**2. Domestication as a science**

#### **2.1. Definition**

Domestication was defined by De Wet [8] as "changes in adaptation that insure total fitness in habitats especially prepared by man for his cultigens". Van Raamsdonk [7] refined this definition by taking into account Simmond's [6] observations on plant domestication syn‐ drome because a considerable number of crop plants are dependent on man for establishing new generations due to non-dehiscence, non-shattering, and absence of seed dormancy. Domestication was thus better defined by van Raamsdonk as a process leading to character‐ istics that are beneficial to humans but generally unprofitable for plants in natural habitats and in the decrease or total lack of capability to disseminate viable offspring [7]. As such defined, the goal for crop domestication appears obvious: setting plant for human's benefits. However, the paths and process followed, and the tools used towards developing a new crop from its wild related plant can greatly vary (Table 1).

#### **2.2. Domestication process and goal**

An artificial selection results in a phenotypic evolution [10]. In fact, agriculture started ~10,000 years ago by probing the diversity present within wild plant species and by planting the selected specimens, first in the garden and then in the field setting, a process known as domestication. Although all crops and plant varieties known to man today did not undergo through this classic process (case of known semi-domesticates) [3], the vast majority did go through, and thus being fully or super domesticated [3], depending on era, needs and advances in technology. Domestication is generally considered to be the end-point of a continuum that starts with exploring wild plants, continues through cultivation of plants selected from the wild but not yet genetically different from wild plants, and terminates in the fixation (at some extent), through human selection, of morphological and hence genetic differences distinguish‐ ing a domesticate from its wild progenitor. Wild and cultivated populations differ statistically in various characters targeted by human selection, although the cultivated plants may be morphologically indistinguishable from the wild plants [3]. Therefore, cultivated populations are not genetically fixed for any characters distinguishing them from wild populations, but the frequencies of alleles governing the characters subjected to human selection presumably differ [3]. Casas et al. [11] considered that changes in allele frequencies resulting from human selection constitute at least an incipient domestication, i.e. a nascent domestication. These authors analyzed the morphological variations in wild, managed *in situ*, and cultivated populations of the columnar cactus *Stenocereus stellatus* in central Mexico. They investigated whether morphological divergence has occurred between manipulated and wild populations by the domestication processes. Multivariate statistical analyses showed that individuals grouped according to management options and the fruit characteristics were the most relevant for grouping. Sweet fruits with non-red pulp colors were more frequent in cultivated popu‐ lations. The fruits were also larger, contained more and bigger seeds, had thinner peel, and fewer spines in cultivated populations than fruits in wild individuals. Phenotypes common in managed *in situ* and cultivated populations generally occur also in the wild but at lower frequencies. However, Gepts [12] considered cultivation as a necessary but insufficient condition for domestication which, at least incipient or semi-domestication, may occur without cultivation by selective removal of undesirable phenotypes and/or enhancement of desirable phenotypes in wild populations [11]. How these different domestication processes and the available tools may apply to wild rosehip is one of the main topics developed in this review.

#### **2.3. Domestication tools**

#### *2.3.1. Ancient tools*

have increased to include health and wellbeing. As a consequence more specific and defined traits such as a targeted and defined ingredient or metabolite are sought. To date, the pace of plant domestication has slowed down mainly due to the loss of biodiversity but also because of our ability to satisfy our current food needs. Nevertheless, few new crops species are still being introduced into farming system to fill the growing gaps in the need of humans and pets. Although domestication, as a concept, is not the main focus of this chapter (reader can refer to [3, 4, 6-9]), this review will look at some aspects of plant domestication in the 21st century as compared with ancient domestication process, the extent of genetic diversity within North American roses, the challenges associated with the domestication and agronomy of Atlantic Canada wild rose species taken as an example, and how the current biotechnology tools can

Domestication was defined by De Wet [8] as "changes in adaptation that insure total fitness in habitats especially prepared by man for his cultigens". Van Raamsdonk [7] refined this definition by taking into account Simmond's [6] observations on plant domestication syn‐ drome because a considerable number of crop plants are dependent on man for establishing new generations due to non-dehiscence, non-shattering, and absence of seed dormancy. Domestication was thus better defined by van Raamsdonk as a process leading to character‐ istics that are beneficial to humans but generally unprofitable for plants in natural habitats and in the decrease or total lack of capability to disseminate viable offspring [7]. As such defined, the goal for crop domestication appears obvious: setting plant for human's benefits. However, the paths and process followed, and the tools used towards developing a new crop from its

An artificial selection results in a phenotypic evolution [10]. In fact, agriculture started ~10,000 years ago by probing the diversity present within wild plant species and by planting the selected specimens, first in the garden and then in the field setting, a process known as domestication. Although all crops and plant varieties known to man today did not undergo through this classic process (case of known semi-domesticates) [3], the vast majority did go through, and thus being fully or super domesticated [3], depending on era, needs and advances in technology. Domestication is generally considered to be the end-point of a continuum that starts with exploring wild plants, continues through cultivation of plants selected from the wild but not yet genetically different from wild plants, and terminates in the fixation (at some extent), through human selection, of morphological and hence genetic differences distinguish‐ ing a domesticate from its wild progenitor. Wild and cultivated populations differ statistically in various characters targeted by human selection, although the cultivated plants may be morphologically indistinguishable from the wild plants [3]. Therefore, cultivated populations

contribute to an economic crop production.

38 Using Old Solutions to New Problems - Natural Drug Discovery in the 21st Century

wild related plant can greatly vary (Table 1).

**2.2. Domestication process and goal**

**2. Domestication as a science**

**2.1. Definition**

The oldest cultivated garden rose was *R x richardii* grown and depicted in art works by the Minoan civilization in Crete more than 3500 years ago. Roses were extensively cultivated during the Roman era (625 BC- 476 AD). After the demise of the Roman Empire, the lessappreciated wild-growing roses in Europe and Asia, belonging to *Rosa* section *Canina* and known today as Dogroses were maintained in monasteries for their reputed medicinal properties [13]. By the 18th century, five rose species (*R. gallica, R. alba, R. damascena, R. centrifolia, and R. centrifolia moscosa*) sharing a number of features such as double flower, flagrance, flower colour, frost hardiness, spring flowering, resistance to black spot and rust, and susceptibility to mildew had emerged [14]. These five species fall into 5 broad rose classes namely Gallica, Alba, Damask, Centrifolia, and Moss rose, respectively, and referred to as old European roses. These traditional European roses were crossed with roses from China (*R. chinensis*) leading to *Rosa x hybrid*, the modern rose selected for defined traits such as shape, colour and flagrance of the flower bud and flower qualities, stem length, and vase life. During these times, probing the genetic diversity within wild populations and selection of progenies from crosses were solely based on morphology.

#### *2.3.1.1. Probing the genetic diversity*

During ancient times, botanists such as Linnaeus [15] have played a crucial role in probing rose genetic diversity and defining boundaries between species. Linaeus [15] was one of the first botanists to acknowledge the complexity of the genus *Rosa*. In his book "*Species Planta‐* *rum*" Linaeus stated that "the species of the genus *Rosa* are difficult to distinguish and determine, I have the impression that nature combines just for fun a number of them and then forms a new one out of the lot, those who have seen only some distinguish them more easily than those who have examined many". The complexity of the genus has remained enigmatic to taxonomists of the twentieth century [13, 16-19] as the morphological characters are continuous and possibly polygenic making difficult in assigning genotypes that clearly define taxa. Nonetheless, similar to any other plant species, end-uses have been instrumental drivers for probing the genetic diversity and guiding in the selection process.

#### *2.3.1.2. Process and goal for probing the genetic diversity (food and ornamentals)*

During the Middle Ages, dogroses were cultivated at monasteries as a medicinal plant and, all parts including rosehips, seeds, petals, leaves and roots were virtually used. Later on in the 19th century, dogroses served as rootstocks to graft modern rose cultivars either as frost or soil born disease resistance sources [13]. They have also been used as a rustic and hardly living fence for fields and public spaces. In the twentieth century, roses have become important horticultural and cosmetic crops receiving much attention from geneticists, breeders, and general public. Hybrid Tea varieties of roses (*Rosa hybrida* L.) are among the most economically important cut-flower plants. The first Hybrid Tea rose was introduced in 1867, and since then more than 10,000 varieties have been released.

The Centre for Variety Research, the Netherlands, has submitted more than 2,800, predomi‐ nantly Hybrid Tea varieties, for Plant Breeders Rights. This number is increasing annually with 80 applications on average each year. This registration and protection process is based on morphological and physiological characteristics as described by the UPOV (Union Internatio‐ nale pour la Protection des Obtentions Végétales) guidelines [20]. Wild roses, semi-domesti‐ cated and commercial varieties, serve as breeding materials for creating new genetic stocks. These breeding materials generally selected as seed or pollen parents, for flowers that are often flagrant, commonly rose-colored flowers although white or more rarely yellow flowers can be observed in some species [21] are used in crosses. Hence, seedlings of interest with differences in flagrance, colour, shapes, disease resistance genes are selected through extensive field trials and advanced in the registration process [22]. Among the many wild rose species, the selection was obviously based on easy availability, attractiveness of characters, seed set potential, but also the plant morphology such as dwarfness and small size of flowers [22]. During these times less emphasis was made on the wild rose fruit characteristics.

#### *2.3.2. Modern tools*

In modern times, these classical methods become less and less efficient as the number of varieties to be tested increases and the genetic distances between varieties becomes smaller [20]. As well, because the needs, objectives, and challenges associated with the rose industry are now changing both in terms of flower and fruit production, combination of morphological, cytological, conventional breeding and biotechnological methods are being widely used for the determination of *Rosa* species as well as for the development of new rose cultivars [23-28].

#### *2.3.2.1. Probing the genetic diversity*

*rum*" Linaeus stated that "the species of the genus *Rosa* are difficult to distinguish and determine, I have the impression that nature combines just for fun a number of them and then forms a new one out of the lot, those who have seen only some distinguish them more easily than those who have examined many". The complexity of the genus has remained enigmatic to taxonomists of the twentieth century [13, 16-19] as the morphological characters are continuous and possibly polygenic making difficult in assigning genotypes that clearly define taxa. Nonetheless, similar to any other plant species, end-uses have been instrumental drivers

During the Middle Ages, dogroses were cultivated at monasteries as a medicinal plant and, all parts including rosehips, seeds, petals, leaves and roots were virtually used. Later on in the 19th century, dogroses served as rootstocks to graft modern rose cultivars either as frost or soil born disease resistance sources [13]. They have also been used as a rustic and hardly living fence for fields and public spaces. In the twentieth century, roses have become important horticultural and cosmetic crops receiving much attention from geneticists, breeders, and general public. Hybrid Tea varieties of roses (*Rosa hybrida* L.) are among the most economically important cut-flower plants. The first Hybrid Tea rose was introduced in 1867, and since then

The Centre for Variety Research, the Netherlands, has submitted more than 2,800, predomi‐ nantly Hybrid Tea varieties, for Plant Breeders Rights. This number is increasing annually with 80 applications on average each year. This registration and protection process is based on morphological and physiological characteristics as described by the UPOV (Union Internatio‐ nale pour la Protection des Obtentions Végétales) guidelines [20]. Wild roses, semi-domesti‐ cated and commercial varieties, serve as breeding materials for creating new genetic stocks. These breeding materials generally selected as seed or pollen parents, for flowers that are often flagrant, commonly rose-colored flowers although white or more rarely yellow flowers can be observed in some species [21] are used in crosses. Hence, seedlings of interest with differences in flagrance, colour, shapes, disease resistance genes are selected through extensive field trials and advanced in the registration process [22]. Among the many wild rose species, the selection was obviously based on easy availability, attractiveness of characters, seed set potential, but also the plant morphology such as dwarfness and small size of flowers [22]. During these times

In modern times, these classical methods become less and less efficient as the number of varieties to be tested increases and the genetic distances between varieties becomes smaller [20]. As well, because the needs, objectives, and challenges associated with the rose industry are now changing both in terms of flower and fruit production, combination of morphological, cytological, conventional breeding and biotechnological methods are being widely used for the determination of *Rosa* species as well as for the development of new rose cultivars [23-28].

for probing the genetic diversity and guiding in the selection process.

40 Using Old Solutions to New Problems - Natural Drug Discovery in the 21st Century

more than 10,000 varieties have been released.

less emphasis was made on the wild rose fruit characteristics.

*2.3.2. Modern tools*

*2.3.1.2. Process and goal for probing the genetic diversity (food and ornamentals)*

Domestication and crop improvement involve the selection of specific alleles at genes control‐ ling key morphological and agronomic traits, resulting in reduced genetic diversity relative to unselected genes [10]. This artificial selection process that operates also in almost all agro-sys‐ tems, including agroforestry, favours abundance of the preferred targeted phenotypes, and acts with more intensity in household gardens [29]. In the 20th century, probing for crops and their wild relative's genetic diversity has been the focus of extensive investigations. In roses in partic‐ ular, morphometric [13, 30-34], cytological characters [25, 35] were the most used in the *Rosa sp* taxonomy and phylogeny. But these methods have been proven not to be sufficient in assigning individual genotypes that clearly defined taxa [13]. The 21st century is characterized by a re‐ markable explosion of molecular tools, highly polymorphic and with high discrimination pow‐ er, for deciphering differences based on DNA nucleotide sequences. The development of these tools were achieved mostly with the event of polymerase chain reaction (PCR) in the mid 1980's [36], which has revolutionized the field of biology by inspiring the development of many PCRbased technologies, large DNA sequence databases, and increased computer power by bioin‐ formatics. Despite the success of these powerful tools and its speed in advancing our current knowledge of the *Rosa* phylogeny [16, 17, 19, 37-43], there is still not exist at present a single method or tool for tracing a clear cut relative phylogenetic position between *Rosa* subgenera, sections and species within the genus [16], mainly due to low sequence divergence, natural hy‐ bridization between taxa, and polyploidy [44]. Rather, complementary methods (morpho-cy‐ tology, ploidy level, and DNA sequences from both chloroplast and nuclear genomes) using extensive data computing, with iterations and bootstrapping, are now the approach commonly sought [16, 17, 39, 40, 44, 45, 46, 47]. Nonetheless, for well-defined *Rosa* species, the DNA se‐ quence analysis for single nucleotide polymorphism [47] and SSR polymorphism [48] are the preferred choice for distinguishing between genotypes and varieties [20]. The current *Rosa* phy‐ logeny relies mainly on Rehder [49] who subdivided the genus into 4 subgeneras: *Hulthemia, Platyrhodon, hesperhodon,* each with 1 or 2 species, and *Rosa*. Likewise, the large *Rosa* subgenus was divided into 10 sections (*Pimpinellifoliae*, *Rosa*, *Caninae*, *Carolinae*, *Cinnamomae*, *Synstylae*, *In‐ dicae*, *Banksianae*, *Laevigatae*, *Bracteatae*). However, recent molecular evidences do not support distinct subgenera status [16, 50] but did support the presence of 2 main clades. One clade in‐ cludes subgenera *Rosa* species of sections *Carolinae*, *Cinnamomae,* and *Pimpinellifoliae* (clade 1) and the other clade (clade 2) includes all remaining subgenera *Rosa* sections, excluding the sec‐ tion *Banksianae* which comprises *R. Banksiae* (section *Banksianae*), *R. roxburhii* (subgenera *Platyr‐ hodon*), and *R. persica* (subgenera *Hulthemia*), found to be sister to clade 2 [16]. The section *Caninae* DC forms a large and well-defined group of polyploid taxa and known as dogroses. In this section, pentaploids are the most common, but tetraploid and hexaploids also occur [18]. Bruneau et al. [16] also showed that sections *Cinnamomae* and *Carolinae* form a monophyletic group, and should be merged into one section, referred to as sect *Cinnamomae*. Indeed, section *Cinnamomae* comprises more than 40% of the species in the genus *Rosa*.

#### *2.3.2.2. Process and goal (life quality)*

One of the main current questions is whether the process and goal for probing rose genetic diversity has changed over time. Although crop domestication and improvement process is a continuum, it evolves constantly with the available technologies in order to meet and fulfill the societal needs. In the present global economy, the scale of demands for any good has increased and the trade has become multidirectional (selling in all part of globe) with multiple layers (one product could be found in many other products as additive or supplement) (Table 1). Thus, probing the genetic diversity of a plant species which end-product would satisfy these new needs both in terms of quality, quantity, sustainability and stability has become the new challenge for plant products developers. Hence, the need for well characterized germplasm with stable and preserved genetic identity is becoming the landmark for todays and tomor‐ row's natural product designers and developers. Therefore, sophisticated molecular tools [51, 52] as well as mass tissue culture and plant propagation tools are being employed to insure stability and sustainability.


**Table 1.** Comparative pathways of ancient and modern plant domestication processes: purposes, tools, and expectations
