PhD Thesis proposal form
Discipline: Biology
Doctoral School
ED 145: Plant Sciences / Sciences du Végétal
http://www.ed-sciences-du-vegetal.u-psud.fr/en/ecoledoctorale.htm
Thesis subject title:
Study of gene flow between the domesticated apple and wild apple species
 Laboratory name and web site
Laboratoire Ecologie, Systématique et Evolution
http://www.ese.u-psud.fr/article211.html?lang=en
http://www.ese.u-psud.fr/
 PhD supervisor (contact person):
 Name: Tatiana Giraud
 Position: Directrice de Recherches, Directrice adjointe du laboratoire
 email: tatiana.giraud@u-psud.fr
 Phone number: +33 1 69 15 56 69
 Thesis proposal (max 1500 words):
Domestication is a process of increasing codependence between human societies and other
organisms 1, 2. The most fundamental questions regarding the evolutionary process of domestication
include determining the identity and geographic origin of the wild progenitors of domesticated
species 3, the nature of the genetic changes underlying domestication4, 5, the tempo and mode of the
domestication process (e.g. rapid transition vs protracted model of domestication) and the
consequences of domestication on the genetic diversity of domesticates6-9. Understanding the
domestication process provides insights into the general mechanisms of adaptation and the history of
human civilizations but also helps modern breeding programs for further improvement of crops or
livestocks10, 11.
Plant domestication has been most widely studied in seed-propagated annual crops, where
strong domestication bottlenecks have often been inferred, with well-documented examples in selfing
annuals such as wheat, barley and rice10, 12-15. Genetic data generally suggest fairly rapid
domestication and/or spread of domesticated traits, even in some outcrossers such as maize or
sunflower, as well as limited numbers of population/species having contributed to the present-day
observed diversity 9, 16-19. The genetic consequences of domestication, however, have been much less
investigated in other groups of plants, in particular long-lived perennials such as fruit trees 20-22. Yet,
trees exhibit several biological features that make them fascinating and original models for
investigating domestication: they are long lifespan outcrossers with lengthy juvenile phases, and tree
populations are often large and connected by high levels of gene flow.
Differences in life-history traits likely result in marked differences in the mode and tempo of
evolution of trees compared to seed-propagated selfing annuals23-25. Outcrossing for instance makes
domestication more difficult, because of the associated lower probability of fixation of selected
alleles than under selfing12. Highly variable progenies generated by self-incompatibility combined
with long juvenile phases also tend to make breeding a slow and costly process, and hence render
crop improvement uneasy. The development of vegetative propagation via cuttings or grafting has
been key in the domestication of long-live perennials, allowing the maintenance and spread of
superior individuals despite self-incompatibility26. These techniques however have contributed to
reduce further the number of sexual cycles in tree crops since initial domestication, in addition to
long juvenile phases, thereby limiting the genetic divergence between cultivated trees and their wild
progenitors26-29. Overall, domestication is therefore more recent (in terms of number of generations)
in fruit tree crops than in seed propagated selfing annuals.
By weakening selection efficiency per generation and restricting the number of generations on
which humans select, the protracted process of tree domestication has likely caused limited
bottlenecks 21, 27 and a weaker domestication syndrome in trees 30 as compare to seed-propagated
selfing annuals. Many cultivated fruit trees nonetheless clearly display morphological, phenotypic
and physiological features that can be considered as typical of a domestication syndrome, such as
large fruits and high sugar or oil content 28, 31. Because domestication in fruit trees is understudied in
many respects 21, most hypotheses on the consequences of the particular features of trees on their
domestication/diversification remain to be investigated. Recent works on grape, almond and olive
trees provided illuminating insights, such as the importance of outcrossing and interspecific
hybridizations32-34, but additional examples are needed to draw firmer conclusions.
This thesis project addresses the question of the origins of the domesticated apple Malus
domestica Borkh., one of the most emblematic and widespread fruit crop in temperate regions31. A
form of apples corresponding to extant domestic apples appeared in the Near East around 4,000 years
ago35, at the time of the first records of the use of grafting. The domesticated apple was then
introduced in Europe and North Africa by the Greeks and Romans and subsequently spread
worldwide31. Surprisingly, the identity and relative contribution of the wild species that have
participated to the genetic makeup of apple cultivars remain largely unknown, despite the potential
importance of this knowledge for plant breeding and for our understanding of the process of
domestication in fruit trees.
Previous studies have identified the wild Central Asian species M. sieversii (Ldb.) M. Roem
as the main contributor to the M. domestica genepool, based on fruit and tree morphological
similarity and genetic data36-39. The Tien Shan forests were pinpointed as the original geographic area
of apple domestication based on huge intra-specific morphological variability of wild apple
populations in this region40, 41. Nucleotide variation at 23 DNA fragments even suggested that M.
sieversii and M. domestica belonged to a single gene pool (that would be called M. pumila Mill.),
phylogenetic networks showing intermingled individuals from the two taxa39. Some authors have also
suggested possible contributions of additional wild species present along the Silk Road: M. baccata
(L.) Borkh native of Siberia, M. orientalis Uglitz., a Caucasian species of the western sections of the
ancient trade routes, and M. sylvestris Mill., a European native species42-45. These hypotheses were
based on the history of human migrations and trade, on the lack of phylogenetic resolution between
M. domestica and the four wild species37, 38, on some genetic evidence of hybridization at a local
scale between domesticated apple and M. sylvestris36, and more recently on the finding of sequence
haplotype sharing between M. sylvestris and M. domestica 46. However such secondary contributions
are still debated47. The three wild species occurring along the Silk Road all bear small, astringent, tart
fruits. Although none of these species have the fruit quality of M. sieversii, they may have
contributed other valuable horticultural traits, such as later blooming, resistance to pests and diseases,
capacity for longer storage or climate adaptation. Their organoleptic properties may also have been
used for the preparation of apple-based beverages, such as ciders42, 48. Cider apples are indeed
smaller, bitter and more astringent, bearing similarities with M. sylvestris apples. Some evidence
indicate that Europeans from the Neolithic and Bronze Age were in fact already making use of M.
sylvestris35.
The domesticated apple is one of the most important fruit crops of temperate regions. Yet,
despite centuries of apple breeding worldwide, the commercial apple has a narrow genetic base and
commercial production is based on very few cultivars. This situation raises concern about our ability
to enhance or simply sustain production in the face of dynamic environmental and biotic threats. For
instance, almost all commercially leading apple cultivars are highly susceptible to the ‘apple scab’
disease, which requires up to 15 fungicide treatments per year. In this context, a key priority is to
enrich the cultivated gene pools by incorporating novel genes that will positively impact on apple
improvement.
Wild relatives have early been recognized as a valuable genetic resource for the domesticated
apple, potentially containing more genetic diversity for important horticultural and environmentally
adapted traits. However, the use of wild apple resources in breeding programs has to be based on
knowledge of their genetic potential: the genetic diversity, origins, and genealogical relationships of
wild and cultivated genomes are key practical guides for the discovery of novel alleles and for the
identification of germplasms more sexually compatible with the domesticated apple. This knowledge
is also of paramount importance for the design of optimal conservation strategies, which should aim
at safeguarding the evolutionary potential of the wild species.
The aim of the project is to use a comprehensive set of apple accessions and wild apple samples
sampled throughout Eurasia and 26 microsatellite markers distributed across the genome to
investigate the following questions: 1) What was the contribution of wild species to the genome of M.
domestica, in addition to the Asian main contributor M. sieversii? 2) Does M. domestica exhibit a
genetic structure that can be associated with the different possible uses of apples (e.g. between cider
or dessert cultivars) and/or associated with region of origin? 3) Can the level of introgression from
the European crab apple M. sylvestris to the M. domestica genome be associated with the different
possible uses of apples (e.g. between cider or dessert cultivars) and/or associated with region of
origin? 4) What is the population structure of the European crab apple M. sylvestris? 5) What is the
level of introgression from M. domestica into the European crab apple M. sylvestris? Does it depend
on the geographical region and or on the agroecological history? Can we identify “pure” M. sylvestris
population that would be suitable to be re-introduced in agrosystems in Europe?
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 Publications of the laboratory in the field (max 5):
Lê Van A., Gladieux P., Lemaire C., Cornille A., Giraud T., Durel C.-E., Caffier V. and Le Cam B.
(2012) Evolution of pathogenicity traits in the apple scab fungal pathogen in response to the
domestication of its host. Evolutionary Applications in press.
Gladieux P, Guérin F, Giraud T , Caffier V, Parisi L, Didelot F, Lemaire C, Le Cam B. (2011)
Emergence of novel fungal pathogens by ecological speciation: importance of the reduced
viability of immigrants. Mol Ecol 20: 4521–4532.
Vercken E, Fontaine MC, Gladieux P, Hood ME, Jonot O, and Giraud T. (2010) Glacial refugia in
pathogens: European genetic structure of anther smut pathogens on Silene latifolia and S.
dioica. PloS Pathogens 6: e1001229.
Gladieux P, Vercken E, Fontaine MC, Hood ME, Jonot O, Couloux A and Giraud T (2011)
Maintenance of fungal pathogen species that are specialized to different hosts: allopatric
divergence and introgression through secondary contact. Mol Biol Evol 28:459–471.
Gladieux P, Giraud T, Shykoff JA, Genton B, Jonot O and Kiss L (2011) Distinct invasion sources of
common ragweed (Ambrosia artemisiifolia) in Eastern and Western Europe. Biological
invasions 13:933–944.
 Specific requirements to apply, if any: