Domestication to crop improvement: genetic resources for Sorghum and Saccharum (Andropogoneae)

BACKGROUND: Both sorghum (Sorghum bicolor) and sugarcane (Saccharum officinarum) are members of the Andropogoneae tribe in the Poaceae and are each other's closest relatives amongst cultivated plants. Both are relatively recent domesticates and comparatively little of the genetic potential of these taxa and their wild relatives has been captured by breeding programmes to date. This review assesses the genetic gains made by plant breeders since domestication and the progress in the characterization of genetic resources and their utilization in crop improvement for these two related species. GENETIC RESOURCES: The genome of sorghum has recently been sequenced providing a great boost to our knowledge of the evolution of grass genomes and the wealth of diversity within S. bicolor taxa. Molecular analysis of the Sorghum genus has identified close relatives of S. bicolor with novel traits, endosperm structure and composition that may be used to expand the cultivated gene pool. Mutant populations (including TILLING populations) provide a useful addition to genetic resources for this species. Sugarcane is a complex polyploid with a large and variable number of copies of each gene. The wild relatives of sugarcane represent a reservoir of genetic diversity for use in sugarcane improvement. Techniques for quantitative molecular analysis of gene or allele copy number in this genetically complex crop have been developed. SNP discovery and mapping in sugarcane has been advanced by the development of high-throughput techniques for ecoTILLING in sugarcane. Genetic linkage maps of the sugarcane genome are being improved for use in breeding selection. The improvement of both sorghum and sugarcane will be accelerated by the incorporation of more diverse germplasm into the domesticated gene pools using molecular tools and the improved knowledge of these genomes.     

Importance of genetic characterization and conservation of plant genetic resources: The breeding system and genetic diversity of wild soybean (Glycine soja)

Abstract Plant genetic resources play an important role in the improvement of cultivated plants. To characterize and evaluate the ecological and reproductive features of wild soybean ( Glycine soja Sieb. et Zucc.), which is the most probable ancestor of cultivated soybean ( G. max (L) Merr.), the breeding system and genetic diversity of G. soja were investigated. The extent of natural cross-pollination of G. soja was estimated in four populations along the Omono River in Akita Prefecture, Japan by examining allozyme variation. Although it has been previously believed that G. soja is autogamous, as is cultivated soybean, the mean multilocus outcrossing rate ( t m) estimate was 13%. These values are much higher than the outcrossing rate previously reported for both G. soja and G. max . Frequent visits by honeybees and carpenter bees to flowers were also observed, which supported this conjecture. Furthermore, to evaluate the genetic variation of G. soja as a genetic resource, the genetic structure of 447 populations over Japan were analyzed. Wild soybean populations had a higher degree of variation of isozyme loci. The G ST coefficient of gene differentian values among the sites within the district were particularly high, revealing that the isozyme genotype was greatly different among site populations and homogeneous within the sites. The genetic differentiation among nine districts was observed in the allele frequencies of a few loci, indicating that geographic isolation in the wild soybean population was effectively created through the distance between the districts. The difference in the allele frequency among the districts may be produced under genetic drift. Finally, the importance of the preservation of natural plant populations and the habitats of wild progenitors (i.e. the in situ conservation of plant genetic resources) was emphasized.     

Quantitative genetic diversity and conservation strategies for an allogamous annual species,Dasypyrum villosum (L.) Candargy (Poaceae)

Dasypyrum villosum (L.) Candargy is a weedy annual diploid (2n = 14, VV genomes) allogamous grass species (Poaceae, Triticeae). Genetic variation for 12 traits was studied in 43 natural populations (31 from Italy and 12 from Croatia and Montenegro of former Yugoslavia) grown in a common field environment in California. Although 7 of 12 traits followed the theoretical prediction that a larger proportion of genetic variation was distributed within populations than among populations, exceptions were found for spike length, plant height, and days to flag-leaf emergence, heading, and anthesis. Covariate analysis showed that developmentally closely related characters were more likely correlated at both population and family within population levels. Geographically closer populations shared more genetic similarity than distant populations as indicated by mean coefficients of variation and cluster analysis of the Euclidean distances among populations. As few as five populations, each population with five or more half-sib seeds taken randomly from 5 plants, is expected to capture more than 95% of the total genetic variation of this species in the region sampled, but sampling a much larger number of seeds per population (> 1000) for long-term storage would supply research and plant breeding needs for several decades. If seed regeneration is required, populations can be sampled from clusters having similar genetic variation, and grown in reproductive isolation or bulked seed samples from all populations of each cluster group can be grown in isolation. The former is recommended if population integrity is desired while the latter is sufficient to provide genetic resources for plant-breeding purposes.     

Spatio-temporal genetic variation in populations of wild emmer wheat, <Emphasis Type="Italic">Triticum turgidum</Emphasis> ssp. <Emphasis Type="Italic">dicoccoides</Emphasis>, as revealed by AFLP analysis

Genetic structure of natural populations of wild crop relatives has been the subject of many studies. Yet, most of them focused on the assessment of spatial genetic diversity, while information on long-term variation, affected by yearly changes, has been considered only in few cases. The present study aimed therefore, to estimate the spatio-temporal genetic variation in populations of wild emmer wheat, the progenitor of domesticated wheat, and to assess the contribution of spatial versus temporal factors to the maintenance of genetic variation in a population. Single spikes were collected in the years 1988 and 2002 from plants that grew in the same sampling points, from six different habitats in the Ammiad conservation site, Eastern Galilee, Israel. Seeds were planted in a nursery and DNA was extracted from each plant and analyzed by the AFLP method. Fourteen primer combinations yielded 1,545 bands of which 50.0 and 48.8% were polymorphic in the years 1988 and 2002, respectively. Genetic diversity was much larger within populations than between populations and the temporal genetic diversity was considerably smaller than the spatial one. Nevertheless, population genetic structure may vary to some degree in different years, mainly due to fluctuations in population size because of yearly rainfall variations. This may lead to predominance of different genotypes in different years. Clustering the plants by their genetic distances grouped them according to their habitats, indicating the existence of genotype-environment affinities. The significance of the results in relation to factors affecting the maintenance of polymorphism in natural populations is discussed. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Soil seed bank contributes significantly to genetic variation of Hypericum sinaicum in a changing environment

The contribution of soil seed bank of a desert endemic plant species in maintaining genetic diversity has been addressed in this paper through investigating the differences in genetic diversity and structure (using AFLP markers) between plants grown from soil seed bank and standing crop plants within and among five populations of H. sinaicum growing at St. Katherine Protectorate, southern Sinai, Egypt. Standard genetic diversity measures showed that the molecular variation within and among populations was highly significantly different between standing crop and soil seed bank. While soil seed bank had lower genetic diversity than standing crop populations, pooling soil seed bank with standing crop samples resulted in higher diversity. The results revealed also that soil seed bank had lower differentiation (7 %) than among populations of the standing crop (18 %). Results of neighbor-joining, Bayesian clustering and principal coordinate analysis showed that soil seed banks had a separate gene pool different from standing crop. The study came to the conclusion that the genetic variation of the soil seed bank contributes significantly to the genetic variation of the species. This also stresses the importance of elucidating the genetic diversity and structure of the soil seed bank for any sound and long-term conservation efforts for desert species. These have been growing in small-size populations for a long time that any estimates gained only from aboveground sampling of populations may be ambiguous.     

Genetic polymorphism in varietal identification and genetic improvement

Summary New sources of genetic polymorphisms promise significant additions to the number of useful genetic markers in agricultural plants and animals, and prompt this review of potential applications of polymorphic genetic markers in plant and animal breeding. Two major areas of application can be distinguished. The first is based on the utilization of genetic markers to determine genetic relationships. These applications include varietal identification, protection of breeder's rights, and parentage determination. The second area of application is based on the use of genetic markers to identify and map loci affecting quantitative traits, and to monitor these loci during introgression or selection programs. A variety of breeding applications based on these possibilities can be envisaged for Selfers, particularly for those species having a relatively small genome size. These applications include: (i) screening genetic resources for useful quantitative trait alleles, and introgression of chromosome segments containing these alleles from resource strain to commercial variety; (ii) development of improved pure lines out of a cross between two existing commercial varieties; and (iii) development of crosses showing increased hybrid vigor. Breeding applications in segregating populations are more limited, particularly in species with a relatively large genome size. Potential applications, however, include: (i) preliminary selection of young males in dairy cattle on the basis of evaluated chromosomes of their proven sire; (ii) genetic analysis of resource strains characterized by high values for a particular quantitative trait, and introgression of chromosome segments carrying alleles contributing to the high values from resource strain to recipient strain.Contribution from The Agricultural Research Organization, The Volcani Center, Bet Dagan, Israel, No. 767-E, 1983 Series     

Multi-parent populations in crops: a toolbox integrating genomics and genetic mapping with breeding

Crop populations derived from experimental crosses enable the genetic dissection of complex traits and support modern plant breeding. Among these, multi-parent populations now play a central role. By mixing and recombining the genomes of multiple founders, multi-parent populations combine many commonly sought beneficial properties of genetic mapping populations. For example, they have high power and resolution for mapping quantitative trait loci, high genetic diversity and minimal population structure. Many multi-parent populations have been constructed in crop species, and their inbred germplasm and associated phenotypic and genotypic data serve as enduring resources. Their utility has grown from being a tool for mapping quantitative trait loci to a means of providing germplasm for breeding programmes. Genomics approaches, including de novo genome assemblies and gene annotations for the population founders, have allowed the imputation of rich sequence information into the descendent population, expanding the breadth of research and breeding applications of multi-parent populations. Here, we report recent successes from crop multi-parent populations in crops. We also propose an ideal genotypic, phenotypic and germplasm ‘package’ that multi-parent populations should feature to optimise their use as powerful community resources for crop research, development and breeding.Subject terms: Plant genetics, Plant breeding, Agricultural genetics, Quantitative trait

Over recent years, numerous multi-parent populations (MPPs) have been successfully developed in crops (Huang et al. 2015; Cockram and Mackay 2018). MPPs bring together key genomic, phenotypic and germplasm resources to form a platform for research and development. In this review, we examine three themes covering new developments in crop MPP research: (1) we survey the rapidly expanding variety of crop MPPs, explaining how differences in their design and construction affect their power and precision in mapping quantitative trait loci (QTL), on which we provide a brief primer. (2) We review the use of genomic technologies in MPPs, which have proven particularly suitable for gathering dense genomic information across large populations. We make general recommendations for collecting genotypic resources in MPPs. (3) We discuss successful applications of MPPs, particularly where they have been used for breeding and pre-breeding. This includes the identification of QTL, the application of genomic prediction to MPPs, and the direct use of MPP lines as germplasm for varietal release or pre-breeding. These recent developments have shown the potential of MPPs for crop improvement.     

云南省作物种质资源的研究现状及利用前景

云南是中国作物种质资源最为丰富的省份之一,已收集保存各类作物种质资源2万余份,并在水稻、小麦、玉米、甘蔗、茶叶、油料、花卉等资源的利用方面开展了一系列的研究,取得了丰硕的成果。本文将在分析云南作物种质资源利用研究的基础上,论述云南作物种质资源在育种、科研、国际交流等方面的利用途径与发展前景。     

A population genetic evaluation of ecological restoration with the case study on <Emphasis Type="Italic">Cyclobalanopsis myrsinaefolia</Emphasis> (Fagaceae)

The ultimate goal of ecological restoration is to create a self-sustaining ecosystem that is resilient to perturbation without further assistance. Genetic variation is a prerequisite for evolutionary response to environmental changes. However, few studies have evaluated the genetic structure of restored populations of dominant plants. In this study, we compared genetic variation of the restored populations with the natural ones in Cyclobalanopsis myrsinaefolia, a dominant species of evergreen broadleaved forest. Using eight polymorphic microsatellite loci, we analyzed samples collected from restored populations and the donor population as well as two other natural populations. We compared the genetic diversity of restored and natural populations. Differences in genetic composition were evaluated using measurements of genetic differentiation and assignment tests. The mean number of alleles per locus was 4.65. Three parameters (A, A _R, and expected heterozygosity) of genetic variation were found to be lower, but not significantly, in the restored populations than they were in the natural populations, indicating a founder effect during the restoration. Significant but low F _ST (0.061) was observed over all loci, indicating high gene flow among populations, as expected from its wind-pollination. Differentiation between the two restored populations was smallest. However, differences between the donor population and the restored populations were higher than those between other natural populations and the restored populations. Only 13.5% and 25.7% individuals in the two restored populations were assigned to the donor population, but 54.1 and 40% were assigned to another natural population. The genetic variation of the donor population was lowest, and geographic distances from the restoration sites to the donor site were much higher than the other natural populations, indicating that the present donor likely was not the best donor for these ecological restoration efforts. However, no deleterious consequences might be observed in restored populations due to high observed heterozygosity and high gene flow. This study demonstrates that during the restoration process, genetic structures of the restored populations may be biased from the donor population. The results also highlight population genetic knowledge, especially of gene flow-limited species, in ecological restoration.     

Analysis of microsatellite variation in the spider mite pest Tetranychus turkestani (Acari: Tetranychidae) reveals population genetic structure and raises questions about related ecological factors

The habitat fragmentation that characterizes agricultural systems made up of an array of sympatric crop and weed biotopes might be a major determinant of the population structure of plant‐feeding arthropods. Spider mites are interesting in this regard as several species are highly polyphagous, possibly generating homogenization by plant shifting, but also have the potential of forming host plant races which promotes specialization. This study analyses genetic diversity and structure in natural populations of a spider mite pest, Tetranychus turkestani, collected on both crops and weeds. Five microsatellite markers were used to genotype 283 individuals collected from 15 samples in four locations in southern France. The markers revealed considerable genetic variation, with an average heterozygosity of 0.68. Pairwise Φ_ST estimates calculated between localities showed differentiation in all comparisons. Although geographical distance appears to be a factor that influences T. turkestani population genetic structure at a regional scale, there was no clear evidence for differentiation between mites living on different host plants. A hierarchical analysis of the distribution of the genetic diversity within and between habitats showed that more than 97% of the observed genetic variation accounted for the differentiation between mites collected on the same host plant in a given locality. Significant heterozygote deficiency was found in 11 out of the 15 samples studied. Considering the biology of the mite, a Wahlund effect and inbreeding might explain such an excess of homozygosity. The data support the view that the plants in a given locality are colonized by mites that originate from diverse sources. They also support previous data suggesting that the demographic structure is made up of small demes of inbred individuals. The agricultural‐level implications of the data are discussed, notably the fact that mites may well be capable of moving between host plants, making weeds surrounding the crop fields potential reservoirs for the pest. © 2004 The Linnean Society of London, Biological Journal of the Linnean Society, 2004, 82 , 69–78.     

Progress in the genetic understanding of plant iron and zinc nutrition

In this review, we describe the need and progress to improve the iron and zinc contents in crop plants by genetic means. To achieve this goal either by transgenic approaches or classical breeding, knowledge about the physiological and molecular mechanisms of mineral uptake and mineral homeostasis will be very helpful. The progress in our understanding of the molecular processes and genes is described, and the use of the identified genes by transgenic approaches is illustrated. Genetic mapping of the existing variation will allow marker-assisted breeding to exploit the available natural variation in crop plants. For this application, ultimately the knowledge of the genes underlying this quantitative variation, called quantitative trait loci (QTL), will be required. It is expected that research in this field in the model species Arabidopsis thaliana , where the molecular tools are available, might help in the identification of the allelic variation at QTL.     

Genetic diversity and conservation and utilization of plant genetic resources

Biodiversity refers to variation within the living world, while genetic diversity represents the heritable variation within and between populations of organisms, and in the context of this paper, among plant species. This pool of genetic variation within an inter-mating population is the basis for selection as well as for plant improvement. Thus, conservation of this plant genetic diversity is essential for present and future human well-being. During recent years, there has been increasing awareness of the importance of adopting a holistic view of biodiversity, including agricultural biodiversity, conservation for sustainable utilization and development. These principles have been enshrined in the Convention on Biological Diversity and the Global Plan of Action of the Food and Agriculture Organization of the United Nations. The emphasis is now to understand the distribution and extent of genetic diversity available to humans in plant species, so that the genetic diversity can be safely conserved and efficiently used. It is generally recognized that plant genetic diversity changes in time and space. The extent and distribution of genetic diversity in a plant species depends on its evolution and breeding system, ecological and geographical factors, past bottlenecks, and often by many human factors. Much of the large amount of diversity of a species may be found within individual populations, or partitioned among a number of different populations.A better understanding of genetic diversity and its distribution is essential for its conservation and use. It will help us in determining what to conserve as well as where to conserve, and will improve our understanding of the taxonomy and origin and evolution of plant species of interest. Knowledge of both these topics is essential for collecting and use of any plant species and its wild relatives. In order to mange conserved germplasm better, there is also a need to understand the genetic diversity that is present in collections. This will help us to rationalize collections and develop and adopt better protocols for regeneration of germplasm seed. Through improved characterization and development of core collections based on genetic diversity information, it will be possible to exploit the available resources in more valuable ways.     

Population structure and phylogeography of Solanum pimpinellifolium inferred from a nuclear gene

Phylogeographical studies are emerging as a powerful tool for understanding the population structure and evolution of wild relatives of crop species. Because of their value as genetic resources, there is great interest in exploring the distribution of variation in wild relatives of cultivated plants. In this study, we use sequence variation from the nuclear gene, fruit vacuolar invertase (Vac), to investigate the population history of Solanum pimpinellifolium. Solanum pimpinellifolium is a close relative of the cultivated tomato and has repeatedly served as a source of valuable traits for crop improvement. We sequenced the second intron of the Vac gene in 129 individuals, representing 16 populations from the northern half of Peru. Patterns of haplotype sharing among populations indicate that there is isolation by distance. However, there is no congruence between the geographical distribution of haplotypes and their genealogical relationships. Levels of outcrossing decrease towards the southernmost populations, as previously observed in an allozyme study. The geographical pattern of Vac variation supports a centre of origin in northern Peru for S. pimpinellifolium and a gradual colonization along the Pacific coast. This implies that inbreeding populations are derived from outcrossing ones and that variation present at the Vac locus predates the spread of S. pimpinellifolium. The expansion of cities and human agricultural activity in the habitat of S. pimpinellifolium currently pose a threat to the species.     

1. The importance of genetic resources in plant breeding

Modern agricultural technology and the introduction of new high-yielding varieties are largely eliminating the wide range of crop genetic diversity that has evolved during the five to ten thousand years since food plants were first domesticated. Related wild species are also on the decline because of new land use policies. These gene pools (or what is left of them) are generally spoken of as genetic resources, and are vitally needed in the creation of new crop varieties by plant breeders. Wild species and land races often furnish genes conferring resistance to diseases and pests and adaptation to environmental stresses which cannot be found in the modern crop varieties.
The study of genetic diversity of crops, its storage in gene banks or in natural reserves, its evaluation and enhancement, are briefly described. The genetic resources work of the Food and Agriculture Organisation of the United Nations (FAO) and other international agencies such as the International Board for Plant Genetic Resources (IBPGR) is outlined.     

论克隆植物的遗传多样性

概述了克隆植物的类型与特点 ,对克隆植物的遗传多样性及其遗传结构的一些特点进行了综述 ,并讨论了克隆植物遗传变异的来源。总体而言 ,克隆植物拥有比早期推测大得多的遗传变异 ,虽然克隆种与其近缘有性繁殖种相比 ,遗传多样性较低 ,但广泛的遗传单态性却很罕见。克隆植物种群的遗传结构有所改变 ,广布基因型很少 ,大多数基因型仅分布于某一种群之内 ,种群间基因型多态性存在广泛的变异。不同克隆植物之间遗传多样性相差很大 ,遗传结构也有巨大差异。说明除生殖模式外 ,其他的一些因素 ,如地理分布范围、生境特点 ,散布方式和种群历史等都对克隆植物遗传多样性有重要影响。     

中华水韭遗传多样性的RAPD分析

采用RAPD方法对珍稀濒危植物中华水韭(Isoetes sinensis)4个自然居群的48个样品进行了DNA多态性分析。从60个随机引物中筛选出14个有效引物,共产生124条DNA片段,其中72条为多态性条带,总的多态位点百分率(PPB)为58．06％。各居群间多态位点百分率差异显著(0．81％-12．90％)。AMOVA分析结果表明,4个居群间基因分化系数Фst=0．5894,即遗传变异中有相当一部分来源于群体间(58．94％)。日益缩小的种群规模而导致的居群内近交和遗传漂变的发生以及居群间有限的基因交流可能是中华水韭目前遗传结构的主要成因。鉴于目前中华水韭居群内个体数偏少、遗传多样性较低的现状,建议对其进行就地保护并保护尽可能多的生境,对不同自然居群内的个体进行植株相互移栽和育苗移栽,以提高不同居群间的基因交流,尽可能地保护中华水韭的遗传多样性。     

Analysis of genetic variability of South American wild rice populations (Oryza glumaepatula) with isozymes and RAPD markers

The knowledge of population structure and genetic diversity of wild relatives of rice is needed to investigate their evolutionary history and potential use in breeding programs. Very little is known about the wild rice species ( Oryza spp.), particularly those that are native to South America. A study using isozyme and RAPD markers was conducted to estimate the level of genetic diversity of four South American wild rice populations ( Oryza glumaepatula ) recently collected in the Amazon forest and western Brazil rivers. F -statistics and genetic diversity parameters calculated from isozyme and RAPD markers indicated high values for inbreeding coefficients and differentiation among the four populations. In agreement with this, a pattern of greater variation between than within populations was observed with both types of markers. These findings were corroborated by an AMOVA analysis, which indicated that a large portion of the total genetic variation was attributed to regional divergence. The partition of the AMOVA analysis among populations showed that most of the genetic diversity was due to differences among populations. This distribution pattern of genetic variation of O. glumaepatula populations is in agreement with the expectation for an autogamous species and provides important baseline data for conservation and collection strategies for this species.     

The impact of hybrids between genetically modified crop plants and their related species: general considerations

Factors influencing the fate and impact of hybrids between crop plants and their related species operate from the early zygote, through to plant establishment in different habitats, to their ability to form self-sustaining populations. Many of the classes of genes being introduced by modern methods of genetic modification are similar to those manipulated by conventional plant breeding. In assessing the impact of transgenes in hybrids between crops and related species, therefore, it is important to be informed about the consequences of hybridization between conventionally bred varieties and their relatives. Some transgenes will have novel effects (e.g. production of pharmaceutical substances or certain fatty acids) on plants, and are likely to need specific assessment studies to determine their impact on hybrids. This will be particularly important if there is the possibility of these transgenes becoming established in wild populations. Some recommendations for further research are outlined.     

Reproductive biology and genetic structure in Lloydia serotina

Concern regarding the conservation status of small, isolated populations of the arctic-alpine plant species Lloydia serotina prompted research to establish the status and performance of this species in Wales, in comparison with large populations in its more typical alpine habitat. Relationships between reproductive strategies and genetic variation were investigated in a number of populations, representing a wide habitat, geographic and population size range. In all populations, vegetative reproduction predominates over sexual reproduction, but seed produced is viable and germinates readily under controlled conditions. Smaller, peripheral populations produced fewer flowers and seeds than the larger ones, but all populations studied supported significant percentages (>30%) of male plants, due to either the occurrence of androdioecy in this species or to a resource limited breeding system. Analysis of allozyme variation in sixteen populations from North America, the European Alps and Wales showed lower levels of genetic variation in smaller populations which averaged 1.1–1.2 alleles per locus and 10–20% of loci polymorphic, whereas larger populations averaged 1.4 alleles per locus and 30–40% polymorphic loci. This applied especially to the most northerly and southerly populations in North America, suggesting the occurrence of genetic drift in these small, peripheral populations. F-statistics suggest relatively high levels of differentiation among smaller populations, even among those closely related geographically, but genetic variation has been retained in all but one population, possibly due to infrequent sexual reproduction by long lived clones. RAPD analysis of four small populations in Wales provided further evidence of clonal growth and possible inbreeding dominating a mixed mating reproductive system with consequent genetic structuring in these populations.     

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.