Main Gene Pools Research Articles

Population genetics of Mediterranean and Saharan olives: geographic patterns of differentiation and evidence for early generations of admixture

The olive (Olea europaea subsp. europaea) was domesticated in the Mediterranean area but its wild relatives are distributed over three continents, from the Mediterranean basin to South Africa and south-western Asia. Recent studies suggested that this crop originated in the Levant while a secondary diversification occurred in most westward areas. A possible contribution of the Saharan subspecies (subsp. laperrinei) has been highlighted, but the data available were too limited to draw definite conclusions. Here, patterns of genetic differentiation in the Mediterranean and Saharan olives are analysed to test for recent admixture between these taxa. Nuclear microsatellite and plastid DNA (ptDNA) data were compiled from previous studies and completed for a sample of 470 cultivars, 390 wild Mediterranean trees and 270 Saharan olives. A network was reconstructed for the ptDNA haplotypes, while a Bayesian clustering method was applied to identify the main gene pools in the data set and then simulate and test for early generations of admixture between Mediterranean and Saharan olives. Four lineages of ptDNA haplotypes are recognized: three from the Mediterranean basin and one from the Sahara. Only one haplotype, primarily distributed in the Sahara, is shared between laperrinei and europaea. This haplotype is detected once in 'Dhokar', a cultivar from the Maghreb. Nuclear microsatellites show geographic patterns of genetic differentiation in the Mediterranean olive that reflect the primary origins of cultivars in the Levant, and indicate a high genetic differentiation between europaea and laperrinei. No first-generation hybrid between europaea and laperrinei is detected, but recent, reciprocal admixture between Mediterranean and Saharan subspecies is found in a few accessions, including 'Dhokar'. This study reports for the first time admixture between Mediterranean and Saharan olives. Although its contribution remains limited, Laperrine's olive has been involved in the diversification of cultivated olives.

Loss of genetic diversity as a signature of apricot domestication and diffusion into the Mediterranean Basin.

BackgroundDomestication generally implies a loss of diversity in crop species relative to their wild ancestors because of genetic drift through bottleneck effects. Compared to native Mediterranean fruit species like olive and grape, the loss of genetic diversity is expected to be more substantial for fruit species introduced into Mediterranean areas such as apricot (Prunus armeniaca L.), which was probably primarily domesticated in China. By comparing genetic diversity among regional apricot gene pools in several Mediterranean areas, we investigated the loss of genetic diversity associated with apricot selection and diffusion into the Mediterranean Basin.ResultsAccording to the geographic origin of apricots and using Bayesian clustering of genotypes, Mediterranean apricot (207 genotypes) was structured into three main gene pools: ‘Irano-Caucasian’, ‘North Mediterranean Basin’ and ‘South Mediterranean Basin’. Among the 25 microsatellite markers used, only one displayed deviations from the frequencies expected under neutrality. Similar genetic diversity parameters were obtained within each of the three main clusters using both all SSR loci and only 24 SSR loci based on the assumption of neutrality. A significant loss of genetic diversity, as assessed by the allelic richness and private allelic richness, was revealed from the ‘Irano-Caucasian’ gene pool, considered as a secondary centre of diversification, to the northern and southwestern Mediterranean Basin. A substantial proportion of shared alleles was specifically detected when comparing gene pools from the ‘North Mediterranean Basin’ and ‘South Mediterranean Basin’ to the secondary centre of diversification.ConclusionsA marked domestication bottleneck was detected with microsatellite markers in the Mediterranean apricot material, depicting a global image of two diffusion routes from the ‘Irano-Caucasian’ gene pool: North Mediterranean and Southwest Mediterranean. This study generated genetic insight that will be useful for management of Mediterranean apricot germplasm as well as genetic selection programs related to adaptive traits.

Climate oscillations and species interactions: large‐scale congruence but regional differences in the phylogeographic structures of an alpine plant and its monophagous insect

AbstractAim To predict the fate of alpine interactions involving specialized species, using a monophagous beetle and its host plant as a case study.Location The Alps.Methods We investigated genetic structuring of the herbivorous beetle Oreina gloriosa and its specific host‐plant Peucedanum ostruthium. We used genome fingerprinting (in the insect and the plant) and sequence data (in the insect) to compare the distribution of the main gene pools in the two associated species and to estimate divergence time in the insect, a proxy for the temporal origin of the interaction. We quantified the similarity in spatial genetic structures by performing a Procrustes analysis, a tool from shape theory. Finally, we simulated recolonization of an empty space analogous to the deglaciated Alps just after ice retreat by two lineages from two species showing unbalanced dependence, to examine how timing of the recolonization process, as well as dispersal capacities of associated species, could explain the observed pattern.Results Contrasting with expectations based on their asymmetrical dependence, patterns in the beetle and plant were congruent at a large scale. Exceptions occurred at a regional scale in areas of admixture, matching known suture zones in Alpine plants. Simulations using a lattice‐based model suggested these empirical patterns arose during or soon after recolonization, long after the estimated origin of the interaction c. 0.5 million years ago.Main conclusions Species‐specific interactions are scarce in alpine habitats because glacial cycles have limited the opportunities for co‐evolution. Their fate, however, remains uncertain under climate change. Here we show that whereas most dispersal routes are paralleled at a large scale, regional incongruence implies that the destinies of the species might differ under changing climate. This may be a consequence of the host dependence of the beetle, which locally limits the establishment of dispersing insects.

Genetic diversity of maize landraces from lowland and highland agro‐ecosystems of Southern South America: implications for the conservation of native resources

AbstractThe North of Argentina is one of the southernmost areas of maize landrace cultivation. Two distinct centres of diversity have been distinguished within this region: Northwestern Argentina (NWA), and Northeastern Argentina (NEA). Nowadays, maize landraces from this area are faced with two main risks. On the one hand, significant structural and functional changes have modified the rural environment with the boundaries of cropland areas experiencing a rapid expansion at the expense of northern natural forests and rangelands; and on the other, native gene pools are increasingly threatened by hybrids and commercial varieties which are more attractive relative to landraces. The first step towards any conservational action is the acquisition of an inclusive knowledge of the biological resources. For this purpose, our study assesses the genetic diversity and population dynamics of maize landraces from Northern Argentina using microsatellite markers. The Northeastern lowland region (NEA) was represented by 12 landraces (19 populations). In addition, six landraces (eight populations) from the Northwestern highland region (NWA) were used for comparison. For the NEA data set, a total of 126 alleles were found, with an average of 10.5 alleles per locus. Mean Ho, He and Rs were 0.350, 0.467 and 2.72, respectively. Global fit to Hardy–Weinberg proportions was observed in 7 of 19 populations. Global estimates of FST revealed significant differentiation among populations. Bayesian analyses of population structure allowed the recognition of two main gene pools (popcorns versus floury landraces). When NWA was added to the analysis, three clusters were distinguished: NEA popcorns, NEA flours and NWA racial complexes. Additional information on the relationships among these groups was retrieved from cluster analyses. This study shows that lowland landraces from Northern Argentina harbour considerable levels of genetic diversity, with contributions from different gene pools. Further studies encompassing a larger number of populations from the NEA region will certainly help to detect additional genetic variation, which may prove highly valuable in germplasm conservation and management. Future conservation efforts should focus on preserving NEA popcorns, NEA floury and NWA racial complexes as different management units.

Genetic structure and core collection of the World Olive Germplasm Bank of Marrakech: towards the optimised management and use of Mediterranean olive genetic resources

The conservation of cultivated plants in ex-situ collections is essential for the optimal management and use of their genetic resources. For the olive tree, two world germplasm banks (OWGB) are presently established, in Córdoba (Spain) and Marrakech (Morocco). This latter was recently founded and includes 561 accessions from 14 Mediterranean countries. Using 12 nuclear microsatellites (SSRs) and three chloroplast DNA markers, this collection was characterised to examine the structure of the genetic diversity and propose a set of olive accessions encompassing the whole Mediterranean allelic diversity range. We identified 505 SSR profiles based on a total of 210 alleles. Based on these markers, the genetic diversity was similar to that of cultivars and wild olives which were previously characterised in another study indicating that OWGB Marrakech is representative of Mediterranean olive germplasm. Using a model-based Bayesian clustering method and principal components analysis, this OWGB was structured into three main gene pools corresponding to eastern, central and western parts of the Mediterranean Basin. We proposed 10 cores of 67 accessions capturing all detected alleles and 10 cores of 58 accessions capturing the 186 alleles observed more than once. In each of the 10 cores, a set of 40 accessions was identical, whereas the remaining accessions were different, indicating the need to include complementary criteria such as phenotypic adaptive and agronomic traits. Our study generated a molecular database for the entire OWGB Marrakech that may be used to optimise a strategy for the management of olive genetic resources and their use for subsequent genetic and genomic olive breeding.Electronic supplementary materialThe online version of this article (doi:10.1007/s10709-011-9608-7) contains supplementary material, which is available to authorized users.

Phylogeography of einkorn landraces in the Mediterranean basin and Central Europe: population structure and cultivation history

Einkorn (Triticum monococcum L.) was one of the first cereals to be domesticated in the Old World ca. 10,000 years ago and to spread towards Europe and North Africa. Its cultivation declined before the Iron Age and it remains today only as a relic crop in remote areas. To investigate if the geographic distribution of genetic diversity in modern einkorn landrace accessions could be informative about the movement of this crop during prehistory, we genotyped 50 accessions of einkorn from Europe, North Africa and the Near East. Using nuclear and chloroplast microsatellites and clustering methods, we detected two main gene pools in einkorn. The distribution of these lineages revealed differences between accessions from Morocco and the Iberian Peninsula from the rest of Europe and the Near East and suggests different regional dynamics in the spread of this crop.

Grafting versus seed propagated apricot populations: two main gene pools in Tunisia evidenced by SSR markers and model-based Bayesian clustering.

Apricot was introduced into the Mediterranean Basin from China and Asian mountains through the Middle-East and the Central Europe. Traditionally present in Tunisia, we were interested in accessing the origin of apricot species in the country, and in particular in the number and the location of its introductions. A set of 82 representative apricot accessions including 49 grafted cultivars and 33 seed propagated ‘Bargougs’ were genotyped using 24 microsatellite loci revealing a total of 135 alleles. The model-based Bayesian clustering analysis using both Structure and InStruct programs as well as the multivariate method revealed five distinct genetic clusters. The genetic differentiation among clusters showed that cluster 1, with only four cultivars, was the most differentiated from the four remaining genetic clusters, which constituted the largest part of the studied germplasm. According to their geographic origin, the five identified groups (north, centre, south, Gafsa oasis and other oases groups) enclosed a similar variation within group, with a low level of differentiation. Overall results highlighted the distinction of two apricot gene pools in Tunisia related to the different mode of propagation of the cultivars: grafted and seed propagated apricot, which enclosed a narrow genetic basis. Our findings support the assumption that grafting and seed propagated apricots shared the same origin.

Microsatellite Marker Characterization of Chilean Common Bean (Phaseolus vulgaris L.) Germplasm

ABSTRACTThe Chilean national common bean germplasm collection consists of 1200 accessions, most of which have not been characterized or used in breeding programs. As part of the characterization of this germplasm we have formed a core collection of 246 accessions that represent 21% of the whole collection and that consists of many race Chile representatives as well as varieties from other races that are traditionally grown in the country. The specific objectives of this work were to use microsatellites to evaluate the level of polymorphism in the Chilean core collection and to determine the genetic variability of race Chile and its relationships with other races. The results indicate that the level of polymorphism detected with microsatellites was higher than that obtained with previous molecular or biochemical markers. The number of microsatellite alleles varied from 2 to 14 and the polymorphism information content (PIC) values were 0.08 to 0.84. Heterozygosity ranged from 0 to 0.052 for each of the markers. Euclidean genetic distance ranged from 0.12% between race Chile and race Nueva Granada to 0.71% between race Chile and race Mesoamerica. Multiple correspondence analysis (MCA) showed clustering of the accessions into the two main genepools, with race Chile genotypes grouping mainly with race Nueva Granada genotypes.

Population Genetic Structure of Laurus nobilis L. Inferred From Transferred Nuclear Microsatellites

Abstract Species with fragmented populations and low population size often display low within-population genetic diversity and strong among-population differentiation. Laurus nobilis L. (Lauraceae), common laurel, has a scattered distribution throughout the Mediterranean, with only few autochthonous populations. Our goal was to elucidate if this species has range-wide genetic structure and if planted material can be traced back to its origin. Genetic diversity was investigated using 4 polymorphic nuclear microsatellites (nSSR) transferred from two species of Lauraceae. Sixty-six laurel trees were selected from 7 widely separated populations within the Mediterranean distribution area of the species. A total of 34 alleles (9 alleles per locus on average) were found. Mean genetic diversity within-population (Hs), was 0.558. Genetic differentiation among populations (GST = 0.243) was high compared to that of other angiosperms. Laurus nobilis can be separated into two main gene pools, one from western (Tunisia, Algeria and France) and the other from eastern Mediterranean (Turkey). The Algerian, Tunisian and French populations presented a strong genetic similarity, compatible with the fact that North African laurel populations could be recently introduced from north-western Mediterranean stock.

Microsatellite variation in maize landraces from Northwestern Argentina: genetic diversity, population structure and racial affiliations

The highland region or Northwestern Argentina (NWA) is one of the southernmost areas of native maize cultivation and constitutes an expansion of the peruvian Andes sphere of influence. To examine the genetic diversity and racial affiliations of the landraces cultivated in this area, 18 microsatellite markers were used to characterize 147 individuals from 6 maize races representative of traditional materials. For the whole data set, a total of 184 alleles were found, with an average of 10.2 alleles per locus. The average gene diversity was 0.571. The observed patterns of genetic differentiation suggest that historical association is probably the main factor in shaping population structure for the landraces studied here. In agreement with morphological and cytogenetic data, Bayesian analysis of NWA landraces revealed the occurrence of three main gene pools. Assessment of racial affiliations using a combined dataset including previous data on American landraces showed a clear relationship between one of these gene pools and typical Andean races, whereas the remaining two gene pools exhibited a closer association to Caribbean accessions and native germplasm from the United States, respectively. These results highlight the importance of integrating regional genetic studies if a deeper understanding of maize diversification and dispersal is to be achieved.

Molecular markers for the assessment of chicken biodiversity

Three main aspects of chicken biodiversity are dealt within this report: (a) cluster analysis based on autosomal microsatellites, (b) microsatellites on the sex chromosomes, and (c) SNP-based biodiversity.(a) Cluster analysis of autosomal microsatellites: We used 29 microsatellites to genotype 2000 chickens randomly selected from 65 different populations representing various chicken types and various geographical regions. The computer program Structure placed the 65 populations into clusters that are in agreement with their geographic origin and breed history. Only at two predefined clusters, there is little admixture between non-commercial populations originating from Asia and those from Europe. In contrast, commercial broilers and brown egg layers appeared as admixed populations of these two main gene pools. Increasing the number of clusters resulted in generation of specific clusters of commercial lines, having very low admixture with other clusters. In addition, we identified seven mixed populations, each of which shared portions of their genome with several other genetic clusters.(b) Microsatellites on the sex chromosomes: We predicted 173 potential microsatellites on chromosome W by in-silico analysis of the chicken genome assembly (version WASHUC1). Twenty five microsatellites of the highest sequence quality were tested in the lab for gender specificity. Unexpectedly, PCR products were generated in both sexes. Moreover, 14 selected microsatellites were mapped (using the East Lansing reference panel) and in all cases, the “W specific” microsatellites were mapped to chromosome Z and except for one locus, to the same ∼6 cM region. We conclude that the draft assembly for chromosome W is quite inaccurate.(c) SNP-based biodiversity: Ten distinct chicken breeds were genotyped at 145 single nucleotide polymorphisms (SNPs) located at 14 random DNA fragments and twenty five, each from different and unlinked genes. Microsatellite genotypes of the same ten breeds were used for comparison. Applying bootstrap values as the criterion for tree's reliability, we found that: (1) increasing the number of SNPs had a higher impact on the reliability of the analysis than increasing the number of individuals per population, and (2) the bootstrap values of phylogenetic un-rooted trees based on microsatellites were relatively low.

Population Genetics, Lethal Yellowing Disease, and Relationships among Mexican and Imported Coconut Ecotypes

Lethal Yellowing (LY) is one the main diseases affecting coconut worldwide, making the research for resistant germplasm vital to production. Study objectives were to: (i) estimate diversity and genetic structure within four commercial Mexican ecotypes and five imported ecotypes; (ii) analyze the genetic relationships between Mexican ecotypes and the main coconut gene pools identified worldwide; and (iii) measure the correlation between the genetic distance among these ecotypes and Malayan Yellow Dwarf and their percentage mortality due to LY. The Mexican pool had high genetic diversity (pl = 94; HT = 0.34 ± 0.02) similar to that of the populations imported from the world's main gene pools (pl = 94; HT = 0.36 ± 0.01). Both molecular variance and Wright's index of differentiation indicated strong differentiation among Mexican ecotypes (FST = 0.32) despite significant gene flow (Nm = 1.4 to 5.6). UPGMA analysis and exact tests of differentiation suggested that the Indo‐African gene pool is found along the Caribbean and Gulf of Mexico coasts, while the Asian‐Pacific pool is found on the Pacific coast. High positive correlations were found between genetic distance and LY mortality percentages under severe incidence conditions during 9‐ and 14‐yr periods (r2 = 0.80; P = 0.02; r2 = 0.78; P = 0.04), suggesting that genetic distance may be useful for the estimation of the potential LY mortality in regions as yet unaffected and identification of potential parents for LY resistance breeding.

Chloroplast microsatellite analysis reveals the presence of population subdivision in Norway spruce (Picea abiesK.)

Three chloroplast microsatellites (cpSSRs), previously sequence characterized and for which paternal inheritance was tested and confirmed, were used to assess their usefulness as informative markers for phylogeographic studies in Norway spruce (Picea abies K.) and to detect spatial genetic differentiation related to the possible recolonization processes in the postglacial period. Ninety-seven populations were included in the survey. Some 8, 7, and 6 different size variants for the three cpSSRs, respectively, were scored by analysing 1105 individuals. The above 21 variants combined into 41 different haplotypes. The distribution of some haplotypes showed a clear geographic structure and seems to be related to the existence of different refugia during the last glacial period. The analysis of chloroplast SSR variation detected the presence of two main gene pools (Sarmathic-Baltic and Alpine - Centre European) and a relatively low degree of differentiation (RSTof about 10%), characteristic of tree species with large distribution and probably influenced by an intensive human impact on this species. Based on our data, we were not able to detect any evidence concerning the existence of additional gene pools (e.g., from Balkan and Carpathian glacial refugia), though we cannot exclude the existence of genetic discontinuity within the species' European range. A large proportion of population-specific haplotypes were scored in this species, thus indicating a possible usefulness of these markers for the identification of provenances, seed-lots, and autochthonous stands. Key words: haplotypic diversity, phylogeography, chloroplast microsatellites, recolonization.

Chloroplast microsatellite analysis reveals the presence of population subdivision in Norway spruce (<i>Picea abies</i> K.)

Three chloroplast microsatellites (cpSSRs), previously sequence characterized and for which paternal inheritance was tested and confirmed, were used to assess their usefulness as informative markers for phylogeographic studies in Norway spruce (Picea abies K.) and to detect spatial genetic differentiation related to the possible recolonization processes in the postglacial period. Ninety-seven populations were included in the survey. Some 8, 7, and 6 different size variants for the three cpSSRs, respectively, were scored by analysing 1105 individuals. The above 21 variants combined into 41 different haplotypes. The distribution of some haplotypes showed a clear geographic structure and seems to be related to the existence of different refugia during the last glacial period. The analysis of chloroplast SSR variation detected the presence of two main gene pools (Sarmathic-Baltic and Alpine--Centre European) and a relatively low degree of differentiation (RST of about 10%), characteristic of tree species with large distribution and probably influenced by an intensive human impact on this species. Based on our data, we were not able to detect any evidence concerning the existence of additional gene pools (e.g., from Balkan and Carpathian glacial refugia), though we cannot exclude the existence of genetic discontinuity within the species' European range. A large proportion of population-specific haplotypes were scored in this species, thus indicating a possible usefulness of these markers for the identification of provenances, seed-lots, and autochthonous stands.

Isozyme variation among teak (Tectona grandis L.f.) provenances

Fourteen enzyme systems were analysed in leaf parenchyma of nine native and introduced populations of teak. These enzyme systems were encoded by 20 putative loci of which 18 were polymorphic. Populations showed a general lack of heterozygosity (average FIS = 0.11). On average over the 18 polymorphic loci, the genetic differentiation among provenances varied according to the estimator: 0.09 for GST, 0.12 for FST and 0.19 for δ. The cluster analysis showed two main gene pools, the first consisted of the Indian provenances and the second of African, Indonesian and Thai provenances. Genetic distances among populations of the same group were similar, and lower than the genetic distances between populations from different groups. The factorial analysis on genotypes of seedlings also showed the same geographic differentiation into two major groups. The possible natural distribution of teak in Java is discussed.