Publications
in limbo veritas
T Bataillon, A. A. T. Smith, T Mailund, A-C Thuillet
Genetics, accepted pending revisions
Recent experimental evidence has demonstrated that mutation rates of microsatellites are allele-specific rather than locus-specific. Although numerous population genetics models have been devised to accommodate the peculiarities of the microsatellite mutational model, allowing for stepwise mutation events, virtually no population genetics model incorporating variation in mutation rate among alleles at a same locus has been studied. We have developed a simple urn model that allows the simulation of microsatellite data from a stationary Wright Fisher population that incorporates allele-specific mutation patterns. An approximate Bayesian framework for the estimation of long term effective size, Ne, is proposed. The method uses rejection sampling to approximate the likelihood of joint summary statistics describing the data. The performance of the method is examined using Monte Carlo simulations of datasets, and is then illustrated by reanalyzing microsatellite data obtained from an earlier study of Triticum diccoicoides where the relationship between allele length and allele mutability had been established from direct observations of mutation rates.
S De Mita, J Ronfort, H I. McKhann, C Poncet, R El Malki and T Bataillon
Genetics, in press
Symbiotic nitrogen-fixing rhizobia are able to trigger root deformation in their Fabaceae host plants, allowing their intracellular accommodation. They do so by delivering molecules called Nod factors. We analyzed the patterns of nucleotide polymorphism of five genes controlling early Nod factor perception in the Fabaceae Medicago truncatula, in order to understand the selective forces shaping the evolution of these genes. We used 30 Medicago truncatula genotypes sampled in a genetically homogeneous region of the species distribution range. We first sequenced 24 independent loci and detected a genome-wide departure from the hypothesis of neutrality and demographic equilibrium that suggests a population expansion. These data were used to estimate parameters of a simple demographic model incorporating population expansion. The selective neutrality of genes controlling Nod factor perception was then examined using a combination of two complementary neutrality tests, Tajima's D and Fay and Wu's standardized H. The joint distribution of D and H expected under neutrality was obtained under the fitted population expansion model. The gene DMI1 only, which is expected to regulate the downstream signal, shows a pattern consistent with a putative selective event (P = 0.022). In contrast, receptor-encoding genes NFP and NORK show no significant signatures of selection. Among the genes we analyzed, only DMI1 should be viewed as a candidate for adaptation in the recent history of M. truncatula.
2007
S De Mita, J Ronfort, H I. McKhann, C Poncet, R El Malki and T Bataillon
Genetics,177:2123-2133
Symbiotic nitrogen-fixing rhizobia are able to trigger root deformation in their Fabaceae host plants, allowing their intracellular accommodation. They do so by delivering molecules called Nod factors. We analyzed the patterns of nucleotide polymorphism of five genes controlling early Nod factor perception in the Fabaceae Medicago truncatula, in order to understand the selective forces shaping the evolution of these genes. We used 30 Medicago truncatula genotypes sampled in a genetically homogeneous region of the species distribution range. We first sequenced 24 independent loci and detected a genome-wide departure from the hypothesis of neutrality and demographic equilibrium that suggests a population expansion. These data were used to estimate parameters of a simple demographic model incorporating population expansion. The selective neutrality of genes controlling Nod factor perception was then examined using a combination of two complementary neutrality tests, Tajima's D and Fay and Wu's standardized H. The joint distribution of D and H expected under neutrality was obtained under the fitted population expansion model. The gene DMI1 only, which is expected to regulate the downstream signal, shows a pattern consistent with a putative selective event (P = 0.022). In contrast, receptor-encoding genes NFP and NORK show no significant signatures of selection. Among the genes we analyzed, only DMI1 should be viewed as a candidate for adaptation in the recent history of M. truncatula.
S De Mita, S Santoni, J Ronfort and T Bataillon
Background
The NODULATION RECEPTOR KINASE (NORK) gene encodes a Leucine-Rich Repeats (LRRs) receptor-like protein and controls infection of symbiotic rhizobia and endomycorrhizal fungi in Legumes. Occurrence of numerous amino acid (AA) changes driven by directional selection have been reported in this gene, using a limited number of EST sequences but the functional of these changes remain obscure. The Medicago genus, where changes in rhizobial associations have been previously examined, is a good model to test whether the evolution of NORK is influenced by rhizobial interactions.
Results
We sequenced a region of 3610 nucleotides (encoding a 392 amino acid-long region of the NORK protein) in 32 Medicago species. We confirm that positive selection in NORK has occurred within the Medicago genus and find that the amino acid positions targeted by selection occur in sites outside of solvent-exposed regions in LRRs, and other sites in the 5' region of the protein. We examined if branches of the Medicago phylogeny where changes of rhizobial symbionts occurred also display accelerated rates of of aa changes. Only one external branch, leading to M. noeana, out of five tested displays such a pattern. Conversely, at least one branch with no a priori regarding rhizobial symbiosis has likely undergone positive selection.
Conclusions
Adaptive changes in the sequence of the NORK receptor have involved the LRRs, but targeted different sites than in most previous studies of LRR proteins evolution. The fact that positive selection in NORK tends not to be associated to changes in rhizobial specificity indicates that this gene was likely not involved in evolving rhizobial preferences. Other explanations (e.g. coevolutionary arms races) must be tested to explain the adaptive evolution of NORK.
A Haudry, A Cenci, C Ravel, T Bataillon, D Brunel, C Poncet, I Hochu, S Poirier, S Santoni, S Glémin and J David
Several demographic and selective events occurred during the domestication of wheat from the allotetraploid wild emmer (Triticum turgidum ssp. dicoccoides). Cultivated wheat has since been affected by other historical events. We analysed nucleotide diversity at 21 loci in a sample of 101 individuals representing four taxa corresponding to representative steps in the recent evolution of wheat (wild, domesticated, cultivated durum and bread wheats), to unravel the evolutionary history of cultivated wheats and to quantify its impact on genetic diversity. Sequence relationships are consistent with a single domestication event and identify two genetically different groups of bread wheat. The wild group is not highly polymorphic, with only 212 polymorphic sites among the 21,720 bp sequenced, and, during domestication, diversity was further reduced in cultivated forms — by 69% in bread wheat and 84% in durum wheat — with considerable differences between loci, some retaining no polymorphism at all. Coalescent simulations were performed and compared with our data, to estimate the intensity of the bottlenecks associated with domestication and subsequent selection. Based on our 21-locus analysis, the average intensity of domestication bottleneck was estimated at about 3 — giving a population size for the domesticated form about one third that of wild dicoccoides. The most severe bottleneck, with an intensity of about 6, occurred in the evolution of durum wheat. We investigated whether some of the genes departed from the empirical distribution of most loci, suggesting that they might have been selected during domestication or breeding. We detected a departure from the null model of demographic bottleneck for the hypothetical gene HgA. However, the atypical pattern of polymorphism at this locus might reveal selection on the linked locus Gsp1A, which may affect grain softness — an important trait for end-use quality in wheat.
Bodil K. Ehlers & Thomas Bataillon
New Phytologist 174 (1), 194–211
(1) We evaluate the role of the mating environment for the maintenance of a labile sex expression, i.e. the ability of some genotypes to develop as functional hermaphrodites, in sub-dioecious plant species.
(2) We use a literature survey to explore which factors correlate with the occurrence of hermaphrodites in significant numbers. The maintenance of hermaphrodites under both low and high population density is also explored theoretically.
(3) We found that significant frequency of hermaphrodites mainly occurred in animal pollinated species where the hermaphrodite morph bore perfect flowers. Hermaphrodite morphs were mainly “inconstant” males, suggesting that these species evolved dioecy through the gynodioecious pathway. Models showed that pollen limitation in females creates a niche allowing hermaphrodites to be maintained either transiently or in stable manner (when assuming a dominant genetic modifier in the pollen of hermaphrodites).
(4) Labile sex expression can be selectively maintained in sub-dioecious species when females occasionally experience pollen limitation thus hindering the evolution of pure dioecy.
2006
J.Ronfort, T. Bataillon, S. Santoni, M. Delalande, J. David, J-M. Prosperi.
BMC Plant Biology 6:28
BACKGROUND: Exploiting genetic diversity requires previous knowledge of the extent and structure of the variation occurring in a species. Such knowledge can in turn be used to build a core-collection, i.e. a subset of accessions that aim at representing the genetic diversity of this species with a minimum of repetitiveness. We investigate the patterns of genetic diversity and population structure in a collection of 346 inbred lines representing the breadth of naturally occurring diversity in the Legume plant model Medicago truncatula using 13 microsatellite loci distributed throughout the genome.
RESULTS: We confirm the uniqueness of all these genotypes and reveal a large amount of genetic diversity and allelic variation within this autogamous species. Spatial genetic correlation was found only for individuals originating from the same population and between neighbouring populations. Using a model-based clustering algorithm, we identified four main genetic clusters in the set of individuals analyzed. This stratification matches broad geographic regions. We also identified a set of "admixed" individuals that do not fit with this population structure scheme.
CONCLUSION: The stratification inferred is discussed considering potential historical events like expansion, refuge history and admixture between neighbouring groups. Information on the allelic richness and the inferred population structure are used to build a nested core-collection. The set of inbred lines and the core collections are publicly available and will help coordinating efforts for the study of naturally occurring variation in the growing Medicago truncatula community.
S. Glemin, L. Vimond, J.Ronfort, T. Bataillon, A. Mignot.
Heredity 97(4):304-11
Various methods have been proposed to estimate inbreeding depression and to assess its consequences for natural populations. As an alternative to controlled crosses, the use of molecular markers has allowed direct investigation of inbreeding depression in natural populations, but usually suffers from low statistical power. Here, we investigated the effect of inbreeding depression on survival in two populations of the rare species Brassica insularis, using both controlled crosses and a marker-based approach. We compare the respective merits of the two approaches for studying inbreeding depression. We also use information from the molecular markers to dissect in detail patterns of inbreeding depression in this species. A posteriori, we find that combining the approaches was not necessary to obtain simple point estimates of inbreeding depression. However, using molecular markers may give insight into the genetic basis of inbreeding depression, such as the occurrence of epistatic interactions among deleterious alleles or purging.
T. Bataillon, T. Mailund, S. Thorlacius, E. Steingrimsson,
T. Rafnar, M.M. Halldorsson, V. Calian, and M.H. Schierup
in press for European Journal of Human Genetics
Characterizing the extent of linkage disequilibrium (LD) in
the genome is a pre-requisite for association mapping
studies. Patterns of LD also contain information about the
past demography of populations. On this study we focus on
the Icelandic population where LD was investigated in 12
regions of ~15 cM using regularly spaced microsatellite
loci. In total 1753 individuals were genotyped for 179
markers. LD was estimated using a composite disequilibrium
measure based on unphased data. LD decreases with distance
in all 12 regions and can be detected over approximately 4
cM for the given sample size. Differences in the patterns
of decrease of LD with distance among genomic regions were
mostly due to two regions exhibiting respectively higher
and lower proportions of pairs in LD than average within
the first 4 cM. We pooled data from all regions except
these two and summarized patterns of LD by computing the
proportion of pairs of loci exhibiting significant LD (at
the 5% level) as a function of distance. We compared
observed patterns of LD with simulated datasets obtained
under scenarios with varying demography and intensity of
recombination. We show that unphased data allow to make
inferences on scaled recombination rates from patterns of
LD. Patterns of LD in Iceland suggest a genome-wide scaled
recombination rate of ρ* = 200 [130–330]
per cM which is equivalent to a long term effective
population size of ~5000 in the range of estimates recently
reported in three populations using extensive SNPs data
from the HapMap project. We discuss the implication of our
findings for association mapping studies using the
Icelandic population and expected pattern of LD between
SNPs markers.
S. De Mita, S. Santoni, I. Hochu, J. Ronfort and T. Bataillon
Understanding the selective constraints of partner specificity in mutually beneficial symbiosis is a significant, yet largely unexplored, prospect of evolutionary biology. These selective constraints can be explored through the study of nucleotide polymorphism at loci controlling specificity. The membrane-anchored receptor NORK (nodulation receptor kinase) of the Legume Medicago truncatula controls early steps of root infection by two symbiotic microorganisms: nitrogen-fixing bacteria (rhizobia) and endomycorrhizal fungi (Glomales). We analyzed the diversity of the gene NORK by sequencing 4 kilobases in 28 inbred lines sampled from natural populations. We detected 33 polymorphic sites with only one non-synonymous change. Analysis based on Tajima's D and Fay and Wu's H summary statistics revealed no departure from the neutral model. We analyzed divergence using sequences from the closely related species M. coerulea. The McDonald-Kreitman test indicated a significant excess of non-synonymous changes contributing to this divergence. Furthermore, maximum-likelihood analysis of a molecular phylogeny of a few Legume species indicated that a number of amino acid sites, likely located in the receptor domain of the protein, evolved under the regime of positive selection. Further research should focus on the rate and direction of molecular co-evolution between microorganisms' signaling molecules, and Legumes' receptors.
R. Kassen and T. Bataillon
The extent to which a population diverges from its ancestor through adaptive evolution depends on variation supplied by novel beneficial mutations. Extending earlier work recent theory makes two predictions that appear to be robust to biological details: the distribution of fitness effects among beneficial mutations prior to selection should be (i) exponential; and (ii) invariant, meaning it is always exponential regardless of the fitness rank of the wild type allele. Here we test these predictions by assaying the fitness of 665 independently-derived single-step mutations in the bacterium, Pseudomonas fluorescens, across a range of environments. We show that the distribution of fitness effects among beneficial mutations is indistinguishable from an exponential despite marked variation in the fitness rank of the wild type across environments. These results suggest that the initial step in adaptive evolution - the production of novel beneficial mutants from which selection sorts - is remarkably general, being characterized by an approximate exponential distribution with many mutations of small effect and few of large effect. We also document striking variation in the pleiotropic costs of antibiotic resistance, a result that may have implications for strategies aimed at eliminating resistant pathogens in animal and human populations.
M-F Ostrowski, J. David, S. Santoni, H. McKhann, X. Reboud, V. Le Corre, C. Camilleri, D. Brunel, D. Bouchez, B. Faure and T. Bataillon
The existence of a large-scale population structure was investigated in
Arabidopsis thaliana
by studying patterns of polymorphism in a set of 71 European accessions. We used
sequence polymorphism surveyed in 10 fragments of ~
600 nucleotides and a set of nine
microsatellite markers. Population structure was investigated using a model-based inference
framework. Among the accessions studied, the presence of four groups was inferred
using genetic data, without using prior information on the geographical origin of the accessions.Significant genetic isolation by geographical distance was detected at the group
level, together with a geographical gradient in allelic richness across groups. These results
are discussed with respect to the previously proposed scenario of postglacial colonization
of Europe from putative glacial refugia. Finally, the contribution of the inferred structure
to linkage disequilibrium among 171 pairs of essentially unlinked markers was also investigated. Linkage disequilibrium analysis revealed that significant associations detected in
the whole sample were mainly due to genetic differentiation among the inferred groups.
We discuss the implication of this finding for future association studies in
A .thaliana.
2005
A.-C. THUILLET, T. BATAILLON, S. POIRIER, S. SANTONI, and J. L. DAVID
Estimation of long-term effective population size (Ne) from polymorphism data alone requires an independent knowledge of mutation rate. Microsatellites provide the opportunity to estimate Ne because their high mutation rate can be estimated from observed mutations. We used this property to estimate Ne in allotetraploid wheat Triticum turgidum at four stages of its history since its domestication. We estimated the mutation rate of 30 microsatellite loci. Allele-specific mutation rates µ were predicted from the number of repeats of the alleles. Effective population sizes were calculated from the diversity parameter {theta} = 4Neµ. We demonstrated from simulations that the unbiased estimator of {theta} based on Nei's heterozygosity is the most appropriate for estimating Ne because of a small variance and a relative robustness to variations in the mutation model compared to other estimators. We found a Ne of 32,500 individuals with a 95% confidence interval of [20,739; 45,991] in the wild ancestor of wheat, 12,000 ([5790; 19,300]) in the domesticated form, 6000 ([2831; 9556]) in landraces, and 1300 ([689; 2031]) in recent improved varieties. This decrease illustrates the successive bottlenecks in durum wheat. No selective effect was detected on our loci, despite a complete loss of polymorphism for two of them.
B. Ehlers, S. Maurice and T. Bataillon
Gynodioecy is defined as the coexistence of two different sexual morphs in a population: females and
hermaphrodites. This breeding system is found among many different families of angiosperms and is
usually under nucleo-cytoplasmic inheritance, with maternally inherited genes causing male sterility and
nuclear factors restoring male fertility. Numerous theoretical models have investigated the conditions for
the stable coexistence of females and hermaphrodites. To date, all models rest on the assumption that
restoration of a given male sterile genotype is controlled by a single Mendelian factor. Here, we review data
bearing on the genetic determinism of sex inheritance in three gynodiecious plant species.We suggest that
restoration of male fertility is probably best viewed as a quantitative trait controlled by many loci. We
develop a threshold model that accommodates an underlying polygenic trait, which is resolved at the
phenotypic level in discrete sexual morphs. We use this model to reanalyse data in Thymus vulgaris, Silene
vulgaris and Plantago coronopus. A simple Mendelian inheritance of sex determinism is unlikely in all three
species. We discuss how our model can shed additional light on the genetics of restoration and point
towards future efforts in the modelling of gynodioecy.
2004
I. Goldringer and T. Bataillon
The effective population size (Ne) is frequently estimated using temporal changes in allele frequencies
at neutral markers. Such temporal changes in allele frequencies are usually estimated from the standardized
variance in allele frequencies (Fc). We simulate Wright-Fisher populations to generate expected distributions
of Fc and of Fc averaged over several loci. We explore the adjustment of these simulated Fc
distributions to a chi-square distribution and evaluate the resulting precision on the estimation of Ne for
various scenarios. Next, we outline a procedure to test for the homogeneity of the individual Fc across
loci and identify markers exhibiting extreme Fc-values compared to the rest of the genome. Such loci are
likely to be in genomic areas undergoing selection, driving Fc to values greater (or smaller) than expected
under drift alone. Our procedure assigns a P-value to each locus under the null hypothesis (drift is
homogeneous throughout the genome) and simultaneously controls the rate of false positive among loci
declared as departing significantly from the null. The procedure is illustrated using two published data
sets: (i) an experimental wheat population subject to natural selection and (ii) a maize population
undergoing recurrent selection.
J. Bechsgaard, T. Bataillon, and M.H. Schierup
Self-incompatibility in Arabidopsis lyrata is sporophytically controlled by the
multi-allelic S-locus. Self-incompatibility alleles (S-alleles) are under strong
negative frequency dependent selection because pollen carrying common
S-alleles have fewer mating opportunities. Population genetics theory predicts
that deleterious alleles can accumulate if linked to the S-locus. This was tested
by studying segregation of S-alleles in 11 large full sib families in A. lyrata.
Significant segregation distortion leading to an up to fourfold difference in
transmission rates was found in six families. Differences in transmission rates
were not significantly different in reciprocal crosses and the distortions
observed were compatible with selection acting at the gametic stage alone. The
S-allele with the largest segregation advantage is also the most recessive, and is
very common in natural populations concordant with its apparent segregation
advantage. These results imply that frequencies of S-alleles in populations of
A. lyrata cannot be predicted based on simple models of frequency-dependent
selection alone.
Heather I. McKhann, Christine Camilleri, Aurelie Berard, Thomas Bataillon, Jacques L. David, Xavier Reboud, Valerie Le Corre, Christophe Caloustian, Ivo G. Gut, Dominique Brunel
A-C. Thuillet, T. Bataillon, P. Sourdille and J. L. David
Theoretical & Applied Genetics
doi:tbf
The effects of factors known to influence the
level of polymorphism at microsatellite loci were studied
using 99 markers and seven lines of bread wheat.
Mutational factors as well as indirect selective events
shape diversity at these loci. Theory predicts that the
selection of favorable alleles should reduce polymorphism
at neutral neighboring loci in genomic areas with
low recombination rates. In wheat, local recombination
rate is positively correlated with physical distance from
the centromere. Seventy four loci among the 99 used
could be physically located on the chromosome. We
studied how the following affected the diversity among a
set of inbred lines: the length of the alleles, the motif (CA
versus CT), the structure of the loci (perfect versus
imperfect) and the chromosomal position of the loci. For
each locus, we determined whether the polymorphism
observed at a locus was compatible with the Stepwise
Mutation Model (SMM) or the Two-Phase Model (TPM).
Both the mutation rate and the compatibility with the
SMM or the TPM were shown to be variable between
loci. Wheat microsatellite loci were found to be more
variable when segregating alleles were perfect and had
long motifs (composed of many repetitions). Diversity
observed at 19 loci was not compatible with the SMM.
Loci located in distal regions, with presumably high
recombination rates, had longer allele sizes and were
more polymorphic than loci located in proximal regions.
We conclude that both mutation factors and indirect
selective events vary according to the local recombination
rate and therefore jointly influence the level of polymorphism
at microsatellite loci in wheat.
2003
T. Bataillon
Trends in Ecology & Evolution , 18(7):315-317
doi:tbf Glemin, S., J. Ronfort and T. Bataillon
Theoretical & Applied Genetics
doi:tbf 2002
Thuillet, A. C., D. Bru, J. David, P. Roumet, S. Santoni, P.Sourdille, and T. Bataillon
2001
Gouesnard, B., T. M. Bataillon, et al.
Glemin, S., Bataillon, T., Ronfort, J., Mignot, A., & Olivieri, I.
2000
T. Bataillon
Keightley, P. D. and T. Bataillon
T. Bataillon and M. Kirkpatrick
We studied the effects of population size on the inbreeding depression and genetic load caused by
deleterious mutations at a single locus. Analysis shows how the inbreeding depression decreases as
population size becomes smaller and}or the rate of inbreeding increases. This pattern contrasts
with that for the load, which increases as population size becomes smaller but decreases as
inbreeding rate goes up. The depression and load both approach asymptotic limits when the
population size becomes very large or very small. Numerical results show that the transition
between the small and the large population regimes is quite rapid, and occurs largely over a range
of population sizes that vary by a factor of 10. The effects of drift on inbreeding depression may
bias some estimates of the genomic rate of deleterious mutation. These effects could also be
important in the evolution of breeding systems in hermaphroditic organisms and in the
conservation of endangered populations
1999
M. Kirkpatrick and T. Bataillon
1998
Ronfort, J., E. Jenczewski, T. Bataillon and F. Rousset.
Population structure parameters commonly used for diploid species are reexamined for the particular
case of tetrasomic inheritance (autotetraploid species). Recurrence equations that describe the evolution
of identity probabilities for neutral genes in an \u201cisland model\u201d of population structure are derived assuming
tetrasomic inheritance. The expected equilibrium value of FST is computed. In contrast to diploids, the
correlation of genes between individuals within populations with respect to genes between populations
(FST) may vary among loci due to the particular segregation patterns expected under tetrasomic inheritance
and is consequently inappropriate for estimating demographic parameters in such populations. We thus
define anew parameter (ρ)and derive its relationship withNm. This relationship is shown to be independent
from both the selfing rate and the proportion of double reduction. Finally, the statistical procedure
required to evaluate these parameters using data on gene frequencies distribution among autotetraploid
populations is developed.
Schoen, D. J., J. L. David and T. M. Bataillon
The accumulation of mildly deleterious mutations
accompanying recurrent regeneration of plant germ
plasm was modeled under regeneration conditions characterized
by different amounts of selection and genetic drift. Under
some regeneration conditions (sample sizes >75 individuals
and bulk harvesting of seed) mutation accumulation was
negligible, but under others (sample sizes <75 individuals or
equalization of seed production by individual plants) mutation
numbers per genome increased significantly during 25\u201350
cycles of regeneration. When mutations also are assumed to
occur (at elevated rates) during seed storage, significant
mutation accumulation and fitness decline occurred in 10 or
fewer cycles of regeneration regardless of the regeneration
conditions. Calculations also were performed to determine the
numbers of deleterious mutations introduced and remaining
in the genome of an existing variety after hybridization with
a genetic resource and subsequent backcrossing. The results
suggest that mutation accumulation has the potential to
reduce the viability of materials held in germ plasm collections
and to offset gains expected by the introduction of
particular genes of interest from genetic resources.
1997
Morgan M. T., D. J. Schoen, and T. M. Bataillon
American Naturalist 150: 618-638
doi:tbf 1996
T. Bataillon, J.L. David and D.J. Schoen
This study examines the use of neutral genetic markers to guide sampling from a large germplasm collection with the objective of establishing from it a smaller, but genetically representative sample. We simulated evolutionary change and germplasm sampling in a subdivided population of a diploid hermaphrodite annual plant to create an initially large collection. Several strategies of sampling from this collection were then compared. Our results show that a strategy based on information obtained from marker genes led to retention of the maximum number of neutral and nonneutral alleles in the smaller sample. This occurred when demes were composed of self-fertilizing individuals or when no migration occurred among demes, but not when demes of an outcrossing population were connected by high levels of migration.
How does self pollination evolve? Inferences from floral ecology and molecular genetic variation.
D.J. Schoen, M.T. Morgan, and T. Bataillon
Phil. Trans Royal Soc. London B series 351:1281-1290
doi:tbf Conference Papers
2006
T BATAILLON, N CHANTRET, A CENCI,
M-F GAUTIER, P JOUDRIER,AHAUDRY, M-H MULLER,C PONCET,
J-M PROSPERI, J. RONFORT, P. ROUMET,S SANTONI, A-C THUILLET, J. DAVID
The comparative study of patterns
of genetic diversity in crops and their wild ancestors coupled with recent advance
in coalescent theory opens the way for making some historical inference on
the demographic (and possibly selective) processes that have shaped genetic diversity
in crops since domestication. Demographic events affect genome-wide levels of
polymorphisms and the spectrum of allelic frequencies. Some forms of selection, in
particular recent selective sweeps are expected to reduce diversity locally that is at
the target of selection and in surrounding areas in the genome. Although a full
reconstruction of the demographic history seems impossible based on patterns of
polymorphism alone, contemporary polymorphism data can be used to calibrate
simplified demographic models that can account for amounts and patterns of currently
observable diversity. We illustrate that approach in two crop species with
contrasted histories and mating systems. First, patterns of diversity are studied in
the (allo)tetraploid wheat (Triticum turgidum) complex a species with a mixed mating
system dominated by high levels of selfing. The intensity of bottlenecks associated
with major historical episodes of domestication and subsequent selection are quantified
using microsatellite markers. Patterns of microsatellite diversity are also compared with patterns of sequence polymorphism detected at the Gsp-1 locus. We find
that domestication and subsequent selection resulted in a massive loss of genetic
diversity and estimated a several fold reduction in the long term effective size realized
in cultivated wheats relative to their wild ancestors (even after accounting for
the probable loss of diversity in wild populations due to extensive habitat loss since
Neolithic times). Next we analyze patterns of nucleotide diversity in alfalfa (Medicago
sativa) an autotetraploid and outcrossing crop species. Sequence polymorphism
among individuals spanning a wide geographic distribution was surveyed and analyzed
at two intronic regions. These were located in respectively the alfalfa NADHdependent
glutamate synthase and PO146, a pollen pectate lyase-like gene. These
genes were chosen while searching in GenBank a public genetic sequence database
for nucleotidic sequences of M. sativa and not chosen with any phenotypic ŕ priori.
This allowed us to i) quantify the extent of genetic divergence between wild and
cultivated populations and thereby assess the impact of domestication on this divergence,
ii) assess the originality of the genetic makeup of wild Spanish populations of
alfalfa relative to the rest of extant population throughout the species range, iii)
determine whether there is likely ongoing (recent) gene-flow among wild and cultivated
populations in Spain.
M. SEGUIN, A. ATTARD, T. BATAILLON,
C. BILLOT, A. CENCI, N. CHANTRET,et al.
Statistical dependence between alleles
at a pair of loci, or linkage disequilibrium (LD) was studied in rice, sorghum, wheat,
rubber tree and Medicago truncatula using samples drawn from germplasm collections.
LD was studied in restricted genomic areas which required to develop closely linked
markers. Approaches using BAC resulted in the development of microsatellite
markers in localized genomic area. In rubber tree, BACs were localized using
mapped markers. The BAC end sequences were used to detect microsatellites motifs.
On wheat and Medicago, primers were designed to allow direct sequencing of
gene fragments. The high number of alleles for the microsatellite markers necessitated
to group alleles with close sizes into the same allelic class in order to estimate
LD. The genetic structure observed on the cultivated crops yielded a strong noise
on LD, while LD was low in the samples drawn from collections of wild selfing
species. Among the varietal groups defined for the cultivated crops, LD was lower
than in the global sample and decayed rather rapidly, sometimes differently between
groups. The decay is around 100 kb in rice and 500 kb in sorghum. Therefore, a
good knowledge of the species diversity appears as a necessary pre-requisite. Those
conditions fulfilled, association genetics studies should be successful in the different
species studied here.
2005
C. Lavigne, I. Goldringer, V. Le Corre, E. Porcher, A-L. Raquin, X. Reboud, T. Bataillon, J. Enjalbert
2003
T. Bataillon, I. Bonnin, J. David et al.
Actes du BRG 1:1-13
2001
T. Bataillon, S. Poirier, P Roumet and J. David
EUCARPIA: Quantitative genetics and breeding methods: the way ahead . A. Gallais , C Dillmann and I. Goldringer (eds) INRA Editions pp 251-257
J. Ronfort, S. Glemin, T. Bataillon
EUCARPIA: Quantitative genetics and breeding methods: the way ahead . A. Gallais , C Dillmann and I. Goldringer (eds) INRA Editions pp 41-48
Reboud, X., McKhann, H., Scarcelli, N., Le Corre, V., Roux, F., David, J. L., Bataillon, T., Camilleri,
C., Bérard, A. & D.Brunel
pp 135-142
in Plant adaptation: molecular biology and ecology 2005 (ed. Q. C. Cronk, J. Whitton and I. E. P. Taylor). Ottawa: NRC Research Press.
How does self pollination evolve? Inferences
from floral ecology and molecular genetic variation.
D. Schen, M. Morgan and T. Bataillon
pp 77-102 in Plant Life Histories: Ecology
Phylogeny & Evolution (1997) Edited by J. Silvertown, M. Franco and J.L. Harper, Cambridge University
Press.