AJPSAmerican Journal of Plant Sciences2158-2742Scientific Research Publishing10.4236/ajps.2019.107083AJPS-93866ArticlesBiomedical&Life Sciences Genetic Diversity and Population Structure of Tomato (<i>Solanum lycopersicum</i>) Germplasm Developed by Texas A&M Breeding Programs DeviR. Kandel1ReneshH. Bedre1KranthiK. Mandadi2KevinCrosby3CarlosA. Avila3*Texas A&amp;M AgriLife Research and Extension Center, Weslaco, TX, USADepartment of Horticultural Sciences, Texas A&amp;M University, College Station, TX, USADepartment of Plant Pathology and Microbiology, Texas A&amp;M University, College Station, TX, USA1107201910071154118029, May 201922, July 2019 25, July 2019© Copyright 2014 by authors and Scientific Research Publishing Inc. 2014This work is licensed under the Creative Commons Attribution International License (CC BY). http://creativecommons.org/licenses/by/4.0/

Genetic variation developed in plant breeding programs is fundamental to creating new combinations that result in cultivars with enhanced characteristics. Over the years, tomato ( Solanum lycopersicum ) breeding programs associated with the Texas A&M University system have developed morphologically diverse lines of tomatoes selected for heat tolerance, fruit quality, and disease resistance to adapt them to Texas growing conditions. Here we explored the intraspecific genetic variations of 322 cultivated tomato genotypes, including 300 breeding lines developed by three Texas A&M breeding programs, as an initial step toward implementing molecular breeding approaches. Genotyping by sequencing using low coverage whole-genome sequencing (SkimGBS) identified 10,236 high-quality single-nucleotide polymorphisms (SNPs) that were used to assess genetic diversity, population structure, and phylogenetic relationship between genotypes and breeding programs. Model-based population structure analysis, phylogenetic tree construction, and principal component analysis indicated that the genotypes were grouped into two main clusters. Genetic distance analysis revealed greater genetic diversity among the products of the three breeding programs. The germplasm developed at Texas A&M programs at Weslaco, College Station, and by Dr. Paul Leeper exhibited genetic diversity ranges of 0.175 - 0.434, 0.099 - 0.392, and 0.183 - 0.347, respectively, suggesting that there is enough variation within and between the lines from the three programs to perform selection for cultivar development. The SNPs identified here could be used to develop molecular tools for selecting various traits of interest and to select parents for future tomato breeding.

Genetic Diversity Single-Nucleotide Polymorphism (SNP) <i>Solanum lycopersicum</i> Tomato Genotyping by Sequencing (GBS)1. Introduction

Tomato (Solanum lycopersicum L.) is a major vegetable crop widely grown around the world [1] [2] [3] . In the USA, fresh and processed tomatoes accounted for more than $1.85 billion in US farm cash receipts in 2018 [4] . The two leading states for fresh-market tomato production are Florida and California, which together comprise almost two-thirds of the total US fresh tomato acreage. Historically, Texas grew as many acres of tomatoes as the leading producing states, with 13,315 ha planted in the 1960s. Because of the lack of adequate cultivars, pest/disease pressure, inefficient production practices, and competition from other production areas, however, Texas growers later migrated to other crops, largely abandoning fresh market tomatoes (harvesting only 304 ha. in 2017) [5] . To satisfy customer demand, Texas imports an estimated 2.4 billion pounds/year [6] . A recent study found that Texas consumers frequently request tomatoes with “vine ripe” flavor, aroma, and texture, and will pay a premium for locally produced selections [7] . This situation represents a great opportunity for local producers to re-claim their share of the Texas tomato market. For this to be possible, however, new cultivars and production practices need to be developed to support the industry.

The Texas A&M AgriLife Research tomato breeding programs at Weslaco and College Station have been breeding tomatoes for heat tolerance, fruit quality, and disease resistance adapted to Texas growing conditions for the past five and eighteen years, respectively. Recognizing that high temperatures significantly impact tomato flavor and appearance, our work has focused on introgressing heat tolerance and high-temperature fruit set genes. The two tomato breeding programs combined have developed more than 400 families, including heat-tolerant lines with disease resistance and diverse heirloom selections with multiple fruit colors and unique flavors. Much of this work targeted improvements in both flavor and content of beneficial phytochemicals [8] . This high-yielding, heat-tolerant base germplasm was developed over a period of 37 years at Weslaco by former Texas A&M breeder Dr. Paul Leeper and has been used extensively by the current Texas A&M breeding programs and others programs in tropical regions, including the cultivars Chico III, Chico, El Monte, Monte Grande, La Pinta, Chico Grande, and Saladette [9] [10] [11] [12] . To date, elite lines in our breeding programs have been selected using conventional phenotypic selection approaches, in which large populations are screened for several breeding cycles. Although this approach has produced high-quality, high-yield cultivars, it is time-consuming and requires substantial resources to develop each new cultivar.

An alternative approach to improve breeding efficiency involves the use of modern molecular breeding techniques for population management, including methods to obtain desired genetic heterogeneity in the end-product cultivars. One of the first steps in implementing molecular breeding approaches is to estimate the genetic variation within the breeding lines. Genetic heritable variability is indispensable in plant breeding aimed at developing new cultivars that express desirable characteristics generation after generation [13] . Furthermore, the development of improved varieties is enhanced when parents are selected based on genetic heterogeneity [14] , making genetic variation estimation necessary in breeding programs to allow the selection of parental lines either to increase breeding population variation or to develop hybrids for cultivar release [15] .

Genetic variation between breeding lines can be effectively determined through the use of molecular markers. In tomato, genetic diversity has been extensively studied using a wide range of molecular data. Miller and Tanksley (1990) [16] used restriction-fragment-length polymorphism (RFLP) markers for genetic diversity analysis of self-incompatible and self-compatible tomato species. To unveil the genetic variations that underlie fruit sugar and organic acid production, Zhao et al. (2016) [17] conducted a genetic diversity analysis of 174 tomato accessions using simple sequence repeat (SSR) markers. To gain insight into the morphological traits of fruits, Sacco et al. (2015) [18] performed a genetic diversity analysis of 123 tomato genotypes using single-nucleotide polymorphisms (SNPs). Similarly, Lin et al. [19] and Aflitos et al. [20] performed an evolutionary study of tomato and its wild relatives involving SNPs.

The advent of next-generation sequencing technologies coupled with bioinformatics has led genetic diversity studies into a new era. Sequencing of tomato has resulted in the discovery of large numbers of SNPs distributed throughout the genome [20] [21] [22] . Furthermore, cultivated tomato genome has been fully sequenced [23] and the genotyping by sequencing (GBS) has emerged as a powerful tool for sequencing large populations. The availability of large numbers of SNPs distributed throughout the genome, a reference genome, and the GBS technique [23] [24] [25] has made large intraspecific studies possible. This is important as most prior studies focused on interspecific variations and only a few intraspecific studies have been performed [19] [20] [26] [27] . The SNPs postulated from such intraspecific studies offer better clues to the genetic control of agronomic traits and can be used to deduce phylogenetic relationships. Parent selection based on such genetic information can greatly enhance breeding efficiency and help to achieve breeding goals such as high quality (flavor, color, shape), long shelf life, disease resistance, and heat tolerance.

In the present study, we used three representative sets of tomato breeding lines from the current Texas A&M AgriLife Research breeding programs at Weslaco and College Station and from former Texas A&M breeder Dr. Paul Leeper to assess genotypic intraspecific variations within Texas A&M germplasm. Sequencing of these lines yielded 10,236 high-quality polymorphic SNPs. Genetic distance analysis revealed that the tomato breeding lines developed by the Texas A&M breeding programs possess a high level of genetic diversity that, upon selection, can be used to develop high-yielding adapted cultivars for Texas production. Furthermore, intraspecific SNPs identified in the present study could be used to identify economically important traits in cultivated tomatoes. Finally, based on the results of phylogenetic and genetic distance analyses, hybridization strategies can be developed to increase diversity and optimize hybrid development within and between breeding programs.

2. Materials and Methods2.1. Plant Material

A total of 322 tomato (Solanum lycopersicum) genotypes were evaluated in this study. Among them, 300 genotypes were developed by three independent tomato breeding programs in the Texas A&M University (TAMU) system. Out of them, 127 were developed by Dr. Kevin Crosby’s breeding program at Texas A&M University, College Station, TX (designated TAM-CS); 125 by Dr. Carlos Avila’s breeding program at the Texas A&M AgriLife Research and Extension Center at Weslaco, TX (designated TAM-W); and 48 by the breeding program of Dr. Paul Leeper, a former TAMU breeder at Weslaco, Texas (designated TAM-L) (Table S1). These genotypes were developed by hybridizations of Texas A&M germplasm with a diverse set of parents including accessions from the USDA National Germplasm System and other public breeding programs mentioned below and subsequent selfing up to the F9 generation. Pedigree information for all the breeding lines developed in Leeper’s program and some from Crosby’s program have been lost (Table S1). Breeding lines developed from all the three breeding program harbor good phenotypic variations in tomato fruit shape, size, and color. Besides the genotypes from the Texas A&M University breeding programs, 16 genotypes from the USDA collection, 3 from the Asian Vegetable Research and Development Center (AVRDC), and 3 developed by University of Florida tomato breeding program (designated FLA) were also included in the present study (Table S1).

2.2. DNA Extraction

Leaves from twelve four-week-old seedlings of the respective genotypes were collected and combined into a single bulk sample. Tissue was lyophilized, homogenized, and stored at −20˚C until extraction. Genomic DNA was extracted from 50 mg of homogenized tissue using the CTAB method [28] . Qualitative and quantitative tests of the DNA were performed by electrophoresis and Qubit 2.0 fluorometry (Life Technologies, Carlsbad, CA), respectively. For each sample, 1.2 mg of DNA was sent to the Texas A&M Genomics and Bioinformatics services (College Station, TX) for sequencing.

2.3. GBS, SNP Discovery, and Population Structure

Genotyping of 322 tomato genotypes was performed using low-coverage whole-genome sequencing (SkimGBS [29] ) with a paired-end approach (150 bp × 150 bp) (Illumina HiSeq 4000) at the Texas A&M Genomics and Bioinformatics service (College Station, TX). Raw sequences from the 322 genotypes were filtered to remove low-quality reads and adapter sequences. High-quality sequence data were mapped to the tomato reference genome (S. lycopersicum v3.00) [23] using bowtie2 [30] . The aligned BAM files were sorted, quality filtered for mapping, and filtered for duplicate reads using SAMtools [31] and Picard (http://broadinstitute.github.io/picard/index.html). The GATK HaplotypeCaller (HC) [32] was used for SNP calling from the aligned data of the 322 tomato genotypes. These raw polymorphic SNPs were filtered to remove SNPs with a high percentage of missing genotypes and low minimum allele frequency (MAF). The resulting genotypes were imputed using Beagle (v4.00) [33] . The imputed genotypes were further filtered to keep only genotypes with probability ≥0.9. The polymorphic SNPs were subsequently filtered to remove the SNPs with >30% missing genotypes.

The population structure and hybrid forms of tomato genotypes were inferred using the Bayesian model-based clustering program STRUCTURE (v2.3.4) [34] using polymorphic SNPs obtained from the GBS analysis. To determine the number of populations in a given genotype, the STRUCTURE was run with 5000 burn-in periods with 5000 Markov-chain Monte Carlo (MCMC) steps using an admixture model and correlated allele frequencies among populations. The program was run independently three times for each value K ranging from 1 to 10. To detect the true value of K (population), we used the uppermost level of structure calculated using the ΔK method as described in Evanno et al., 2005 [35] . The tomato genotypes were assigned to each true population (Q) based on the value obtained for the proportion of population membership for a given K. The population structure of 322 tomato genotypes was visualized using a bar plot (sorted by Q) in the Python matplotlib package.

2.4. Phylogenetic and Principal Component Analysis

Phylogenetic analysis was performed using the unweighted pair-group method with arithmetic mean (UPGMA) algorithm implemented in TASSEL v5.2.52 [36] . The phylogenetic tree obtained from TASSEL was visualized using iTOL v4.3.3 and each population was annotated using customized annotation files [37] . The pairwise genetic distance matrix between each pair of genotypes was calculated using TASSEL v5.2.52 and visualized using the Python matplotlib package. The PCA was performed using the PCA function in TASSEL. The first three principal components were exported and visualized as a three-dimensional (3D) scatter plot using the Python matplotlib package.

3 Results3.1. Generation of High-Quality Tomato GBS Data

We generated a total of ~598 million sequence reads (paired-end, 150 bp) using low-coverage (average ~0.37×) whole-genome sequencing across 322 tomato genotypes. The raw sequence data were filtered to remove low-quality bases, adapter contamination, and uncalled bases to produce high-quality sequence data (~522 million reads). On an average, ~95% of high-quality reads mapped to the tomato reference genome for SNP discovery. In total, we obtained ~3.2 million SNPs from tomato SkimGBS data from the 322 genotypes, which we subsequently filtered to remove SNPs with >50% missing, rare alleles with MAF <5% across all 322 tomato genotypes, and SNPs with low genotype probability (<0.9) (Figure S1 and Figure S2). We used the remaining 10,236 high-quality SNPs for downstream analysis. SNPs were not distributed evenly across all chromosomes (Figure 1). Chromosome 12 and 1 had the highest numbers of identified SNPs with 1337 and 1208, respectively, whereas chromosomes 6 and 4 had the lowest number of identified SNPs with 173 and 255, respectively. In addition, 1279 SNPs were mapped to unanchored scaffolds (Chr00).

3.2. Genetic Distance between Tomato Genotypes

We calculated the pairwise genetic distance matrix for the 322 tomato genotypes in TASSEL v5.2.52. Genetic distance between tomato genotypes ranged from 0.092 to 0.443, with an average distance of 0.270 (Table 1 and Table S2). Among them, the combination of genotypes TAM-CS-138 and USDA-273 revealed the smallest genetic distance (0.092). Genotype TAM-CS-138 is an F5 inbred heirloom type with large, pink fruit, developed by the Texas A&M College Station breeding program, and genotype USDA-273 is a cherry tomato that produces small red fruit, from the USDA germplasm bank (Table S1). Among all possible 100,142 combinations between the 322 genotypes, the largest genetic distance (0.443) was observed between genotypes TAM-CS-111 and TAM-W-322 (Table 1). Genotype TAM-CS-111 is an F5 inbred that produces small, round red fruit, from

Genetic distances among tomato genotypes developed by different groups
Genotype sourceNo. of genotypesMinimum diversityMaximum diversityMean Genetic distance
Genotype combinationGenetic distanceGenotype combinationGenetic distance
Overall322TAM-CS-138 and USDA-2730.092TAM-CS-111 and TAM-W-3220.4430.270
TAM-W125TAM-W-315 and TAM-W-3160.175TAM-W-322 and TAM-W-1720.4340.264
TAM-CS127TAM-CS-138 and TAM-CS-2300.099TAM-CS-111 and TAM-CS-1650.3920.282
TAM-L48TAM-L-13 and TAM-L-540.183TAM-L-51 and TAM-L-160.3470.255
USDA16USDA-238 and USDA-2730.192USDA-259 and USDA-3200.2920.234
AVRDC3AVRDC-119 and AVRDC-1330.289AVRDC-119 and AVRDC-1260.3090.296
FLA3FLA-154 and FLA-1610.276FLA-147 and FLA-1540.3150.298

Note: AVRDC = Asian Vegetable Research and Development Center; TAM-CS = Dr. Kevin Crosby’s breeding program at Texas A&M at College Station; TAM-W = Dr. Carlos Avila’s breeding program at Texas A&M AgriLife Research and Extension Center at Weslaco, TX; TAM-W = Dr. Paul Leeper’s breeding program at Texas A&M AgriLife Research and Extension Center at Weslaco, TX; FLA = Florida Tomato Breeding Program; USDA = United States Department of Agriculture.

the Texas A&M College Station breeding program, while TAM-W-322 is an F9 inbred that produces medium Roma-type pink fruit, developed by the Texas A&M AgriLife breeding program at Weslaco.

The genetic distances between the genotypes from the three Texas A&M University Breeding programs and control outgroups from the USDA, AVRDC, and Florida are presented in Table 1. Breeding lines developed by the Texas A&M College Station, Weslaco, and Leeper programs had overall intra-program genetic distance means of 0.282, 0.264, and 0.255, respectively (Table 1). The genetic diversity between germplasms from the different Texas A&M breeding programs indicates a high potential for introducing variability between programs. In regard to within-program variation, among lines from the Texas A&M AgriLife breeding program at Weslaco, the largest genetic distance (0.434) was between genotypes TAM-W-172 and TAM-W-322; among lines from the Texas A&M College Station breeding program, the largest genetic distance (0.392) was between TAM-CS-111 and TAM-CS-165; and for those from the Texas A&M Leeper program, the largest genetic distance (0.347) was between TAM-L-51 and TAM-L-16. The genotypes developed by the USDA were overall the least diverse group, with a mean genetic distance of 0.234 and a range of 0.192 - 0.292. Within that group, the genotype combination of USDA-259 and USDA-320 showed the largest genetic distance (Table 1). The sets of genotypes from the AVRDC and Florida breeding programs used in the present study showed mean genetic diversities of 0.296 and 0.298, respectively (Table 1).

3.3. Population Structure

We explored the population structure of tomato genotypes using a model-based clustering method implemented with STRUCTURE v2.3.4. The maximum value for ΔK was observed when K = 2 (Figure 2(a)), indicating the presence of two

main population clusters (Q1 and Q2) (Figure 2(b)). Out of the entire population evaluated in this study, 32 tomato genotypes (9.9%) were grouped into Q1, while the remaining 290 genotypes were placed into Q2 (90.1%) (Table 2). Of the two clusters, the genetic diversity assessment indicated that Q1 is more diverse, and it included the two genotypes with the largest genetic distance observed (genotypes TAM-W-322 and TAM-CS-111, Figure 3(a)). The range of genetic distances between genotypes assigned to cluster Q1 was 0.288 - 0.443, and the mean was 0.346 (Figure 3(a)). In cluster Q2, the range of genetic distances between genotypes was 0.092 - 0.334, with a mean of 0.268, and this cluster included the two genotypes with the smallest genetic distance (0.092), TAM-CS-138 and USDA-273 (Figure 3(b)).

The population structure analysis also revealed that genotypes from the breeding programs were distributed between the Q1 and Q2 clusters, while all evaluated genotypes from the USDA collection belonged to the Q2 cluster (Table 2 and Table S1). The majority of genotypes (62%) in the Q1 cluster were developed by the Texas A&M College Station breeding program, while germplasm developed by the Texas A&M AgriLife Weslaco and Leeper breeding programs accounted for 18.75% and 12.5%, respectively (Table 2). On the other hand, the Weslaco and College Station breeding programs contributed roughly equally (41% and 36.89%, respectively) to cluster Q2, with the Leeper program accounting for 12.5% (Table 2). The Q2 cluster included most of the genotypes from each of the three breeding programs, accounting for 95.2% of those from the Weslaco program, 84.26% of those from the College Station program, and 91.66% of those from the Leeper program.

Distribution of tomato genotypes from six different sources into two clusters. A model-based structure analysis performed on 322 genotypes divided them into two clusters Q1 and Q2
Genotype sourceNo. genotypesNo. of genotypes in each clusterPercentage of genotypes in each cluster
Q1Q2Q1Q2
Overall322322909.990.1
TAM-W12561194.895.2
TAM-CS1272010715.7484.26
TAM-L484448.3491.66
USDA160160100
AVRDC31233.3466.64
Florida31233.3466.64

Note: AVRDC = Asian Vegetable Research and Development Center; TAM-CS = Dr. Kevin Crosby’s breeding program at Texas A&M at College Station; TAM-W = Dr. Carlos Avila’s breeding program at Texas A&M AgriLife Research and Extension Center at Weslaco, TX; TAM-W = Dr. Paul Leeper’s breeding program at Texas A&M AgriLife Research and Extension Center at Weslaco, TX; FLA = Florida Tomato Breeding Program; USDA = United States Department of Agriculture.

3.4. Phylogenetic Tree and Principal Component Analysis

Next, we constructed a phylogenetic tree based on the 10,236 SNPs and found that it also divided the 322 tomato population into two groups and that these groups corresponded with the two population clusters Q1 and Q2 (Figure 4). Thus, the phylogenetic tree displayed consistency with the population structure revealed by the model-based clustering analysis with STRUCTURE v2.3.4 (Figure 2). Figure 4 shows that the genotypes producing the smallest genetic distance (USDA-273 and TAM-CS-138) had the shortest branches arising from the lowermost clade. Similarly, genotype TAM-W-322, which was one of the two genotypes producing the largest genetic distance with another, was placed on the

extreme other side of the phylogenetic tree in the longest uppermost clade (Figure 4). The phylogenetic tree indicated that the genotypes TAM-W-322, TAM-CS-111, and TAM-L-16, from the Texas A&M Weslaco, College Station, and Leeper breeding programs, respectively, had the potential to yield greater genetic diversity when combined with other genotypes. We also performed PCA to check the number of population structure groups; Figure 5 presents the distribution of tomato genotypes in scatter plots of the first three principal components in a 3D space. This PCA also revealed that the tomato genotypes clustered into two groups, with some overlap indicative of the small genetic distances between some genotypes in Q1 and Q2.

4. Discussion

Genetic diversity studies have increased in recent years due to advances in high-throughput sequencing technologies and the availability of high-resolution SNPs. For example, 5.4 million SNPs were identified between wild and cultivated tomato genomes during the sequencing of the tomato reference genome from the cultivar Heinz 1706 [23] . Likewise, 11.6 million SNPs were found from the sequencing of 360 accessions that included both cultivated and wild tomato species [19] and 180,000 - 350,000 SNPs from the sequencing of four large-fruited cultivated tomato accessions [38] . In the present study, sequencing of 322 tomato genotypes from cultivated S. lycopersicum resulted in the discovery of 3.2 million SNPs. After filtering on the basis of quality parameters, 10,236 high-quality SNPs were obtained and used for genetic diversity analysis. Among them, the largest number of SNPs were observed in chromosome 12, followed by chromosome 1 and 10 (Figure 1). The existence of unanchored scaffolds (Chr00) and the large

number of SNPs mapped to it (1279 in total) indicate that numerous genomic regions have not yet properly placed in chromosomes [2] . It also highlights the importance of identifying new intraspecific SNPs in the tested tomato breeding lines.

Past efforts to develop diverse breeding populations in Texas A&M University breeding programs are reflected in the range of genetic diversity within and between the groups of tomato lines developed by the three Texas A&M programs as well as in comparison to the outgroup lines. High ranges were expected, since some of these lines were generated from diverse sets of parents, including some that the USDA, Florida, and AVRDC programs contributed to Texas A&M diversity (Table 1 and Table S1). Among the breeding programs, the highest range and mean of genetic diversity were detected among the genotypes from the Texas A&M Weslaco (genetic distance range 0.175 - 0.434, mean 0.264) and College Station (range 0.099 - 0.392, mean 0.282) breeding programs (Table 1). These results can be explained by the possibility that a significant proportion of common parents shared has been shared between Texas A&M breeding programs and subsequent selections between programs. The largest genetic diversity was achieved from the combination of genotypes from the Weslaco and College Station programs (genetic distance of 0.443 between genotypes TAM-W-322 and TAM-CS-111), indicating that crossing germplasm from the two programs should generate more variation for cultivar development. However, in looking at the genetic diversity between the Weslaco and College Station breeding programs, we found that there was in general greater genetic diversity within than between programs, perhaps because the recently initiated program at Weslaco used College Station material for breeding population development. The broad range of genetic diversity of breeding lines within a breeding program was also reflected in the population structure analysis and the phylogenetic tree (Figure 3 and Figure 4). Genotypes from all three Texas A&M breeding programs and also from AVRDC and Florida lines were observed in both the Q1 and Q2 clusters (Figure 4). Additionally, the grouping of genotypes into two clusters with some overlaps was further validated by the PCA.

Several inbred lines developed by the Texas A&M Weslaco and College Station breeding programs were developed from the hybridization of heirloom tomato parents with morphologically diverse fruit characteristics, including color, size, and shape, in an attempt to improve quality. Though distinct in nature, heirloom tomatoes possess comparatively low genetic diversity [2] [39] [40] . Thus, a genotype developed by hybridizing two heirloom tomato strains is expected to have low genetic diversity compared to genotypes evolved from contemporary lines since heirloom genotypes that are different only in shape and color may differ only by a handful of genes [41] [42] [43] . This may have contributed to the lower genetic diversity in some of the Texas A&M Weslaco and College Station breeding program lines in the Q2 cluster.

On the other hand, some of the breeding lines were developed by introgressing one or more disease-resistance genes. Disease-resistance genes are primarily introgressed from wild relatives, which have been reported to carry 20 times higher genetic diversity than that of cultivated tomato [19] [20] , and which thereby contributed to the high genetic diversity in Texas A&M breeding populations. Some examples of introgressed resistance genes in the Texas A&M AgriLife breeding population include the gene Mi-1, which confers resistance against root knot nematode caused by Meloidogyne spp. and was introgressed from Solanum peruvianum [44] ; Sw-5, which confers resistance to the tomato spotted wilt virus (TSWV), introgressed from S. peruvianum [45] [46] ; Ty-2 and Ty-3, which confer resistance to tomato yellow leaf curl virus (TYLCV), introgressed from S. habrochaites [47] [48] and S. chilense [49] , respectively; and I-2 and I-3, conferring resistance to vascular wilt caused by Fusarium oxysporum race 2 (Fol2) and Fol1, Fol2, and Fol3, were introgressed from S. pimpinellifolium [50] and S. pennellii [51] [52] , respectively. Thus, introgressions of disease-resistance genes during hybridization could have played an important role in producing the genetic diversity among breeding lines observed in the present study and thus in grouping the genotypes into two clusters.

The present study revealed that the tomato breeding lines developed by the Texas A&M breeding programs possess a high level of genetic diversity and thus should be capable, upon selection, of yielding a variety of cultivars adapted for Texas production. Furthermore, the broad genetic base of the breeding lines and the higher recombination generated through hybridization could be utilized to uncover QTLs for complex traits. As the SNPs identified here were intraspecific, they could be valuable for uncovering economically important traits within cultivated tomato. Finally, our work here suggests that through the use of a phylogenetic tree and genetic distances, it is possible to develop crossing strategies to increase diversity and encourage hybrid development within and between breeding programs.

Acknowledgements

We are grateful to the USDA ARS Plant Genetic Resources Unit, the AVRDC, and Samuel Hutton at the University of Florida for providing seeds for this study. We would like to thank the Bioinformatics Genomics and Bioinformatics services, College Station, TX, for performing the GBS on tomato genotypes. We appreciate the help of Samantha Serna, Alexandra Hernandez, and Alondra Menchaca for planting tomato genotypes in the greenhouse, and Henry Awika and Sonia del Rio for tissue collection, lyophilization, and homogenization. This research was funded by Texas A&M AgriLife Research seed grant FY18-124353 assigned to C.A.A. and K.C. and Texas A&M AgriLife Research Insect-vectored Disease Seed Grant (114190-96210) to K.M.

Conflicts of Interest

The authors declare that they have no competing interests.

Cite this paper

Kandel, D.R., Bedre, R.H., Mandadi, K.K., Crosby, K. and Avila, C.A. (2019) Genetic Diversity and Population Structure of Tomato (Solanum lycopersicum) Germplasm Developed by Texas A&M Breeding Programs. American Journal of Plant Sciences, 10, 1154-1180. https://doi.org/10.4236/ajps.2019.107083

Supplementary The details of 322 tomato genotypes used in genetic diversity analysis. All the genotypes were from cultivated tomato Solanum lycopersicum
Genotype sourceGenotype IDClusterPedigreeGenerationFruit type*Fruit SizeFruit color
TAM-CSTAM-CS-1Q2Lost pedigreeF5RoundSRed
TAM-CSTAM-CS-2Q2bl46 HDF5CherryXSOrange
TAM-CSTAM-CS-3Q2T105F5RomaSRed
TAM-CSTAM-CS-4Q2BL30 med polated redF5RomaSRed
TAM-CSTAM-CS-5Q2bl39 vroom small pinkF5RomaSRed
TAM-WTAM-W-6Q2Pink Ponderosa#3 × I-2F6PearSRed
TAM-WTAM-W-7Q21500 × AVT1106 Plant 4F6RoundSRed
TAM-WTAM-W-8Q2275SBR × AVT1001 Plant BF6RomaSRed
TAM-CSTAM-CS-9Q2Alamo T11 VRF7RomaSRed
TAM-CSTAM-CS-10Q2Alamo T13F7RoundSRed
TAM-LTAM-L-11Q235RomaSRed
TAM-LTAM-L-12Q2106RoundSRed
TAM-LTAM-L-13Q2203
TAM-LTAM-L-14Q2221BeefsteakMRed
TAM-LTAM-L-15Q2249RomaSRed
TAM-LTAM-L-16Q1265
TAM-LTAM-L-17Q2489RomaSRed
TAM-LTAM-L-19Q2530RomaMRed
TAM-LTAM-L-20Q2701RomaSRed
TAM-LTAM-L-22Q2725RomaMRed
TAM-LTAM-L-23Q2761RomaMRed
TAM-LTAM-L-24Q2782RoundSRed
TAM-LTAM-L-25Q21116
TAM-LTAM-L-26Q21125RomaSRed
TAM-LTAM-L-27Q21131RoundSRed
TAM-LTAM-L-28Q21504RomaSRed
TAM-LTAM-L-29Q21525RomaMRed
TAM-LTAM-L-30Q21531
TAM-LTAM-L-31Q21538RomaMRed
TAM-LTAM-L-32Q21547RomaSRed
TAM-LTAM-L-33Q21555BeefsteakLRed
TAM-LTAM-L-35Q21576PearSRed
TAM-LTAM-L-37Q21587BeefsteakLRed
TAM-LTAM-L-38Q21603BeefsteakMRed
TAM-LTAM-L-39Q21615BeefsteakLRed
TAM-LTAM-L-40Q21633PearSRed
TAM-LTAM-L-41Q21656BeefsteakMRed
TAM-LTAM-L-42Q21666RomaLRed
TAM-LTAM-L-43Q21672RoundMRed
TAM-LTAM-L-44Q21678BeefsteakLRed
TAM-LTAM-L-45Q21689BeefsteakLRed
TAM-LTAM-L-46Q21695
TAM-LTAM-L-47Q21792
TAM-LTAM-L-49Q21804RoundSRed
TAM-LTAM-L-50Q21813RomaMRed
TAM-LTAM-L-51Q11838PearMRed
TAM-LTAM-L-52Q21869BeefsteakMRed
TAM-LTAM-L-53Q21894RomaMRed
TAM-LTAM-L-54Q21987RomaMRed
TAM-LTAM-L-55Q22001RomaMRed
TAM-LTAM-L-56Q22022RomaSRed
TAM-LTAM-L-57Q2W-9BeefsteakXLRed
TAM-WTAM-W-58Q2275SBR × DELICIOUS PI639212F5RoundSRed
TAM-W-59Q2HealaniRoundMRed
TAM-WTAM-W-60Q2W25 × CHEROKEE PURPLE P1639211F5RoundSPink
TAM-WTAM-W-61Q2W25 × CHEROKEE PURPLE P1639211F5RoundLPink
TAM-WTAM-W-62Q2W25 × DELICIOUS PI639212F5BeefsteakLRed
TAM-LTAM-L-63Q2W-12BeefsteakLRed
TAM-WTAM-W-64Q2W25 × I-2F5RomaSPink
TAM-WTAM-W-65Q2W25 × I-2F5BeefsteakLRed
TAM-W-66Q2Vit KasparCherryXSRed
TAM-WTAM-W-67Q2W29 × YELLOW PEACHF5RoundSRed
TAM-CSTAM-CS-68Q2bl49F5CherryXSRed
TAM-WTAM-W-69Q2W9 × HILLBILLY POTATO LEAF PI 639219F5RoundSRed
TAM-LTAM-L-70Q2W-25RoundMRed
TAM-CSTAM-CS-71Q2bl44F5CherryXSYellow
TAM-WTAM-W-72Q2W25 × DELICIOUS PI639212F5BeefsteakLRed
TAM-WTAM-W-73Q2W9 × HILLBILLY POTATO LEAF PI 639219F5BeefsteakMRed
TAM-CSTAM-CS-74Q2RG1F5BeefsteakXLPink
TAM-CSTAM-CS-75Q2T106F5BeefsteakLRed
TAM-CSTAM-CS-76Q2RG1F5HeirloomXLPink
TAM-LTAM-L-77Q2W-29RomaSRed
TAM-CSTAM-CS-78Q2bl49F5HeirloomXLPink
TAM-CSTAM-CS-79Q2Lost pedigreeF5BeefsteakXLPink
TAM-CSTAM-CS-80Q2T65F5RoundSYellow
TAM-CSTAM-CS-81Q2T22F5BeefsteakLPink
TAM-CSTAM-CS-82Q2RG2F5BeefsteakXLPink
TAM-CSTAM-CS-83Q2T74F5BeefsteakLRed
TAM-LTAM-L-84Q1275 SBRRoundSRed
TAM-CSTAM-CS-85Q2T74F5BeefsteakXLRed
TAM-CSTAM-CS-86Q2Lost pedigreeF5BeefsteakLPink
TAM-CSTAM-CS-87Q2T74F5HeirloomXLPink
TAM-CSTAM-CS-88Q2RG2F5RoundLTiger stripe
TAM-CSTAM-CS-89Q2RG2F5HeirloomXLTiger stripe
TAM-CSTAM-CS-90Q2T36F5BeefsteakXLRed
TAM-LTAM-L-91Q2276 SBRRomaSRed
TAM-CSTAM-CS-92Q2BL10F5BeefsteakXLYellow
TAM-CSTAM-CS-93Q1T37F5BeefsteakXLPink
TAM-CSTAM-CS-94Q2bl9F5BeefsteakXLRed
TAM-CSTAM-CS-95Q2bl9F5BeefsteakXLRed
TAM-CSTAM-CS-97Q2Lost pedigreeF5BeefsteakXLRed
TAM-LTAM-L-98Q1277 SBRBeefsteakLRed
TAM-CSTAM-CS-99Q2RG6F5BeefsteakLRed
TAM-CSTAM-CS-100Q2BL 27 F’15F5BeefsteakLRed
TAM-CSTAM-CS-101Q2BL 30 v small round yellowF5CherrySYellow
TAM-CSTAM-CS-102Q2T67F5BeefsteakLRed
TAM-CSTAM-CS-103Q2BL12F5BeefsteakLRed
TAM-CSTAM-CS-104Q2BL27 @ redF5RoundLRed
TAM-CSTAM-CS-105Q2HT-1HeirloomXLPink
TAM-CSTAM-CS-106Q2T37F5BeefsteakXLPink
TAM-CSTAM-CS-107Q2T39F5BeefsteakXLPink
TAM-CSTAM-CS-108Q2RG2F5BeefsteakXLTiger stripe
TAM-CSTAM-CS-109Q2Lost pedigreeF5BeefsteakLRed
TAM-CSTAM-CS-110Q2Lost pedigreeF5RoundLRed
TAM-CSTAM-CS-111Q1T105F5RoundSRed
TAM-CSTAM-CS-112Q2TAM Hot TyBeefsteakXLRed
TAM-CSTAM-CS-113Q1t38F5BeefsteakLRed
TAM-CSTAM-CS-114Q2bl50F5CherrySRed
TAM-CSTAM-CS-115Q2T104F5RoundMRed
TAM-CSTAM-CS-116Q1T94F5BeefsteakLRed
TAM-CSTAM-CS-117Q1T69F5BeefsteakMRed
TAM-CSTAM-CS-118Q2RG2F5BeefsteakLPink
AVRDCAVRDC-119Q2AVT1001BeefsteakMRed
TAM-CSTAM-CS-120Q1RG2F5RoundMPink
TAM-CSTAM-CS-121Q2BL17F5BeefsteakLRed
TAM-CSTAM-CS-122Q2BL9F5RomaSRed
TAM-CSTAM-CS-123Q2T40F5BeefsteakLPink
TAM-CSTAM-CS-124Q2TSW3P4F5BeefsteakLPink
TAM-CSTAM-CS-125Q1T73F5BeefsteakLRed
AVRDCAVRDC-126Q1AVT1106RomaSRed
TAM-CSTAM-CS-127Q2BL15F5BeefsteakLPink
TAM-CSTAM-CS-128Q2RG2F5HeirloomXLPink
TAM-CSTAM-CS-129Q2Diablo bc vrF5RoundSRed
TAM-CSTAM-CS-130Q2Lost pedigreeF5RoundLRed
TAM-CSTAM-CS-131Q2T20F5RoundLRed
TAM-CSTAM-CS-132Q1T101F5RoundMRed
AVRDCAVRDC-133Q2AVT1110RoundMRed
TAM-CSTAM-CS-134Q2BL15F5BeefsteakXLRed
TAM-CSTAM-CS-135Q1bl41 vroom bulk small redF5CherryXSYellow
TAM-CSTAM-CS-136Q2BL15F5RomaSRed
TAM-CSTAM-CS-137Q2T44F5BeefsteakXLRed
TAM-CSTAM-CS-138Q2T102F5HeirloomXLPink
TAM-CSTAM-CS-139Q2T19F5BeefsteakLRed
TAM-CSTAM-CS-141Q2T53F5BeefsteakLPink
TAM-CSTAM-CS-142Q1bl46 @ small redF5BeefsteakLRed
TAM-CSTAM-CS-143Q2T107F5BeefsteakLRed
TAM-CSTAM-CS-144Q1T99F5CherrySYellow
TAM-CSTAM-CS-145Q2BL30F5BeefsteakMRed
TAM-CSTAM-CS-146Q2t58 @ red cherryF5CherrySRed
FLAFLA-147Q1Fla8624BeefsteakLRed
TAM-CSTAM-CS-148Q2T97F5CherrySYellow
TAM-CSTAM-CS-149Q1T55F5HeirloomXLPink
TAM-CSTAM-CS-150Q1T61F5CampariSRed
TAM-CSTAM-CS-151Q2RG1P4F2F5BeefsteakMPink
TAM-CSTAM-CS-152Q2BL30 vr lg redF5BeefsteakLRed
TAM-CSTAM-CS-153Q2BL16F5BeefsteakXLYellow
FLAFLA-154Q2Fla417-8RoundMRed
TAM-CSTAM-CS-155Q2T82F5BeefsteakXLRed
TAM-CSTAM-CS-156Q2T79F5ItalianMRed
TAM-CSTAM-CS-157Q2T27F5BeefsteakXLRed
TAM-CSTAM-CS-158Q1T33F5
TAM-CSTAM-CS-159Q2T39F5BeefsteakLRed
TAM-CSTAM-CS-160Q2T89F5CampariSPink
FLAFLA-161Q2154712-1BeefsteakLRed
TAM-CSTAM-CS-162Q1BL12F5HeirloomLTiger stripe
TAM-CSTAM-CS-163Q2BL18F5CherrySYellow
TAM-CSTAM-CS-164Q2b38 red round pink fleshF5BeefsteakXLPink
TAM-CSTAM-CS-165Q1t59 @ red cherryF5BeefsteakMOrange
TAM-CSTAM-CS-166Q2T23F5RoundMRed
TAM-CSTAM-CS-167Q2T35F5BeefsteakLRed
TAM-CSTAM-CS-168Q2Mi-1BeefsteakXLRed
TAM-CSTAM-CS-169Q2T57F5BeefsteakMPink
TAM-CSTAM-CS-170Q1T62F5HeirloomXLPink
TAM-CSTAM-CS-171Q2RG6WESF2P2F5BeefsteakMRed
TAM-WTAM-W-172Q1PI 633505 Yellow Peach × I-3 Ty-3F6CampariSYellow
TAM-WTAM-W-173Q1PI 633505 Yellow Peach × I-3 Ty-3F6CampariSPink
TAM-WTAM-W-174Q2PI 633505 Yellow Peach × I-3 Ty-3F6RoundMRed
TAM-CSTAM-CS-175Q2I-3 Ty-2BeefsteakXLRed
TAM-WTAM-W-176Q2PI 633505 Yellow Peach × I-3 Ty-3F6RoundMYellow
TAM-WTAM-W-177Q2PI 639208 Black from Tula × LA4440 Plant AF6RoundMRed
TAM-WTAM-W-178Q2PI 639209 Brandywine#1 × I-2 Ty-2F6BeefsteakMRed
TAM-WTAM-W-179Q2PI 639213 Juane Flamme × I-2 Ty-2F6HeirloomMYellow
TAM-WTAM-W-180Q2PI 639213 Juane Flamme × I-2 Ty-2F6BeefsteakSRed
TAM-WTAM-W-181Q2PI 639213 Juane Flamme × I-3 Ty-3F6RoundMYellow
TAM-CSTAM-CS-182Q1I-2-Ty-2RoundSRed
TAM-WTAM-W-183Q2PI 639213 Juane Flamme × I-3 Ty-3F6BeefsteakLOrange
TAM-WTAM-W-184Q2PI 639215 Principe Borguese × I-2 Ty-2F6RoundXSRed
TAM-WTAM-W-185Q2PI 639215 Principe Borguese × I-3 Ty-3F6CherrySRed
TAM-WTAM-W-186Q2PI 639215 Principe Borguese × I-3 Ty-3F6CherryXSRed
TAM-WTAM-W-187Q2PI 639217 Striped Cavern × I-2 Ty-2F6HeirloomSTiger stripe
TAM-WTAM-W-188Q2PI 639217 Striped Cavern × I-2 Ty-2F6BeefsteakSRed
TAM-CSTAM-CS-189Q2I2BeefsteakMRed
TAM-WTAM-W-190Q2PI 639217 Striped Cavern × I-2 Ty-2 Plant AF6HeirloomMTiger stripe
TAM-WTAM-W-191Q2PI 647526 Brandywine#1 × I-2 Ty-2F6BeefsteakXLRed
TAM-WTAM-W-192Q2PI 647526 Brandywine#1 × I-2 Ty-2F6HeirloomXLPink
TAM-WTAM-W-193Q2PI 647526 Brandywine#1 × I-2 Ty-2F6HeirloomXLRed
TAM-WTAM-W-194Q2PI 639215 Principe Borguese × I-2 Ty-2F6HeirloomMRed
TAM-WTAM-W-195Q2PI639209 Brandywine#1 × AVT1001 Plant AF6BeefsteakMPink
TAM-CSTAM-CS-196Q2I3BeefsteakLRed
TAM-WTAM-W-197Q2PI639209 Brandywine#1 × AVT1001 Plant BF6RoundMRed
TAM-WTAM-W-198Q1PI639209 Brandywine#1 × AVT1001 Plant BF6RoundMRed
TAM-WTAM-W-199Q1PI639209 Brandywine#1 × AVT1001 Plant CF6RoundMRed
TAM-WTAM-W-200Q2Supersteak#1 × I-2 Ty-2F6BeefsteakLRed
TAM-WTAM-W-201Q2Supersteak#1 × I-2 Ty-2F6BeefsteakLRed
USDAUSDA-203Q2440RoundXSBlack
TAM-WTAM-W-204Q2W-25#1 × Mi-1F6BeefsteakXLRed
TAM-WTAM-W-205Q2W-25#2 × I-3 Ty-3F6RoundSRed
TAM-WTAM-W-206Q2W-25#4 × Mi-1F6
TAM-WTAM-W-207Q2W-25#4 × Mi-1F6BeefsteakLRed
TAM-WTAM-W-208Q1W-29#3 × LA3473 Plant AF6RoundSRed
TAM-WTAM-W-209Q2PI 639208 Black from Tula × LA4440 Plant AF7RoundSRed
USDAUSDA-210Q2ProsperoBeefsteakMRed
TAM-WTAM-W-211Q2W-9#1 × I-3 Ty-3F6BeefsteakMRed
TAM-WTAM-W-212Q2W-9#1 × LA3473F6BeefsteakXLRed
TAM-WTAM-W-213Q2W-9#2 × Mi-1F6BeefsteakXLRed
TAM-WTAM-W-214Q2W-9#2 × Mi-1F6BeefsteakXLRed
TAM-WTAM-W-215Q2W9#1 × FLA417-8F6BeefsteakLRed
TAM-WTAM-W-216Q2PI 639211 Cherokee Purple × I-2 Ty-2F6BeefsteakMRed
USDAUSDA-217Q2Ailsa CraigRoundSRed
TAM-WTAM-W-218Q2PI 639211 Cherokee Purple × I-2 Ty-2F6BeefsteakLRed
TAM-WTAM-W-219Q2PI 639213 Juane Flamme × I-3 Ty-3F6BeefsteakLOrange
TAM-WTAM-W-220Q2PI 639217 Striped Cavern × I-2 Ty-2F6HeirloomMTiger stripe
TAM-WTAM-W-221Q2PI 639217 Striped Cavern × I-2 Ty-2F6Bell pepperMTiger stripe
TAM-WTAM-W-222Q2Supersteak#2 × I-2 Ty-2F6RoundLRed
TAM-WTAM-W-223Q2W-25#2 × I-3 Ty-3F6BeefsteakMRed
USDAUSDA-224Q2MoneymakerRoundSRed
TAM-WTAM-W-225Q2W-25#2 × Mi-1F6BeefsteakLRed
TAM-WTAM-W-226Q2W-25#3 × Mi-1F6BeefsteakLRed
TAM-WTAM-W-227Q2W-25#3 × Mi-1F6BeefsteakXLRed
TAM-WTAM-W-228Q2PI 639217 Striped Cavern × FLA417-8 Plant AF6HeirloomXLRed
TAM-CSTAM-CS-229Q2AVT1110 × RedlineF6CherrySPink
TAM-CSTAM-CS-230Q2AVT1001 × Black TulaF6BeefsteakLRed
USDAUSDA-231Q2Tres CantosRoundMRed
TAM-WTAM-W-232Q2106 × AVT1110 Plant BF7
TAM-WTAM-W-233Q2106 × AVT1110 Plant CF7RoundLRed
TAM-WTAM-W-234Q21212 × AVT1001 Plant AF7PearLRed
TAM-WTAM-W-235Q21212 × AVT1001 Plant AF7BeefsteakLRed
TAM-WTAM-W-236Q21212 × AVT1001 Plant BF7RoundSRed
TAM-WTAM-W-237Q21212 × AVT1001 Plant BF7BeefsteakSRed
USDAUSDA-238Q2Chico GrandeRomaMRed
TAM-WTAM-W-239Q21500 × AVT1110F7RoundMRed
TAM-WTAM-W-240Q21680 × AVT1106F7RoundMRed
TAM-WTAM-W-241Q21790 × AVT1001 Plant AF7RoundMRed
TAM-WTAM-W-242Q21790 × AVT1001 Plant BF7BeefsteakMRed
TAM-WTAM-W-243Q21790 × AVT1001 Plant BF7RoundSRed
TAM-WTAM-W-244Q21790 × AVT1106 Plant AF7RomaMRed
USDAUSDA-245Q2Heinz 1350BeefsteakMRed
TAM-WTAM-W-246Q21803 × AVT1001 Plant AF7RoundMRed
TAM-WTAM-W-247Q21803 × AVT1001 Plant BF7RoundSRed
TAM-WTAM-W-248Q21820 × AVT1110 Plant 2F7PearSRed
TAM-WTAM-W-249Q21820 × AVT1001 Plant AF7BeefsteakXLRed
TAM-WTAM-W-250Q21999 × AVT1001 Plant BF7BeefsteakMRed
TAM-WTAM-W-251Q21999 × AVT1001 Plant BF7RoundMRed
USDAUSDA-252Q2Heinz 1370RoundMRed
TAM-WTAM-W-253Q21999 × FLA417-8 Plant AF7BeefsteakLRed
TAM-WTAM-W-254Q22015 × AVT1001 Plant AF7BeefsteakLRed
TAM-WTAM-W-255Q2203 × AVT1001 Plant AF7BeefsteakLRed
TAM-WTAM-W-256Q2W12 × AVT1106 Plant AF7RomaSRed
TAM-WTAM-W-257Q2277SBR × AVT1001 Plant AF7RoundMRed
TAM-CSTAM-CS-258Q2T5 × NC946 (Ty-2, Sw-5, I-3)F7CherrySPink
USDAUSDA-259Q2NC 50-7BeefsteakLRed
TAM-WTAM-W-260Q2330 × AVT1106 Plant AF7RomaSRed
TAM-WTAM-W-261Q2330 × AVT1106 Plant AF7RoundLRed
TAM-WTAM-W-262Q2330 × FLA417-8 Plant AF7RoundMRed
TAM-WTAM-W-263Q2W12 × AVT1001 Plant AF7BeefsteakXLRed
TAM-WTAM-W-264Q2W12 × AVT1001 Plant AF7RoundMRed
TAM-WTAM-W-265Q2W12 × AVT1001 Plant BF7BeefsteakXLRed
USDAUSDA-266Q2Peto 460RomaLRed
TAM-WTAM-W-267Q2W12 × FLA417-8 Plant 1F7
TAM-WTAM-W-268Q2W4 × AVT1106 Plant 1F7
TAM-WTAM-W-269Q2W4 × AVT1106 Plant 2F7RoundMRed
TAM-WTAM-W-270Q2W4 × AVT1106 Plant 2F7RoundMRed
TAM-WTAM-W-271Q2106 × AVT1001 Plant AF7BeefsteakMRed
TAM-WTAM-W-272Q2106 × AVT1106 Plant AF6RoundMRed
USDAUSDA-273Q2Baxter’s Early Bush CherryCherryXSRed
TAM-WTAM-W-274Q22015 × AVT1001 Plant BF7HeartSRed
TAM-WTAM-W-275Q2203 × AVT1001 Plant AF7BeefsteakSRed
TAM-WTAM-W-276Q2275SBR × AVT1001 Plant AF7RoundSRed
TAM-WTAM-W-277Q2275SBR × AVT1106 Plant AF7RoundSRed
TAM-WTAM-W-278Q2277SBR × AVT1001 Plant AF7BeefsteakXLRed
TAM-CSTAM-CS-279Q2T5 × NC946 (Ty-2, Sw-5, I-3)F7RomaSRed
USDAUSDA-280Q2NC 8288BeefsteakXLRed
TAM-CSTAM-CS-281Q2T5 × NC946 (Ty-2, Sw-5, I-3)F7RoundSRed
TAM-CSTAM-CS-282Q2T5 × NC946 (Ty-2, Sw-5, I-3)F7RomaMRed
TAM-WTAM-W-283Q2CLN2498XFLA619yF9RomaMRed
TAM-WTAM-W-284Q2130710 × T55F8BeefsteakXLRed
TAM-WTAM-W-285Q2130710 × T55F8BeefsteakXLRed
TAM-WTAM-W-286Q2130710 × T55F8RoundLRed
USDAUSDA-287Q2Yellow PeachCherrySYellow
TAM-WTAM-W-288Q2130710 × T55F8BeefsteakLRed
TAM-WTAM-W-289Q2T11-5-1 × T55F8BeefsteakMRed
TAM-WTAM-W-290Q2PI 639208 Black from Tula × LA4440 Plant CF8
TAM-CSTAM-CS-291Q2T215 VR × ManyellF8BeefsteakXLYellow
TAM-CSTAM-CS-292Q2Gold Nugget × T5F8BeefsteakXLRed
TAM-CSTAM-CS-293Q2Black Seaman × T215F8BeefsteakXLPink
USDAUSDA-294Q2RosaHeirloomXLPink
TAM-CSTAM-CS-295Q2AVT1110 × RedlineF8HeirloomLPink
TAM-CSTAM-CS-296Q2Alamo T13F8HeirloomXLPink
TAM-CSTAM-CS-297Q1T215 VR × ManyellF8BeefsteakXLRed
TAM-CSTAM-CS-298Q2Gold Nugget × SungoldF8RoundMOrange
TAM-CSTAM-CS-299Q2Estrella × AVT1109F8ItalianLRed
TAM-CSTAM-CS-300Q2Gold Nugget × T5F8RoundMRed
TAM-CSTAM-CS-301Q2Black icicle × T5F8PearLRed
TAM-CSTAM-CS-302Q2AVT1110 × RedlineF8BeefsteakMRed
TAM-CSTAM-CS-303Q1T135 × Black TulaF8BeefsteakLRed
TAM-CSTAM-CS-304Q2AVT1110 × BL60F8BeefsteakLRed
TAM-CSTAM-CS-305Q2AVT1104 × J & D 7F8CherrySYellow
TAM-CSTAM-CS-306Q2AVT 1001 × Black CherryF8CherrySPink
USDAUSDA-307Q2Flora-dadeBeefsteakXLRed
TAM-CSTAM-CS-308Q2AVT 1001 × Black CherryF8CherrySPink
TAM-CSTAM-CS-309Q2Gypsy × T135 VRF8BeefsteakLPink
TAM-CSTAM-CS-310Q2AVT1104 × J & D 7F8BeefsteakLYellow
TAM-CSTAM-CS-311Q2AVT1104 × J & D 7F8RoundMOrange
TAM-CSTAM-CS-312Q2P278 × AVT 1106F8RomaSRed
TAM-WTAM-W-313Q2AVT1108 × BL100F9RoundLPink
TAM-WTAM-W-314Q2CLN2498XFLA619yF9RomaMPink
TAM-WTAM-W-315Q2CLN2498XFLA619yF9PearLPink
TAM-WTAM-W-316Q2CLN2498XFLA619yF9RomaLPink
TAM-WTAM-W-317Q2CLN2498XFLA619yF9RoundMRed
TAM-WTAM-W-318Q2CLN2498XFLA619y Plant BF9RoundSRed
TAM-WTAM-W-319Q2Zapotec × Avt1104F9RomaSRed
USDAUSDA-320Q2Pomodoro Superselezione di MarmandeHeirloomLRed
TAM-WTAM-W-321Q2T75= (WT 501 × Merced) × (T2-25 × CLN2498) F6F9HeirloomMPink
TAM-WTAM-W-322Q1Zapotec × Avt1104 Plant AF9RomaMPink
TAM-WTAM-W-323Q2Zapotec × Avt1104 Plant BF9
TAM-WTAM-W-324Q2CLN2498XFLA619yF9RoundMRed
TAM-WTAM-W-325Q2FLA417-8 × FM9F10BeefsteakMRed
TAM-WTAM-W-326Q2FLA417-8 × FM9F10RoundLRed
TAM-WTAM-W-327Q2FLA417-8 × FM9F10RoundMRed
TAM-WTAM-W-328Q2FLA417-8 × FM9F10RoundMRed
TAM-CSTAM-CS-329Q2AVT1104 × J & D 7F8RoundMOrange
TAM-CSTAM-CS-330Q2(Merced F6 × (Black Krim × FLA 417-8)F11BeefsteakLPink

AVRDC = Asian Vegetable Research and Development Center; TAM-CS = Dr. Kevin Crosby’s breeding program at Texas A&M at College Station; TAM-W = Dr. Carlos Avila’s breeding program at Texas A&M AgriLife Research and Extension Center at Weslaco, TX; TAM-W = Dr. Paul Leeper’s breeding program at Texas A&M AgriLife Research and Extension Center at Weslaco, TX; FLA = Florida tomato breeding program; USDA = United States Department of Agriculture; *Fruit size: XS = extra small, S = small, M = medium, L = large, XL = extra large.

<xref ref-type="table" rid="table">Table </xref>S2. Distance Matrix of 322 Genotypes Based on Identified SNPs Markers

https://agrilife.org/avilalab/

Abbreviations

AVRDC = Asian Vegetable Research and Development Center

GBS = Genotyping by Sequencing

HC = Haplotype Caller

MAF = Minor Allele Frequency

PCA = Principal Component Analysis

SNP = Single-Nucleotide Polymorphism

TAMU = Texas A&M University

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