Progress 03/15/18 to 03/14/22
Outputs
Target Audience:The target audience of this project includes tomato producers in areas affected by Fusarium wilt race 3 (both fresh market and processing markets); and tomato breeders, geneticists and pathologists in public and private sectors. Changes/Problems:Prior to the start of this grant, it was unclear whether the negative effects associated with I-3 were due to linkage drag or pleiotropy. We planned to investigate this using both conventional breeding methods and gene editing with CRIPSR. Early field trials indicated that reducing the I-3introgression resolves the negative effects, supporting that these problems are not due to pleiotropy. We therefore discontinued efforts to manipulate the I-3 gene using CRISPR, and we invested our efforts on the remaining objectives. Several project delays occurred in 2020-2021 due to the Covid-19 pandemic, which led to a University shutdown and workplace restrictions, and coincided with several staff changes in the Vallad lab. Research resumed fully in 2021-2022 and allowed the successful completion of each of the project's goals. What opportunities for training and professional development has the project provided?Jessica Chitwood-Brown was trained as a PhD student on this project until her graduation in August 2020; Dr. Chitwood-Brown then continued to work on this project as a post-doctoral researcher until she began a new faculty position in March, 2022. Dr. Joseph Carrillo, post-doctoral researcher, carried out work on project from July 2020 until he began a new position with Syngenta Crop Protection in August 2021. Dr. Katia Xavier, post-doctoral researcher, carried out work on the project from January 2020 until leaving for a position with Invaio Sciences in June 2020. Dr. Juliana Aparecid Pereira, post-doctoral researcher, carried out work on the project from May 2018 until she took a position with Bayer Crop Sciences in August 2019. Several undergraduates worked on this project in 2020-2021 including Andrea Karina Suazo Tejada (Zamorano University, Honduras) and Hannah Mather (University of Florida, Microbiology). Gurleen Kaur, PhD student in the Lee lab, contributed to this research project in 2018. Samuel Ipinyomi, a new PhD student in the Hutton lab, has carried out research on this project since August 2021. How have the results been disseminated to communities of interest?Chitwood-Brown, J., Vallad, G., Lee, T.G., and Hutton, S.F. (2018). Taking a closer look at Fusarium wilt resistance in tomato. Proc. Florida Tomato Institute. PRO 534:4-5 Chitwood-Brown, J (2020). Improving Resistance to Fusarium Wilt Race Three of Tomato (Solanum lycopersicum). [Doctoral dissertation, University of Florida]. Chitwood-Brown J, Vallad GE, Lee TG, Hutton SF (2021)Characterization and elimination of linkage-drag associated with Fusarium wilt race 3 resistance genes.Theor Appl Genet. https://doi.org/10.1007/s00122-021-03810-5 Chitwood-Brown, J, GE Vallad, TG Lee, and SF Hutton (2021) Breeding for resistance to fusarium wilt of tomato: a review. Genes 12:1673. https://doi.org/10.3390/ genes12111673 Li, J, J Chitwood-Brown, G Kaur, JA Labate, GE Vallad, TG Lee, and SF Hutton (2022) Novel sources of resistance to Fusarium oxysporum f. sp. lycopersici race 3 among Solanum pennellii accessions. J. Amer. Soc. Hort. Sci. 147:35-44. Members of the Hutton lab gave research presentations that highlighted the work from this project: Chitwood-Brown, J., Hutton, S.F., Lee, T.G., and Vallad, G.E. (2018). "A dual strategy to advance resistance to Fusarium wilt race 3 of tomato." Poster presented at Florida Ag Expo. 2018 November 7. Wimauma, FL. Chitwood-Brown, J., Hutton, S.F., Lee, T.G., and Vallad, G.E. (2018). "A Closer Look at Fusarium Wilt Resistance in Tomato." Oral presentation at annual seminar of Florida Seed Association. 2018 May 30. Gainesville, FL. Chitwood-Brown, J., Hutton, S.F., Lee, T.G., and Vallad, G.E. (2018). "The improvement of resistance to fusarium wilt race 3 of tomato." Poster presented at Ohio State University Plant Sciences Symposium. 2018 April 7. Wooster, OH. Chitwood-Brown, J., and Hutton, S.F. (2018). "Discovery and improvement of novel and known resistance to Fusarium wilt race three of tomato." Oral presentation at 47th Tomato Breeders Roundtable. 2018 April 4-6. Wooster, OH. Chitwood-Brown, J., Hutton, S.F., Lee, T.G., and Vallad, G.E. (2018). "Improving resistance to Fusarium wilt race 3 of tomato." Oral presentation at University of Minnesota Plant Sciences Symposium. 2018 March 22-23. St. Paul, MN. Chitwood-Brown, J. (2019) "Improving Resistance in Tomato to Fusarium Wilt Race 3 of Tomato." Oral presentation at UF Horticultural Sciences Department Seminar Series. 2019 Feb 4. Gainesville, FL. Chitwood-Brown, J., Hutton, S.F., Lee, T.G., and Vallad, G.E. (2019) "Mission in Progress: Improving Disease Resistance in Tomato to Help Save the World." Oral presentation at GCREC Seminar Series. 2019 Sept 5. Wimauma, FL. Chitwood-Brown, J. (2019) "Reducing Linkage Drag Associated with the I-3 Gene." Oral presentation at GCREC Three Minute Thesis competition. 2019 Nov 14. Wimauma, FL. Hutton, S., Vallad, G., Lee, T., Chitwood-Brown, J., Pereira, J. (2019). "NIFA: Advancing resistance to Fusarium wilt of tomato through the pyramiding of available and novel resistance genes." Poster presented at National Association of Plant Breeders annual meeting. 2019 August 27. Pine Mountain, GA. Chitwood-Brown, J., Hutton, S.F., Lee, T.G., Vallad, G.E. (2019). "Breaking Free: Eliminating linkage-drag to improve resistance to Fusarium wilt race 3 in tomato." Poster presented at joint meeting of 48th annual Tomato Breeders Roundtable and Tomato Disease Workshop. 2019 November 18. Clearwater, FL. Chitwood-Brown, J, Vallad, GE, Lee, TG, and Hutton, S "Improving Resistance to Fusarium Wilt Race 3 of Tomato by Addressing Negative Association at the I-3 Locus." Oral presentation at the American Society for Horticultural Science annual conference. 2020 August 11. Virtual conference. Hutton, SF "Current breeding strategies to address decades-old disease challenges in Florida fresh market tomato." Texas A&M Horticultural Sciences Department Seminar. 2020 March 5. College Station, TX. Hutton, SF "Current breeding strategies to address decades-old disease challenges in Florida fresh market tomato." Oral presentation at the Gadsden Tomato Forum. 2021 December 9. Quincy, FL. Members of the Vallad lab gave research presentations that highlighted the work from this project: Carrillo, J.D. and G.E. Vallad. 2021. Evaluation of biological and conventional pesticides for Fusarium wilt management on tomato and watermelon. GCREC Virtual Field Day, Feb. 2021. Presentation during the Florida AgExpo in Nov. of 2020 (n=30) on the identification and characterization of FOL and FORL in a workshop for plant health specialists. Participants learn about the symptoms caused by each pathogen and available management options. Carrillo, J.D., F. Martin and G.E. Vallad. 2021. Effector screening of secreted in xylem (SIX) genes from Fusarium oxysporum f. sp. lycopersici reveals several race 3 isolates containing AVR1. Plant Health 2021. Virtual poster presentation. Vallad, G.E. 2021. Integrated approaches to disease management for tomatoes. 2021 Gadsden Tomato Growers Meeting, Quincy, FL. Presentations during the Florida AgExpo in Nov. of 2018 (n=50 individuals) 2019 (n=50), 2020 (n=30), and 2021 (n=50) on the identification and characterization of FOL and FORL in a workshop for plant health specialists. Participants learn about the symptoms caused by each pathogen and available management options. What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
Objective 1. Backcrossing was used to incorporate the reduced I-3 introgression into four elite UF/IFAS breeding lines to the BC4 generation. Segregating F2 populations were evaluated over three field seasons for bacterial spot, yield, and fruit size, and all trials demonstrated that the reduced I-3 introgression has no effect on bacterial spot sensitivity or fruit size in any of the four backgrounds. The I-7 gene was likewise backcrossed into an elite breeding line background, and evaluation of a segregating BCF2 population over two seasons demonstrated that the I-7 gene/introgression has no effect on bacterial spot or fruit size. The genomes of three breeding lines carrying the reduced I-3 introgression and larger introgression sizes were re-sequenced using Illumina HiSeq technology for delineation of introgression boundaries and gene content. The reduced I-3 introgression was shown to be approximately 140 kb in length. Including the I-3 gene/ortholog (according to the SL4.0 tomato genome assembly and ITAG 4.1 annotations), this interval contains 14 annotated genes in the S. lycopersicum reference genome (Heinz 1706) and 18 annotated genes in S. pennellii accession LA716. Breeding lines containing the reduced I-3 introgression have been developed and made available via MTA upon request from researchers and breeders. Breeding efforts have continued to advance the reduced I-3 introgression into improved backgrounds and elite parental lines and to advance I-7 into an improved fresh market background. These materials will continue to be available via MTA upon request from breeders. Objective 2. A modified backcrossing approach incorporating seedling disease screens coupled with field evaluations was used to advance Fol3 resistance from S. pennellii accessions into an elite tomato breeding line. Seedling disease assays were conducted to select Fol3 resistance, while field evaluations were conducted on resistant plants in order to select for superior horticultural traits. Three BC5F4 populations showing clear segregation for resistance over multiple seasons were selected for genetic study. Bulk segregant sequencing analysis identified two resistance loci on chromosome 3 (from the LA1522) and chromosome 10 (from the LA750). Backcrossing was further used to advance novel resistance alleles on chromosome 10 from LA750 and on chromosome 3 from LA1522 into an elite tomato background, as well as to develop an improved line combining the I-3 and I-7 genes together with I and I-2. Simultaneously, each of the previously known and available Fol resistance genes (I, I-2, I-3, I-7) were advanced (singly) into a commong background for the development of near isogenic lines (NILs) that will be available for subsequent genetic and pathology studies. A genome-wide SNP panel was employed to quantify percent background recovery for each of the backcrosses, and these results will support a future breeding line release of these materials. Objective 3. Eighty-eight Fusarium oxysporum isolates were collected from tomato throughout the U.S. (California, n=5; Florida, n=52; Georgia, n=1; Kentucky, n=6; Louisiana, n=1; Ohio, n=1; North Carolina, n=3; Tennessee, n=1; Texas, n=1) and abroad (France, n=2; Netherlands, n=3; Spain, n=1). Florida isolates represented eight counties where commercial tomato production. Out of the 88, 76 isolates were typed as F. oxysporum f.sp. lycopersici (FOL), 5 as F. oxysporum f.sp. radicis-lycopersici (FORL), and 7 as non-pathogenic F. oxysporum (FOXY) on the susceptible tomato cv. Bonny Best. Fifty-seven FOL isolates were characterized with standard set of Fusarium wilt differentials, 8 were FOL race 1 (FOL1), 13 were FOL race 2 (FOL2), and 36 were FOL race 3. Sequence-based analysis of these 88 Fusarium oxysporum isolates collected from throughout the U.S. was performed on several housekeeping loci (ITS, RPB2-1, RPB2-2, and TUB) and on SIX gnees. Translation elongation factor (TEF) 1-α provided the most informative polymorphisms to phylogenetically group FOL strains into two distinct phylogenetic clades, corresponding to F. nirenbergiae and F. languescens, as recently proposed by Lombard et al. (2019). While FOL and non-pathogenic FOXY isolates were represented in both clades, the FORL isolates (n=5) were all in F. nirenbergiae. FOL isolates were typed for SIX genes, including sequencing of SIX3 and SIX4. For most FOL isolates, the predicted race based on SIX gene profiling matched phenotype based on Fusarium wilt differentials. Several FOL2 and FOL3 strains maintained a copy of SIX4 (Avr1), while others lacked SIX5, SIX6, and SIX7. Several non-pathogenic FOXY and FORL isolates contained some or all of the SIX genes. Based on SIX3 sequencing, several amino acid changes corresponded to FOL3 isolates including G121A, G134A, and G137C; within the collection, G121A was the most common SIX3 allele and only observed within F. nirenbergiae FOL isolates. Overall, these results demonstrate the inability to rely on SIX genotyping alone to differentiate FOL isolates from other pathogenic and non-pathogenic FOXY isolates or to reliably determine race in the absence of host differentials. Regardless SIX gene profiles, the tomato differential line carrying I, I-2 and I-3 was effective against all tested FOL3 isolates. Studies evaluating unusual FOL isolates with near isogenic lines (NILs) that contain, singly, the I, I-2, I-3 and I-7 resistance alleles are in progress.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2021
Citation:
Chitwood-Brown, J, GE Vallad, TG Lee, and SF Hutton (2021) Breeding for resistance to fusarium wilt of tomato: a review. Genes 12:1673. https://doi.org/10.3390/ genes12111673
- Type:
Journal Articles
Status:
Published
Year Published:
2022
Citation:
Li, J, J Chitwood-Brown, G Kaur, JA Labate, GE Vallad, TG Lee, and SF Hutton (2022) Novel sources of resistance to Fusarium oxysporum f. sp. lycopersici race 3 among Solanum pennellii accessions. J. Amer. Soc. Hort. Sci. 147:35-44
|
Progress 03/15/20 to 03/14/21
Outputs
Target Audience:The target audience of this project includes tomato producers in areas affected by Fusarium wilt race 3 (both fresh market and processing markets); and tomato breeders, geneticists and pathologists in public and private sectors. Changes/Problems:Several project delays occurred in 2020-2021 due to the Covid-19 pandemic, which led to a University shutdown and workplace restrictions, and coincided with several staff changes in the Vallad lab. What opportunities for training and professional development has the project provided?Jessica Chitwood-Brown, the PhD student on this project, graduated in August 2020 with training in plant breeding for disease resistance and gene mapping. Dr. Chitwood-Brown continues to work on this project as a post-doctoral researcher. Dr. Joseph Carrillo, post-doctoral researcher, has carried out work on this project since July 2020. Dr. Katia Xavier, post-doctoral researcher, carried out work on the project from January 2020 until leaving for a position with Invaio Sciences in June 2020. Several undergraduates worked on this project in 2020-2021 including Andrea Karina Suazo Tejada (Zamorano University, Honduras) and Hannah Mather (University of Florida, Microbiology). How have the results been disseminated to communities of interest?Chitwood-Brown J, Vallad GE, Lee TG, Hutton SF (2021)Characterization and elimination of linkage-drag associated with Fusarium wilt race 3 resistance genes.Theor Appl Genet. https://doi.org/10.1007/s00122-021-03810-5 Chitwood-Brown, J (2020). Improving Resistance to Fusarium Wilt Race Three of Tomato (Solanum lycopersicum). [Doctoral dissertation, University of Florida]. Members of the Hutton lab gave research presentations this year that highlighted the work from this project: Chitwood-Brown, J, Vallad, GE, Lee, TG, and Hutton, S "Improving Resistance to Fusarium Wilt Race 3 of Tomato by Addressing Negative Association at the I-3 Locus." Oral presentation at the American Society for Horticultural Science annual conference. 2020 August 11. Virtual conference. Hutton, SF "Current breeding strategies to address decades-old disease challenges in Florida fresh market tomato." Texas A&M Horticultural Sciences Department Seminar. 2020 March 5. College Station, TX. Members of the Vallad lab gave research presentations that highlighted the work from this project: Carrillo, J.D. and G.E. Vallad. 2021. Evaluation of biological and conventional pesticides for Fusarium wilt management on tomato and watermelon. GCREC Virtual Field Day, Feb. 2021. Presentation during the Florida AgExpo in Nov. of 2020 (n=30) on the identification and characterization of FOL and FORL in a workshop for plant health specialists. Participants learn about the symptoms caused by each pathogen and available management options. What do you plan to do during the next reporting period to accomplish the goals?We will continue efforts to pyramid currently available Fusarium wilt resistance genes into an established parental background. Breeding will also pursue development of near isogenic lines (NILs) that contain each of the existing Fol resistance genes (I, I-2, I-3, I-7) as well as the novel resistance genes on chromosomes 3 and 10, singly. NILs will be useful for genetic and pathology study, including comparing each gene's effect against the known races of Fol. Finally, we will pursue two additional publications based on findings from this project.
Impacts
What was accomplished under these goals?
Objective 1. The reduced I-3 introgression was found to have no negative effect on bacterial spot sensitivity or fruit size. Genome sequencing determined this introgression to be approximately 140 kb in length. The interval contains 14 annotated genes, Including the I-3 gene/ortholog (according to the SL4.0 tomato genome assembly and ITAG 4.1 annotations), this interval contains 14 annotated genes in the reference genome and 18 annotated genes in S. pennellii accession LA716. Breeding lines containing the reduced I-3 introgression have been developed and made available via MTA upon request from researchers and breeders. Objective 2. Seedling disease assays were conducted to select Fol3 resistance for the continued backcrossing of novel resistance into an elite, Fol3 susceptible, tomato breeding line. Three BC5F4 populations showing clear segregation for resistance over multiple seasons were selected for genetic study. Bulk segregant sequencing analysis identified two resistance loci on chromosome 3 (from the LA1522) and chromosome 10 (from the LA750). Backcrossing was initiated to advance each of the novel loci into a Fusarium wilt susceptible breeding line for assessing the effects of the novel resistances against races 1 and 2. Crosses were made to combine I-3 and I-7 into a single elite UF/IFAS breeding line (already containing I and I-2) to begin pyramiding the Fusarium wilt resistant genes. Objective 3. Eighty-eight Fusarium oxysporum isolates were collected from tomato throughout the U.S. (California, n=5; Florida, n=52; Georgia, n=1; Kentucky, n=6; Louisiana, n=1; Ohio, n=1; North Carolina, n=3; Tennessee, n=1; Texas, n=1) and abroad (France, n=2; Netherlands, n=3; Spain, n=1). Florida isolates represented eight counties where commercial tomato production. Out of the 88, 76 isolates were typed as F. oxysporum f.sp. lycopersici (FOL), 5 as F. oxysporum f.sp. radicis-lycopersici (FORL), and 7 as non-pathogenic F. oxysporum (FOXY) on the susceptible tomato cv. Bonny Best. Fifty-seven FOL isolates were characterized with standard set of Fusarium wilt differentials, 8 were FOL race 1 (FOL1), 13 were FOL race 2 (FOL2), and 36 were FOL race 3. Studies to further characterize these isolates based on sequence-based analysis of housekeeping loci and of SIX genes are in progress.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2021
Citation:
Chitwood-Brown, J., Vallad, G.E., Leee, TT.G, Hutton SF (2021)G. et al. Characterization and elimination of linkage-drag associated with Fusarium wilt race 3 resistance genes. Theor Appl Genet (2021). https://doi.org/10.1007/s00122-021-03810-5
- Type:
Theses/Dissertations
Status:
Awaiting Publication
Year Published:
2020
Citation:
Chitwood-Brown, J. (2020). Improving Resistance to Fusarium Wilt Race Three of Tomato (Solanum lycopersicum). [Doctoral dissertation, University of Florida].
|
Progress 03/15/19 to 03/14/20
Outputs
Target Audience:The target audience of this project includes tomato producers in areas affected by Fusarium wilt race 3 (both fresh market and processing markets); and tomato breeders, geneticists and pathologists in public and private sectors. Changes/Problems:Prior to the start of this grant, it was unclear whether the negative effects associated with I-3 were due to linkage drag or pleiotropy. We planned to investigate this using both conventional breeding methods and gene editing with CRIPSR. Early field trials suggested, and subsequent field trials confirmed, that reducing the I-3introgression resolves the negative effects, indicating that these problems are not due to pleiotropy. We therefore discontinued efforts to manipulate the I-3 gene using CRISPR, and we invested our efforts the remaining objectives. What opportunities for training and professional development has the project provided?Jessica Chitwood-Brown is the PhD student on this project and is being trained in plant breeding for disease resistance and gene mapping. Juliana Pereira was the postdoc working on this project from 2018-2019 and was trained in fungal plant pathology with emphasis on breeding. Joseph D. Carrillo is the current postdoc leading the research in exploring the diversity of FOL through sequencing and greenhouse studies from populations present in Florida. How have the results been disseminated to communities of interest?- One peer-reviewed research article submitted: Chitwood-Brown, J., G.E. Vallad, and S.F. Hutton. (2020). Characterization and elimination of linkage-drag associated with Fusarium wilt race 3 resistance genes. Theoretical and Applied Genetics. (submitted) - Member of the Hutton lab gave several research presentations this year that highlighted the work from this project: Chitwood-Brown, J. (2019) "Improving Resistance in Tomato to Fusarium Wilt Race 3 of Tomato." Oral presentation at UF Horticultural Sciences Department Seminar Series. 2019 Feb 4. Gainesville, FL. Chitwood-Brown, J., Hutton, S.F., Lee, T.G., and Vallad, G.E. (2019) "Mission in Progress: Improving Disease Resistance in Tomato to Help Save the World." Oral presentation at GCREC Seminar Series. 2019 Sept 5. Wimauma, FL. Chitwood-Brown, J. (2019) "Reducing Linkage Drag Associated with the I-3 Gene." Oral presentation at GCREC Three Minute Thesis competition. 2019 Nov 14. Wimauma, FL. Hutton, S., Vallad, G., Lee, T., Chitwood-Brown, J., Pereira, J. (2019). "NIFA: Advancing resistance to Fusarium wilt of tomato through the pyramiding of available and novel resistance genes." Poster presented at National Association of Plant Breeders annual meeting. 2019 August 27. Pine Mountain, GA. Chitwood-Brown, J., Hutton, S.F., Lee, T.G., Vallad, G.E. (2019). "Breaking Free: Eliminating linkage-drag to improve resistance to Fusarium wilt race 3 in tomato." Poster presented at joint meeting of 48th annual Tomato Breeders Roundtable and Tomato Disease Workshop. 2019 November 18. Clearwater, FL. What do you plan to do during the next reporting period to accomplish the goals?Backcrossing will continue advancement of the reduced I-3 introgression and I-7 in commercially relevant breeding lines. Genome sequences of three breeding lines carrying the reduced I-3 introgression and larger introgression sizes will be compared to delineate introgression boundaries and gene content. To validate the possible novel resistance loci identified, markers will be developed and tested on plants subjected to disease assays to determine whether the loci co-segregate with resistance. These resistances will be backcrossed into a background lacking I and I-2 (which confer resistance to Fusarium wilt races 1 and 2 respectively) in order to test the novel resistance allele(s) for efficacy against these races. Novel resistance alleles will also be pyramided with the known resistance genes, I, I-2 and I-3, in an elite breeding line background. Genome sequence alignments will be compared to identify genetic variations within novel FOL3 resistance accessions and corresponding to regions associated with novel resistance alleles. Since the housekeeping and SIX genes from FOL have been analyzed, the most representative groups from each phylogenetic cluster that are also highly virulent can be used to challenge resistant plants to evaluate the effectiveness of I-3, I-7, and novel Fol3 resistance genes.
Impacts
What was accomplished under these goals?
Objective 1. We continued backcrossing efforts to incorporate the reduced I-3 introgression into four elite UF/IFAS breeding lines to the BC4 generation. We completed evaluation of segregating F2 populations for bacterial spot, yield, and fruit size over a third field season. The reduced I-3 introgression was found to have no effect on bacterial spot sensitivity or fruit size in any of the four backgrounds. Backcrossing was also continued to characterize I-7 in elite breeding lines, and we completed evaluation of a segregating F2 population in one background for bacterial spot, yield, and fruit size over a second field season. The I-7 gene/introgression had no effect on bacterial spot or fruit size. We are continuing backcrossing of the reduced I-3 introgression and I-7 into an advanced breeding line so that these are available for future breeding efforts. The genomes of three breeding lines carrying the reduced I-3 introgression and larger introgression sizes were re-sequenced using Illumina HiSeq technology, and sequence comparisons are underway to delineate introgression boundaries and gene content. Objective 2. Seedling disease assays were conducted to select Fol3 resistance for the continued backcrossing of novel resistance into an elite tomato breeding line. Field evaluations were conducted on resistant plants in order to continue selection for superior horticultural traits. Three BC5F4 populations which segregated for resistance over multiple seasons with ratios suggesting simple inheritance and dominant gene action were selected for sequencing using Illumina NovaSeq6000. Preliminary results have identified a single candidate resistance locus in each population. Further studies are underway to develop markers for validation and for testing for effects of these loci in separate populations with resistance derived from other S. pennellii accessions. Re-sequencing of the genomes of the three donor S. pennellii accessions has also been completed and sequence comparisons are underway. Objective 3. We obtained 67 Fusarium oxysporum isolates from across the U.S. and received 3 isolates from the Netherlands, adding to the 20 isolates already in the lab collection. Isolates were characterized by inoculating plants carrying different combinations of I genes and further sequencing of Secreted in Xylem (SIX) genes to determine races through molecular assays as well as with greenhouse differential assays. Housekeeping genes and SIX genes have been sequenced and analyzed to evaluate F. oxysporum genetic diversity among isolates pathogenic to tomato. The confirmed FOL isolates from all races reside in two phylogenetic species groups described by Crous et al. (2019) as F. languescens and F. nirenbergiae from housekeeping gene sequencing. In examining 7 SIX genes from molecular assays, diversity from examined from isolates was observed from Florida isolates and isolates representing other areas. From differential assays, virulent isolates were identified which will be useful in downstream assays testing the resistance from novel tomato hybrids.
Publications
- Type:
Journal Articles
Status:
Submitted
Year Published:
2020
Citation:
Chitwood-Brown, J., G.E. Vallad, and S.F. Hutton. (2020). Characterization and elimination of linkage-drag associated with Fusarium wilt race 3 resistance genes. Theoretical and Applied Genetics. (submitted)
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2019
Citation:
Hutton, S., Vallad, G., Lee, T., Chitwood-Brown, J., Pereira, J. (2019). NIFA: Advancing resistance to Fusarium wilt of tomato through the pyramiding of available and novel resistance genes. Poster presented at National Association of Plant Breeders annual meeting. 2019 August 27. Pine Mountain, GA.
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2019
Citation:
Chitwood-Brown, J., Hutton, S.F., Lee, T.G., Vallad, G.E. (2019). Breaking Free: Eliminating linkage-drag to improve resistance to Fusarium wilt race 3 in tomato. Poster presented at joint meeting of 48th annual Tomato Breeders Roundtable and Tomato Disease Workshop. 2019 November 18. Clearwater, FL.
|
Progress 03/15/18 to 03/14/19
Outputs
Target Audience:The target audience of this project includes tomato producers in areas affected by Fusarium wilt race 3 (both fresh market and processing markets); and tomato breeders, geneticists and pathologists in public and private sectors. Changes/Problems:As mentioned previously, prior to the start of this grant, it was unclear whether the negative effects associated with I-3 were due to linkage drag or pleiotropy. We planned to investigate this using both conventional breeding methods and gene editing with CRIPSR. Early field trials demonstrated that reducing the I-3introgression resolved the negative effects, indicating that these problems are not due to pleiotropy. We therefore, decided to forego the manipulation of I-3 gene using CRISPR, and to further invest our efforts into other worthwhile objectives. What opportunities for training and professional development has the project provided?Jessica Chitwood-Brown is the PhD student on this project and is being trained in plant breeding for disease resistance and gene mapping. Juliana Pereira is the postdoc on this project and is being trained in fungal plant pathology with emphasis on breeding. How have the results been disseminated to communities of interest?Member of the Hutton lab gave several research presentations this year that highlighted the work from this project: Chitwood-Brown, J., Hutton, S.F., Lee, T.G., and Vallad, G.E. (2018). "A dual strategy to advance resistance to Fusarium wilt race 3 of tomato." Poster presented at Florida Ag Expo. 2018 November 7. Wimauma, FL. Chitwood-Brown, J., Hutton, S.F., Lee, T.G., and Vallad, G.E. (2018). "A Closer Look at Fusarium Wilt Resistance in Tomato." Oral presentation at annual seminar of Florida Seed Association. 2018 May 30. Gainesville, FL. Chitwood-Brown, J., Hutton, S.F., Lee, T.G., and Vallad, G.E. (2018). "The improvement of resistance to fusarium wilt race 3 of tomato." Poster presented at Ohio State University Plant Sciences Symposium. 2018 April 7. Wooster, OH. Chitwood-Brown, J., and Hutton, S.F. (2018). "Discovery and improvement of novel and known resistance to Fusarium wilt race three of tomato." Oral presentation at 47th Tomato Breeders Roundtable. 2018 April 4-6. Wooster, OH. Chitwood-Brown, J., Hutton, S.F., Lee, T.G., and Vallad, G.E. (2018). "Improving resistance to Fusarium wilt race 3 of tomato." Oral presentation at University of Minnesota Plant Sciences Symposium. 2018 March 22-23. St. Paul, MN. The Hutton lab also produced an article for the Florida Tomato Institute: Chitwood-Brown, J., Vallad, G., Lee, T.G., and Hutton, S.F. (2018). Taking a closer look at Fusarium wilt resistance in tomato. Proc. Florida Tomato Institute. PRO 534:4-5 What do you plan to do during the next reporting period to accomplish the goals?For the continued characterization of the reduced I-3 introgression and I-7 gene, we will conduct two field seasons in which we will evaluate segregating populations for bacterial spot sensitivity, yield, and fruit size. Backcrossing will continue to incorporate both genes into elite breeding lines. To map the causal mutations in novel loci, we will perform genotyping on pools of genomic DNA from different pools of segregating phenotypic groups and their parents. Upon mapping of resistance loci, linked molecular markers will be used to select for distinct alleles that account for variation of Fol3 resistance. We will resequence selected Solanum pennellii accessions using the Illumina HiSeq method to investigate allelic variation in sequence. Aligned read data will be used to predict sequence variants. We will also clone and sequence the housekeeping and SIX genes, searching for genetic variability of Fusarium oxysporum. We will then choose the most representative groups from each phylogenetic cluster with which we will challenge Fol3 resistant plants to evaluate the effectiveness of I-3, I-7, and novel Fol3 resistance genes.
Impacts
What was accomplished under these goals?
Objective 1. Backcrossing continued to incorporate the reduced I-3 introgression into four elite UF/IFAS breeding lines to the BC4 generation. Segregating F2 populations were evaluated over two field seasons for bacterial spot, yield, and fruit size. Backcrossing was also continued to characterize I-7 in elite breeding lines, and a segregating F2 population in one background was evaluated over one field season for bacterial spot, yield, and fruit size. Prior to the start of this grant, it was unclear whether the negative effects associated with I-3 were due to linkage drag or pleiotropy, and we planned to investigate this using both conventional breeding methods and gene editing with CRIPSR. Early field trials demonstrated that reducing the introgression resolved the negative effects, indicating that these problems are not due to pleiotropy. We therefore, decided to forego the manipulation of I-3 gene using CRISPR, and to further invest our efforts into other worthwhile objectives. Objective 2. SNP data was generated using the Tomato Illumina SNP array for four populations segregating for Fol3 resistance from S. pennellii accessions. This data will be used to map the resistance loci. Seedling disease assays were conducted to select resistance for the continued backcrossing of novel resistance into an elite tomato breeding line. Field evaluations were also conducted on resistant plants in order to continue selection for superior horticultural traits. Objective 3. We obtained 35 Fusarium oxysporum isolates from across the U.S. and received one isolate from the Netherlands, adding to the 20 isolates already in the lab collection. Isolates were characterized by inoculating plants carrying different combinations of I genes and further sequencing of SIX3 to determine races. Housekeeping genes and SIX genes are being cloned, sequenced and analyzed to evaluate Fusarium oxysporum genetic diversity.
Publications
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