Since the domestication of crop species, humans have derived specific varieties for particular uses and shaped the genetic diversity of these varieties. Here, using an interdisciplinary approach ...combining ethnobotany and population genetics, we document the within‐variety genetic structure of a population‐variety of bread wheat (Triticum aestivum L.) in relation to farmers’ practices to decipher their contribution to crop species evolution. Using 19 microsatellites markers, we conducted two complementary graph theory‐based methods to analyze population structure and gene flow among 19 sub‐populations of a single population‐variety Rouge de Bordeaux (RDB). The ethnobotany approach allowed us to determine the RDB history including diffusion and reproduction events. We found that the complex genetic structure among the RDB sub‐populations is highly consistent with the structure of the seed diffusion and reproduction network drawn based on the ethnobotanical study. This structure highlighted the key role of the farmer‐led seed diffusion through founder effects, selection and genetic drift because of human practices. An important result is that the genetic diversity conserved on farm is complementary to that found in the genebank indicating that both systems are required for a more efficient crop diversity conservation.
BACKGROUND: and Aims Dynamic management (DM) of genetic resources aims at maintaining genetic variability between different populations evolving under natural selection in contrasting environments. ...In 1984, this strategy was applied in a pilot experiment on wheat (Triticum aestivum). Spatio-temporal evolution of earliness and its components (partial vernalization sensitivity, daylength sensitivity and earliness per se that determines flowering time independently of environmental stimuli) was investigated in this multisite and long-term experiment. METHODS: Heading time of six populations from the tenth generation was evaluated under different vernalization and photoperiodic conditions. Key Results Although temporal evolution during ten generations was not significant, populations of generation 10 were genetically differentiated according to a north-south latitudinal trend for two components out of three: partial vernalization sensitivity and narrow-sense earliness. CONCLUSIONS: It is concluded that local climatic conditions greatly influenced the evolution of population earliness, thus being a major factor of differentiation in the DM system. Accordingly, a substantial proportion (~25 %) of genetic variance was distributed among populations, suggesting that diversity was on average conserved during evolution but was differently distributed by natural selection (and possibly drift). Earliness is a complex trait and each genetic factor is controlled by multiple homeoalleles; the next step will be to look for spatial divergence in allele frequencies.
Experimental populations evolving under natural selection represent an interesting tool to study genetic bases of adaptation. Evolution of genes possibly involved in adaptive response can be followed ...together with the corresponding phenotypic traits. Using experimental populations of hexaploid wheat, we studied the evolution of flowering time, a major adaptive trait that synchronizes the initiation of reproduction and the occurrence of favourable environmental conditions. During 12 generations, three populations were grown in contrasted environments (Vervins North France, Le Moulon near Paris, Toulouse South France) under the influence of natural selection, drift, mutation and recombination. Evolution of diversity at the major gene VRN-1 involved in wheat vernalization response has been analysed jointly with earliness estimated in controlled conditions. Whatever the population, rapid phenotypic changes as well as parallel genotypic variations were observed in the first seven generations, probably as the result of selection acting on this major gene which explains 80% of the trait variation overall. Different allelic combinations at physically unlinked copies of VRN-1 located on distinct genomes (A, B and D) were selected between populations. As theoretically expected, due to population differentiation, a high level of genetic diversity was maintained overall in generation 12. Surprisingly, in two populations out of three, the emergence of new alleles by mutation or migration, coupled with temporal variable selection or frequency-dependent selection, allowed to maintain within-population diversity despite local genetic drift and natural selection. This result may plead for an evolutionary approach of wheat genetic resource conservation.
Abstract Phenological match/mismatch between cultivated plants and their pest could impact pest infestation dynamics in the field. To explore how such match/mismatch of plant and pest phenologies may ...interact with plant defense dynamics, we studied the infestation dynamics of maize by one of its main pests in Europe, the European Corn Borer (Ostrinia nubilalis; Lepidoptera: Crambidae). A two-year field experiment was carried out on a collection of 23 maize inbred lines contrasted for their earliness. Each inbred line was sown at three different dates in order to expose different developmental stages of maize to natural European corn borer infestation. The effect of the sowing date depended on the inbred line, the pest generation, and the year. In 2021, the final pest incidence ranged from 36% to 91% depending on inbred lines and sowing date. In 2022, it ranged from 2% to 77%. This variability in final pest incidence can be related to variations in plant development during plant exposure to pest infestation. However, this relationship was not straightforward. Indeed, the shape and intensity of the relationship depended on the timing of the onset of the pest infestation. When infestation occurred while plants were in a vegetative stage, a nonlinear relationship between development and pest incidence was observed with the least and most developed plants being the most infested. When infestation occurred when all plants were in the mature phase, the most developed plants were the least infested. Our results highlight the effect of plant–pest phenological match/mismatch on pest infestation dynamics and underline the importance of taking plant–pest interactions into account to propose relevant control strategies.
The modification of flowering date is considered an important way to escape the current or future climatic constraints that affect wheat crops. A better understanding of its genetic bases would ...enable a more efficient and rapid modification through breeding. The objective of this study was to identify chromosomal regions associated with earliness in wheat. A 227-wheat core collection chosen to be highly contrasted for earliness was characterized for heading date. Experiments were conducted in controlled conditions and in the field for 3 years to break down earliness in the component traits: photoperiod sensitivity, vernalization requirement and narrow-sense earliness. Whole-genome association mapping was carried out using 760 molecular markers and taking into account the five ancestral group structure. We identified 62 markers individually associated to earliness components corresponding to 33 chromosomal regions. In addition, we identified 15 other significant markers and seven more regions by testing marker pair interactions. Co-localizations were observed with the Ppd-1, Vrn-1 and Rht-1 candidate genes. Using an independent set of lines to validate the model built for heading date, we were able to explain 34% of the variation using the structure and the significant markers. Results were compared with already published data using bi-parental populations giving an insight into the genetic architecture of flowering time in wheat.
While modern agriculture relies on genetic homogeneity, diversifying practices associated with seed exchange and seed recycling may allow crops to adapt to their environment. This socio‐genetic model ...is an original experimental evolution design referred to as on‐farm dynamic management of crop diversity. Investigating such model can help in understanding how evolutionary mechanisms shape crop diversity submitted to diverse agro‐environments. We studied a French farmer‐led initiative where a mixture of four wheat landraces called ‘Mélange de Touselles’ (MDT) was created and circulated within a farmers' network. The 15 sampled MDT subpopulations were simultaneously submitted to diverse environments (e.g. altitude, rainfall) and diverse farmers' practices (e.g. field size, sowing and harvesting date). Twenty‐one space‐time samples of 80 individuals each were genotyped using 17 microsatellite markers and characterized for their heading date in a ‘common‐garden’ experiment. Gene polymorphism was studied using four markers located in earliness genes. An original network‐based approach was developed to depict the particular and complex genetic structure of the landraces composing the mixture. Rapid differentiation among populations within the mixture was detected, larger at the phenotypic and gene levels than at the neutral genetic level, indicating potential divergent selection. We identified two interacting selection processes: variation in the mixture component frequencies, and evolution of within‐variety diversity, that shaped the standing variability available within the mixture. These results confirmed that diversifying practices and environments maintain genetic diversity and allow for crop evolution in the context of global change. Including concrete measurements of farmers' practices is critical to disentangle crop evolution processes.
Participatory plant breeding (PPB) is based on the decentralization of selection in farmers’ fields and their involvement in decision-making at all steps of the breeding scheme. Despite the evidence ...of its benefits to develop population varieties adapted to diversified and local practices and conditions, such as organic farming, PPB is still not widely used. There is a need to share more broadly how the different programs have overcome scientific, practical, and organizational issues and produced a large number of positive outcomes. Here, we report on a PPB program that started on bread wheat in France in 2006 and has achieved a range of outcomes, from the emergence of new organization among actors, to specific experimental designs and statistical methods developed, and to populations varieties developed and cultivated by farmers. We present the results of a two-year agronomic evaluation of the first population varieties developed within this PPB program compared to two commercial varieties currently grown in organic agriculture. We found that several PPB varieties were of great agronomic interest, combining relatively good performance even under the most favorable conditions of organic agriculture and good robustness, i.e., the ability to maintain productivity under more constraining conditions. The PPB varieties also tended to show a good temporal dynamic stability and appeared promising for the farmers involved.
Microsatellite markers are extensively used to evaluate genetic diversity in natural or experimental evolving populations. Their high degree of polymorphism reflects their high mutation rates. ...Estimates of the mutation rates are therefore necessary when characterizing diversity in populations. As a complement to the classical experimental designs, we propose to use experimental populations, where the initial state is entirely known and some intermediate states have been thoroughly surveyed, thus providing a short timescale estimation together with a large number of cumulated meioses. In this article, we derived four original gene genealogy-based methods to assess mutation rates with limited bias due to relevant model assumptions incorporating the initial state, the number of new alleles, and the genetic effective population size. We studied the evolution of genetic diversity at 21 microsatellite markers, after 15 generations in an experimental wheat population. Compared to the parents, 23 new alleles were found in generation 15 at 9 of the 21 loci studied. We provide evidence that they arose by mutation. Corresponding estimates of the mutation rates ranged from 0 to 4.97 x 10(-3) per generation (i.e., year). Sequences of several alleles revealed that length polymorphism was only due to variation in the core of the microsatellite. Among different microsatellite characteristics, both the motif repeat number and an independent estimation of the Nei diversity were correlated with the novel diversity. Despite a reduced genetic effective size, global diversity at microsatellite markers increased in this population, suggesting that microsatellite diversity should be used with caution as an indicator in biodiversity conservation issues.
Because organic systems present complex environmental stress, plant breeders may either target very focused regions for different varieties, or create heterogeneous populations which can then evolve ...specific adaptation through on-farm cultivation and selection. This often leads to participatory plant breeding (PPB) strategies which take advantage of the specific knowledge of farmers. Participatory selection requires increased commitment and engagement on the part of the farmers and researchers. Projects may begin as researcher initiatives with farmer participation or farmer initiatives with researcher participation and over time evolve into true collaborations. These projects are difficult to plan in advance because by nature they change to respond to the priorities and interests of the collaborators. Projects need to provide relevant information and analysis in a time-frame that is meaningful for farmers, while remaining scientifically rigorous and innovative. This paper presents two specific studies: the first was a researcher-designed experiment that assessed the potential adaptation of landraces to organic systems through on-farm cultivation and farmer selection. The second is a farmer-led plant breeding project to select bread wheat for organic systems in France. Over the course of these two projects, many discussions among farmers, researchers and farmers associations led to the development of methods that fit the objectives of those involved. This type of project is no longer researcher-led or farmer-led but instead an equal collaboration. Results from the two research projects and the strategy developed for an ongoing collaborative plant breeding project are discussed.
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