Since domestication and for thousands of years, crops have been grown as populations (i.e., landraces) and selected on-farm, therefore allowing among population (varietal) and within population (genetic) diversification. These two levels of diversity confer crop adaptability to contrasting environmental conditions and farmers’ practices [1
]. However, with the advancement of knowledge, especially in plant breeding and genetics (Mendelism, F1 hybrid development, pure line breeding, etc.), and modernization of agriculture from the middle of the nineteenth century in western countries, these genetically diverse landraces have been progressively replaced by genetically uniform modern varieties. This was particularly the case after the Second World War with the introduction of seed regulations such as distinctness, uniformity and stability (DUS) that a new variety had to meet to be registered and marketed [5
]. The breeding history of varieties is thus really informative.
The increased use of genetically uniform crops since the Green Revolution has significantly improved yields and helped to alleviate the problem of hunger in the world. However, these modern varieties are highly dependent on inputs. The widespread use of these products in a context of climate change, water restrictions, pesticide resistance and rising prices for petroleum-derived chemicals is beginning to raise real concerns for society. One typical example of the impact of diseases on modern varieties is the corn leaf blight epidemics in America in 1970, which caused a
reduction in the estimated production [6
]. Similar events have been described in other studies [7
]. In the case of oat, the impact of the disease was found to be 25% less for landraces than for modern varieties [10
]. The causal relationship between genetic diversity and disease tolerance has been demonstrated for rice in China [11
] showing a lower impact of plant disease for mixtures of varieties compared to single varieties. In some cases, higher robustness and stress tolerance have been observed due to genetic diversity and higher level of heterozygosity [12
]. Mobilizing among-variety genetic diversity through mixtures and within-variety genetic diversity by growing landraces or population varieties has become more important than ever before with global climate change and thus the increased risk of environmental variability in the near future [13
These changes in the environmental conditions have made the conservation and use of genetic diversity crucially important. The scientific community has raised awareness about genetic erosion since the pioneer works accomplished by Vavilov or Harlan from the first part of the twentieth century [15
]. Two types of conservation methods are generally employed for plant genetic resources: (i) Ex situ conservation and (ii) in situ conservation. Ex situ conservation is a static evolutionary strategy that involves the storage of samples (seeds, propagules and plants) outside their environment of origin such as in gene banks, botanical gardens, DNA banks, etc. [16
]. In situ conservation is an evolutionary dynamic strategy in which genetic diversity is maintained in habitats where such diversity arose and continues to grow, i.e., for crop plants, in areas where that particular species has been domesticated and is continuously selected by farmers [20
]. This in situ conservation is usually considered to be on-farm conservation (mainly landraces). This approach ensures the conservation of genetic diversity over time through the action of evolutionary forces (genetic drift, selection, mutation, migration) [1
]. The adaptive response that a population shows when encountering a changing environment largely depends on the level and the structure of genetic diversity within the population [24
Several studies were carried out in the recent past to understand the trends of crop genetic diversity in the last century. These studies generally neglected the within-variety (within-accession) diversity as they analysed very small sample sizes (1–5 individuals per landrace, accession or even species), and very often investigated either released varieties or ex situ conserved landraces [26
]. Consequently, few studies have compared the effects of ex situ and in situ conservation on crop population genetic diversity. Sun et al. found higher genetic diversity and more alleles in landraces conserved in situ compared to the landraces conserved ex situ in rice [29
]. Further, the evaluation of 600 landraces of rice conserved on-farm revealed that the genetic diversity was maintained even after 27 years strengthening the case of advantages of on-farm conservation [30
]. In contrast, a decrease in genetic diversity due to genetic drift during regeneration with limited sample sizes in ex situ conservation has been shown in bean [31
] and barley [32
]. While 88% of total natural diversity was found in ex situ conserved Vatica guangxiensis
], a better maintenance of genetic diversity of Parashorea chinensis
was observed in in situ conservation than in ex situ conservation [34
]. The effects of conservation of crop biodiversity by the two methods (in situ and ex situ) was studied in more detail by Negri and Tiranti [35
], who identified reduced population size as the main factor causing the reduction of genetic variation, followed by ex situ multiplication, which increased subpopulation differentiation due to different environmental conditions compared to the adaptation area. In a recent study, the comparison of genetic diversity of rice landraces conserved ex situ in 1980 as well as conserved on-farm until 2014 showed that the on-farm conservation system maintained more alleles and higher genetic diversity compared to ex situ conserved landraces indicating that on-farm conservation provides the opportunity of evolution along with conservation [36
]. Various other studies in crops species such as maize [1
], rice [37
], common bean [35
], barley [32
] and sorghum [38
], have confirmed that in situ conservation, especially on-farm conservation, was highly capable of maintaining and enriching the within-population genetic diversity and heterozygosity. In these studies, diversity was found within each population cultivated under the name of a given landrace variety and to a lesser extent among those populations. Such heterogeneity is compatible with good productivity and quality under low input conditions, probably due to better local adaptation and more buffering capacity under stress conditions, as shown for instance in the case of an Italian landrace of celery [39
Therefore, from a plant genetic resource management perspective, it is important to evaluate the effect of factors such as the mating system, the breeding history of the variety, the farmer’s practices and the conservation strategies on the extent of the genetic population structure of varieties. We propose to describe the role of three of them: The breeding history of the variety, the conservation strategy and the population composition. Three modalities are considered for the breeding history of the varieties: Landraces, historical and modern varieties. Landraces are varieties developed by farmers before the 1850s. historical varieties were developed between the 1850s and the 1960s. Modern varieties are those developed since the 1960s. The conservation strategy discriminates ex situ conservation and in situ conservation. The composition of the population distinguishes between single varieties and mixtures.
In this study, using a set of eight populations of bread wheat (Triticum aestivum
L., 2n = 6x = 42, AABBDD, self-pollinating species) with varying breeding histories and management practices (conservation and composition) provides an opportunity to understand the influence of all these three factors on population structure (Table 1
). In such a set of populations, different genetic structures are expected to arise depending upon their history and farmer practices in the area. Based on our knowledge and the literature, we hypothesized that there was a gradient of increasing genetic diversity from modern varieties to mixture of landraces. This hypothesis was used to examine the diversifying processes in action in farmers’ fields.
These eight populations (described in Table 1
) were characterized using 41 neutral molecular markers. Genetic diversity was analysed at three levels: The allelic, haplotypes and genetic group level to search for a possible gradient within these eight populations. Additionally, the fine population structure of the different varieties has been revealed using a discriminant analysis and a kinship network analysis. The consequences of conservation and management methods on these different population structures are discussed in light of the different history of each variety and the genetic structure depicted in this study.
3.1. Multi-Level Genetic Diversity and Population Structure of Samples
Heterogeneous levels of neutral genetic diversity were found among the eight samples corresponding to different variety types (modern variety, historical varieties, landraces and mixtures) and different management strategies (ex situ vs in situ conservation and mono-varietal vs mixtures). The following sections provide a description of each sample using a multi-level analysis of the genetic diversity: the unbiaised Nei’s diversity at the allelic (
), haplotype (
) and genetic group (
) levels (Table 2
3.1.1. Single Variety Conserved Ex Situ and Modern Variety
Genetic diversity analysis revealed similar characteristics for one of the two landraces, “Haute Loire” (HL), which is managed as a single variety and conserved ex situ, and the modern variety, Renan. The other landrace (Piave) showed a contrasted pattern. “Haute Loire” was the most homogeneous sample with a single genetic group (Figure 1
) denoted as “HL1”. Consistently HL had a very low genetic diversity at the genetic group level (
), but also at the allelic level (
) and haplotypic level (
). We noticed that the observed heterozygosity was also an order of magnitude lower in this sample than in the others (
for the others).
Similar to HL, all the individuals from the modern variety Renan (RN) were also characterized to have a unique genetic group named “RN1” (Figure 1
and Figure S2
). Moreover, the very low genetic diversity at all the three levels (
) indicated very low within-population genetic diversity.
Piave (PI) the second ex situ landrace clearly showed a different pattern of genetic diversity and ultimately different genetic structure compared to the two previous samples. PI showed higher genetic diversity values at the allelic level (
, haplotypic level
and genetic group level
) than the two other samples. PI was a composite variety with two specific groups denoted PI1 and PI2 (Figure 1
3.1.2. Single Variety Conserved In Situ (HV and LR)
The Rouge de Bordeaux (RB) variety showed a composite structure with three genetic groups (Figure 1
), i.e., two main specific groups (RB1 and RB2) and one shared group (CG1) with Redon. In addition, genetic diversity at allelic, haplotypic and genetic group levels were relatively high for RB (
, respectively, Table 2
) compared to the previously discussed varieties.
Solina d’Abruzzo (SO) also had a composite population structure with four specific genetic groups (SO1, SO2, SO3, SO4) and one shared group (CG2) with Touselles (Figure 1
) indicating highly complex population structure. Interestingly, the probability that some individuals of this landrace fall in one specific group was relatively weak, but they always fall in groups specific to this landrace or in the CG2 group. A high level of genetic diversity at the haplotypic and genetic group levels was observed for SO (
, respectively, Table 2
), but a relatively low allelic diversity (
) was observed compared to RB.
3.1.3. Mixtures In Situ Conserved (MIXMV and MIXLR)
Zonne Hoeve (ZH) was structured into two main fixed groups (ZH1 and ZH2) and one shared group (CG3) with Touselles. ZH2 represented almost
of the mixture, explaining the relatively low genetic group diversity
observed for a mixture. The allelic diversity and haplotypic diversity (
) were also intermediate (Table 2
The “Touselles” (TO) sample was composed of five main specific groups (TO1, TO2, TO3, TO4 and TO5) and two groups (CG2 and CG3) shared, respectively, with SO and ZH (Figure 1
), consistent with the expectation that this mixture would have a complex population structure based on its history. A high level of genetic diversity was observed for the different genetic indices:
indicating that the TO population was genetically diverse (Table 2
Similar to TO, Redon (RD) also presented a composite structure with four main specific groups (RD1, RD2, RD3 and RD4) and one group (CG1) shared with RB (Figure 1
). Genetic diversity indices were relatively high at the three levels:
confirming the diverse nature of this population (Table 2
3.1.4. Relationship among Genetic Indices
The correlations between
was significant and positive (Figure 2
). The correlations between
was also significant and posotive (Figure 2
However, some samples like RB, ZH and SO were relatively far from the regression line (Figure 2
). For RB, an excess of allelic diversity, deficit of haplotypic diversity, and excess of genetic group diversity was observed compared to the other samples. ZH showed an excess of haplotype diversity and a deficit of allelic diversity and genetic group diversity compared to the other samples. SO showed an excess of haplotypic and genotype group diversity and a deficit of allelic diversity compared to the other samples.
3.2. Deciphering the Varietal Relatedness
Dendrogram confidently separated the eight populations into three clusters (bootstrap support of
, Figure 3
). The first one is composed of ZH and PI which are themselves relatively different (
, bootstrap support equal to
). The second cluster grouped RD and RB, two closed varieties (
) which are distinguished with intermediate confidence (bootstrap support equal to
). The third group is composed of TO, SO, RN and HL in which varieties cannot be clearly distinguished (bootstrap support
) even if their genetic distances ranged from 0.14 to 0.53. RN is the most distant population compared to the other populations, then it is ZH and PI. RN and PI are the two far populations (
provided additional information (Table S1
). Very strong differentiation was observed between the two varieties which are almost fixed: HL and RN, with a pairwise-
close to 1. Strong genetic differentiation was observed for pairs involving one of these two varieties with pairwise-
ranging from 0.74 to 0.92. Intermediate pairwise-
values ranging from 0.73 to 0.64, were observed when populations with a limited amount of genetic diversity such as PI, SO and ZH were involved. The lowest differentiation values were observed when one or both populations were genetically diverse with a pairwise-
ranging from 0.25 to 0.63.
The kinship network analysis performed on 245 haplotypes after filtering (KNA, Figure 4
) revealed that: (1) Genetic groups from the same variety were not always strongly related, and (2) genetic groups from two different varieties could be related.
and , the two main haplotypes from the modern variety RN were only related to each other. The main haplotype from PI2 genetic group, , was related to few haplotypes belonging to the same genetic group and not connected to the other haplotypes, indicating that this component of Piave variety was genetically very different from the rest. , the main haplotype of the PI1 genetic group was connected to haplotypes belonging to several TO genetic groups, revealing that the PI1 genetic group appeared to be more related to TO rather than to its second genetic group PI2. was the main haplotype of the HL variety. It showed some relatedness with different haplotypes from several TO genetic groups and with only one SO haplotype (), respectively.
The KNA analysis confirmed the composite characteristic of the mono-varietal in situ conserved FV, (RB and SO). was the main haplotype of RB which was present in the genetic group RB1 and was connected to the other haplotypes present in this genetic group. haplotype, the main haplotype of genetic group RB2, was not connected to other haplotypes, showing a clearly distinct genetic make-up compared to other haplotypes from RB, as well as other samples. belonging to the CG1 genetic group was the same haplotype detected in RB and RD. This haplotype seemed very distinct from the other genetic groups. The landrace variety SO showed the most diverse population structure compared to other samples investigated in this experiment. Many haplotypes with mostly very low haplotypic frequencies were observed. Interestingly, most of these haplotypes were connected together, revealing a very strong relatedness among them. was the main and the most central haplotype within SO.
As expected, mixtures showed a high haplotypic diversity. For ZH, , the main haplotype of genetic group ZH1 was not connected to the other haplotypes of its genetic group, appearing to be weakly related to the rest of ZH as well as of other FV. , the main haplotype of ZH2 was connected with haplotypes belonging the ZH1 genetic group. is the main ZH haplotypes assigned to the CG3 genetic group. The other ones were more related to ZH1 and ZH2.
Among different genetic groups of the RD mixture, the main haplotypes assigned to RD1 and RD2 like , , or were strongly related as the make a cluster. They were weakly connected with SO haplotypes. By contrast, the main haplotypes from the genetic group RD3 and RD4 like or showed a strong genetic relatedness with haplotypes of SO. The KNA applied to the TO mixture revealed that TO1 was very distinct from rest of the genetic groups as , the main haplotype of this genetic group, was not connected to any other haplotype except . The genetic groups TO3 and TO4 were composed by only one haplotype (respectively, and ). These two haplotypes were related to each other, but were not connected to the rest. The different haplotypes belonging to genetic group TO2 were connected to each other, as well as to the (the main haplotype of PI1 genetic group as described above). In addition, they were also connected with some other haplotypes belonging to TO5 genetic group indicating that TO2 was genetically more related to TO5 as compared to other genetic groups of TO.
In this paper, we considered different crop varieties and mixtures of bread wheat ex situ conserved or continuously grown in situ on-farm. Our results revealed an increase in the complexity of genetic structure as we move on the gradient of variety types (from modern single variety to in situ on-farm mixtures of landraces). We have shown that two on-farm management practices increased genetic diversity: Mixtures of varieties and in situ on-farm management of landraces. When these management practices are combined, they substantially increase the different levels of genetic diversity of the populations (allelic, haplotypic, genetic groups diversity), and consequently improve their adaptability.
Indeed, genetic analyses of the mixtures revealed that, despite a very high selfing rate in wheat, growing in evolutionary mixtures promotes recombination between different genetic components of the mixture, a second way to increase the level of haplotype diversity. More surprisingly, an excess of haplotype diversity compared to the level of allelic diversity was observed for Solina d’Abruzzo (SO) in Italy, one of the landraces continuously cultivated in situ on-farm. Different evolutionary mechanisms have already been proposed to describe distribution of genetic diversity in self-pollinated species, but none of them is sufficient to explain the distribution observed in SO. The most likely scenario to explain such an organization of genetic diversity is a very large effective size through collective management by local farmers that combines seed circulation with mixing and selection of their seeds in addition to natural selection. These practices promote recombination between different genotypes and the fixation of neutral and adaptive mutations. In-depth investigation by simulation and experimentation is needed to decipher precisely the evolutionary mechanisms in action which allowed such features to emerge.
All these findings confirm the need to develop and manage evolving diversified large populations on-farm. In an era of global climate shift, where modern varieties have shown low adaptive potential to changing environmental conditions, especially in organic and low input areas, the use of highly diverse landraces and historical varieties in mixtures could solve the problem to a certain extent because on-farm diversified populations have a higher potential to adapt to their local environment than uniform varieties. Such diversifying practices need to be generalized, in particular when promoting agroecological and sustainable agriculture. The new EU seed legislation on heterogeneous material in 2018 is opening new opportunities in this direction. However, the evolutionary characteristics of these populations are still poorly understood by researchers and need to be better considered in the future.
Our conclusions invite crop diversity managers such as genebank curators, community seed bank managers and farmers’ organizations to adapt their management strategies to the type of variety they wish to manage, because we have shown that their choices have a strong influence on the genetic composition of the crop populations.