Validation of KASP-SNP markers in cassava germplasm for marker-assisted selection of increased carotenoid content and dry matter content.

Provitamin A biofortification and increased dry matter content are important breeding targets in cassava improvement programs worldwide. Biofortified varieties contribute to the alleviation of provitamin A deficiency, a leading cause of preventable blindness common among pre-school children and pregnant women in developing countries particularly Africa. Dry matter content is a major component of dry yield and thus underlies overall variety performance and acceptability by growers, processors, and consumers. Single nucleotide polymorphism (SNP) markers linked to these traits have recently been discovered through several genome-wide association studies but have not been deployed for routine marker-assisted selection (MAS). This is due to the lack of useful information on markers' performances in diverse genetic backgrounds. To overcome this bottleneck, technical and biological validation of the loci associated with increased carotenoid content and dry matter content were carried out using populations independent of the marker discovery population. In the present study, seven previously identified markers for these traits were converted to a robust set of uniplex allele-specific polymerase chain reaction (PCR) assays and validated in two independent pre-breeding and breeding populations. These assays were efficient in discriminating marker genotypic classes and had an average call rate greater than 98%. A high correlation was observed between the predicted and observed carotenoid content as inferred by root yellowness intensity in the breeding (r = 0.92) and pre-breeding (r = 0.95) populations. On the other hand, dry matter content-markers had moderately low predictive accuracy in both populations (r< 0.40) due to the more quantitative nature of the trait. This work confirmed the markers' effectiveness in multiple backgrounds, therefore, further strengthening their value in cassava biofortification to ensure nutritional security as well as dry matter content productivity. Our study provides a framework to guide future marker validation, thus leading to the more routine use of markers in MAS in cassava improvement programs.

Breedbase: a digital ecosystem for modern plant breeding.

Modern breeding methods integrate next-generation sequencing and phenomics to identify plants with the best characteristics and greatest genetic merit for use as parents in subsequent breeding cycles to ultimately create improved cultivars able to sustain high adoption rates by farmers. This data-driven approach hinges on strong foundations in data management, quality control, and analytics. Of crucial importance is a central database able to (1) track breeding materials, (2) store experimental evaluations, (3) record phenotypic measurements using consistent ontologies, (4) store genotypic information, and (5) implement algorithms for analysis, prediction, and selection decisions. Because of the complexity of the breeding process, breeding databases also tend to be complex, difficult, and expensive to implement and maintain. Here, we present a breeding database system, Breedbase (https://breedbase.org/, last accessed 4/18/2022). Originally initiated as Cassavabase (https://cassavabase.org/, last accessed 4/18/2022) with the NextGen Cassava project (https://www.nextgencassava.org/, last accessed 4/18/2022), and later developed into a crop-agnostic system, it is presently used by dozens of different crops and projects. The system is web based and is available as open source software. It is available on GitHub (https://github.com/solgenomics/, last accessed 4/18/2022) and packaged in a Docker image for deployment (https://hub.docker.com/u/breedbase, last accessed 4/18/2022). The Breedbase system enables breeding programs to better manage and leverage their data for decision making within a fully integrated digital ecosystem.

Genome-wide association analysis reveals new insights into the genetic architecture of defensive, agro-morphological and quality-related traits in cassava.

KEY MESSAGE: More than 40 QTLs associated with 14 stress-related, quality and agro-morphological traits were identified. A catalogue of favourable SNP markers for MAS and a list of candidate genes are provided. Cassava (Manihot esculenta) is one of the most important starchy root crops in the tropics due to its adaptation to marginal environments. Genetic progress in this clonally propagated crop can be accelerated through the discovery of markers and candidate genes that could be used in cassava breeding programs. We carried out a genome-wide association study (GWAS) using a panel of 5130 clones developed at the International Institute of Tropical Agriculture-Nigeria. The population was genotyped at more than 100,000 SNP markers via genotyping-by-sequencing (GBS). Genomic regions underlying genetic variation for 14 traits classified broadly into four categories: biotic stress (cassava mosaic disease and cassava green mite severity); quality (dry matter content and carotenoid content) and plant agronomy (harvest index and plant type) were investigated. We also included several agro-morphological traits related to leaves, stems and roots with high heritability. In total, 41 significant associations were uncovered. While some of the identified loci matched with those previously reported, we present additional association signals for the traits. We provide a catalogue of favourable alleles at the most significant SNP for each trait-locus combination and candidate genes occurring within the GWAS hits. These resources provide a foundation for the development of markers that could be used in cassava breeding programs and candidate genes for functional validation.

Current status and impending progress for cassava structural genomics.

KEY MESSAGE: We demystify recent advances in genome assemblies for the heterozygous staple crop cassava (Manihot esculenta), and highlight key cassava genomic resources. Cassava, Manihot esculenta Crantz, is a crop of societal and agricultural importance in tropical regions around the world. Genomics provides a platform for accelerated improvement of cassava's nutritional and agronomic traits, as well as for illuminating aspects of cassava's history including its path towards domestication. The highly heterozygous nature of the cassava genome is widely recognized. However, the full extent and context of this heterozygosity has been difficult to reveal because of technological limitations within genome sequencing. Only recently, with several new long-read sequencing technologies coming online, has the genomics community been able to tackle some similarly difficult genomes. In light of these recent advances, we provide this review to document the current status of the cassava genome and genomic resources and provide a perspective on what to look forward to in the coming years.

Can Cross-Country Genomic Predictions Be a Reasonable Strategy to Support Germplasm Exchange? - A Case Study With Hydrogen Cyanide in Cassava.

Genomic prediction (GP) offers great opportunities for accelerated genetic gains by optimizing the breeding pipeline. One of the key factors to be considered is how the training populations (TP) are composed in terms of genetic improvement, kinship/origin, and their impacts on GP. Hydrogen cyanide content (HCN) is a determinant trait to guide cassava's products usage and processing. This work aimed to achieve the following objectives: (i) evaluate the feasibility of using cross-country (CC) GP between germplasm's of Embrapa Mandioca e Fruticultura (Embrapa, Brazil) and The International Institute of Tropical Agriculture (IITA, Nigeria) for HCN; (ii) provide an assessment of population structure for the joint dataset; (iii) estimate the genetic parameters based on single nucleotide polymorphisms (SNPs) and a haplotype-approach. Datasets of HCN from Embrapa and IITA breeding programs were analyzed, separately and jointly, with 1,230, 590, and 1,820 clones, respectively. After quality control, ∼14K SNPs were used for GP. The genomic estimated breeding values (GEBVs) were predicted based on SNP effects from analyses with TP composed of the following: (i) Embrapa genotypic and phenotypic data, (ii) IITA genotypic and phenotypic data, and (iii) the joint datasets. Comparisons on GEBVs' estimation were made considering the hypothetical situation of not having the phenotypic characterization for a set of clones for a certain research institute/country and might need to use the markers' effects that were trained with data from other research institutes/country's germplasm to estimate their clones' GEBV. Fixation index (FST) among the genetic groups identified within the joint dataset ranged from 0.002 to 0.091. The joint dataset provided an improved accuracy (0.8-0.85) compared to the prediction accuracy of either germplasm's sources individually (0.51-0.67). CC GP proved to have potential use under the present study's scenario, the correlation between GEBVs predicted with TP from Embrapa and IITA was 0.55 for Embrapa's germplasm, whereas for IITA's it was 0.1. This seems to be among the first attempts to evaluate the CC GP in plants. As such, a lot of useful new information was provided on the subject, which can guide new research on this very important and emerging field.

A population based expression atlas provides insights into disease resistance and other physiological traits in cassava (Manihot esculenta Crantz).

Cassava, a food security crop in Africa, is grown throughout the tropics and subtropics. Although cassava can provide high productivity in suboptimal conditions, the yield in Africa is substantially lower than in other geographies. The yield gap is attributable to many challenges faced by cassava in Africa, including susceptibility to diseases and poor soil conditions. In this study, we carried out 3'RNA sequencing on 150 accessions from the National Crops Resources Research Institute, Uganda for 5 tissue types, providing population-based transcriptomics resources to the research community in a web-based queryable cassava expression atlas. Differential expression and weighted gene co-expression network analysis were performed to detect 8820 significantly differentially expressed genes (DEGs), revealing similarity in expression patterns between tissue types and the clustering of detected DEGs into 18 gene modules. As a confirmation of data quality, differential expression and pathway analysis targeting cassava mosaic disease (CMD) identified 27 genes observed in the plant-pathogen interaction pathway, several previously identified CMD resistance genes, and two peroxidase family proteins different from the CMD2 gene. Present research work represents a novel resource towards understanding complex traits at expression and molecular levels for the development of resistant and high-yielding cassava varieties, as exemplified with CMD.

Comprehensive genotyping of a Brazilian cassava (Manihot esculenta Crantz) germplasm bank: insights into diversification and domestication.

KEY MESSAGE: Brazilian cassava diversity was characterized through population genetics and clustering approaches, highlighting contrasted genetic groups and spatial genetic differentiation. Cassava (Manihot esculenta Crantz) is a major staple root crop of the tropics, originating from the Amazonian region. In this study, 3354 cassava landraces and modern breeding lines from the Embrapa Cassava Germplasm Bank (CGB) were characterized. All individuals were subjected to genotyping-by-sequencing (GBS), identifying 27,045 single-nucleotide polymorphisms (SNPs). Identity-by-state and population structure analyses revealed a unique set of 1536 individuals and 10 distinct genetic groups with heterogeneous linkage disequilibrium (LD). On this basis, a density of 1300-4700 SNP markers were selected for large-effect quantitative trait loci (QTL) detection. Identified genetic groups were further characterized for population genetics parameters including minor allele frequency (MAF), observed heterozygosity [Formula: see text], effective population size estimate [Formula: see text]) and polymorphism information content (PIC). Selection footprints and introgressions of M. glaziovii were detected. Spatial population structure analysis revealed five ancestral populations related to distinct Brazilian ecoregions. Estimation of historical relationships among identified populations suggests an early population split from Amazonian to Atlantic forest and Caatinga ecoregions and active gene flows. This study provides a thorough genetic characterization of ex situ germplasm resources from cassava's center of origin, South America, with results shedding light on Brazilian cassava characteristics and its biogeographical landscape. These findings support and facilitate the use of genetic resources in modern breeding programs including implementation of association mapping and genomic selection strategies.

Large-scale genome-wide association study, using historical data, identifies conserved genetic architecture of cyanogenic glucoside content in cassava (Manihot esculenta Crantz) root.

Manihot esculenta (cassava) is a root crop originating from South America that is a major staple in the tropics, including in marginal environments. This study focused on South American and African germplasm and investigated the genetic architecture of hydrogen cyanide (HCN), a major component of root quality. HCN, representing total cyanogenic glucosides, is a plant defense component against herbivory but is also toxic for human consumption. We genotyped 3354 landraces and modern breeding lines originating from 26 Brazilian states and 1389 individuals were phenotypically characterized across multi-year trials for HCN. All plant material was subjected to high-density genotyping using genotyping by sequencing. We performed genome-wide association mapping to characterize the genetic architecture and gene mapping of HCN. Field experiments revealed strong broad- and narrow-sense trait heritability (0.82 and 0.41, respectively). Two major loci were identified, encoding for an ATPase and a MATE protein, and contributing up to 7 and 30% of the HCN concentration in roots, respectively. We developed diagnostic markers for breeding applications, validated trait architecture consistency in African germplasm and investigated further evidence for the domestication of sweet and bitter cassava. Fine genomic characterization revealed: (i) the major role played by vacuolar transporters in regulating HCN content; (ii) the co-domestication of sweet and bitter cassava major alleles are dependent upon geographical zone; and (iii) the major loci allele for high HCN in M. esculenta Crantz seems to originate from its ancestor, M. esculenta subsp. flabellifolia. Taken together, these findings expand our insights into cyanogenic glucosides in cassava roots and its glycosylated derivatives in plants.

The Ontologies Community of Practice: A CGIAR Initiative for Big Data in Agrifood Systems.

Heterogeneous and multidisciplinary data generated by research on sustainable global agriculture and agrifood systems requires quality data labeling or annotation in order to be interoperable. As recommended by the FAIR principles, data, labels, and metadata must use controlled vocabularies and ontologies that are popular in the knowledge domain and commonly used by the community. Despite the existence of robust ontologies in the Life Sciences, there is currently no comprehensive full set of ontologies recommended for data annotation across agricultural research disciplines. In this paper, we discuss the added value of the Ontologies Community of Practice (CoP) of the CGIAR Platform for Big Data in Agriculture for harnessing relevant expertise in ontology development and identifying innovative solutions that support quality data annotation. The Ontologies CoP stimulates knowledge sharing among stakeholders, such as researchers, data managers, domain experts, experts in ontology design, and platform development teams.

High density genotype storage for plant breeding in the Chado schema of Breedbase.

Modern breeding programs routinely use genome-wide information for selecting individuals to advance. The large volumes of genotypic information required present a challenge for data storage and query efficiency. Major use cases require genotyping data to be linked with trait phenotyping data. In contrast to phenotyping data that are often stored in relational database schemas, next-generation genotyping data are traditionally stored in non-relational storage systems due to their extremely large scope. This study presents a novel data model implemented in Breedbase (https://breedbase.org/) for uniting relational phenotyping data and non-relational genotyping data within the open-source PostgreSQL database engine. Breedbase is an open-source, web-database designed to manage all of a breeder's informatics needs: management of field experiments, phenotypic and genotypic data collection and storage, and statistical analyses. The genotyping data is stored in a PostgreSQL data-type known as binary JavaScript Object Notation (JSONb), where the JSON structures closely follow the Variant Call Format (VCF) data model. The Breedbase genotyping data model can handle different ploidy levels, structural variants, and any genotype encoded in VCF. JSONb is both compressed and indexed, resulting in a space and time efficient system. Furthermore, file caching maximizes data retrieval performance. Integration of all breeding data within the Chado database schema retains referential integrity that may be lost when genotyping and phenotyping data are stored in separate systems. Benchmarking demonstrates that the system is fast enough for computation of a genomic relationship matrix (GRM) and genome wide association study (GWAS) for datasets involving 1,325 diploid Zea mays, 314 triploid Musa acuminata, and 924 diploid Manihot esculenta samples genotyped with 955,690, 142,119, and 287,952 genotype-by-sequencing (GBS) markers, respectively.

Comparative assessment of genetic diversity matrices and clustering methods in white Guinea yam (Dioscorea rotundata) based on morphological and molecular markers.

Understanding the diversity and genetic relationships among and within crop germplasm is invaluable for genetic improvement. This study assessed genetic diversity in a panel of 173 D. rotundata accessions using joint analysis for 23 morphological traits and 136,429 SNP markers from the whole-genome resequencing platform. Various diversity matrices and clustering methods were evaluated for a comprehensive characterization of genetic diversity in white Guinea yam from West Africa at phenotypic and molecular levels. The translation of the different diversity matrices from the phenotypic and genomic information into distinct groups varied with the hierarchal clustering methods used. Gower distance matrix based on phenotypic data and identity by state (IBS) distance matrix based on SNP data with the UPGMA clustering method found the best fit to dissect the genetic relationship in current set materials. However, the grouping pattern was inconsistent (r = - 0.05) between the morphological and molecular distance matrices due to the non-overlapping information between the two data types. Joint analysis for the phenotypic and molecular information maximized a comprehensive estimate of the actual diversity in the evaluated materials. The results from our study provide valuable insights for measuring quantitative genetic variability for breeding and genetic studies in yam and other root and tuber crops.

Genomic characterization of Ugandan smallholder farmer-preferred cassava varieties.

Understanding the genetic relationships among farmer-preferred cassava (Manihot esculenta Crantz) varieties is indispensable to genetic improvement efforts. In this study, we present a genetic analysis of 547 samples of cassava grown by 192 smallholder farmers, which were sampled at random within four districts in Uganda. We genotyped these samples at 287,952 single nucleotide polymorphisms using genotyping-by-sequencing and co-analyzed them with 349 cassava samples from the national breeding program in Uganda. The samples collected from smallholders consisted of 86 genetically unique varieties, as assessed using a genetic distance-based approach. Of these varieties, most were cultivated in only one district (30 in Kibaale, 19 in Masindi, 14 in Arua, and three in Apac), and only three were cultivated across all districts. The genetic differentiation we observed among farming districts in Uganda (mean fixation index [F ST] = .003) is similar to divergence observed within other countries. Despite the fact that none of the breeding lines were directly observed in farmer fields, genetic divergence between the populations was low (F ST = .020). Interestingly, we detected the presence of introgressions from the wild relative M. glaziovii Müll. Arg. on chromosomes 1 and 4, which implies ancestry with cassava breeding lines. Given the apparently similar pool of alleles in the breeding germplasm, it is likely that breeders have the raw genetic material they require to match the farmer-preferred trait combinations necessary for adoption. Our study highlights the importance of understanding the genetic makeup of cassava currently grown by smallholder farmers and relative to that of plant breeding germplasm.

Phenotypic and molecular assessment of genetic structure and diversity in a panel of winged yam (Dioscorea alata) clones and cultivars.

A better understanding of the structure and extent of genetic variability in a breeding population of a crop is essential for translating genetic diversity to genetic gain. We assessed the nature and pattern of genetic variability and differentiation in a panel of 100 winged-yam (Dioscorea alata) accessions using 24 phenotypic traits and 6,918 single nucleotide polymorphism (SNP) markers. Multivariate analysis for phenotypic variability indicated that all phenotypic traits assessed were useful in discriminating the yam clones and cultivars. Cluster analysis based on phenotypic data distinguished two significant groups, while a corresponding analysis with SNP markers indicated three genetic groups. However, joint analysis for the phenotypic and genotypic data provided three clusters that could be useful for the identification of heterotic groups in the D. alata breeding program. Our analysis for phenotypic and molecular level diversity provided valuable information about overall diversity and variation in economically important traits useful for establishing crossing panels with contrasting traits of interest. The selection and hybridization of parental lines from the different heterotic groups identified would facilitate maximizing diversity and exploiting population heterosis in the D. alata breeding program.

Historical Introgressions from a Wild Relative of Modern Cassava Improved Important Traits and May Be Under Balancing Selection.

Introgression of alleles from wild relatives has often been adaptive in plant breeding. However, the significance of historical hybridization events in modern breeding is often not clear. Cassava (Manihot esculenta) is among the most important staple foods in the world, sustaining hundreds of millions of people in the tropics, especially in sub-Saharan Africa. Widespread genotyping makes cassava a model for clonally propagated root and tuber crops in the developing world, and provides an opportunity to study the modern benefits and consequences of historical introgression. We detected large introgressed Manihot glaziovii genome-segments in a collection of 2742 modern cassava landraces and elite germplasm, the legacy of a 1930s era breeding to combat disease epidemics. African landraces and improved varieties were, on average, 3.8% (max 13.6%) introgressed. Introgressions accounted for a significant (mean 20%, max 56%) portion of the heritability of tested traits. M. glaziovii alleles on the distal 10 Mb of chr. 1 increased dry matter and root number. On chr. 4, introgressions in a 20 Mb region improved harvest index and brown streak disease tolerance. We observed the introgression frequency on chr. 1 double over three cycles of selection, and that later stage trials selectively excluded homozygotes from consideration as varieties. This indicates a heterozygous advantage of introgressions. However, we also found that maintaining large recombination-suppressed introgressions in the heterozygous state allowed the accumulation of deleterious mutations. We conclude that targeted recombination of introgressions would increase the efficiency of cassava breeding by allowing simultaneous fixation of beneficial alleles and purging of genetic load.

Meta-analysis of genome-wide association studies provides insights into genetic control of tomato flavor.

Tomato flavor has changed over the course of long-term domestication and intensive breeding. To understand the genetic control of flavor, we report the meta-analysis of genome-wide association studies (GWAS) using 775 tomato accessions and 2,316,117 SNPs from three GWAS panels. We discover 305 significant associations for the contents of sugars, acids, amino acids, and flavor-related volatiles. We demonstrate that fruit citrate and malate contents have been impacted by selection during domestication and improvement, while sugar content has undergone less stringent selection. We suggest that it may be possible to significantly increase volatiles that positively contribute to consumer preferences while reducing unpleasant volatiles, by selection of the relevant allele combinations. Our results provide genetic insights into the influence of human selection on tomato flavor and demonstrate the benefits obtained from meta-analysis.

BrAPI-an application programming interface for plant breeding applications.

MOTIVATION: Modern genomic breeding methods rely heavily on very large amounts of phenotyping and genotyping data, presenting new challenges in effective data management and integration. Recently, the size and complexity of datasets have increased significantly, with the result that data are often stored on multiple systems. As analyses of interest increasingly require aggregation of datasets from diverse sources, data exchange between disparate systems becomes a challenge. RESULTS: To facilitate interoperability among breeding applications, we present the public plant Breeding Application Programming Interface (BrAPI). BrAPI is a standardized web service API specification. The development of BrAPI is a collaborative, community-based initiative involving a growing global community of over a hundred participants representing several dozen institutions and companies. Development of such a standard is recognized as critical to a number of important large breeding system initiatives as a foundational technology. The focus of the first version of the API is on providing services for connecting systems and retrieving basic breeding data including germplasm, study, observation, and marker data. A number of BrAPI-enabled applications, termed BrAPPs, have been written, that take advantage of the emerging support of BrAPI by many databases. AVAILABILITY AND IMPLEMENTATION: More information on BrAPI, including links to the specification, test suites, BrAPPs, and sample implementations is available at https://brapi.org/. The BrAPI specification and the developer tools are provided as free and open source.

Identification of major loci and genomic regions controlling acid and volatile content in tomato fruit: implications for flavor improvement.

Plant metabolites are important to world food security due to their roles in crop yield and nutritional quality. Here we report the metabolic profile of 300 tomato accessions (Solanum lycopersicum and related wild species) by quantifying 60 primary and secondary metabolites, including volatile organic compounds, over a period of 2 yr. Metabolite content and genetic inheritance of metabolites varied broadly, both within and between different genetic groups. Using genotype information gained from 10 000 single nucleotide polymorphism markers, we performed a metabolite genome-wide association mapping (GWAS) study. We identified 79 associations influencing 13 primary and 19 secondary metabolites with large effects at high resolution. Four genome regions were detected, highlighting clusters of associations controlling the variation of several metabolites. Local linkage disequilibrium analysis and allele mining identified possible candidate genes which may modulate the content of metabolites that are of significant importance for human diet and fruit consumption. We precisely characterized two associations involved in fruit acidity and phenylpropanoid volatile production. Taken together, this study reveals complex and distinct metabolite regulation in tomato subspecies and demonstrates that GWAS is a powerful tool for gene-metabolite annotation and identification, pathways elucidation, and further crop improvement.

Use of modern tomato breeding germplasm for deciphering the genetic control of agronomical traits by Genome Wide Association study.

KEY MESSAGE: A panel of 300 tomato accessions including breeding materials was built and characterized with >11,000 SNP. A population structure in six subgroups was identified. Strong heterogeneity in linkage disequilibrium and recombination landscape among groups and chromosomes was shown. GWAS identified several associations for fruit weight, earliness and plant growth. Genome-wide association studies (GWAS) have become a method of choice in quantitative trait dissection. First limited to highly polymorphic and outcrossing species, it is now applied in horticultural crops, notably in tomato. Until now GWAS in tomato has been performed on panels of heirloom and wild accessions. Using modern breeding materials would be of direct interest for breeding purpose. To implement GWAS on a large panel of 300 tomato accessions including 168 breeding lines, this study assessed the genetic diversity and linkage disequilibrium decay and revealed the population structure and performed GWA experiment. Genetic diversity and population structure analyses were based on molecular markers (>11,000 SNP) covering the whole genome. Six genetic subgroups were revealed and associated to traits of agronomical interest, such as fruit weight and disease resistance. Estimates of linkage disequilibrium highlighted the heterogeneity of its decay among genetic subgroups. Haplotype definition allowed a fine characterization of the groups and their recombination landscape revealing the patterns of admixture along the genome. Selection footprints showed results in congruence with introgressions. Taken together, all these elements refined our knowledge of the genetic material included in this panel and allowed the identification of several associations for fruit weight, plant growth and earliness, deciphering the genetic architecture of these complex traits and identifying several new loci useful for tomato breeding.

Genomic variation in tomato, from wild ancestors to contemporary breeding accessions.

BACKGROUND: Domestication modifies the genomic variation of species. Quantifying this variation provides insights into the domestication process, facilitates the management of resources used by breeders and germplasm centers, and enables the design of experiments to associate traits with genes. We described and analyzed the genetic diversity of 1,008 tomato accessions including Solanum lycopersicum var. lycopersicum (SLL), S. lycopersicum var. cerasiforme (SLC), and S. pimpinellifolium (SP) that were genotyped using 7,720 SNPs. Additionally, we explored the allelic frequency of six loci affecting fruit weight and shape to infer patterns of selection. RESULTS: Our results revealed a pattern of variation that strongly supported a two-step domestication process, occasional hybridization in the wild, and differentiation through human selection. These interpretations were consistent with the observed allele frequencies for the six loci affecting fruit weight and shape. Fruit weight was strongly selected in SLC in the Andean region of Ecuador and Northern Peru prior to the domestication of tomato in Mesoamerica. Alleles affecting fruit shape were differentially selected among SLL genetic subgroups. Our results also clarified the biological status of SLC. True SLC was phylogenetically positioned between SP and SLL and its fruit morphology was diverse. SLC and "cherry tomato" are not synonymous terms. The morphologically-based term "cherry tomato" included some SLC, contemporary varieties, as well as many admixtures between SP and SLL. Contemporary SLL showed a moderate increase in nucleotide diversity, when compared with vintage groups. CONCLUSIONS: This study presents a broad and detailed representation of the genomic variation in tomato. Tomato domestication seems to have followed a two step-process; a first domestication in South America and a second step in Mesoamerica. The distribution of fruit weight and shape alleles supports that domestication of SLC occurred in the Andean region. Our results also clarify the biological status of SLC as true phylogenetic group within tomato. We detect Ecuadorian and Peruvian accessions that may represent a pool of unexplored variation that could be of interest for crop improvement.