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: Characterization of adaptive variation along altitudinal gradients in teosinte wild
populations
 Laboratory name and web site:
UMR de Génétique Végétale (UMR GV)
Equipe: Génétique Evolutive : Adaptation et Redondance (Responsable C. Damerval)
http://moulon.inra.fr/index.php/en
 PhD supervisor (contact person):
 Name: Tenaillon Maud (http://moulon.inra.fr/~mtenaillon/)
 Position: Chargé de Recherche 1, CNRS
 email: tenaillon@moulon.inra.fr
 Phone number: +33 (0) 1 69 33 23 34
 Thesis proposal (max 1500 words):
In the face of current and future drastic climate changes, a better understanding of the genetic
mechanisms of adaptation and a characterization of the adaptive potential of species are essential.
This project will focus on the wild reservoir of a major crop species, maize. Maize has been
domesticated from teosintes around 9,000 years ago in Mexico. As a result of domestication and
subsequent improvement, maize has undergone a massive diversity shrinkage (about 20%) resulting
in a loss of adaptive variation. Hence, several authors have reported the pervasiveness of cryptic
adaptive variability in wild progenitors of crop species and selection from standing variation seems to
a major contributor of local adaptation. In teosintes, for instance, cryptic nucleotide variability has
largely contributed to the establishment of the cultivated phenotype and also largely contributes to
quantitative phenotypic variability. The wild populations therefore represent an unexploited reservoir
of variability that could greatly contribute to enhance the adaptive potential of maize.
Studies on the genetic of adaptation have revealed some of the newest and most fascinating
research in the past decade. Convincing examples of the role of nucleotide variants in both coding
and non-coding regions, of the role of Transposable Elements (TEs) and chromatin states in
adaptation are accumulating and it is becoming clear that various genomic components including the
unsuspected ‘junk DNA’ contribute to phenotypic variation. Next Generation Sequencing (NGS) of
both, DNA and RNA, has created a unique opportunity to assess and correlate genome wide variation
in sequence, expression and chromatin structure. One approach that has been proposed to investigate
the genetic determinants of the adaptation is to analyze the nucleotide differentiation between
populations submitted to contrasted environment by whole genome sequencing of pooled individuals.
Pools allow estimating allele frequencies of polymorphisms within and between populations useful
for a genome-wide investigation of evolutionary processes.
The ultimate goal of the proposed project will be to identify variation that contributes to local
adaptation in the wild gene pools to be transferred in the cultivated gene pool. To mimic climate
variation, we will rely on a vast sample of populations collected along two altitudinal gradients.
Those populations are subjected to contrasted abiotic conditions such as temperature, rainfall, soil
content, day length, and contrasted biotic conditions. The proposed project is articulated around three
distinct yet complementary objectives defining 3 main tasks: (1) to detect selection in populations
subjected to contrasted environmental conditions (gradients) and characterize nucleotide and
structural polymorphisms (TE indels) linked to climate adaptation; (2) to investigate in greater details
adaptation in controlled crosses between individuals growing in extreme environments; (3) to
validate the association between variation at candidate polymorphisms and phenotypic variation at
adaptive traits related to plant life cycle, architecture and yield.
Task1 1 will produce a description of various types of polymorphisms using NGS of pooled
individuals belonging to two wild populations growing in the most ‘extreme’ environments
(‘extreme’ populations) of the gradients. We propose to develop an innovative assay for the detection
of polymorphisms of insertion-deletion of TEs by NGS of transposon display reactions. Statistical
analyses and modeling will provide a list of candidate SNPs (Single Nucleotide Polymorphisms) and
TE insertions for adaptation. The SNPs will be used to build an Illumina VeraCode containing a set
of candidate and some control SNPs. The VeraCode and candidate adaptive TE insertions will be
genotyped on a broad sample of 31 populations. We will carry out population genomic analyses to
confirm that patterns of allelic variation are consistent with adaptation and measure the degree of
parallel/convergent evolution between gradients.
Task 2 will use expression and small RNA data from reciprocal crosses of individuals
sampled in the most ‘extreme’ populations to assess variation in small RNA and differential
expression between the parents. Using allele specific expression in F1 hybrids we will determine the
proportion of cis versus trans regulation of gene expression genome-wide. In addition, results from
reciprocal crosses will also provide information on maternal and paternal inheritance of gene
expression. A paternal dominance of trans-eQTLs in one way cross maize hybrids has been proposed
but requires further validation in two ways crosses. Our design will allow to statistically test whether
cis-polymorphisms or coding mutations are preferentially targeted during adaptation by comparing
the percentage of cis-regulation among selected genes versus the percentage of cis-regulation
observed genome wide.
Task 3 will validate the association between variation at candidate polymorphisms and
phenotypic variation, measured in natural conditions, at adaptive and agronomic traits related to plant
life cycle, architecture and yield. We will rely on the Illumina Veracode and candidate TE indels to
perform association mapping.
In summary, the proposed project will make use of all the most recent available NGS to
explore the multiple facets of adaptation and ultimately help characterizing the adaptive variation in
the wild gene pools of maize. We envision multiple outcomes that will be useful for the research
community but also plant breeders, those include: a better understanding of plant adaptation; a
measure of the degree of parallel evolution between gradients; the identification of functional
variation associated with climate variation. The project will be conducted in close collaboration with
colleagues at UMR GV (Domenica Manicacci, Clémentine Vitte, Matthieu Falque, Yohann Joets),
Yves Vigouroux and Daniel Grimanelli (UMR DIADE, Montpellier, France). In addition the PhD
student will benefit from a exchnages with the laboratories of Brandon Gaut (University of
California, Irvine, USA) and Luis Eguiarte (Institute of Ecology, University Nacional Autonoma de
Mexico, Mexico).
 Publications of the laboratory in the field (max 5):
Tenaillon M.I., Hufford M., Gaut B.S., Ross-Ibarra J. (2011). Genome size and transposable element
content as determined by high-throughput sequencing in maize and Zea luxurians. Genome
Biology and Evolution. 3: 219-229.
Tenaillon M.I., Hollister J., Gaut B.S. (2010). A triptych of the evolution of plant transposable
elements. Trends in Plant Science. 15(8): 471-478.
Zerjal T., Joets J., Alix K., Grandbastien M-A., Tenaillon M.I. (2009). Contrasting evolutionary
patterns and target specificities among three Tourist-like MITE families in the maize genome.
Plant Molecular Biology. 71:99-114.
Camus-Kulandaivelu L., Chevin L-M., Tollon C., Charcosset A., Manicacci D., Tenaillon M.I.
(2008). Patterns of variation of the Tb1-D8 region shed light into early maize evolutionary
history. Genetics. 180:1107-1121.
Tenaillon M.I. and Tiffin P.L. (2008). The quest for adaptive evolution: a theoretical challenge in a
maze of data. Curr. Opin. Plant Biol. 11(2):110-115.
Specific requirements to apply, if any: A strong background in population genetics, statistics and
bioinformatics is required with an interest for evolutionary questions and experimental design.