Caroline Pont

Caroline Pont

session, year:
2017 2nd


Receiving laboratory:
UCSC, University of California Santa Cruz, Santa Cruz, CA

Country of origin:


Country of destination:

United States of America

Last available contact


Download Curriculum Vitae

Mobility project

Ancient DNA to reveal plant evolutionary trajectories in response to climate modification and domestication during the Holocene

Climate change, steady population growth and increasing needs from emerging economies are threatening food security over the world. The development of high-yielding, durably stress-resistant crops/trees is thus essential to ensure future human needs. This challenge can be partly addressed through the identification, conservation and valorisation of key polymorphisms underlying plant adaptation, and their proper exploitation in current genome-informed conservation and breeding strategies. Signatures of adaptation in response to natural or human-driven selection are embedded in the genome of modern populations/species, allowing past selective processes to be inferred from the analysis of spatial patterns of extant genetic variations. Such a synchronic (i.e. indirect) approach has clearly demonstrated the power of natural and artificial selection in creating local adaptations. However, in complement of relying on traditional single time point data sets (i.e. modern diversity for a given species), adding a temporal dimension from genomic ‘snapshots’ of the population at several time points, before, during and after the start of a selective sweep (i.e a direct or allochronic approach) can uniquely illuminate the parameters underlying the adaptive history of plant species. PaleoPLANT is aimed at opening the new scientific area of plant paleogenomics, through ancient DNA analysis from archaeobotanical remains. Our main objectives are to quantify the rate of molecular evolution during the Holocene (a period during which crop plants were domesticated and where major climatic changes took place) and determine the genomic targets of plant adaptation. Combining past and present-day genetic variation will help in identifying the genomic signatures of adaptation to climate changes and domestication and will provide a list of key alleles to be prioritized in modern conservation and breeding programs.

Biography & research interests

I work at INRA, the French National Institute for Agricultural Research, since 2003 in plant genomics (initially as a technician) in the paleogenomic and evolution group. I have completed a master in Genomic, Production and Plant Ecophysiology and then a PhD in Physiology and Molecular Genetics. I investigated, during my PhD wheat evolutionary history to unveil the molecular basis of plant adaptation to climate constraints. Combining skills and competences in molecular biology, genomics, genetics and bioanalysis, I conducted a research program that provided novel insights into the role of hybridization as a major evolutionary mechanisms in wheat to enhance genomic plasticity (via the accumulation of mutations, gene loss or expression modification). I would like to realize a rewarding experience abroad that will value my expertise acquired during my thesis as it should be during a post-doc. I am currently AgreenSkills outgoing fellow in Beth Shapio’s Lab at University of Santa Cruz (CA) where I work in a paleogenomic lab specialized in ancient DNA sequencing from remains. My objective is to determine the genomic targets of plant adaptation and plant domestication during the Holocene (last 10 000 years) with a large collection of archaeobotanical samples. This mobility gives me the unique opportunity to develop new skills, to build long-term collaboration and then to develop a new laboratory in my institute in France.

Selected publications

Pont C., Salse J., 2017. Wheat paleohistory created asymmetrical genomic evolution. Curr Opin Plant Biol. 6;36:29-37. Doi: 10.1016/j.pbi.2017.01.001.

El Baidouri M, Murat F, Veyssiere M, Molinier M, Flores R, Burlot L, Alaux M, Quesneville H, Pont C, Salse J., 2017. Reconciling the evolutionary origin of bread wheat (Triticum aestivum). New Phytol. 213(3):1477-1486.  *Co-corresponding authors.

Murat F, Pont C, Salse J, 2014. Paleogenomics in Triticeae for translational research, Current Plant Biology, 1, 34-39. Doi: 10.1016/j.cpb.2014.08.003.

Murat F, Armero A, Pont C, Klopp C, Salse J., 2013. Reconstructing the genome of the most recent common ancestor of flowering plants. Nat Genet. 49,4, 490. Doi: 10.1038/ng.3813.

Pont C, Murat F, Guizard S, Flores R, Foucrier S, Bidet Y, Quraishi UM, Alaux M, Doležel J, Fahima T, Budak H, Keller B, Salvi S, Maccaferri M, Faure S, Feuillet C, Steinbach D, Quesneville H, Salse J. Wheat, 2013. Syntenome unveils new evidences of contrasted evolutionary plasticity between paleo- and neoduplicated subgenomes. Plant J. 76(6):1030-44.


ancient DNA, paleogenomic, selection, sub-genome, hexaploidization, wheat, domestication, climate change