Project 3: Biodiversity and Genetic Resources (BioGen)

Last update date: Friday 21 August 2026
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1) A first topic in plant genetics: genetic variability of medicinal and aromatic plants in association with their secondary metabolite content.

2) A second topic in animal genetics: molecular analysis of the major genes involved in disease resistance in small ruminants in Tunisia.

Name of project leader:

BEN SLIMEN Hichem

Theme 1: Genetic variability of medicinal and aromatic plants in association with their secondary metabolite content.

At a time when the use of herbal remedies is experiencing unprecedented popularity, and when the threats to these plants are becoming increasingly serious, not only as a result of overexploitation but also due to the harmful effects of global change, little attention is being paid to the conservation and promotion of these plants in several countries, including Tunisia.

The sustainable management of aromatic and medicinal plants has become an urgent priority, not only because of their value as a potential source of new medicines and wellness products that are attracting growing interest from the pharmaceutical, cosmetics, and agri-food industries, but also because of the increasing reliance of local populations to these plants for healthcare purposes, on the one hand, and the weakening of the ecosystems that host these plants under the effects of climate change, on the other. These constraints are often associated with a decrease in genetic diversity, leading to erosion of biodiversity and a reduction in the ability of species to adapt to pathogens and changes in their environment.

Advances in knowledge of the plant genome have led to the development of molecular markers targeting different regions of the nuclear, chloroplast, and mitochondrial genomes. The development of genomics provides access to genes that control adaptive traits, which are very important for the management and conservation of genetic resources. The key task of genetic resource conservation is to preserve, through in situ methods, the evolutionary/adaptive potential of species, communities, and ecosystems. This is especially true for medicinal and aromatic plants, which are characterized by limited and fragmented distribution. Population genetics provides information on the problems of genetic diversity reduction and the factors contributing to this reduction, such as genetic drift and inbreeding. It also makes it possible to assess gene flow between populations and identify small isolated populations threatened with extinction. In the first part of this project, we propose to assess the genetic diversity of different species and populations of medicinal and aromatic plants in Tunisia. This will enable better management of these genetic resources and the development of rational decisions for their conservation.

On the other hand, the pharmaceutical use of plants, either in their natural state or in a more or less purified form, is limited by the very high variability in the content of secondary compounds within a single plant species. The phytochemical composition is directly influenced by genetic diversity and by all the factors that characterize the soil and climate environment in which the plants grow. Indeed, several studies have suggested that environmental characteristics (light, temperature, soil nutrient content, etc.) affect the genes involved in the synthesis of phenolic compounds and their transcription factors. In addition, recent studies based on genomic and transcriptomic approaches have revealed significant associations between the polymorphism of several genes in the phenolic compound biosynthesis pathway and their content of these compounds (Kariñho-Betancourt et al., 2019; Lei et al. 2018; Padilla-González et al. 2019).

In this second part of the project, analysis of genetic variability in the genes encoding the enzymes involved in the biosynthesis pathway of phenolic compounds and their transcription factors will reveal a probable association between variation in the quantity and quality of secondary metabolites and specific genotypes/alleles.

Theme 2: Molecular analysis of major genes involved in disease resistance in small ruminants in Tunisia.

Small ruminant farming is a traditional activity deeply rooted in the agricultural societies of North African countries. Indeed, this activity continues to represent one of the essential, if not exclusive, sources of income for a significant portion of the agricultural populations in these regions. In Tunisia, the small ruminant population consists of four sheep breeds and one goat breed. Sheep farming accounts for 39% of total red meat production (OEP, 2014) with more than 6.8 million head, including approximately 3.9 million ewes (ONAGRI, 2012) belonging to four different breeds: Barbarine (60.3%), Queue ﬁne de l’Ouest (34.6%), Noir de Thibar (2.1%) and Sicilo Sarde (0.7%).

The Barbarine breed, known locally as “Nejdi” or “fat-tailed sheep,” is the most widespread in Tunisia and is mainly used for meat production in extensive farming systems (Djemali et al., 1994). The second breed is the “Queue ﬁne de l’Ouest” breed, also known as “Bergui,” which is mainly found in the steppes of central Tunisia. The Black Thibar breed is a composite black-wool sheep found in the sub-humid region of northern Tunisia and used for meat production. Finally, the Sicilo Sarde breed is the only dairy sheep breed in North Africa. It is the result of a cross between two imported Italian dairy breeds (Sarde and Sicilienne) from Sicily and is currently limited to areas in northwestern Tunisia (Djemali, 2000).

The Tunisian goat population numbers around 1.5 million, including 900,000 breeding females. The majority of goats are found in the southern regions of Tunisia. Around 95% of this population is made up of a native black-coated breed known as the “Arbi” breed.

Diseases have a negative impact on animal production and welfare. The costs they generate are estimated at 17% of total animal production income in developed countries and between 30% and 50% in developing countries. However, to date, there are few breeding programs for disease resistance in place that have yielded conclusive results.

Diseases caused by parasites, bacteria, or viruses have always been a major obstacle to efficient sheep and goat production worldwide. Controlling or eliminating infectious agents in farm animals has always depended on the use of vaccines, drugs, and/or the elimination of sick animals. However, these measures have failed to eradicate some of the major infectious diseases in livestock. Indeed, prolonged use of antibiotics, vaccines, or other treatments often leads to the development of resistant strains of pathogens or parasites. This significantly reduces the effectiveness of treatments. The use of genetic improvement through research into disease defense mechanisms will provide new approaches to combating diseases affecting livestock. Differential genetic resistance to disease in livestock has been known for a long time (Hutt, 1958). The discovery of immune response genes has provided new impetus for studying the genetic control of the immune response in livestock. However, genetic selection methods for disease resistance in small ruminants have not been widely used, as selection for meat production traits has ignored the improvement of disease resistance traits. Furthermore, due to the complexity of infectious diseases caused by multiple pathogens, selection becomes ineffective in controlling all types of diseases. Finally, basic research has not identified enough genes that can be used in selection for pathogen resistance.

As part of this project, we looked at various genes involved in the immune response. Two main categories of immune responses can be distinguished: innate immunity and adaptive immunity (Medzhitov, 2007). Among the molecules involved in immunity, those of the major histocompatibility complex (MHC) play an essential role in the activation of adaptive immune responses, while Toll-like receptors (TLRs) are involved in innate immunity mechanisms by recognizing molecular motifs conserved in many pathogens. On the other hand, cytokines are important mediators of the immune system involved in intercellular communication and responsible for initiating, amplifying, and regulating inflammation in response to a pathogen challenge. They perform several roles associated with their functions as mediators of innate and adaptive immune responses (Downing et al., 2010).

A review of the most recent knowledge on these gene groups in different livestock models confirms their central role in controlling immune mechanisms. Functional studies have revealed numerous associations between these genes and various physiological traits, including both the quality of the immune response to various pathogens and zootechnical performance in terms of production and reproduction (Maillard, 1998). Several studies have been conducted, mainly in sheep, with the aim of identifying significant associations between MHC gene polymorphism and resistance to nematodes, bacteria, and viruses (Shen et al., 2014). However, a significant association has only been observed between DRB1 and DQB1 gene polymorphism and resistance to cystic echinococcosis (Shen et al., 2014). In addition, certain MHC alleles have been associated with resistance to bovine leukemia virus (Gutierrez et al., 2016).

On the other hand, analysis of TLR genes in several livestock species has shown a significant association between their polymorphism and resistance to certain pathogens. Indeed, TLR2 has been associated with susceptibility/resistance to tuberculosis in cattle and has been suggested as a selection target in breeding programs. Polymorphism in the TLR4 and TLR5 genes has been associated with resistance to brucellosis and Mycobacterium avium, respectively (Bhaladhare et al., 2016).

Finally, polymorphism in certain cytokine genes (GM-CSF, IL-4, IL-8, IL-12a, and IL-13) has been associated with resistance/susceptibility to various diseases (Downing et al., 2010).

There are several reasons for using selection rather than traditional methods to control diseases. Selection for disease resistance could improve the economic performance of herds by both reducing the subclinical effect of diseases on production and decreasing the number and severity of clinical cases.