Commercial Tomato Panel
We offer the Commercial Tomato Panel for full-service, PlexSeq genotyping to be used as a tool to conduct molecular breeding and production quality control tests.
The Commercial Tomato panel, which consists of 1039 SNPs, was developed by a consortium of academic and industry researchers and breeders from the tomato community.
We also offer the Commercial Tomato panel to the public at a discounted price and expedited turnaround through the AgriPlex Connect program (submission deadline 10/31/23).
* The following is derived from the White Paper
Introduction
Both molecular markers in general and SNPs specifically are used by geneticists to construct high-density genetic maps (2021), which in turn, are used to identify quantitative trait loci (QTLs) associated with important traits such as fruit quality, disease resistance, stress tolerance (21) and Enhanced Nutritional Content by increasing lycopene content (22, 23).
For breeders, the use of molecular markers permits accurate and early selection of individuals of interest, reduction of the number of selection cycles required (24), implementation of new breeding schemes such as marker-assisted selection, background genome selection (24, 25, 26), and genomic selection (27, 28). Overall, the utilization of molecular markers in breeding reduces the time to market of new lines at a lower cost of breeding.
We describe here a new, mid-density, multiplexed SNP panel designed for various research and breeding applications on the PlexSeq NGS genotyping platform.
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The Initial Fresh Market Tomato Panel
The Commercial Tomato SNP panel was developed as an extension and update of a Fresh Market Tomato (FMT) panel that was created as part of an initiative of the Solanaceae Coordinated Agricultural Project (SolCap). This FMT panel contained 384 SNPs. SolCap was established with the help of the United States Department of Agriculture (USDA) to bridge the gap between breeding and genomics. The project has identified and validated 7,720 SNPs (Illumina’s Tomato Infinium array) through whole transcriptome sequencing of cultivated tomato varieties and two wild species, S. pimpinellifolium and the weedy S. lycopersicum var. cerasiforme (https://emea.illumina.com/library-prep-array-kit-selector/kits-and-arrays/thesolcap-tomato-consortium.html). High density SNP arrays are an excessive and expensive genotyping tool for many applications; therefore, two 384 subsets of SNPs were further selected from the 7K SNP array. Molecular markers for these panels were chosen to:
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Provide coverage of all 12 chromosomes
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Maintain a 0.2 cM or 0.2 Mbp distance between adjacent SNPS (corresponding to the expected recombination rate)
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The DNA sequences that are flanking the SNP lend them self to primer design.
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Include common SNPs between populations but also population specific SNPs
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One of these 384 SNPs subsets was created for Commercial Processing Tomatoes while the other was created for Fresh Market Tomatoes. The 384 SNP Fresh Market Tomato subset was introduced by AgriPlex Genomics in early 2018. The SNPs were multiplexed and validated as a PlexSeq panel and offered to tomato breeders and researchers since June of that year.
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The new Commercial Tomato Panel was designed by a consortium of leading tomato breeders and geneticists. Marker selection was conducted and led by Dr. Tong Geon Lee of the University of Florida (Currently at Bayer) with contributions from Professor David Francis of The Ohio State University.
The need to expand upon the Fresh Market Tomato panel rose for several reasons:
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To obtain higher genome coverage by closing gaps of unqueried genomic intervals between adjacent markers in the current Fresh Market Tomato panel.
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To augment the existing panel with more trait-related markers
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To provide one panel that can be utilized by both Commercial Processing and Fresh Market Tomato studies and breeding.T
The Commercial Tomato panel contains 1039 SNPs that span across all 12 tomato chromosomes. The additional markers were derived from genotypic datasets of diverse cultivated tomato inbreds, wild accessions, and their segregating populations. The various sources include (Table 1) transcriptome sequencing of Solanum lycopersicum, S.pimpinellifolium, S. pennellii (29, 30), whole genome sequencing of S. lycopersicum (31, 32, 33) and individual contributions of various tomato researchers.
The improvements in genome coverage of the Commercial Tomato Panel compared to the preceding FMT panel are depicted in Figure 1. The illustration represents the relative markers density in both panels. These improvements are further captured in Table 2:
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The marker density per chromosome has increased on average 2.7-fold, going from an average number of 32 markers per chromosome in the FMT panel to an average 87 SNPs per chromosome for the Commercial Tomato Panel.
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Consequently, the average inter-marker gap decreased to 0.773 Mbp which is a 64.9% improvement compared to the previous distance between adjacent markers in the FMT panel.
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To provide continuity with the widely used 384 SNP FMT panel and to retain its quality in capturing the genetic variations within the Fresh Market Tomato class, 360 of the best performing SNPs (94%) of the Fresh Market Tomato Panel have been preserved in the Commercial Tomato Panel (Figure 1).
The Mid-Density, Commercial Tomato Panel
Table 1: Summary of the SNP numbers by species and source of the Commercial Tomato Panel. TS, transcriptome sequencing, WGS, whole genome sequencing, NA, not available.
Figure 1. Chromosomal distribution of 1,039 SNPs in the Commercial Tomato SNP panel. The physical positions of SNPs are indicated by circles to the right of the chromosome. â…¹ symbol, left to the chromosome mark the positions of markers that were already included in the initial FMT panel. Estimated genetic map lengths (cM) based on contemporary U.S. Fresh Market Tomato populations (31,32,33) are indicated immediately below to the corresponding chromosome. Courtesy of Tong Geon Lee (University of Florida; Bayer).
Table 2. Number of markers per chromosome, and average distance (Mbp) between adjacent markers in the initial Fresh Market Tomato panel and the updated Commercial Tomato Panel.
The Commercial Tomato contains 384 trait-associated markers, 274 of which are associated with gene coding for major biochemical functions such as transcription and replication regulation, cell division and cellular structure proteins, photosynthesis, disease resistance to fusarium, late blight resistance, and Verticillium wilt disease resistance protein (please see Appendix A for a complete list). The remaining 110 SNPs are associated with genes of unknown factors.
A study was conducted by AgriPlex Genomics and a consortium of tomato researchers and breeders to characterize and validate the Commercial Tomato panel; 2726 samples were submitted for this purpose from four academic tomato genetics and breeding programs.
The success rate varied between 76.8 % to 96.2% among the different submissions and averaged 86.48%. When addressing the 4 different breeding programs as populations, the average % polymorphism of the panel ranged from 62.6% to 75.3%, and averaged 66.96%, or on the average 696 markers were polymorphic. The Average Minor Allele Frequency was 0.19 ± 0.166 (corresponding to a coefficient of variance of 86.5%).
It is important to note that the germplasm used for these experiments consisted of a variety of cultivated lines as well as wild tomato species; thus, the observed variation in performance parameters is expected for a panel designed to include common SNPs between populations as well as population-specific SNPs.
Applications
Genomic Selection
The Commercial Tomato SNP panel will enable genomic selection; the level of polymorphism observed indicates that there is a high likelihood of obtaining sufficient polymorphic markers.
for imputation to a higher marker density level. The average Genomic Selection predictive ability will vary for different combinations of parental lines and in different years.
The combination of rapid, cost-effective genotyping of a prediction population during the last generation of line fixation saves expenses on the cost of field space for seed increase and allows rapid recycling of progeny as parents.
Marker-assisted backcrossing:
​The Commercial Tomato SNP panel can be used for background recovery estimates in marker assisted backcrossing programs. The combination of informative background markers and a selection of trait markers allows for the accurate estimation of background recovery, ensures recovery of valuable genes from the recipient line, and can provide additional confirmation that a target gene is carried by the selected progeny. Background selection can reduce by 2 or more the number of backcross generations required to achieve >95% recipient parent recovery.
QTL Mapping
​While not the primary target application, the Commercial Tomato SNP panel can be used for biparental mapping purposes. The density of polymorphic markers may, in some cases, be lower than what is desirable (largely dependent on the parents involved), which may lead to gaps in the linkage map. However, the panel does provide an option for genotyping much of the genome. Any remaining gaps could then be filled in with other marker systems or by further panel customization.
Trait Profiling
The Commercial Tomato SNP panel contains high-value trait markers (Appendix A), covering a range of traits related to disease resistance, enzymatic profile, abiotic stress tolerance, taste, and others. These markers are designed to characterize the targeted genes and QTLs across different Solanum species and accessions including some wild relatives and are highly informative within the larger tomato U.S. germplasm, enabling interrogation of traits from/into lines of interest.
Seed Purity and Hybridity
The genome coverage of the Commercial Tomato SNP panel includes the number of markers that will allow for the identification of diagnostic marker subsets for seed quality applications such as genetic purity testing (uniformity) and varietal identification in commercial production operations.
Conclusions
AgriPlex Genomics’ implementation of the Commercial Tomato SNP panel is providing an excellent, cost-effective alternative for applications requiring mid-density SNP numbers over any number of sample throughput. The panel fits with rapid line fixation protocols due to its low cost-per-sample and rapid turnaround time. This panel will allow for major-locus selection as part of genomic selection, or backcross introgressions amongst tomato accessions, or the transfer of genes and QTLs of interest from wild tomato species into cultivated germplasm. The panel presents a valuable tool for saving critical time, expenses, and shortening the “time to market.” The panel primarily enables molecular breeding applications. However, the suite of trait markers and genome coverage expands its usefulness in a range of other research applications.
The flexibility of the PlexSeq platform permits continual revision and upgrading of the panel, ensuring the process keeps pace with the current breeding and seed production needs of the tomato breeding and research communities.
For the full white paper and list of References, click here.