Stéphanie Mariette

Comparison of microsatellites and amplified fragment length polymorphism markers for parentage analysis

This study compares the properties of dominant markers, such as amplified fragment length polymorphisms (AFLPs), with those of codominant multiallelic markers, such as microsatellites, in reconstructing parentage. These two types of markers were used to search for both parents of an individual without prior knowledge of their relationships, by calculating likelihood ratios based on genotypic data, including mistyping. Experimental data on 89 oak trees genotyped for six microsatellite markers and 159 polymorphic AFLP loci were used as a starting point for simulations and tests. Both sets of markers produced high exclusion probabilities, and among dominant markers those with dominant allele frequencies in the range 0.1–0.4 were more informative. Such codominant and dominant markers can be used to construct powerful statistical tests to decide whether a genotyped individual (or two individuals) can be considered as the true parent (or parent pair). Gene flow from outside the study stand (GFO), inferred from parentage analysis with microsatellites, overestimated the true GFO, whereas with AFLPs it was underestimated. As expected, dominant markers are less efficient than codominant markers for achieving this, but can still be used with good confidence, especially when loci are deliberately selected according to their allele frequencies.

Sampling within the genome for measuring within‐population diversity: trade‐offs between markers

Experimental results of diversity estimates in a set of populations often exhibit contradictory patterns when different marker systems are used. Using simulations we identified potential causes for these discrepancies. These investigations aimed also to detect whether different sampling strategies of markers within the genome resulted in different estimates of the diversity at the whole genome level. The simulations consisted in generating a set of populations undergoing various evolutionary scenarios which differed by population size, migration rate and heterogeneity of gene flow. Population diversity was then computed for the whole genome and for subsets of loci corresponding to different marker techniques. Rank correlation between the two measures of diversity were investigated under different scenarios. We showed that the heterogeneity of genetic diversity either between loci (genomic heterogeneity, GH) or among populations (population heterogeneity, PH) varied greatly according to the evolutionary scenario considered. Furthermore, GH and PH were major determinants of the level of rank correlation between estimates of genetic diversities obtained using different kinds of markers. We found a strong positive relationship between the level of the correlation and PH, whatever the marker system. It was also shown that, when GH values were constantly low during generations, a reduced number of microsatellites was enough to predict the diversity of the whole genome, whereas when GH increased, more loci were needed to predict the diversity and amplified fragment length polymorphism markers would be more recommended in this case. Finally the results are discussed to recommend strategies for gene diversity surveys.

Genetic diversity within and among Pinus pinaster populations: comparison between AFLP and microsatellite markers.

Twenty-three populations of Pinus pinaster (13 Aquitaine populations and 10 Corsican populations) were analysed at three microsatellite loci and 122 AFLP loci. The aims of the study were: (i) to compare levels of within-population and among-population diversity assessed with both kinds of markers; (ii) to compare Aquitaine and Corsican provenances of P. pinaster; and (iii) to know if both markers gave the same information for conservation purposes. Classical population genetics statistics were estimated and the ranking of populations obtained using different markers and/or parameters were compared by computing Spearman’s rank correlations. Even though microsatellites showed a higher within-population diversity, they showed the same level of differentiation as AFLP markers. Moreover, both markers also showed a higher genetic diversity in the Aquitaine provenance and a higher differentiation among Corsican populations. AFLPs and microsatellites gave different population diversity rankings. Consequently, the results do not support the potential population identification within each provenance for conservation purposes.

Population structure and genetic bottleneck in sweet cherry estimated with SSRs and the gametophytic self-incompatibility locus

BackgroundDomestication and breeding involve the selection of particular phenotypes, limiting the genomic diversity of the population and creating a bottleneck. These effects can be precisely estimated when the location of domestication is established. Few analyses have focused on understanding the genetic consequences of domestication and breeding in fruit trees. In this study, we aimed to analyse genetic structure and changes in the diversity in sweet cherry Prunus avium L.ResultsThree subgroups were detected in sweet cherry, with one group of landraces genetically very close to the analysed wild cherry population. A limited number of SSR markers displayed deviations from the frequencies expected under neutrality. After the removal of these markers from the analysis, a very limited bottleneck was detected between wild cherries and sweet cherry landraces, with a much more pronounced bottleneck between sweet cherry landraces and modern sweet cherry varieties. The loss of diversity between wild cherries and sweet cherry landraces at the S-locus was more significant than that for microsatellites. Particularly high levels of differentiation were observed for some S-alleles.ConclusionsSeveral domestication events may have happened in sweet cherry or/and intense gene flow from local wild cherry was probably maintained along the evolutionary history of the species. A marked bottleneck due to breeding was detected, with all markers, in the modern sweet cherry gene pool. The microsatellites did not detect the bottleneck due to domestication in the analysed sample. The vegetative propagation specific to some fruit trees may account for the differences in diversity observed at the S-locus. Our study provides insights into domestication events of cherry, however, requires confirmation on a larger sampling scheme for both sweet cherry landraces and wild cherry.

Comparison of genetic diversity estimates within and among populations of maritime pine using chloroplast simple-sequence repeat and amplified fragment length polymorphism data

We compared the genetic variation of Pinus pinaster populations using amplified fragment length polymorphism (AFLP) and chloroplast simple‐sequence repeat (cpSSR) loci. Populations’ levels of diversity within groups were found to be similar with AFLPs, but not with cpSSRs. The high interlocus variance associated with the AFLP loci could account for the lack of differences in the former. Although AFLPs revealed much lower genetic diversity than cpSSRs, the levels of among‐population differentiation found with the two types of marker were similar, provided that loci showing fewer than four null‐homozygotes, in any population, were pruned from the AFLP data. Moreover, the French and Portuguese populations were clearly differentiated from each other, with both markers. The Mantel test showed that the genetic distance matrix calculated using the AFLP data was correlated with the matrix derived from the cpSSRs. Because of the concordance found between markers we conclude that gene flow was indeed the predominant force shaping nuclear and chloroplastic genetic variation of the populations within regions, at the geographical scale studied.

Geographical diversity and genetic relationships among Cedrus species estimated by AFLP

Genetic diversity was described in 17 cedar populations covering the geographical range of the four species of the genus Cedrus. The study was conducted using amplified fragment length polymorphism (AFLP) on haploid tissues (megagametophytes). Eleven selective AFLP primer pairs generated a total of 107 polymorphic amplification products. Correspondence and genetic distance analyses indicated that Cedrus deodara constitutes a separate gene pool from the Mediterranean cedars. Within Mediterranean cedars, we distinguished two groups: the first one is made of Cedrus atlantica, while the second one is made of Cedrus libani and Cedrus brevifolia, these latter two species being genetically similar despite important divergence previously observed for morphological and physiological traits. The lowest intrapopulation variability was found in the two C. deodara populations analyzed. Surprisingly, C. brevifolia, the endemic taxon from the island of Cyprus that is found in small and fragmented populations, showed one of the highest levels of diversity. This unexpected pattern of diversity and differentiation observed for C. brevifolia suggests a recent divergence rather than a relictual, declining population. Patterns of diversity within- and among-populations were used to test divergence and fragmentation hypotheses and to draw conclusions for the conservation of Cedrus gene pools.

Family‐based linkage and association mapping reveals novel genes affecting Plum pox virus infection in Arabidopsis thaliana

Sharka is a devastating viral disease caused by the Plum pox virus (PPV) in stone fruit trees and few sources of resistance are known in its natural hosts. Since any knowledge gained from Arabidopsis on plant virus susceptibility factors is likely to be transferable to crop species, Arabidopsiss natural variation was searched for host factors essential for PPV infection. To locate regions of the genome associated with susceptibility to PPV, linkage analysis was performed on six biparental populations as well as on multiparental lines. To refine quantitative trait locus (QTL) mapping, a genome-wide association analysis was carried out using 147 Arabidopsis accessions. Evidence was found for linkage on chromosomes 1, 3 and 5 with restriction of PPV long-distance movement. The most relevant signals occurred within a region at the bottom of chromosome 3, which comprises seven RTM3-like TRAF domain-containing genes. Since the resistance mechanism analyzed here is recessive and the rtm3 knockout mutant is susceptible to PPV infection, it suggests that other gene(s) present in the small identified region encompassing RTM3 are necessary for PPV long-distance movement. In consequence, we report here the occurrence of host factor(s) that are indispensable for virus long-distance movement.

Genome‐wide association links candidate genes to resistance to Plum Pox Virus in apricot (Prunus armeniaca)

In fruit tree species, many important traits have been characterized genetically by using single-family descent mapping in progenies segregating for the traits. However, most mapped loci have not been sufficiently resolved to the individual genes due to insufficient progeny sizes for high resolution mapping and the previous lack of whole-genome sequence resources of the study species. To address this problem for Plum Pox Virus (PPV) candidate resistance gene identification in Prunus species, we implemented a genome-wide association (GWA) approach in apricot. This study exploited the broad genetic diversity of the apricot (Prunus armeniaca) germplasm containing resistance to PPV, next-generation sequence-based genotyping, and the high-quality peach (Prunus persica) genome reference sequence for single nucleotide polymorphism (SNP) identification. The results of this GWA study validated previously reported PPV resistance quantitative trait loci (QTL) intervals, highlighted other potential resistance loci, and resolved each to a limited set of candidate genes for further study. This work substantiates the association genetics approach for resolution of QTL to candidate genes in apricot and suggests that this approach could simplify identification of other candidate genes for other marked trait intervals in this germplasm.

Linkage disequilibrium in French wild cherry germplasm and worldwide sweet cherry germplasm

A basic knowledge on linkage disequilibrium (LD) is necessary in order to determine resolution of association studies. We investigated the extent and patterns of LD in a self-incompatible species (Prunus avium L.), in 3 groups (wild cherry, sweet cherry landraces and sweet cherry modern varieties), using a set of 35 microsatellite markers and the gametophytic self-incompatibility locus. Since population structure might create spurious LD, we thus used the information provided by a structure analysis published in a previous study to perform the LD analysis. In the current study, we detected a greater LD extent in sweet cherry than in wild cherry, which is plausibly due to the bottleneck associated with domestication and breeding. Higher LD values in sweet cherry sub-groups may be explained by smaller sample sizes. We also showed that the remaining structure in the groups of sweet cherry, in particular landraces, is responsible for a part of the LD extent. Intra-group relatedness may also account for extensive LD in two sub-groups. These results demonstrate, if ever necessary, the importance of controlling the genetic structure and relatedness when estimating LD. Moreover, LD decays very rapidly with genetic linkage distance in both wild and sweet cherries, which seems promising for future association studies.

Genetic diversity and fitness in small populations of partially asexual, self-incompatible plants.

How self-incompatibility systems are maintained in plant populations is still a debated issue. Theoretical models predict that self-incompatibility systems break down according to the intensity of inbreeding depression and number of S-alleles. Other studies have explored the function of asexual reproduction in the maintenance of self-incompatibility. However, the population genetics of partially asexual, self-incompatible populations are poorly understood and previous studies have failed to consider all possible effects of asexual reproduction or could only speculate on those effects. In this study, we investigated how partial asexuality may affect genetic diversity at the S-locus and fitness in small self-incompatible populations. A genetic model including an S-locus and a viability locus was developed to perform forward simulations of the evolution of populations of various sizes. Drift combined with partial asexuality produced a decrease in the number of alleles at the S-locus. In addition, an excess of heterozygotes was present in the population, causing an increase in mutation load. This heterozygote excess was enhanced by the self-incompatibility system in small populations. In addition, in highly asexual populations, individuals produced asexually had some fitness advantages over individuals produced sexually, because sexual reproduction produces homozygotes of the deleterious allele, contrary to asexual reproduction. Our results suggest that future research on the function of asexuality for the maintenance of self-incompatibility will need to (1) account for whole-genome fitness (mutation load generated by asexuality, self-incompatibility and drift) and (2) acknowledge that the maintenance of self-incompatibility may not be independent of the maintenance of sex itself.