Permanent staff

Research interest

As a population geneticist, I am interested in the evolution, conservation and adaptation of domesticated species. My activities focus on the dynamics of the diversity of African cereals, mainly pearl millet (Pennisetum glaucum) in Sahelian Africa. How is genetic diversity organized? What are the impacts of climate changes and societal changes on the evolution of this diversity? What adaptive potential has been mobilized in recent decades to cope with these changes?

On older time scales, I study the links between cultivated and wild pearl millet, i.e. the history of domestication and the role of gene flow, particularly the introgression of adaptations. As such, I am leading the PemilAdapt project (ANR 2020-2024) on adaptive introgression in pearl millet.

Current research

My current research focus on understanding plants adaptation to climate conditions, especially African crops such as pearl millet. 

Ongoing projects aim at identifying the adaptive potential of wild relatives of crops as a reservoir of adaptation for crops improvement in regard to future climate changes. Our approach is to use NGS data to perform genomic scan and identify signature of selections linked to environmental variables.

Current projects

PemilAdapat (ANR-19-CE02-006-1; 2020-2024)

Understanding how species adapt is paramount to biodiversity. Species/populations adaptive potential largely depends on their genetic variability, which relies either on standing genetic variation or on de novo mutation. However, if rates of environmental changes are too rapid, occurrence of de novo mutations might be too slow of a process. When gene flow between species/populations occurs through recurrent backcrosses over generations, allowing foreign DNA to become part of recipient species’ genetic pool, it is named genetic introgression. If the genetic introgression from donor species/population increases the fitness of the recipient species/population then it is called “Adaptive Introgression" (AI). Despite the occurrence of hybridization in nature, relatively limited evidences supporting AI have been gathered until recently. Striking evidences of AI were found between archaic and modern humans. For crops, wild relatives represent a reservoir of adaptations that could refuel crops genetic diversity. With the advance of genomics, it is becoming evident that wild-crops gene flow was far more complex and protracted than previously considered. A compelling example of the potential adaptive outcome of introgression is the adaptation to altitude acquired by highland maize landraces from wild populations. Nonetheless, conclusive evidence for AI is restricted to a limited number of cases. For AI to take place, we will first need crosses and introgression to be successful. When selection against hybrids is weak and backcrosses are possible, genomic heterogeneity in terms of permeability to gene flow will affect introgression rates. Gaps knowledge on the genomic heterogeneity to introgression need to be fulfil particularly for crops. In addition, most evidence for AI comes from hard-selective sweeps, while soft-selective sweeps might be the dominant mode of adaptation. The main objective of the PEMILADAPT project is to understand how introgression from wild relatives can favour crops adaptation. The PEMILADAPT projects aims at responding the following specific questions:

1) How frequent wild introgression is and how is it distributed along the cultivated genome?

2) What modes (hard vs. soft) of selection are acting on introgressed alleles?

3) What are the functional implications of wild introgression in the cultivated genome?

To answer the above questions, we will focus on the pearl millet crop (Pennisetum glaucum). Pearl millet is the sixth most important cereal grain worldwide and it is a key cereal in arid and semi-arid regions where it is a staple food for over 90 million small farmers. Wild and cultivated pearl millet are found in sympatry and gene flow between the two forms is well recognized. By taking the opportunities coming from cutting edge technologies for high-throughout genomic sequencing and for artificial intelligence for powerful machine learning approaches, the project PEMILADAPT is expected to be at the leading front of evolutionary research questions. In addition to the fundamental knowledge on evolution that PEMILADAPT will produce, it may have significant impacts for on–going worldwide environmental challenges and sustainable development. Understanding selection forces and genomic landscape of introgression will likely help breeders in improving efficiency of their breeding strategies to adapt future varieties to on-going climate changes.

ASSET

ASSET (2018-2022) main objective is to evaluate the role of crop diversity to reduce the vulnerability of food production and livelihoods to climatic instability and shocks.

Combining ecology, agronomy and ethnoecology, the project will provide new insights into where (field, landscape, regions) and what components (variety, species, functions) of crop diversity (i.e. agrobiodiversity) are critical for the resilience of food production under climate change. We are also strongly engaging with farmers in France, Morocco and Senegal to understand how they currently use agrobiodiversity to face increasing risks linked to climate variability and extremes. The ASSET project will yield novel insights for the design and implementation of adaptation strategies that are based on a deep understanding of the agroecological systems investigated, but which remain rooted in the practicalities of on-the-ground food production.

The project ASSET is lead by Delphine Renard who is s a contractual researcher at Centre d’Ecologie Fonctionnelle et Evolutive in Montpellier (France). More information on the project can be found at: https://www.asset.cnrs.fr.

Formation and research experience

2013-Present

Senior researcher, IRD, UMR DIADE, DYNADIV

Research subject: Genetic diversity and adaptation of African cereals

2012-2013

Post doctoral position, IRD , UMR DIADE, DYNADIV

Research subject: Genetics diversity and adaptation of wild pearl millet populations (Pennisetum glaucum)

2010-2012

Post doctoral position, Center for Invasion Biology, University of Stellenbosch, South Africa

Pr Bettine van Vuren, Dr Cang Hui, Dr Jaco Le Roux & Dr Berndt Janse van Rensburg

Research subject: Colonisation dynamics of invasive birds: common mynas (Acridotheres tristis) & common starlings (Sturnus vulgaris)

2008-2009

Post doctoral position, CIRAD-AGIRs

Dr Johan Michaux

Research subject: Spatial genetics and phylogeography of domesticated animal species

2003-2008

Ph.D in Genetic Diversity and Population Genetics, ABIES-AgroParisTech

Supervisors: Pr Etienne Verrier (INRA-AgroParisTech) and  Dr Jean-Charles Maillard (CIRAD)

Research subject: Characterisation of the cattle, buffalo and chicken populations in the Northern Vietnamese province of Ha Giang-BIODIVA Project.

Past projects

DIVAGRO (Co-PI), 2018-2020, SEP2D, 30000€

AMMA50 (Co-I), 2015-2019, ANR, 3M£

CERAO (Co-I), 2014-18, ANR, 740 000€

MILDIV (PI),2012-2015, ANR, 160 000 €

ADAPTINCROPS (PI), 2015-2018, Fondation Agropolis, 180 000 €

Teaching activities

2016- present

Master MPTPA – UGB University Gaston Berger, St Louis, Sénégal, Agrobiodiversity course

2014-present

Master BIOVEM –UCAD University of Dakar, Senegal: Population Genetics course

Publications

 Salson, M., Orjuela, J., Mariac, C., Zekraoui, L., Couderc, M., Arribat, S., ... & Berthouly-Salazar, C. (2023). A strongly improved assembly of the pearl millet reference genome using Oxford Nanopore long reads and optical mapping.  G3: Genes|Genomes|Genetics accepted, https://doi.org/10.1101/2023.01.06.522873

Faye, A., Barnaud, A., Kane, N. A., Cubry, P., Mariac, C., Burgarella, C., ... & Berthouly-Salazar, C. (2022). Genomic footprints of selection in early-and late-flowering pearl millet landraces. Frontiers in plant science. 13:880631. https://doi.org/10.3389/fpls.2022.880631

Cissé, A., Clermont-Dauphin, C., Sall, S. N., Sakmi, G. I. E., Groupement, M. P., Ndiaye, A.,... & Berthouly-Salazar, C. (2022). Sahelian smallholders' varietal mixtures reconcile yield and agrobiodiversity conservation. Basic and Applied Ecology. https://doi.org/10.1016/j.baae.2022.12.006

Diack, O., Kanfany, G., Gueye, M. C., Sy, O., Fofana, A., Tall, H., Serba, D. D., Zekraouï, L., Berthouly-Salazar, C., Vigouroux, Y, Diouf, D., and Kane, N. A. (2020). GWAS unveils features between early- and late-flowering pearl millets. BMC Genomics, 21(1), 777. https://doi:10.1186/s12864-020-07198-2

Rhoné, B., Defrance, D., Berthouly-Salazar, C., Mariac, C., Cubry, P., Couderc, M., ... Vigouroux, Y. (2020). Pearl millet genomic vulnerability to climate change in West Africa highlights the need for regional collaboration. Nature Communications, 11(1). https://doi:10.1038/s41467-020-19066-4

Olodo, K. F., Barnaud, A., Kane, N. A., Mariac, C., Faye, A., Couderc, M., ... and Berthouly-Salazar, C. (2020). Abandonment of pearl millet cropping and homogenization of its diversity over a 40 year period in Senegal. PLoS ONE, 15, 1-18. https://doi:10.1371/journal.pone.0239123

Jankowski, F., Louafi, S., Kane, N. A., Diol, M., Camara, A. D., Pham, J. L., Berthouly-Salazar, C. and Barnaud, A. (2020). From texts to enacting practices: defining fair and equitable research principles for plant genetic resources in West Africa. Agriculture and Human Values, 37(4), 1083-1094. https://doi:10.1007/s10460-020-100393

Vignal, A., Boitard, S., …, Berthouly-Salazar C, …, & Warren, W. C. (2019). A guinea fowl genome assembly provides new evidence on evolution following domestication and selection in galliformes. Molecular ecology resources, 19(4), 997-1014. https://doi.org/10.1111/1755-0998.13017

Burgarella, C., Barnaud, A., Kane, N. A., Jankowski, F., Scarcelli, N., Billot, C., ... & Berthouly-Salazar, C. (2019). Adaptive introgression: An untapped evolutionary mechanism for crop adaptation. Frontiers in plant science, 10, 4. https://doi.org/10.3389/fpls.2019.00004

Burgarella, C., Cubry, P., Kane, N. A., Varshney, R. K., Mariac, C., Liu, X., ... Berthouly-Salazar C, Vigouroux Y. A western Sahara centre of domestication inferred from pearl millet genomes. Nature ecology & evolution, 2018, vol. 2, no 9, p. 1377-1380. https://doi.org/10.1038/s41559-018-0643-y

Rajeev K Varshney, …, Berthouly-Salazar C, …, Xun Xu (2017) Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments. Nature Biotechnology 35(10):969-976. doi: 10.1038/nbt.3943

Rhoné B, Mariac C, Couderc M, Berthouly-Salazar C, Ousseini IS, Vigouroux Y (2017) No Excess of Cis-Regulatory Variation Associated with Intraspecific Selection in Wild Pearl Millet (Cenchrus americanus). Genome biology and evolution 9(2):388-397

Diack O, Kane NA, Berthouly-Salazar C, Gueye MC, Diop BM, Fofana A, Sy O, Tall H, Zekraoui L, Piquet M, Couderc M, Vigouroux Y, Diouf D,Barnaud A (2017) New Genetic Insights into Pearl Millet Diversity As Revealed by Characterization of Early- and Late-Flowering Landraces from Senegal. Frontiers in plant science 8:818

Ousseini IS, Bakasso Y, Kane NA, Couderc M, Zekraoui L, Mariac C, Manicacci D, Rhoné B, Barnaud A, Berthouly-Salazar C, Assoumane A, Moussa D, Moussa T, Vigouroux Y (2017) Myosin XI is associated with fitness and adaptation to aridity in wild pearl millet. Heredity

Berthouly‐Salazar C, Thuillet AC, Rhoné B, Mariac C, Ousseini IS, Couderc M, Vigouroux Y (2016) Genome scan reveals selection acting on genes linked to stress response in wild pearl millet. Molecular ecology 25(21):5500-5512

Berthouly-Salazar C, Mariac C, Couderc M, Pouzadoux J, Floc'h JB, Vigouroux Y (2016) Genotyping-by-sequencing SNP identification for crops without a reference genome: using transcriptome based mapping as an alternative strategy. Frontiers in Plant Science 7:777.

Scarcelli N, Mariac C, Couvreur TLP, Faye A, Richard D, Sabot F, Berthouly-Salazar C, Vigouroux Y (2016) Intra-individual polymorphism in chloroplasts from NGS data: where does it come from and how to handle it?. Molecular Eciology Resources 16(2):434-445

Miguel E, Grosbois V, Berthouly-Salazar C, Roger F (2013) Review and meta-analysis of epidemiological studies of newcastle disease in African agro-systems (1980-2009). Epidemiology & Infection doi:10.1017/S0950268812002610

Smitz N, Berthouly-Salazar C, Cornelis D, Heller R, Chardonnet P, Prins HHT, De Iongh HH, Michaux JR (2013) A pan-african phylogeographical study of the African buffalo: investigating subspecies divergence. PLoS ONE

Mang Hung P, Wei-Hua C, Berthouly-Salazar C, Der-Yuh L, Yen-Pai L, Tixier-Boichard M, Chih-Feng C (2013) Genetic characterisation of Taiwan commercial native chickens ascertained by microsatellite markers. Poultry Science 50:290-299

Mang Hung P, Berthouly-Salazar C, Tran XH, Wei-Hua C, Der-Yuh L, Croijmans RPMA, Yen-Pai Lee, Hoang VT, Tixier-Boichard M, Chih-Feng C (2013) Genetic characterisation of Vietnamese local chickens as decision-making support for conservation strategy. Animal Genetics 44: 509-521

Berthouly-Salazar C, Hui C, Blackburn T, Gaboriaud C, van Rensburg B, van Vuuren B, Le Roux J (2013) Long-distance dispersal maximizes evolutionary potential during rapid geographic range expansion. Molecular Ecology 22:5793-5804

Barnaud A, Kalwij J, Berthoul-Salazar C, McGeoh M, van Vuuren B (2013) A road verges corridors for weed invasion? Insights from the fine-scale spatial genetic structure of Raphanus raphanistrum. Weed research 53:362-369

Le Roux J, Blignault M, Gildenhuys E, Mavengere N, Berthouly-Salazar C (2013) The genetic of biological invasions: What do we know about non-additive genetic effects and invasion success? Biological Invasion DOI:10.1007/s10530-013-0568-y

Trevennec K Chevalier V, Grosbois V, Ho Thu H, Berthouly-Salazar C, Roger F (2012) Are remote areas free from swine influenza? A case study in Northern Vietnam. Acta Tropica 122:160-163

Berthouly-Salazar C, van Rensburg B, Le Roux J, van Vuuren B, Hui C (2012) Development and characterization of 13 new, and cross amplification of 3, polymorphic nuclear microsatellite loci in the common myna (Acridotheres tristis). Conservation genetic resources 4:621-624

Berthouly-Salazar C, Thévenon S, Nhu Van T, Trong Nguyen B, Doan Pham L,Vu Chi C, Maillard JC (2012) Uncontrolled admixture and loss of genetic diversity in a local Vietnamese pig breed. Ecology & Evolution 2:962-97

Berthouly-Salazar C, van Rensburg B, Le Roux J, van Vuuren B, Hui C (2012) Spatial sorting drives morphological variation in the invasive bird, Acridotheres tristis. PLoS ONE 7:e38145

Chang CS, Chen CF, Berthouly-Salazar C, Chazara O, Lee YP, Chang CM, Chang KH, Bed’Hom B, Tixier-Boichard M (2011) A global analysis of molecular markers and phenotypic traits in local chicken breeds in Taiwan. Animal Genetics 43:172-182

Trevennec K Chevalier V, Grosbois V, Garcia JM, Ho Thu H, Berthouly-Salazar C, Peiris JSM, Roger F (2011) Looking for animal influenza in remote areas. A case study in Northern Vietnam. Acta Tropica 120:160-166

Berthouly C, Maillard JC, Doan Pham L, Nhu Van T, Bed’Hom B, Leroy G, Hoang Thang H, Laloë D, Bruneau N, Vu Chi C, Nguyen Dang V, Verrier E, Rognon X (2011) Revealing fine scale subpopulations structure in the Vietnamese H’mong cattle breed breed for conservation purposes. BMC Genetics 11:45-55

Berthouly-Salazar C, Rognon X, Nhu Van T, Gely M, Vu Chi C, Tixier-Boichard M, Bed’Hom B, Bruneau N, Verrier E, Maillard JC, Michaux RJ (2011) Vietnamese chickens: a gate towards Asian genetic diversity. BMC Genetics 11:53-64

Berthouly C, Leroy G, Nhu Van T, Hoang Thanh H, Bed’Hom B, Trong Nguyen B, Vu Ci C, Monicat F, Verrier E, Maillard JC, Rognon X (2009) Genetic Analysis of local Vietnamese chickens provides evidence of gene flow between domestic and wild populations. BMC Genetics 10:1-8

Berthouly C, Rognon X, Nhu Van T, Thanh Hoang H, Bed’Hom B, Laloë D, Vu Chi C, Verrier E, Maillard JC (2009) Genetic and morphometric characterisation of a local Vietnamese Swamp buffalo population. Journal of Animal Breeding and Genetics 127:74-84

Berthouly C, Do Ngoc D, ThévennonS, Bouchel D, Nhu Van T, Danes D, Grosbois V, Hoang Thanh H, Vu Chi C, Maillard JC (2009) How does farmer connectivity influence livestock genetics structure? A case study in a Vietnamese goat population. Molecular Ecology 18:3980-3991

Berthouly C, Bed’Hom B, Tixier-Boichard M, Chen CF, Lee YP, Laloë D, Legros H, Verrier E, Rognon X (2008) Using Molecular markers and multivariate methods to study the genetic diversity on local European and Asian chickens breeds. Animal Genetics 39:121-129

Maillard JC, Phan Van K, Nguyen T, Nhu Van T, Berthouly C, Libeau G, Kwiatek O (2008) Examples of probable host-pathogen co-adaptation/co-evolution in isolated farmed animal populations in the mountainous regions of North Vietnam. Annals of the New York Academy of sciences 1149:259-262