Population Structure of Barley Landrace Populations and Gene-Flow with Modern Varieties

Landraces are heterogeneous plant varieties that are reproduced by farmers as populations that are subject to both artificial and natural selection. Landraces are distinguished by farmers due to their specific traits, and different farmers often grow different populations of the same landrace. We used simple sequence repeats (SSRs) to analyse 12 barley landrace populations from Sardinia from two collections spanning 10 years. We analysed the population structure, and compared the population diversity of the landraces that were collected at field level (population). We used a representative pool of barley varieties for diversity comparisons and to analyse the effects of gene flow from modern varieties. We found that the Sardinian landraces are a distinct gene pool from those of both two-row and six-row barley varieties. There is also a low, but significant, mean level and population-dependent level of introgression from the modern varieties into the Sardinian landraces. Moreover, we show that the Sardinian landraces have the same level of gene diversity as the representative sample of modern commercial varieties grown in Italy in the last decades, even within population level. Thus, these populations represent crucial sources of germplasm that will be useful for crop improvement and for population genomics studies and association mapping, to identify genes, loci and genome regions responsible for adaptive variations. Our data also suggest that landraces are a source of valuable germplasm for sustainable agriculture in the context of future climate change, and that in-situ conservation strategies based on farmer use can preserve the genetic identity of landraces while allowing adaptation to local environments.     

Resistance of Maize Landraces to the Maize Weevil Sitophilus zeamais Motsch. (Coleoptera: Curculionidae)

The maize weevil Sitophilus zeamais Motsch. is an important pest of maize that attacks the grain both in the field and during storage. The damage caused by the maize weevil S. zeamais on maize landraces, Amarelo Antigo, Asteca, Caiano, Carioca, and Ferrinho, was evaluated by no-choice tests under laboratory conditions. The commercial varieties Sol da Manh?, BR 106, BR 451, and the synthetics PC 0203 and PC 9903 were evaluated for comparisons with the maize landraces. The parameters evaluated were susceptibility index, number of weevil progeny, development time, weevil progeny dry weight, and grain dry weight loss. The landraces were more susceptible to the maize weevil as compared to the commercial varieties. Based on the cluster analysis, two groups of susceptibility to the maize weevil were observed: one of more susceptible populations formed by local landraces and BR 451, and another less susceptible, with commercial varieties, synthetics, and the landrace Amarelo.     

Assessing the allozyme variation in cultivars and Swedish landraces of rye (Secale cereale L.)

Genetic interpretation and diversity of 9 isozyme loci have been estimated in 7 improved varieties and 19 landraces from Sweden by means of starch gel electrophoresis. The isozyme systems were ACO, DIA, GPI, MDH, PGD and PGM. For the statistic analysis we used the following measures: average number of alleles per locus, percentage of polymorphic loci, average heterozygosity direct count and average heterozygosity Hardy-Weinberg expected unbiased estimate. The measures were made on species and population levels. The distribution of the total genetic diversity among populations was also calculated. To illustrate the genetic relationships among populations, genetic distances were measured and principal component analysis performed. As expected in a cross-pollinated crop we found high genetic diversity and a larger variation within than among the populations. Somewhat unexpectedly, however, we found that the currently used varieties have the same high level of heterozygosity as the landraces but in the dendrogram the two groups are separated. The dendrogram showed three main clusters. The large cluster included 21 populations and the two small clusters were clearly distinguishable from the rest. The landrace spring-type could not be separated from the landraces winter-type, but we did detect a difference between different spring types. A few populations had unique alleles for certain loci.     

Identification of Indian Landraces of Opium Poppy Papaver somniferum Resistant to Damping-off and Downy Mildew Fungal Diseases

A set of 32 landraces (traditional local cultivars) of poppy Papaver somniferum originating in the Indian states of Rajasthan, Madhya Pradesh, Uttar Pradesh and Tamilnadu, and four Indian commercial varieties were screened over four cropping seasons for their reaction to downy mildew disease caused by Peronospora arborescens and damping-off disease caused by Pythium dissotocum under both field and artificial inoculation conditions. The landrace 1018 was found to be resistant to damping-off disease and the landraces 1014 and N3 were resistant to downy mildew disease. A yield trial conducted over two seasons showed that the damping-off disease-resistant landrace 1018 was superior to all the commercial varieties in seed, morphine and/or codeine yield. The experiments provided further evidence that there is considerable genetic variability between the landraces.     

Genetic diversity and population structure of common bean (<Emphasis Type="Italic">Phaseolus vulgaris</Emphasis> L<Emphasis Type="Italic">.</Emphasis>) landraces from the East African highlands

The East African highlands are a region of important common bean production and high varietal diversity for the crop. The objective of this study was to uncover the diversity and population structure of 192 landraces from Ethiopia and Kenya together with four genepool control genotypes using morphological phenotyping and microsatellite marker genotyping. The germplasm represented different common bean production ecologies and seed types common in these countries. The landraces showed considerable diversity that corresponded well to the two recognized genepools (Andean and Mesoamerican) with little introgression between these groups. Mesoamerican genotypes were predominant in Ethiopia while Andean genotypes were predominant in Kenya. Within each country, landraces from different collection sites were clustered together indicating potential gene flow between regions within Kenya or within Ethiopia. Across countries, landraces from the same country of origin tended to cluster together indicating distinct germplasm at the national level and limited gene flow between the two countries highlighting divided social networks within the regions and a weak trans-national bean seed exchange especially for landrace varieties. One exception to this may be the case of small red-seeded beans where informal cross-border grain trade occurs. We also observed that genetic divergence was slightly higher for the Ethiopian landraces compared to Kenyan landraces and that Mesoamerican genotypes were more diverse than the Andean genotypes. Common beans in eastern Africa are often cultivated in marginal, risk-prone farming systems and the observed landrace diversity should provide valuable alleles for adaptation to stressful environments in future breeding programs in the region.     

Introgression from modern hybrid varieties into landrace populations of maize (Zea mays ssp. mays L.) in central Italy

Landraces are domesticated local plant varieties that did not experience a deliberate and intensive selection during a formal breeding programme. In Europe, maize landraces are still cultivated, particularly in marginal areas where traditional farming is often practiced. Here, we have studied the evolution of flint maize landraces from central Italy over 50 years of on-farm cultivation, when dent hybrid varieties were introduced and their use was widespread. We have compared an 'old' collection, obtained during the 1950s, before the introduction of hybrids, and a recent collection of maize landraces. For comparison, a sample of maize landraces from north Italy, and of improved germplasm, including hybrids and inbred lines were also used. A total of 296 genotypes were analysed using 21 microsatellites. Our results show that the maize landraces collected in the last 5–10 years have evolved directly from the flint landrace gene pool cultivated in central Italy before the introduction of modern hybrids. The population structure, diversity and linkage disequilibrium analyses indicate a significant amount of introgression from hybrid varieties into the recent landrace populations. No evidence of genetic erosion of the maize landraces was seen, suggesting that in situ conservation of landraces is an efficient strategy for preserving genetic diversity. Finally, the level of introgression detected was very variable among recent landraces, with most of them showing a low level of introgression; this suggests that coexistence between different types of agriculture is possible, with the adoption of correct practices that are aimed at avoiding introgression from undesired genetic sources.     

Swiss Mattenklee landraces,a distinct and diverse genetic resource of red clover (<Emphasis Type="Italic">Trifolium pratense</Emphasis> L.)

Genetic variability within and among 19 landraces and cultivars of red clover ( Trifolium pratense L.) was investigated by means of amplified fragment length polymorphism (AFLP) analysis in order to assess the potential value of Swiss Mattenklee landraces as genetic resources for plant breeding and the preservation of biodiversity. Populations were classified into three groups according to their origin and agronomic features: Mattenklee landraces (8), Mattenklee cultivars (8) and field clover cultivars (3). Analysis of molecular variance based on 276 polymorphic AFLP markers revealed 80% of total variability to be due to variability within populations while 12% were attributed to variability among groups. Stepwise discriminant analysis identified a subset of 126 AFLP markers which best separated individual plants into the three respective groups. Genetic distances between populations were considerably larger among groups than among populations within the same group, providing further evidence for the genetic distinction between Mattenklee landraces, Mattenklee cultivars and field clover cultivars. AFLP markers identified two landrace clusters, containing three and four populations respectively, which, together with one additional landrace, may sufficiently represent the genetic variability of all eight landraces investigated. The results of this study strongly suggest that Swiss Mattenklee landraces form a genetically distinct group of red clover. The data obtained provide criteria on how to efficiently manage, preserve and exploit Mattenklee germplasm.     

山东小麦种质资源品质特性多样性研究及利用

连续2年对698份地方品种、育成品种和省外引进品种的淀粉糊化特性、面团揉混特性和面筋蛋白特性等进行了详细的研究,并对不同生态类型区地方品种的品质特性进行了分析。结果表明:(1)不同来源种质资源品质特性表现出一定差异,育成品种和省外引进品种具有较长的面团揉混形成时间和较高的沉淀值,形成时间超过3.5min的品种分别有10和16个,最高值达5.2min;沉淀值水平较高,超过40.0ml的品种分别有32和25个,最高值分别为61.8ml和68.8ml;地方品种表现出较好的淀粉RVA糊化特性和较高的面筋蛋白含量,峰值粘度大于2900cP的有24个,最高峰值粘度高达4099cP,沉淀值在40.0ml以上的品种占48.8%,最高值达58.8ml;(2)不同生态类型区地方品种具有不同的品质特性,胶东丘陵冬性晚熟类型区烟台和青岛的地方品种具有较好的淀粉RVA糊化特性和较高的面筋蛋白含量,鲁西北平原冬性/半冬性晚熟类型区滨州、潍坊和德州的地方品种具有较好的淀粉RVA糊化特性,鲁中山丘川半冬性/冬性中熟类型区临沂、泰安的地方品种具有较高的面筋蛋白含量;(3)筛选出形成时间大于4.5min且沉淀值高于50.0ml的育成品种济南17、济宁16、济麦20、洲元9369和泰麦一号等,沉淀值超过60.0ml的省外引进品种藁优9415、冀5099、临汾6410和临汾6510等,峰值粘度高于3100cP的地方品种半截芒、白秃头(二)、三八麦、白秃头、小白芒(2)、半截红穗,以及沉淀值高于50.0ml的地方品种蚂蚱头、白肚、白气死雾、一穗收、四棱白、白穗红、半截红穗等,这些材料均可作为培育优质小麦的首选亲本。     

Landraces <Emphasis Type="Italic">in situ</Emphasis> Conservation: A Case Study in High-Mountain Home Gardens in Vall Fosca,Catalan Pyrenees,Iberian Peninsula<Superscript>1</Superscript>

Landraces in situ Conservation: A Case Study in High-Mountain Home Gardens in Vall Fosca, Catalan Pyrenees, Iberian Peninsula. Interest in landrace conservation has grown over the last few decades with much research focusing on the maintenance of on-farm crop genetic diversity in the tropics. Research on landraces is less abundant in temperate climates. In this paper we assess landrace conservation status in home gardens in Vall Fosca (Catalan Pyrenees, Iberian Peninsula). We estimate the individual socio-demographic attributes associated with in situ conservation of landraces and explore the reasons for their conservation. Fieldwork was conducted March–September 2008, during which time we surveyed 60 home gardens, owned by 53 tenders from 16 villages. We recorded occurrence, abundance, uses, and management of plants cultivated in home gardens. We also inquired about the informants’ reasons for conserving landraces. We found 148 different species. We identified 39 landraces corresponding to 31 species. Women, people over 65 years of age, experienced gardeners, and people who grow their home garden organically were more likely to conserve landraces than people without those characteristics. Although the informants express a strong preference for landraces, they mainly grow commercial varieties. Landraces seem to be displaced by less labor-intensive commercial varieties.     

Diversity in commercial varieties and landraces of black eggplants and implications for broadening the breeders' gene pool

Black‐coloured eggplants (Solanum melongena) represent the commercially most important group of eggplants in Europe and North America. Most of the modern varieties of black eggplants correspond to F₁ hybrids, which at the same time constitute an elite gene pool for the development of new varieties. However, there are many black landraces and old varieties, which could be useful as sources of variation for black eggplant breeding programmes as well as for the broadening of the genetic diversity of the breeders’ gene pool. We have studied the morphological and molecular [amplified fragment length polymorphism and simple sequence repeat (SSR)] diversity in a collection of 38 black eggplant accessions, including commercial (modern F₁ hybrid and old nonhybrid) varieties and landraces as well as in six nonblack control eggplants, from different origins. The results show that black eggplants contain a considerable morphological and molecular diversity, but commercial varieties, and in particular F₁ hybrids, display a reduced morphological and molecular diversity when compared with landraces. The principal components analysis morphological and principal coordinates analysis molecular analyses show that commercial F₁ hybrids group together, indicating that they share a common and narrow gene pool. Commercial F₁ hybrids present a series of productive advantages, like early production, intense black colour (low L*, a* and b*) values and absence of fruit calyx prickles. However, several of the landraces and old nonhybrid varieties studied present a high yield as well as other traits of interest for eggplant breeding. Furthermore, given the low genetic diversity of F₁ hybrids and the moderate level of SSR heterozygosity found in these materials (0.382), introduction of black landraces and old varieties in the present breeding programmes could contribute to broadening the gene pool used by breeders and this could help increase the heterosis for yield of F₁ hybrids, which is greatly favoured by high heterozygosity levels.     

Conservation and genetic characterisation of common bean landraces from Cilento region (southern Italy): high differentiation in spite of low genetic diversity

Since its introduction from Central-South America to Italy almost 500 years ago, the common bean (Phaseolus vulgaris L.) was largely cultivated across the peninsula in hundreds of different landraces. However, globalisation and technological modernisation of agricultural practices in the last decades promoted the cultivation of few varieties at the expense of traditional and local agro-ecotypes, which have been confined to local markets or have completely disappeared. The aim of this study was to evaluate the genetic diversity and differentiation in 12 common bean landraces once largely cultivated in the Cilento region (Campania region, southern Italy), and now the object of a recovery program to save them from extinction. The analysis conducted using 13 nuclear microsatellite loci in 140 individuals revealed a high degree of homozygosity within each landrace and a strong genetic differentiation that was reflected in the success in assigning individuals to the source landrace. On the contrary, internal transcribed spacers 1 and 2, analysed in one individual per landrace, were highly similar among common bean landraces but allowed the identification of a cowpea variety (Vigna unguiculata Walp.), a crop largely cultivated in the Old World before the arrival of common bean from Americas. In conclusion, our study highlighted that conservation of landraces is important not only for the cultural and socio-economic value that they have for local communities, but also because the time and conditions in which they have been selected have led to that genetic distinctiveness that is at the basis of many potential agronomical applications and dietary benefits.     

Genetic diversity and linkage disequilibrium in Chinese bread wheat (Triticum aestivum L.) revealed by SSR markers

Two hundred and fifty bread wheat lines, mainly Chinese mini core accessions, were assayed for polymorphism and linkage disequilibrium (LD) based on 512 whole-genome microsatellite loci representing a mean marker density of 5.1 cM. A total of 6,724 alleles ranging from 1 to 49 per locus were identified in all collections. The mean PIC value was 0.650, ranging from 0 to 0.965. Population structure and principal coordinate analysis revealed that landraces and modern varieties were two relatively independent genetic sub-groups. Landraces had a higher allelic diversity than modern varieties with respect to both genomes and chromosomes in terms of total number of alleles and allelic richness. 3,833 (57.0%) and 2,788 (41.5%) rare alleles with frequencies of <5% were found in the landrace and modern variety gene pools, respectively, indicating greater numbers of rare variants, or likely new alleles, in landraces. Analysis of molecular variance (AMOVA) showed that A genome had the largest genetic differentiation and D genome the lowest. In contrast to genetic diversity, modern varieties displayed a wider average LD decay across the whole genome for locus pairs with r(2)>0.05 (P<0.001) than the landraces. Mean LD decay distance for the landraces at the whole genome level was <5 cM, while a higher LD decay distance of 5-10 cM in modern varieties. LD decay distances were also somewhat different for each of the 21 chromosomes, being higher for most of the chromosomes in modern varieties (<5 ～ 25 cM) compared to landraces (<5 ～ 15 cM), presumably indicating the influences of domestication and breeding. This study facilitates predicting the marker density required to effectively associate genotypes with traits in Chinese wheat genetic resources.     

Dynamic Management of Maize Landraces in Central Mexico

Conservationists of crop genetic resources have feared that in situ conservation was not viable for agriculture precisely because of changes resulting from introduction of new varieties of existing crops, new crops, and new farm practices. In addition, conservation within farming systems necessarily implies a constantly changing crop population resulting from the processes of crop evolution. Even though in situ conservation of crop genetic resources is now generally understood to be dynamic, there are few examples of how evolution takes place in farmers fields. This study describes several changes in maize landraces in four communities along an altitude transect in Central Mexico (1200 to 2400 masl). While true modern varieties have not been widely adopted in the study region, farmer management results in numerous changes in maize landrace populations. Five types of dynamic management were observed: (1) purposeful hybridization between traditional and modern maize types, (2) possible creation of a new maize landrace by directional selection of the progeny of hybridization between two traditional landraces, (3) displacement of a local landrace by the introduction of a modern variety and a non-local landrace, (4) maintenance of stable populations of a locally dominant landrace, and (5) market-driven selection for a minor variety. We concur that in situ conservation of crops must be conceived as an open process where the objective is not to maintain historic varieties or static genetic conditions. Rather, in situ conservation of crops is totally in the hands of the farmer, although interventions may be designed to influence farmers’ management of agrobiodiversity.     

In Situ conservation of maize in Mexico: Genetic diversity and Maize seed management in a traditional community

Results from a study of maize varieties and seed sources in a traditional community in Jalisco, Mexico, raise questions about the relationship between genetic erosion and the introduction of varieties. The relevance of models for in situ conservation of crop genetic resources based on geographical isolation of a community is discussed. The morphophenological diversity of local materials is shown to be enhanced by introductions of both improved cultivars and landraces from farmers in other communities. On the other hand, the geographical point of reference for defining “local” landrace is shown to be larger than the community itself. Farmers will classify seed obtained from other farmers in and outside the community as that of a local landrace if it resembles their own according to the phenotypic characteristics they use to distinguish varieties. Maize diversity in this community is then the result of a certain level of introduction of genetic material and not of geographical isolation.     

Population structure of rice (Oryza sativa) landraces under farmer management

Greater insight into the dynamics of genetic resources of crop plants is needed in order to pinpoint detrimental evolutionary patterns and draw up conservation priorities. The present study demonstrated farmer management of crop population structure and temporal evolution of rice genetic diversity in traditional production systems. The 16 STMS primers analysed for 11 rice landrace populations indicated enough polymorphism to fully differentiate the inter- and intrapopulation diversity. A total number of 98 alleles were recorded, of which 91 were common and seven were rare. The mean number of alleles per locus was 6.13 and for different groups of rice landrace populations, namely five populations of upland common landrace Jaulia, three populations of irrigated common landrace Thapachini and one population each of three distinct rare landraces were 4.37, 2.75 and 4.37, respectively. The study also compared genebank-conserved ( ex situ ) populations and on-farm-managed ( in situ ) landrace populations of same named landraces Jaulia and Thapachini, and revealed greater number of alleles per locus for on-farm-managed populations as compared to the populations under static management. A substantial number of alleles specific to populations under dynamic management could also be recorded. Further, the rare landrace populations included in the present study were more diverse than the common landrace populations. The rare landraces were distinct genetic entities largely representing locally common alleles. Investigating the population genetic structure is therefore helpful in monitoring change in diversity over time and space, and also for devising a rational plan for management of farmer landraces on-farm.     

Comparative analysis of phenotypic and genotypic diversity among plantain landraces (Musa spp., AAB group)

Genetic diversity amongst 76 plantain landraces has been studied using RAPD analysis at two levels of intensity and compared with groupings based on phenotypic indices and morphotype. There was a good correlation (R²=0.78) between estimates of genetic diversity based on 76 RAPD bands and 164 RAPD bands. However, there was a poor correlation between RAPD-based estimates of genetic diversity and a phenotypic index based on agronomic characters. There was also a poor correlation between RAPD analyses and morphotype group (based on bunch type and stature). These results suggest that the traditional designations of plantain landraces based on morphotype do not provide a true reflection of overall genetic divergence. Similarly, classification systems using phenotypic indices based on agronomic characters may not provide accurate taxonomic differentiation. The level of genetic divergence within morphogroups based on bunch type suggests that True Horn plantains are derived from False Horn plantains which in turn are derived from French plantains. Genetic divergence was found to be generally quite low within the plantain landrace genepool, which is consistent with the proposed evolution of this germplasm through somatic mutation of a relatively small number of introductions. However, putative synonyms/duplicates have been shown to be genetically distinct. In contrast, a group of 12 landraces have been identified that are highly distinct from one another (showing 20–35% dissimilarity). Fertile members of this group may be useful for generating genetically diverse 2x and 4x breeding populations that can be used in breeding secondary triploid hybrid plantain varieties. Received: 8 January 2000 / Accepted: 2 March 2000     

Local genetic diversity of sorghum in a village in northern Cameroon: structure and dynamics of landraces

We present the first study of patterns of genetic diversity of sorghum landraces at the local scale. Understanding landrace diversity aids in deciphering evolutionary forces under domestication, and has applications in the conservation of genetic resources and their use in breeding programs. Duupa farmers in a village in Northern Cameroon distinguished 59 named sorghum taxa, representing 46 landraces. In each field, seeds are sown as a mixture of landraces (mean of 12 landraces per field), giving the potential for extensive gene flow. What level of genetic diversity underlies the great morphological diversity observed among landraces? Given the potential for gene flow, how well defined genetically is each landrace? To answer these questions, we recorded spatial patterns of planting and farmers’ perceptions of landraces, and characterized 21 landraces using SSR markers. Analysis using distance and clustering methods grouped the 21 landraces studied into four clusters. These clusters correspond to functionally and ecologically distinct groups of landraces. Within-landrace genetic variation accounted for 30% of total variation. The average F _is over landraces was 0.68, suggesting high inbreeding within landraces. Differentiation among landraces was substantial and significant (F _st = 0.36). Historical factors, variation in breeding systems, and farmers’ practices all affected patterns of genetic variation. Farmers’ practices are key to the maintenance, despite gene flow, of landraces with different combinations of agronomically and ecologically pertinent traits. They must be taken into account in strategies of conservation and use of genetic resources.     

Distribution of MWG699 polymorphism in Spanish European barleys.

The STS marker MWG699/TaqI is closely linked to the vrs1 locus and has been proposed as a marker of domestication in barley. This study included 257 cultivated barleys of both two- and six-rowed varieties, mainly from the western Mediterranean region. These included many landraces from the Spanish barley core collection, Moroccan landraces, and a set of accessions from other European countries. Restriction analysis of amplified DNA revealed three alleles, as previously described. Most of the two-rowed entries had the same allele, type K. Six-rowed entries showed both types A and D. Indeed, type D was widespread among Spanish landraces and commercial varieties from central Europe. It was also found in some two-rowed landraces originating from Spain and Morocco. Barleys with the D haplotype were predominantly winter types, whereas the A haplotype was evenly distributed among spring and winter types. These results support the existence of two different genetic sources among six-rowed Spanish landraces.     

Landraces of Phaseolus vulgaris (Fabaceae) in Northern Malawi. II. Generation and maintenance of variability

Bean (Phaseolus vulgaris) landraces in northern Malawi were found to be heterogeneous for many qualitative and quantitative traits. An earlier 21- character evaluation of 25 lines in 15 landraces found significant differences in all characters among lines and among landraces. The present study has concentrated on two factors that are likely to be involved in the generation and maintenance of this heterogeneity: seed- handling practices and natural outcrossing. Seed- handling practices during harvest, storage, and marketing at the village, local market, and national levels were found to result in physical and usually nonselective mixing of many seed types. Experiments determined that outcrossing does occur at a low level among beans in Malawi and can result in the generation of many new seed phenotypes. A scenario was developed integrating seed- handling practices and outcrossing that lays a foundation for understanding the generation and maintenance of variability in these bean landraces. The process whereby landrace heterogeneity arises and the ways it is maintained, if understood, should assist plant breeders in the development of improved germplasm for subsistence farmers.     

SNP genotyping reveals genetic diversity between cultivated landraces and contemporary varieties of tomato

Background

The tomato (Solanum lycopersium L.) is the most widely grown vegetable in the world. It was domesticated in Latin America and Italy and Spain are considered secondary centers of diversification. This food crop has experienced severe genetic bottlenecks and modern breeding activities have been characterized by trait introgression from wild species and divergence in different market classes.

Results

With the aim to examine patterns of polymorphism, characterize population structure and identify putative loci under positive selection, we genotyped 214 tomato accessions (which include cultivated landraces, commercial varieties and wild relatives) using a custom-made Illumina SNP-panel. Most of the 175 successfully scored SNP loci were found to be polymorphic. Population structure analysis and estimates of genetic differentiation indicated that landraces constitute distinct sub-populations. Furthermore, contemporary varieties could be separated in groups (processing, fresh and cherry) that are consistent with the recent breeding aimed at market-class specialization. In addition, at the 95% confidence level, we identified 30, 34 and 37 loci under positive selection between landraces and each of the groups of commercial variety (cherry, processing and fresh market, respectively). Their number and genomic locations imply the presence of some extended regions with high genetic variation between landraces and contemporary varieties.

Conclusions

Our work provides knowledge concerning the level and distribution of genetic variation within cultivated tomato landraces and increases our understanding of the genetic subdivision of contemporary varieties. The data indicate that adaptation and selection have led to a genomic signature in cultivated landraces and that the subpopulation structure of contemporary varieties is shaped by directed breeding and largely of recent origin. The genomic characterization presented here is an essential step towards a future exploitation of the available tomato genetic resources in research and breeding programs.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-14-835) contains supplementary material, which is available to authorized users.