Progress 09/01/13 to 08/31/16
Outputs
Target Audience:The molecular regulation of fruit weight among modern tomato varieties is largely unknown despite the importance of this trait in breeding programs. In the fresh market industry, increased fruit weight is desired for plum and beefsteak whereas increased fruit weight is not desired for grape tomato. The focus of this project is on five genes that control tomato fruit weight: FW2.2, FW3.2, FW11.3, FAS and LC. The alleles for FW3.2, FW11.3, FAS and LC are not fixed in cultivated tomato. In addition to weight, FAS and LC also control locule number which is critically important for the internal structure of beefsteak tomato. To extend this finding to economically relevant accessions, we will evaluate the distribution of the alleles for the five genes in tomato breeding germplasm and commercial hybrids. We will create pre-breeding materials where large fruit weight alleles are exchanged in fresh market materials, and evaluate the utility of the alleles for tomato improvement. We will also identify novel QTL controlling fruit weight from underutilized tomato germplasm and identify molecular markers linked to the trait. Collectively, these findings will enable informed decisions tailored to breeding goals that are specific to each market class. The results will be distributed via eXtension, including tutorials describing variation in genes that control tomato fruit morphology. Pre-breeding germplasm will be available via MTA at the institutions of the collaborators. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?
Nothing Reported
How have the results been disseminated to communities of interest?
Nothing Reported
What do you plan to do during the next reporting period to accomplish the goals?The project needs to be transferred to Univ of Georgia. See annual report for more details as nothing new has been accomplished since I moved labs (5 months ago).
Impacts
What was accomplished under these goals?
1.Genotype fruit weight and shape alleles in contemporary breeding tomato lines. Our findings show that the contemporary breeding lines are nearly completely fixed for the fruit weight and shape genes within each market class. For lc, the derived allele is common in beefsteak accessions. For ovate, the derived allele is common in grape accessions. The processing, beefsteak and plum class carry derived alleles for the three fruit weight genes, whereas grape tomato carries the derived allele of fw3.2 only. The vintage/heirloom collection found in the SolCAP germplasm is more genetically diverse for the fruit weight and shape alleles than any of the breeding lines. This finding is consistent with previous published results from our laboratory (Rodriguez et al 2011). These findings suggest a narrow diversity in the market classes for further improvement of tomato. 2.Develop pre-breeding germplasm for plum, beefsteak and grape market classes, and investigate the utility of known fruit weight alleles. For two plum breeding lines, we are exchanging the alleles of fw3.2 and lc. For both populations, selected BC2 F2 plants for each homozygous are being evaluated for fruit weight as well as for horticultural acceptability at Mountain Horticultural Crops Research & Extension Center, Mills River with collaborator Panthee, and also at the Ohio Agricultural Research and Development Center (OARDC) in Wooster. For two grape breeding lines, we are exchanging the three fruit weight alleles. We are currently evaluating the potential interactions of the fruit weight loci with one another and the pleiotropic effects of the loci for fruit weight and shape. For two beefsteak breeding lines, we are exchanging fw3.2 and fas or fw2.2 and fas, respectively. These populations are being evaluated for horticultural acceptability at the Gulf Coast Research and Education Center in Florida with collaborator Hutton. 3.Identify novel fruit weight QTL from populations derived from crosses between underutilized tomato germplasm and those segregating in beefsteak tomato germplasm. The findings from the initial stage of this project suggested that fw11.2 maps to a 62 kb region on chromosome 11. In an effort to better define the fw11.2 region, additional progeny tests were performed on 18 recombinants. Fruit weight and the interactions between fw3.2 and fw11.2 will be evaluated at the end of the season. We performed an additional QTL seq analysis for fruit weight and locule number in one S. l. cerasiforme F2 population. The traits were segregating. However, the bulk segregant coupled with QTL seq analyses showed only putative and minor QTL located in different centromeric regions in the tomato genome. Altogether, none of the putative QTL was highly significant and further analysis will not likely be conducted because of their location in non-recombining regions of the tomato genome. Lastly, we are in the process of identifying fruit weight QTL that are segregating in the beefsteak breeding lines. Average fruit size was measured on 60 plants of the (Fla. 8872B × Fla. 8857) population, and each plant was genotyped for known fruit weight alleles. Neither of the known loci had a significant effect on fruit weight; supporting the hypothesis that larger fruit size in Fla. 8872B is conferred by novel fruit weight QTL. Additional plants of this population will be evaluated in fall 2015 to increase the number of individuals available for QTL-seq identification of fruit weight alleles in Fla. 8872B. Analysis of 75 plants of the (Fla. 8872B × Fla. 8059) population determined that the Fla. 8872B allele at fw2.2 had a minor but significant effect on increasing fruit size. However, the increase in fruit weight arose from the wild allele at this locus which is contrary to data presented in publications. We are further investigating how the fw2.2 allele differs from other known alleles and confirming its effect on fruit size as well as considering whether a locus linked to fw2.2 is in fact increasing fruit size in this population. In beefsteak tomato breeding programs, larger fruit size is obtained in fruit that are globe-shaped vs. flat-round shaped. The globe-shape is undesirable for commercial beefsteak varieties due to increased fruit defects resulting in decreased marketability. Yet because the globe shape is recessive to flat, breeders often develop hybrids by crossing globe parents with flat parents in an effort to increase fruit size in the F1 . The genes controlling globe vs. flat fruit shape have not yet been characterized, and the effect of globe vs. flat shape on fruit size has not been quantified either. In fall 2014 and spring 2015, we evaluated three different F2 populations segregating for globe and flat fruit shape for their effect on fruit size. For all three populations, flat fruits were smaller than globe fruits (181 g vs 217 g; 184 g vs. 208 g; 137 g vs. 150 g). For one of these populations, Fla. 8000 × Fla. 8111B, 87 recombinant inbred lines were evaluated for fruit shape and also genotyped with the SolCAP SNP array, and a novel fruit shape QTL was identified. We confirmed this QTL in an F2 population of the same cross. Ongoing efforts seek to validate the effect of this QTL in additional parents, as well as to determine the gene(s) underlying this QTL.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2015
Citation:
Blanca, J., Montero-Pau, J., Sauvage, C., Bauchet, G., Illa, E., Diez, M.J., Francis, D., Causse, M., van der Knaap, E., Canizares, J. (2015) Genomic variation in tomato, from wild ancestors to contemporary breeding accessions. BMC Genomics 16, 257
- Type:
Journal Articles
Status:
Published
Year Published:
2015
Citation:
Illa-Berenguer, E., Van Houten, J., Huang, Z., van der Knaap, E. (2015) Rapid and reliable identification of tomato fruit weight and locule number loci by QTL-seq. Theor Appl Genet 128, 1329-1342.
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Progress 09/01/14 to 08/31/15
Outputs
Target Audience: The target audiences are: 1) tomato breeders and geneticists and 2) growers and consumers. The size and shape of vegetables and fruits is important to growers and consumers. Depending on the culinary purpose, consumers will not select produce that is too small or large and of the wrong shape. For tomato, the large and smooth round beefsteak is chosen for slicing onto sandwiches whereas the small and oval-shaped grape tomato is chosen for salads and garnish. Growers on the other hand aim for high yield (weight per acre land) and large produce for most market classes except grape tomato. Five genes are known to control the weight and shape of the tomato. Some of the genes lead to increased weight of the produce but come at a cost to the plant and the grower. For example, larger tomatoes tend to ripen slower, feature fewer branches and may display blossom end rot, a physiological disorder causing extensive losses to growers. The goals of this project are to evaluate whether a slight decrease in tomato weight can be offset by fewer undesirable characters and ultimately higher returns for farmers. Our efforts thus far have been to initiate the creation of these lines by conducting crosses and backcrosses, and using molecular markers to aid this process. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Post doctoral reseacher Eudald Illa Berenguer has been trained in the area of developing breeding lines, genome analysis and marker development. How have the results been disseminated to communities of interest?Two manuscripts have been published and one poster presentation at the Plant and Animal Genome meeting in San Diego in 2015. What do you plan to do during the next reporting period to accomplish the goals?We are still evaluating results fromthe field experiments in the Wooster and Mills River locations and will report on the results as well as next years results at the next reporting time.. We will continue to backcross the prebreeding germplasm and work with Sam Hutton and Dilip Panthee to evaluate this newly created materials forfruit weight and quality,and horticultural acceptability. The fine mapping of fw11.2 is going slower than expected due to the difficulty of pinpointing the gene to a defined location in the genome. Also,we foundno putative causitive SNPs in the region. For next year, we plan to evaluate genome structure at the locus.We also are seeking to obtain BAC clones in the fw11.2 region since there are several gaps in the tomato genome contig.These gaps may actually harbor informative SNPs that were missed during the analysis. We plan to conduct a QTL seq experiment with the beefsteak breeding lines developed by Sam Hutton in an effort to map the shape (globe vs round) and fruit weight loci. We willpost our findings including the genotype data for the fruit weight and shape genes at eXtension or another outlet in an effort to post the informationto the public.
Impacts
What was accomplished under these goals?
1.Genotype fruit weight and shape alleles in contemporary breeding tomato lines. Our findings show that the contemporary breeding lines are nearly completely fixed for the fruit weight and shape genes within each market class. For lc, the derived allele is common in beefsteak accessions. For ovate, the derived allele is common in grape accessions. The processing, beefsteak and plum class carry derived alleles for the three fruit weight genes, whereas grape tomato carries the derived allele of fw3.2 only. The vintage/heirloom collection found in the SolCAP germplasm is more genetically diverse for the fruit weight and shape alleles than any of the breeding lines. This finding is consistent with previous published results from our laboratory (Rodriguez et al 2011). These findings suggest a narrow diversity in the market classes for further improvement of tomato. 2.Develop pre-breeding germplasm for plum, beefsteak and grape market classes, and investigate the utility of known fruit weight alleles. For two plum breeding lines, we are exchanging the alleles of fw3.2 and lc. For both populations, selected BC2F2 plants for each homozygous are being evaluated for fruit weight as well as for horticultural acceptability at Mountain Horticultural Crops Research & Extension Center, Mills River with collaborator Panthee, and also at the Ohio Agricultural Research and Development Center (OARDC) in Wooster. For two grape breeding lines, we are exchanging the three fruit weight alleles. We are currently evaluating the potential interactions of the fruit weight loci with one another and the pleiotropic effects of the loci for fruit weight and shape. For two beefsteak breeding lines, we are exchanging fw3.2 and fas or fw2.2 and fas, respectively. These populations are being evaluated for horticultural acceptability at the Gulf Coast Research and Education Center in Florida with collaborator Hutton. 3.Identify novel fruit weight QTL from populations derived from crosses between underutilized tomato germplasm and those segregating in beefsteak tomato germplasm. The findings from the initial stage of this project suggested that fw11.2 maps to a 62 kb region on chromosome 11. In an effort to better define the fw11.2 region, additional progeny tests were performed on 18 recombinants. Fruit weight and the interactions between fw3.2 and fw11.2 will be evaluated at the end of the season. We performed an additional QTL seq analysis for fruit weight and locule number in one S. l. cerasiforme F2 population. The traits were segregating. However, thebulk segregant coupled with QTL seq analyses showed only putative and minor QTL located in different centromeric regions in the tomato genome. Altogether, none of the putative QTL was highly significant and further analysis will not likely be conducted because of their location in non-recombining regions of the tomato genome. Lastly, we are in the process of identifying fruit weight QTL that are segregating in the beefsteak breeding lines. Average fruit size was measured on 60 plants of the (Fla.8872B × Fla.8857) population, and each plant was genotyped for known fruit weight alleles. Neither of the known loci had a significant effect on fruit weight; supporting the hypothesis that larger fruit size in Fla.8872B is conferred by novel fruit weight QTL. Additional plants of this population will be evaluated in fall 2015 to increase the number of individuals available for QTL-seq identification of fruit weight alleles in Fla.8872B. Analysis of 75 plants of the (Fla.8872B × Fla.8059) population determined that the Fla.8872B allele at fw2.2 had a minor but significant effect on increasing fruit size. However, the increase in fruit weight arose from the wild allele at this locus which is contrary to data presented in publications. We are further investigating how the fw2.2 allele differs from other known alleles and confirming its effect on fruit size as well as considering whether a locus linked to fw2.2 is in fact increasing fruit size in this population. In beefsteak tomato breeding programs, larger fruit size is obtained in fruit that are globe-shaped vs. flat-round shaped. The globe-shape is undesirable for commercial beefsteak varieties due to increased fruit defects resulting in decreased marketability. Yet because the globe shape is recessive to flat, breeders often develop hybrids by crossing globe parents with flat parents in an effort to increase fruit size in the F1. The genes controlling globe vs. flat fruit shape have not yet been characterized, and the effect of globe vs. flat shape on fruit size has not been quantified either. In fall 2014 and spring 2015, we evaluated three different F2 populations segregating for globe and flat fruit shape for their effect on fruit size. For all three populations, flat fruits were smaller than globe fruits (181 g vs 217 g; 184 g vs. 208 g; 137 g vs. 150 g). For one of these populations, Fla.8000 × Fla.8111B, 87 recombinant inbred lines were evaluated for fruit shape and also genotyped with the SolCAP SNP array, and a novel fruit shape QTL was identified. We confirmed this QTL in an F2 population of the same cross. Ongoing efforts seek to validate the effect of this QTL in additional parents, as well as to determine the gene(s) underlying this QTL.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2015
Citation:
Blanca, J., Montero-Pau, J., Sauvage, C., Bauchet, G., Illa, E., Diez, M.J., Francis, D., Causse, M., van der Knaap, E., Canizares, J. (2015) Genomic variation in tomato, from wild ancestors to contemporary breeding accessions. BMC Genomics 16, 257
- Type:
Journal Articles
Status:
Published
Year Published:
2015
Citation:
Illa-Berenguer, E., Van Houten, J., Huang, Z., van der Knaap, E. (2015) Rapid and reliable identification of tomato fruit weight and locule number loci by QTL-seq. Theor Appl Genet 128, 1329-1342.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2015
Citation:
llla-Berenguer, Eudald and van der Knaap Esther. Fruit Weight Regulation in Tomato: identification and validation of novel QTLs, in Plant and Animal Genome XXIII Conference. San Diego, CA. USA.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2015
Citation:
Illa-Berenguer, Eudald. QTL-seq: a rapid and efficient way to identify new QTLs in tomato, too, in Bioinformatic Practitioner/R User Group meeting, Molecular and Cellular Imaging Center (MCIC), OARDC/OSU, Wooster, OH, USA.
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Progress 09/01/13 to 08/31/14
Outputs
Target Audience: The target audience are tomato breeders and geneticists. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided? Training has been provided to a post doc in the area of genome analysis, molecular marker development, QTL seq and develpopment of breeding lines. How have the results been disseminated to communities of interest? The first manuscript has been submitted. Collectively, we have presented these findings in three separate oral presentations (two local and one international meeting). What do you plan to do during the next reporting period to accomplish the goals? For goal 2, we plan to evaluate the newly created breeding germplasm for horticultural and fruit quality traits in three locations: Florida, Ohio and North Carolina. For goal 3, we will conduct association mapping to identify the most likely candidate gene underlying fw11.2. Additionally, we will conduct QTL seq to identify new fruit weight and locule number genes in the F2 populations that were phenotyped this summer.
Impacts
What was accomplished under these goals?
Lay abstract:The size and shape of vegetables and fruits is important to growers and consumers. Depending on the culinary purpose, consumers will not select produce that is too small or large and of the wrong shape. For tomato, the large and smooth round beefsteak is chosen for slicing onto sandwiches whereas the small and oval-shaped grape tomato is chosen for salads and garnish. Growers on the other hand aim for high yield (weight per acre land) and large produce for most market classes except grape tomato. Five genes are known to control the weight and shape of the tomato. Some of the genes lead to increased weight of the produce but come at a cost to the plant and the grower. For example, larger tomatoes tend to ripen slower, feature fewer branches and may display blossom end rot, a physiological disorder causing extensive losses to growers. The goals of this project are to evaluate whether a slight decrease in tomato weight can be offset by fewer undesirable characters and ultimately higher returns for farmers. Our efforts thus far have been to initiate the creation of these lines by conducting crosses and backcrosses, and using molecular markers to aid this process. The current knowledge on the regulation of tomato weight and shape is far from complete. The regulation of weight and shape can be viewed as a large puzzle for which we identified only a few pieces out of many. Thus, our project aims to identify novel tomato genes that further explain the size variation of the vegetable. This additional knowledge would greatly enable tomato breeders to develop new varieties for the different market classes featuring the correct shapes and sizes. Prior public support for technology improvement in the area of genome sequencing now allows us to identify candidate genes that control weight of the tomato in a much more expeditious manner than before. Within one year of the project, the Next Generation Sequencing approach resulted in the identification of a very small region in the tomato genome that controls weight with only a few candidate genes that underlie the trait. We are now well positioned to definitively show which of these genes controls weight and determine whether crop improvement is feasible using the different versions of the gene. Specific details: Goal 1 has been accomplished and the manuscript detailing the findings has been submitted for peer review. The data include genotype information for 426 SolCAP accessions and an additional 523 wild, cerasiforme and cultivated tomato accessions. Briefly, for contemporary accessions excluding grape tomato, almost all accessions carry the mutation in the three fruit weight genes. This suggest a too narrow basis in these market classes for the improvement of fruit weight. With respect to locule number, only lc is found in beefsteak tomato. However this mutation can not explain the high locule number found in this tomato type and thus other genes that control this character must be present in the tomato germplasm. Goal 2 We have started to introgress wild type allele for certain fruit weight genes in selected beefsteak and plum tomatoes for 3 generations. Goal 3 Using a bulk segregant and whole genome sequencing approach, we identified a single QTL, fw11.2, associated with fruit weight variation at the distal part of chromosome 11. Although FW11.2 maps close to FAS and FW11.3, it is distinct from these two known fruit weight genes. We confirmed the location to a ~750-kb interval using progeny testing. To better define the fw11.2 region, additional progeny tests were performed on 38 recombinants. The progeny test showed that fw11.2 was fine-mapped to a 62 kb region in chromosome 11. According to the genome annotation, only 8 genes are found in the 62-kb region corresponding to fw11.2 locus. This summer, we phenotypically characterized two additional populations for segregation in fruit weight and locule number. The known fruit weight and locule number genes were not segregating in either population. Thus, the phenotypic results suggested that new fruit weight and two locule number genes are segregating in the populations. Locule number is critical for shaping the beefsteak tomato and this phenotype is not explained by lc alone (see goal 1).
Publications
- Type:
Journal Articles
Status:
Submitted
Year Published:
2014
Citation:
Genomic variation in the tomato, from wild ancestors to contemporary breeding accessions.
Jose M Blanca, Javier Montero-Pau, Christopher Sauvage, Guillaume Bauchet, Eudald Illa, Mar�a J Diez, David Francis, Mathilde Causse, Esther van der Knaap and Joaquin Ca�izares
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2014
Citation:
Local presentation: Illa, Eudald. Identification of novel fruit size QTL in tomato, in Wooster Association of Molecular Biology Area (WAMBA) Seminars. OARDC/OSU, Wooster, OH, USA.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2014
Citation:
State-wide presentation: Illa, Eudald, van Houten, Jason, and van der Knaap, Esther. Identification and Validation of Novel QTLs Linked to Fruit Weight Variation in Tomato, in 2014 Midwestern Section Annual Meeting. Columbus, OH. USA.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2014
Citation:
International meeting: Van der Knaap, Esther. Identification of Novel Genes Controlling Tomato Fruit Weight using a Bulk Segregant and Whole Genome Sequencing Approach. Genome-assisted Biology of Crops and Model Plant Systems. Cold Spring Harbor Asia Conference, Suzhou, China, Apr 21-25, 2014.
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