits. One of these, delicacy giving way to a large mammal-
wild apple domestication being traced to Malus baccata (Siberian Crab), has small, distributed form. Small apples have even
Almaty (Kazakstan). Vavilov reasoned that, red fruits that hang in clusters and are been observed to pass intact through a
because the wild apple bears similar fruits bird-dispersed (Fig. 1). Malus baccata bear’s jaw and guts; it should be noted,
to the domesticated apple, it must have might have had a wider distribution than however, that apple seeds retained in the
been the progenitor. Recent fieldwork in the that of the present day, and we think that apple core do not germinate.
region appears to confirm the similarity populations became ‘trapped’ as the By the time humans began to occupy
between wild and cultivated apples [2,3]. Tien Shan began to rise out of the Tethys the area ~5000–8000 years ago, the
Furthermore, Janick et al. suggested that Ocean. Over seven million years, perhaps early evolution of the apple was almost
‘this area [Central Asia] is the area of complete, and its migration, ably assisted
greatest diversity and the centre of origin’ by the now domesticated horse [10], was
of the domesticated apple [4]. This is linked (a) (b) under way. Over several more thousands
to Vavilov’s ‘oversimplified’idea that the of years, from within this migrating flow
centre of diversity is the place of origin [5,6]. came the many thousands of apple
The Central Asian wild apple (Box 1) is a cultivars now known, as a result of both
diverse species with a wide range of forms, unconscious and conscious selection [11].
colours and flavours [7], whilst its allozyme Based on combined archaeological and
diversity is significantly greater than that molecular data, it seems likely that, in
TRENDS in Genetics
the late Neolithic or early Bronze Age,
* Vavilov, N.I. (1930) Wild progenitors of the fruit travellers on the great trade routes that
trees of Turkistan and the Caucasus and the problem Fig. 1. Range of variation in apple fruit types: (a) Malus
of the origin of fruit trees. International baccata, a bird-dispersed species; and (b) domesticated ran from central China to the Danube
Horticultural Congress Group B, 271–286 apple, a mammal-dispersed species. (Fig. 2), carried the seed of the Central

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Forum TRENDS in Genetics Vol.18 No.8 August 2002 427

Regions of high concentrations of 'ancient' apples Pre-history. Surmized distribution of Malus sieversii 'Silk roads'
TRENDS in Genetics

Fig. 2. Location of great trade routes (‘silk roads’, red), surmized distribution of Malus sieversii (green) and regions of 8-bp duplication that differs by a T residue,
high concentrations of present-day ‘ancient’ apples (yellow). Scale bar = 500 km. whereas duplication II is a perfect 18-bp
duplication. Duplications I and II were
Asian wild apple west, either in saddle the basis of the evidence available from the always present together, suggesting that
bags or horses’ guts. We now know that the living plant’ [1]. However, the molecular each has arisen only once during the
important technique of grafting (described systematics revolution potentially provides evolution of Malus spp. (Fig. 3).
as ‘instant domestication’ [12]), where the an excellent source of potential characters Duplication II was polymorphic in both
variety can be preserved forever, was for analyses of these type. the Central Asian wild apple and the
probably discovered in Mesopotamia at domesticated apple, suggesting that the
Mari, as early as 3800 years ago (S. Dalley, The origin of the domesticated apple and Central Asian wild apple could be the
pers. commun.). The description, on relations with other Malus spp. major maternal contributor, as proposed
cuneiform tablets, concerns vines Combinations of nuclear (nDNA) and by Watkins et al. [20].
(Vitis spp.), but the techniques are easily cytoplasmically [chloroplast (cpDNA) The nuclear ribosomal internal
transferable. From there, the fruits and and mitochondrion (mtDNA)] inherited transcribed spacer (ITS) showed
the necessary technology passed through molecular genetic markers provide 89 phylogenetically informative characters
the Persians and Greeks to the Romans, important clues about the origins of from the 617 bp sequenced. A strongly
who perfected orchard economies. The domesticated plants, for example, supported group comprised the Central
Romans brought the whole package Citrus spp. [16], beans [17] and potatoes Asian wild apple and the domesticated
to Western Europe and, for the last [18]. In Malus, the chloroplast genome apple, as well as M. asiatica, M. orientalis,
2000 years, the domesticated apple has provides data about evolutionary M. niedzwetzkyana and M. prunifolia (all
diversified and flourished worldwide. relationships of the maternal line, whilst from section Malus spp.), although there
Archaeological evidence for the collection biparentally inherited nDNA provides was little resolution within this group
of apples from the wild in Europe can independent data, which, combined with (Fig. 4). Together, data from the chloroplast
be found in Neolithic (11 200 years ago) cpDNA, could enable the origin of the and nuclear genomes support the view that
and Bronze Age (c. 4500 years ago) sites domesticated apple to be determined. the domesticated apple is most closely
throughout Europe [13,14], and for apple Hybridization and introgression are related to the series Malus spp. These data
cultivation as early as 1000 BC in Israel [1]. expected to have been important factors in also indicate that the Central Asian wild
In terms of apple domestication, series the development of domesticated apple apple could be most closely related to the
Malus is the most important group of cultivars. Therefore, for investigations that domesticated apple. Savolainen et al. were
species. However, the nomenclature of the aim to determine the earliest origins of the unable to determine the origin of the
species in series Malus is complex. With domesticated apple, it is necessary to use domesticated apple because of a lack of
few discrete characters to differentiate cultivars that are as ancient as possible. variation in the cpDNA-encoded atpB-rbcL
species, the difficulty of species matK, a cpDNA-encoded region spacer and the absence of the Central Asian
delimitation has hampered investigations ~1800-bp long, of which 1341 bp wild apple in their sample [21]. However,
into the origins of apples [15]; was sequenced, showed only additional phylogenetically useful DNA
morphological characters used to delimit 16 phylogenetically informative characters sequence information should be sought,
species in series Malus are continuous and across the genus Malus, and thus poor so that this hypothesis can be confirmed;
overlapping. Such problems perhaps resolution in the phylogenetic tree [19] additional sampling of Central Asian wild
contributed to Zohary and Hopf’s (Fig. 3). However, two duplications were apples and domesticated apples is needed
statement that ‘it is therefore futile to try to found 39 bp from the 3′ end of the matK to ensure that rare hybridization events
delimit the area of initial domestication on coding region. Duplication I is an imperfect with other Malus spp. that might have

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428 Forum TRENDS in Genetics Vol.18 No.8 August 2002

[Erwinia amylovora (Burill) Winslow


(a)

n
et al.] [26]. As with wild species, the

a ti o
tion
taxonomy of apple varieties is fraught with

pl i c
lica

du
up
problems, including environmental and

pd

-bp
developmental variation within varieties,

8-b

18
and limited numbers of morphological
Series Malus Wild apple and chemical characters to distinguish
Section Malus
Series Baccata Domesticated apple varieties [11]. In addition the triad of
Section Sorbomalus Malus asiatica decreasing budgets, but increasing
Section Eriolobus Malus micromalus collection size and running cost, traps a
Malus sylvestris collection manager whose goal is to have
Section Docyniopsis
Malus baccata a well-characterized but easily utilized
Section Chloromeles
Malus hupehensis collection, and forces choices to be made to
Weak(50–74%) support Malus sieboldii try and minimize genotypic redundancy.
Strong (75–100%) support Malus toringoides Thus, molecular genetic markers provide
Malus fusca a valuable aid to the identification of
Duplication present
Malus tschonoskii duplicates (possible cultivar synonyms),
Duplication polymorphic Malus prattii
correctly naming mis-identified plants
Duplication absent Malus yunnanensis
and enabling managers to make effective
Malus kansuensis
decisions about the reduction of collection
Malus doumeri
size without reducing genetic variation
Docynia delavayi
(i.e. creation of core collections) [27].
Malus orientalis
Two contrasting types of molecular
Malus coronaria
genetic marker can be used to characterize
Malus ioensis
apples. The first type is those that identify
Malus trilobata
few, high information content loci, such as
Malus florentina
microsatellites. The second are those that
Maloid outgroups
identify many, low information content loci,
(b) such as RAPD. Studies of RAPD variation
matK 3′ trnK
in Malus spp. have focused on the diversity
present in domesticated apples and
germplasm collections. Dunemann et al.
investigated RAPD variation at 52 putative
aaattctatttaaatattaaataattaagagataacaaaaaattaagagataacaaaaaattaat loci in a collection of 27 domesticated apple
8-bp duplication I 18-bp duplication II cultivars and were able to differentiate
TRENDS in Genetics
between cultivars [22]. Furthermore,
Fig. 3. Phylogeny of the chloroplast DNA-encoded gene matK in the genus Malus (a). A cartoon of matK is shown RAPD markers have also been used to
in (b) and the positions of the two duplications are indicated. Wild apple refers to the Central Asian wild apple, analyse the maternal and paternal
M. sieversii. Circles indicate the level of statistical support for particular groups. The distribution of the two matK
duplications is shown on the tree.
contributions to pedigrees [22,28,29]. In a
large study by Oraguzie et al., 43 RAPD
contributed to the early domestication of reproducibility, primer structure, markers were used to assess the variation
apples have not been overlooked. dominance, product competition, homology, in a worldwide collection of 50 old
The need for more variable DNA allelic variation, genome sampling and domesticated apple varieties, current
markers has led to analyses of Malus non-independence of loci, whilst similar breeding lines and a collection of 105 other
phylogeny using randomly amplified problems have been highlighted for the use apples, including wild species [30].
polymorphic DNA (RAPD) [22] and nuclear of SSRs in phylogenetic analyses [23–25]. Individual cultivars could be distinguished
microsatellites [single sequence repeats and ~95% of the RAPD variation occurred
(SSR)] [23]. Dunemann et al.’s results Variation within the domesticated apple within cultivars, breeding lines and wild
indicated that M. pumila and M. sylvestris Many thousands of named domestic apple species. Furthermore, Central Asian wild
(section Malus) were involved in the origin varieties (both dessert and cider) have apple accessions were scattered in a
of cultivated apples [23]. However, they been selected for hundreds of years in cluster analysis based on genetic distance.
suggested that M. sylvestris, M. florentina Europe, Asia and North America, and more However, RAPD markers have been
or M. dasyphylla could be the female parent recently in the Southern Hemisphere. criticized for the analysis of genetic
of M. domestica. By contrast, Hokanson Together with wild species, these are variation on both technical and theoretical
et al.’s SSR studies were not useful in maintained in national collections as grounds [24] and, given the problem of
determining the relationships among the genetic resources for breeding, particularly poor inter-laboratory result reproduction,
142 accessions from 23 species analysed as sources of resistance to apple scab arbitrary fragment length polymorphisms
[23]. However, it has been argued that [Venturia inaequalis (Cooke) Winter], could be a more effective way of producing
RAPD data are not appropriate for the powdery mildew [Podosphaera leucotricha genotypes based on many, low information
reconstruction of phylogeny because of (Ellis and Everh) Salmon] and fireblight content, loci [31].

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Forum TRENDS in Genetics Vol.18 No.8 August 2002 429

Eight apple SSR loci (seven dinucleotide


repeat loci and one trinucleotide repeat Series Malus Section Docyniopsis
Section Malus
locus) were developed by Szewc-McFadden Series Baccata Section Chloromeles
and colleagues [27,32] and used by
Section Sorbomalus Weak (50–74%) support
Hokanson [33] to identify the genotypes of
a core collection of 66 domesticated apple Section Eriolobus
Strong (75–100%) support
varieties. All but seven pairs of accessions
(five of these were either mutations or
their progenitors) of the 2145 possible
pair-wise varietal combinations could be
distinguished. The probability of any two
single locus genotypes matching by chance
in this study ranged from 0.027 to 0.970,
although this dropped to 0.156 × 10−8 for
multilocus comparisons. The high
discrimination power shows the value of
SSR markers for varietal genotyping,
whilst their co-dominance and high
repeatability makes them more reliable
markers than RAPDs. SSR loci also appear
Maloid outgroups
Malus doumeri
Malus ioensis
Malus coronaria
Malus angustifolia
Malus tschonoskii
Malus trilobata
Malus florentina
Malus ombrophila
Malus fusca
Malus kansuensis
Malus honanensis
Malus yunnanensis
Malus prattii
Malus yunnanensis
Malus transitoria
Malus toringoides
Malus mandshurica
Malus hupehensis
Malus sargentii
Malus sieboldii
Malus halliana
Malus baccata
Malus niedzwetzkyana
Domesticated apple
Malus prunifolia
Malus orientalis
Malus niedzwetzkyana
Wild apple
Malus niedzwetzkyana
Wild apple
Wild apple
Domesticated apple
Domesticated apple
Malus asiatica
Wild apple
Malus orientalis
Wild apple
Domesticated apple
Domesticated apple
to be very useful anchor markers in apple
genome-mapping projects. The occurrence
of low frequency alleles potentially makes
SSRs valuable markers for pedigree
analysis, although large numbers of
co-dominant markers are likely to be
necessary if complex crossing patterns are
to be disentangled. TRENDS in Genetics
Limited surveys of apple varieties have
revealed two cpDNA mutations that Fig. 4. Phylogeny of the nuclear ribosomal internal transcribed spacer gene in the genus Malus. Where the same
together provide evidence for multiple name appears at different places on the tree, this indicates that multiple accessions were used. Wild apple refers to
the Central Asian wild apple, M. sieversii. Circles indicate the level of statistical support for particular clades.
origins of the maternal component of
the domesticated apple, because apple
cultivars are propagated vegetatively. both the chloroplast and mitochondrial apple cultivars using highly variable
In a survey of 40 cultivars (36 named and genomes of domesticated apples [34,35]. molecular genetic markers such as SSRs,
four unnamed), Savolainen et al. showed identification of DNA sequences that
that cultivars could be divided into two Conclusions allow resolution of the section Malus spp.
cpDNA haplotypes depending on a C→T Two stages appear to have been important a comprehensive taxonomic account
transition at position 17 of the atpB–rbcL in the domestication of apples across the of the genus Malus and additional
spacer [21]. Similarly, Robinson et al., in range of the genus; the initial introduction archaeological evidence of human use of
a survey of nine cultivars, showed that of apples into Western Europe and later apples in Central Asia and the Near East
these could be divided into two groups hybridizations between cultivars and will be important. Clearly, there is still
based on the occurrence of an 18-bp between cultivars and wild species. Based much to be discovered about the origin of
duplication in the matK–3′trnK spacer on molecular data, it was members of the domesticated apple, the processes that
region [19]. The duplication was found section Malus that were important, led to its domestication and the origins of
only in the domesticated apple and one particularly the wild apple, in the initial both dessert and cider apples.
accession of the Central Asian wild apple introduction. The morphological,
following a broad survey of the genus, biochemical and molecular variation Acknowledgements
highlighting the close relationship within wild apple indicates that the We thank The Leverhulme Foundation for
between the Central Asian wild and earliest selections of domesticated apples funding the work described in this article;
domesticated apple. Unfortunately, could have come directly from the wild the Merlin Trust for travel grants; the
because the objectives of these two studies apple, without the involvement of other staff at the USDA-ARS Plant Genetic
were different, complementary cultivars species. However, later hybridizations Resources Unit, Cornell University, in
were not included. However, combining could have been important in the creation particular P. Forsline, H. S. Aldwinkle,
these two markers into the same study of new cultivars that carry economically A. Szewc-McFadden and W. Lamboy, for
might allow major lineages in cultivated important characteristics. The detailed practical help and support; K. Tobutt
and wild apples to be identified. analysis of these stages requires more and the staff at Horticultural Research
Investigations of restriction fragment sampling of the variation within Central International, East Malling, for providing
length polymorphism provide additional Asia. Given the extensive range of the wild wild species material from their
evidence for uncharacterized variation in apple, detailed analysis of known old collections; I. Belolipov and L.Samieva of

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430 Forum TRENDS in Genetics Vol.18 No.8 August 2002

the University of Tashkent for assistance in 11 Morgan, J. (1993) The Book of Apples, Ebony Press 26 Manganaris, A.G. et al. (1994) Isozyme locus Pgm-1
12 Zohary, D. and Spiegel-Roy, P. (1975) Beginnings is tightly linked to a gene (Vf) for scab resistance in
the field collecting in Uzbekistan and
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Kirghistan; the staff of LES-IC, the 187, 319–327 27 Szewc-McFadden, A.K. et al. (1996) Utilisation of
Khirghiz Swiss Forestry Support 13 Hopf, M. (1973) Apfel (Malus communis L.); identified simple sequence repeats (SSRs) in
Programme and the Forestry Institute of Aprikose (Prunus armeniaca L.). In Reallexikon Malus x domestica (apple) for germplasm
der Germanischen Altertumskunde (Vol. 1) characterisation. HortScience. 31, 619
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and the University of Almaty for assistance 15 Rohrer, J.R. et al. (1994) Floral morphology of 29 Landry, B.S. et al. (1994) Phylogeny analysis of 25
in field collecting in Kazakhstan. In Maloideae (Rosaceae) and its systematic apple rootstocks using RAPD markers and tactical
relevance. Am. J. Bot. 81, 574–581 gene tagging. Theor. Appl. Genet. 89, 847–852
particular, we thank R. Wise of the Dept of
16 Moore, G.A. (2001) Oranges and lemons: clues to 30 Oraguzie Nnadozie, C. et al. (2001) Genetic diversity
Plant Sciences, Oxford, UK for all the the taxonomy of Citrus from molecular markers. and relationships in Malus sp. germplasm collections
artwork. B.E.J. is currently a Leverhulme Trends Genet. 17, 536–540 as determined by randomly amplified polymorphic
Emeritus Research Fellow in the Dept of 17 Beccara Veläsquez, V.L. and Gepts, P. (1994) RFLP DNA. J. Am. Soc. Hort. Sci. 126, 318–328
diversity of common bean (Phaseolus vulgaris) in 31 Jones, C.J. et al. (1997) Reproducibility testing of
Plant Sciences, Oxford.
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plants. Trudy Byuro. Prikl. Bot. 16, 139–245 22 Dunemann, F. et al. (1994) Genetic relationships in restriction fragment length polymorphisms in
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horse lineages. Science 291, 474–477 Forstgenetik und Forstpflanzenzüchtung Oxford, UK OX1 3RE.

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