Thierry Robert

Bio: Thierry Robert is an academic researcher from Université Paris-Saclay. The author has contributed to research in topics: Domestication & Population. The author has an hindex of 17, co-authored 44 publications receiving 1172 citations. Previous affiliations of Thierry Robert include Pierre-and-Marie-Curie University & University of Paris.

Unmanaged sexual reproduction and the dynamics of genetic diversity of a vegetatively propagated crop plant, cassava (Manihot esculenta Crantz), in a traditional farming system

Abstract: Occurrence of intervarietal or interspecific natural crosses has been reported for many crop plants in traditional farming systems, underlining the potential importance of this source of genetic exchange for the dynamics of genetic diversity of crop plants. In this study, we use microsatellite loci to investigate the role of volunteer seedlings (plants originating from unmanaged sexual reproduction) in the dynamics of genetic diversity of cassava (Manihot esculenta Crantz), a vegetatively propagated crop, in a traditional farming system in Guyana. A previous field study showed that farmers incorporate such plants into the germplasm for vegetative propagation, and that many of them are likely to be assigned by farmers to recognized varieties. Under strict vegetative propagation clonality of varieties is expected. The high proportion of polyclonal varieties observed suggests that incorporation of seedlings into the germplasm for propagation is a frequent event. The molecular variability assessed with microsatellite markers shows that there is high differentiation among heterozygous varieties, whereas populations of seedlings do not depart from the proportions expected under Hardy–Weinberg assumptions. Assignment of seedlings to a recognized variety on the basis of morphological similarity greatly increases genetic diversity within the variety. We argue that recombination and gene flow play a major role in the dynamics of genetic diversity of cassava in traditional farming systems. Documenting unmanaged sexual reproduction and its genetic consequences is a prerequisite for defining strategies of in situ conservation of crop plant genetic resources.

Traditional management of cassava morphological and genetic diversity by the Makushi Amerindians (Guyana, South America): perspectives for on-farm conservation of crop genetic resources

Abstract: In this paper we present original data on morphological and genetic diversity of cassava managed by the Makushi Amerindians from Guyana. Although they propagate cassava exclusively vegetatively by means of stem cuttings, many Amerindian farmers also use and multiply volunteer plants grown from seeds produced by sexual reproduction. Morphological characters were recorded for 29 varieties cultivated by the Makushi and two populations of plants originating from volunteer cassava seedlings. Genetic characterisation with AFLP markers was available for 21 of the examined varieties. The morphological and agronomic characters were highly variable among varieties. Every variety could be differentiated from any other one, except for one pair of varieties. However, high intra-varietal variability existed, which might lead to confusions between phenotypically similar varieties by the Makushi. Seedlings were on average different from the pool of the varieties studied, but 67% were found to resemble closely enough one of the varieties to be liable to be assigned to it. Confusion between very similar varieties, as well as assignment of seedlings to a variety, should generate genetic variability within varieties, which was detected with AFLP markers. As in other sites in Amazonia, there was only a weak correlation between inter-varietal distances assessed with molecular and with morphological markers, suggesting that diversification of morphological characters has taken place repeatedly and independently across the Amazonian range of the crop. Diversifying selection, exchanges of varieties between farmers, and incorporation of sexually produced volunteer plants are key mechanisms responsible for the high diversity observed. Strategies of conservation of genetic resources should take these dynamic processes into account.

Genetic control of domestication traits in pearl millet (Pennisetum glaucum L., Poaceae).

Abstract: Quantitative trait loci (QTLs) controlling the morphological differences between pearl millet (Pennisetum glaucum ssp. glaucum) and its wild ancestor (Pennisetum glaucum ssp. monodii, form mollissimum) were investigated in a cultivated/wild F2 population by means of RFLP markers. The most critical adaptive changes resulting from the domestication process involved the spikelet structure: non-shedding seeds with reduced bracts and bristles and long involucral pedicel. Major differences also concerned characters describing the plant architecture, phenology and spike sizes. Many morphological differences could be attributed to the effect of a small number of loci with relatively large effects. These loci are mainly concentrated on four linkage groups (2, 5, 6 and 7). The loss of shedding ability, due to the absence of a functional abscission layer, is controlled by a single locus on linkage group 6 (al6). Genetic control of the other spikelet traits involved factors with large effects which are located in the region of linkage group 6 close to al6 and to an esterase gene, Esterase-E. Moreover, QTLs with large effects on plant and spike morphology traits such as plant height, number of spikes and weight of the spike were also mapped on linkage groups 6 and 7. This strong linkage of factors in the domestication syndrome may be involved in the maintenance of the phenotypic identity of wild and cultivated populations in sympatry. This result also brings new arguments in the understanding of the domestication process of this allogamous crop.

Assessment of genetic variability in a traditional cassava (Manihot esculenta Crantz) farming system, using AFLP markers

Abstract: Despite the urgent need to conserve domesticated plant genetic resources, and developing ‘on farm’ strategies of conservation, the impact of traditional farming practices and of their interaction with ecological factors on the structure and evolutionary dynamics of the genetic variability of crop populations has been little documented. We assessed the genetic variability of 31 varieties of cassava (M. esculenta Crantz) traditionally grown by Makushi Amerindians from Guyana, using AFLP markers. We used a sample of 38 varieties from an ex situ core collection as a reference. Accessions of wild cassava were also included. While clonality of the varieties was expected due to the vegetative propagation of cassava, 21 varieties presented intravarietal polymorphism. Among the varieties from a single site in Guyana, genetic diversity was the same as that in the accessions from the core collection. We suggest that incorporation of volunteer seedlings, produced by sexual reproduction, into the stock of varieties grown by the Makushi plays a major role in explaining both intravarietal polymorphism and the high level of genetic diversity. No correspondence was found between the structure of molecular diversity and variation observed for agronomic traits that are targets for selection by cultivators. As found in previous studies, all wild forms of cassava clustered together and separately from the cultivated varieties in a Neighbour-Joining dendrogram. These results are consistent with the hypothesis of a limited domestication event in a restricted area, followed by rapid diffusion of cultivated phenotypes and convergent evolution. Our results show that local varieties are an important source of genetic diversity, and highlight the importance of the interaction between human and ecological factors in the dynamics of this diversity.

Evaluation of the extent of genetic variability among Theobroma cacao accessions using RAPD and RFLP markers

Abstract: Random amplified polymorphic DNA (RAPD) and restriction fragment length polymorphism (RFLP) markers were used to evaluate genetic relationships within the Theobroma cacao species and to assess the organization of its genetic diversity Genetic variability was estimated with 18 primers and 43 RFLP probes on 155 cocoa trees belonging to different morphological groups and coming from various geographic origins The majority of the RFLP probes issued from low-copy DNA sequences On the basis of on the genetic distance matrices, the two molecular methods gave related estimates of the genetic relationship between genotypes Although an influence of cocoa morphological groups and geographical origins of trees was observed, a lack of gene differentiation characterized the T cacao accessions studied The continuous RFLP variability observed within the species may reflect the hybridization and introgressions between trees of different origins Nevertheless, the Nacional type was detected to be genetically specific and different from well-known types such as Forastero, Criollo and Trinitario Some of those genotypes were characterized by a low heterozygosity rate and may constitute the original Nacional pool These results also provide information for the constitution of a cocoa tree core collection

Hundreds of variants clustered in genomic loci and biological pathways affect human height

Abstract: Most common human traits and diseases have a polygenic pattern of inheritance: DNA sequence variants at many genetic loci influence the phenotype. Genome-wide association (GWA) studies have identified more than 600 variants associated with human traits, but these typically explain small fractions of phenotypic variation, raising questions about the use of further studies. Here, using 183,727 individuals, we show that hundreds of genetic variants, in at least 180 loci, influence adult height, a highly heritable and classic polygenic trait. The large number of loci reveals patterns with important implications for genetic studies of common human diseases and traits. First, the 180 loci are not random, but instead are enriched for genes that are connected in biological pathways (P = 0.016) and that underlie skeletal growth defects (P < 0.001). Second, the likely causal gene is often located near the most strongly associated variant: in 13 of 21 loci containing a known skeletal growth gene, that gene was closest to the associated variant. Third, at least 19 loci have multiple independently associated variants, suggesting that allelic heterogeneity is a frequent feature of polygenic traits, that comprehensive explorations of already-discovered loci should discover additional variants and that an appreciable fraction of associated loci may have been identified. Fourth, associated variants are enriched for likely functional effects on genes, being over-represented among variants that alter amino-acid structure of proteins and expression levels of nearby genes. Our data explain approximately 10% of the phenotypic variation in height, and we estimate that unidentified common variants of similar effect sizes would increase this figure to approximately 16% of phenotypic variation (approximately 20% of heritable variation). Although additional approaches are needed to dissect the genetic architecture of polygenic human traits fully, our findings indicate that GWA studies can identify large numbers of loci that implicate biologically relevant genes and pathways.

Evolution of crop species: genetics of domestication and diversification

Abstract: Domestication is a good model for the study of evolutionary processes because of the recent evolution of crop species (<12,000 years ago), the key role of selection in their origins, and good archaeological and historical data on their spread and diversification. Recent studies, such as quantitative trait locus mapping, genome-wide association studies and whole-genome resequencing studies, have identified genes that are associated with the initial domestication and subsequent diversification of crops. Together, these studies reveal the functions of genes that are involved in the evolution of crops that are under domestication, the types of mutations that occur during this process and the parallelism of mutations that occur in the same pathways and proteins, as well as the selective forces that are acting on these mutations and that are associated with geographical adaptation of crop species.

Rice Domestication by Reducing Shattering

Abstract: Crop domestication frequently began with the selection of plants that did not naturally shed ripe fruits or seeds. The reduction in grain shattering that led to cereal domestication involved genetic loci of large effect. The molecular basis of this key domestication transition, however, remains unknown. Here we show that human selection of an amino acid substitution in the predicted DNA binding domain encoded by a gene of previously unknown function was primarily responsible for the reduction of grain shattering in rice domestication. The substitution undermined the gene function necessary for the normal development of an abscission layer that controls the separation of a grain from the pedicel.