Progress 06/01/23 to 05/31/24
Outputs
Target Audience:Target audience includes the scientific community, growers and extension agents. The findings have been shared through national conference, seminars and meetings. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?This project hasallowed two undergraduate students withopportunities to learn and develop greenhouse and laboratory skills including plant maintenance in the green house, sample collection, tissue sectioning using vibratome, imaging using binocular microscope, and a basic understanding of image processing software ImageJ. This project gave the opportunity for a graduate student to get nominated and presenthis research for an E. Broadus Browne outstanding graduate student award at UGA held at University of Georgia. The graduate student also presented research findings in the Department of Crop, Soil and Environmental Sciences, at Auburn University, Alabama, as an initiative of graduate seminar exchange program organized in Spring 2024. How have the results been disseminated to communities of interest?The research findings from the proposed studies have been shared through an oral presentation with the growers and the scientific community at the American Society for Horticultural Science (ASHS) conference held in Orlando. The results were shared with scientists and growers at Auburn University, where findings of abscisic acid application to reduce BER was discussed with growers attending the seminar. What do you plan to do during the next reporting period to accomplish the goals?For Aim 2A, fruit from near isogenic lines (24S9) harboring BER11.1 & BER11.2 have been collected at 7 days post anthesis (DPA), 10 DPA and 14 DPA. Fruit height and diameter data have been collected to analyze for fruit growth rates. Fruit have been stored in a fixative that will be used to make thin sections of the fruit from the proximal and distal ends using a vibratome. The sections will be analyzed for the number of cells per unit area, pericarp thickness, average cell area, and number of cell layers. Further, statistical analysis will be performed to compare the growth rate between 7, 10 and 14 DPA and between two genotypes. This will help us to understand the growth differences and their relation to BER initiation between the two genotypes. For Aim 2D, the effect of physiological changes after ABA treatment in reducing BER will be investigated. These measurements will be focused on determining gas exchange, stomatal density, PSII efficiency, water use efficiency and water uptake rate, xylem developmentacross the NILs BER11.1&2 and between the treatments. We also plan to determine fruit growth rate and changes in calcium distribution due to ABA treatments. For Aim 3, we will further analyze the RNASeq data generated from BER11.1&2 to identify some candidate gene(s), present within the QTL region based on their function and transcript abundance. Further, Gene Ontology (GO) enrichment analysis will be performed to identify cluster of genes/pathways associated with BER.
Impacts
What was accomplished under these goals?
For Aim 2; specifically, for Aim 2A, fruit have been collected from a Near Isogenic Line (NIL; 24S9) harboring BER11.1 & BER11.2. Fruits were collected at 7 days post anthesis (DPA), 10 DPA and 14 DPA since the symptoms of BER initiate between 7 to 14 days. These fruits have been stored in a fixative (CRAFIII) to determine cell expansion rate. For Aim 2D, NILs for QTL BER11.1 & BER11.2 were treated with weekly foliar applications of abscisic acid (ABA) at the rate of 500 ppm. Fruit harvested at breaker stage were phenotyped for BER. ABA treatments reduced BER incidence in the three trials. In susceptible lines, ABA treatments reduced BER incidence between 3 to 13%. Some of the resistant lines displayed BER as well probably due to environmental conditions, however ABA treatments were effective in reducing BER incidence in resistant lines by 4 to 30%. Further experiments are being conducted to determine the effects of ABA on fruit calcium distribution and growth rate and BER incidence. For BER4.1 locus, 56 annotated genes were found based on iTAG 4.0 gene models. Of these, putative candidate gene(s) involved in reactive oxygen species (ROS) seem to be promising due to the involvement of ROS in BER development. The ROS genes spanning BER4.1 included Solyc04g064690 (peroxidase) and Solyc04g064470 (glutathione S transferase). In order to assay for ROS status, hydrogen peroxide (H2O2) was quantified in parental accessions (BGV007900 and BGV008224; resistant, and BGC007936; susceptible). Fruit proximal and distal pericarp tissues were harvested at 7, 10 and 14 DPA. The levels of H2O2 were similar at the proximal part of the fruit, however at 14 DPA, in the distal tissue H2O2 levels were significantly lower in the susceptible parent, BGV007936. These results were contrary to what we expected and suggested that BER induction in the susceptible BGV007936 parent is not associated with higher levels of H2O2. If this discrepancy arose due to pooling of BER affected and healthy tissues, needs further investigation. It is also likely that stress levels are higher in the susceptible line, which may result in a faster detoxification of H2O2. To address this, ratio of reduced glutathione (GSH) and oxidized glutathione (GSSG) was measured. The ratio of GSH:GSSG was dramatically lower at 14 DPA in the susceptible (BGV007936) compared to the resistant line (BGV007900), suggesting increased oxidative stress in the susceptible parent. However, the differences in H2O2 levels and glutathione ratios were not found in the NILs, indicating that BER4.1 is not likely to control ROS signaling. This region also contains, a gene that encodes the bidirectional sugar transporter SWEET1 (Solyc04g064620), and its association with BER in BER4.1 remains to be investigated. For Aim 3, RNASeq analysis has been performed using NILs harboring both QTL BER11.1&11.2. We generated F6 populations (23S62) from a cross between BGV007900 and BGV007936 such that it contains QTL BER11.1&11.2. The left and right border marker for this QTL is18EP951:SL4.0ch11 50569217,21EP212: SL4.0ch11 53644189, respectively, and containing 373 genes in the interval.For the susceptible genotype, no BER signs was observed at the 7 DPA with water-soaked spots appearing at 10 DPA and nearly all fruit showing BER at 14 DPA. Therefore, only 7 DPA and 10 DPA from 4 biological replicates were used for RNASeq. Four tissue types were collected from each fruitconsisting proximal pericarp, proximal inner tissues, distal pericarp and distal inner tissues. Since symptoms initiate at the distal end, only distal pericarp and distal inner tissues were used for RNAseq.RNA extraction was performed using ISOLATE II RNA Mini Kit Meridian-bioscience in the lab.Library construction, andpaired-end 150bp sequencing using Illumina NovaSeq 6000 Sequencing System were performed by Novogene. Next, raw reads that were generated from sequencing were used to trim out the adaptors generating clean reads. These clean reads were aligned with the reference genome to obtain raw read counts. Further, DESeq2 package was used for the differential analysis of RNA-Seq count data using these raw read counts. In the distal pericarp tissue 2,030 and 3,412 genes were upregulated and 2,559 and 3,059 downregulated at 7 and 10 DPA, respectively in the susceptible line compared to the resistant line. In distal inner tissues 3,360 and 719 genes are upregulated, while 3,239 and 1,084 genes are down-regulated at 7 and 10 DPA, respectively in the susceptible line compared to the resistant line. Further analyses are being performed to identify potential candidate gene(s), present within the QTL BER11.1 & 11.2 based on their function and expression levels.
Publications
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2023
Citation:
Singh, Ranveer P., Y. Topcu, E. van der Knaap, and S.U Nambeesan. 2023. Investigating the physiological basis of blossom-end rot in tomato. American Society for Horticultural Sciences Annual Meeting, Orlando, Fl.
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Progress 06/01/22 to 05/31/23
Outputs
Target Audience:Target audience includes the scientific community, growers and extension agents. The efforts for the proposed work will include presentations in international, national, and regional conferences, and publication of scientific research articles. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?Activities for professional development for the students and post-doctoral research associates included presentations in national and international meetings such as the International Plant & Animal Genome Conference 2023, Crops 2022 hosted by Hudson Alpha, Plant Center Retreats (2022 and 2023),and Institute of Plant Breeding, Genetics and Genomic Retreats (2022-2023) hosted by University of Georgia. This project has also helped to train a few undergraduate students to learn different tools and techniques. How have the results been disseminated to communities of interest?The latest findings from these studies were orally presented and discussed with scientists, plant breeders, and representatives from multi-national companiesaround the world in the International Plant & Animal Genome Conference 2023 at the Solanaceae session, which is the largest ag-genomics meeting in the world, held onJanuary 13-18, 2023, in San Diego, Ca/USA. Additionally, poster presentations wereperformed at the Crops 2022 meeting on June 13-16, 2022, in Huntsville, AL/USA.The findings related to ROS and oxidative stress were also presented and discussed with scientists around the nation at the retreats hosted byUniversity of Georgia?. What do you plan to do during the next reporting period to accomplish the goals?To further finemap and identify the candidate genes (Aim1), progeny tests of selected recombinants and recombinant screening approaches will be taken. A recombinant screening (23S1) population will be phenotyped for BER11.1. Progeny testing families for BER4.1 will be conducted in both greenhouse and field conditions. Fruit weight, BER Incidence, and BER Severity traits will be phenotyped. RNA-seq approach will be implemented for BER11.1 and BER11.2/fas QTLs. A progeny family encompassing both loci was already selected and RNA-seq analysis will be performed following the same procedure that was taken previously for BER4.1. Further, oxidative stress responses in BER4.1 Near-isogenic Linesand parents will be measured since the most likely candidate gene is involved in the ROS signaling pathway. In order to investigate the mechanism of resistance, we plan to characterize vascular development and calcium localization in these lines. To better quantify ROS and oxidative stress in resistant and susceptible parents (BGV007900, BGV008224, andBGV007936) further experiments have been designed to measure H2O2 and glutathione rates at 7, 10, and 14 DPA (Days Post Anthesis). First transgenic T0 plants for Glutathione-S transferase will be backcrossed to wild-type (BGV007900) and Cas-9 negative homozygous edited plants will be selected for BER evaluation. Transgenic plants will be developed for the candidate genes identified by the RNA-seq study.Crispr-Cas9 gene editing will be implemented to knock out Bidirectional sugar transporter SWEET and Peroxidase candidate genes. We are also setting up experiments in the greenhouse to determine the effect of hormonal applications such as abscisic acid (ABA) and its effect on calcium distribution in the fruit in BER11.2/fas
Impacts
What was accomplished under these goals?
We identified five loci associated with BER: BER3.1 (first BER locus on chromosome 3), BER3.2, BER4.1, BER11.1, and BER11.2/fas. Currently, we are focusing on fine-mapping BER4.1 and BER11.1. For Aim 1, we previously showed thatBER11.2 overlapped with fas. The underlying gene at fas is SlCLV3, controlling fruit size and fasciated fruit shape. The data showed that highly fasciated fruits are less susceptible to BER. Furthermore, we also identified another QTL on chromosome 11 (renamed as BER11.1) nearby BER11.2/fas and this locus is fixed by the BER11.2 resistance allele. Progeny testing of recombinant plantssuggested that BER11.1 QTL can be mapped to a736,315 bp interval, flanked by 18EP1052 SL4.0ch11 51423399 and18EP1046 SL4.0ch11 52159714 KASP markers. To further fine mapBER11.1 locus, 960 seedlings were screened and 180 plants will be used for the phenotypic evaluation at the University of Georgia greenhouse.With respect to BER4.1,combined progeny testing results suggest that BER4.1 can be further fine-mapped to approximately101,701 bp interval, with two outlier families. In a second genetic background (BGV008224 x BGV007936), phylogenetic tree analysis and detailed investigation of the locus in terms of SNPs, Indels, and Structural analysis showed that there isanother QTL, flanked by22EP227 SL4.0ch04 54773850and22EP230 SL4.0ch04 55,338,932. To further confirm and fine map this locus, 12 progeny families were selected for two genetic backgrounds (BGV007900 x BGV007936, BGV008224 x BGV007936)and transplanted to the fields in Athens/GA, and Blairsville/GA for fruit weight evaluation. The second half of the plants were transplanted to the greenhouse for both BER evaluations. For Aim2, to understand the physiological basis of BER, a pair of isogenic lines, differing for alleles at the BER11.1 locus (resistant allele from BGV007900 resistant accession and susceptible allele derived from BGV007936 susceptible accession) have been used. Leaf calcium analysis suggested that calcium concentration was similar in both the susceptible and resistant genotypes. Further, temporal and spatial distribution of calcium during early fruit growth stages were determined and compared between two NILs containing BER11.1. The inner tissues comprising of placenta and columella displayed higher Ca2+ concentration at 10 DPA (Days Post Anthesis) and 14 DPA in the resistant NIL (Near Isogenic Lines) compared to the susceptible NIL. Calcium translocation to the fruit occurs mainly through the xylem. Functional xylem was analyzed both in the pedicel and fruit tissue. The resistant NIL displayed a higher pedicel cross-sectional area, which in turn allowed for higher functional and total xylem compared to the susceptible NIL. In fruit tissue, the resistant NIL had a higher number of functional vascular bundles per cross-sectional area in the distal pericarp, placenta, and columella compared to the susceptible NIL. These results indicate that a lower number of vascular bundles per cross-sectional area in the BER susceptible NIL may lead to lower calcium influx into the fruit's distal end. The BER4.1 fine-mapped region contained genes of interest related to Reactive Oxygen Species (ROS) detoxification. These genes were of special interest due to the known correlations between high levels of ROS, lipid peroxidation, and blossom-end rot (BER). This high level of lipid peroxidation is one of the proposed causes of the black necrotic lesions that define BER. To better determine the potential physiological function of the genes of interest, an experiment was designed to measure H2O2 and oxidative stress levels in resistant and susceptible plants. This experiment utilized proximal and distal fruit pericarp tissue from a near-isogenic line (NIL) and resistant and susceptible parents. Through this experiment, a pattern of oxidative stress and H2O2concentration was found between both parents and within the NIL. This pattern of H2O2and oxidative stress may be indicative of the mode of resistance in mapped BER QTLs and may elucidate one of the causes of BER and its resistance in tomato fruits. For Aim 3, an F3family (BGV008224 x BGV007936) was used for the RNA-seq experiment. For this purpose, 4 biological reps were used for each genotype. For developmental points, 7 and 10 DPAs were used. While no BER sign was observed at the 7 DPA, water-soaked spots were observed at 10 DPA for the plants with susceptible genotypes. Since an excess amount of BER was observed for both genotypes at 14 DPA, this time point was excluded from the analysis. With respect to tissue types, three tissue types namely proximal pericarp, distal pericarp, and inner part (columella, placenta, and seed) were collected. Total RNA extraction was performed usingISOLATE II RNA Mini Kit Meridian-bioscience, library construction, and paired-end 150bp sequencing usingIllumina NovaSeq 6000 Sequencing System were performed byNovogene company. Next, downstream bioinformatic analysis was performed in the lab. The DESeq2 package was usedfor the differential analysis of RNA-Seq count data. While only a few fold genes were differentially expressed at 7DPA between resistant and susceptible pools for all the tissue types, more than 10- and 29-foldgenes were downregulated and upregulated, respectively for the distal pericarp tissue.Significantly enriched GO terms of the differential expressed genes at 10DPA of distal pericarp tissue (Resistant vs Susceptible) showed thatthere was significant enrichment of differentially expressed genes inresponse to chemical,phosphorylation, response to abiotic stimulus, and oxoacid metabolic process pathways. For the BER4.1 locus, while only two genes were differentially expressed at 7 DPA, 63 genes were differentially expressed at 10 DPA for the distal pericarp tissue for the 22S212 F3 family. Among these genes, we identifieda bidirectional sugar transporter SWEET gene, which involvesvarious developmental and stress responses. Further, we identified a peroxidase gene, which also involves inplant growth, development, and abiotic stress tolerance.
Publications
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2023
Citation:
Topcu, Y., Fleming, Z., and van der Knaap, E. (2023) QTL fine mapping and identification of candidate genes for Blossom-end Rot in tomato (Solanum lycopersicum L.). Plant and Animal Genome (PAG) 30. (Oral&Poster presentation) January 13-18, 2023, San Diego, CA/USA.
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2022
Citation:
Topcu, Y., and van der Knaap, E. (2022) Finemapping of BER4.1 and BER11.1 loci associated with Blossom-end rot in tomato. Crops 2022. June 13-16, 2022, Huntsville, AL/USA.
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2022
Citation:
Fleming, Z. and van der Knaap, E. (2022). Measurement of Oxidative Stress in Near-Isogenic Lines Affecting the Blossom-end Rot QTL BER4.1. Crops 2022. June 13-16, 2022, Huntsville, AL/USA.
- Type:
Conference Papers and Presentations
Status:
Awaiting Publication
Year Published:
2022
Citation:
Fleming, Z. , Van der Knaap, E. (2022, December 12-13). Measurements of H2O2 in Parental and Near Isogenic Lines Differing in Blossom End Rot in Tomato [Poster Presentation]. UGA Plant Center Retreat, Young Harris, GA, United States.
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2023
Citation:
Fleming, Z. , Van der Knaap, E. (2023, May 17-19). Quantification of Hydrogen Peroxide and Glutathione Levels in Blossom End Rot Resistant and Susceptible Tomato [Poster Presentation]. UGA Institute of Plant Breeding Genentics and Genomics Retreat, Columbus, GA, United States.
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Progress 06/01/21 to 05/31/22
Outputs
Target Audience:Target audience includes the scientific community, extension agenst and growers. The efforts for the proposed work will includepresentations in international,national, and reginal conferences, andpublication of scientific research articles. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?This has led to the training of one addition graduate student. Activities for professional development for one of the students included publication of a manuscript in Molecular Horticulture presentations in national and international meetings such as the International Plant & Animal Genome Conference 2022, and Plant Center Retreat 2021 hosted by University of Georgia. How have the results been disseminated to communities of interest?1- The knowledge derived from these studies was published in Molecular Horticulture. Topcu, Y., Nambeesan, S.U. & van der Knaap, E. Blossom-end rot: a century-old problem in tomato (Solanum lycopersicumL.) and other vegetables.Mol Horticulture2,1 (2022). https://doi.org/10.1186/s43897-021-00022-9 2- The latest findings from these studies were presented and discussed with scientists around the world in the International Plant & Animal Genome Conference 2022, which is the largest ag-genomics meetingin the world. Topcu, Y.,& van der Knaap, E. Finemapping of BER4.1 and BER11.1 in Tomato. https://pag.confex.com/pag/xxix/meetingapp.cgi/Paper/45248 What do you plan to do during the next reporting period to accomplish the goals?In order to further finemap and identify the candidate genes (Aim1), progeny tests of selected recombinants and recombinant screening approaches will be taken. We will mainly focus on finemapping of BER3.1 since this locus does not encompass any known fruit weight genes in contrast to BER3.2 and BER11.1 in which two major fruit weight genes (fw3.2 and fas) are located. Further, oxidative stress responses in Near-isogenic Lines related to the Blossom End Rot QTL BER 4.1 will be measured since the most likely candidate gene involves in ROS signaling pathway. In order to investigate the mechanism of resistance, weplanto characterizevascular development and calcium localization in these lines.
Impacts
What was accomplished under these goals?
We identified 4 loci associated with BER: BER3.1 (first BER locus on chromosome 3), BER3.2, BER4.1 and BER11.1 were identified. Currently, we are focusing on finemapping these loci. For Aim 1, the recombinant plants were from selected 17S28 progenies. BER3.2, the major BER QTL on ch3, was narrowed down from 5.68 Mbp to 1.58 Mbp with a 1.5-LOD Support Interval (SI) corresponding to 209 candidate genes. BER3.2 colocalizes with the fruit weight gene FW3.2/SlKLUH, an ortholog of cytochrome P450 KLUH in Arabidopsis. Increase in fruit size is associated with BER incidence and therefore the fruit weight gene SlKLUH may be a likely candidate. BER4.1 was further finemapped to approximately 130 Kb and this region encompassed 12 candidate genes. Further work is being performed to identify the candidate gene. To further finemap BER11.1, we screened 1920 F4:5 seedlings with KASP markers 20EP51 and 18EP1117 to identify recombinants. A total of 209 recombinant plants along with progeny families suggested that BER11.1 was contained in a 338 Kb region. The BER11.1 overlapped with fas. The underlying gene at fas is SlCLV3, controlling fruit size and fasciated fruit shape. The data showed that highly fasciated fruits are less susceptible to BER. For Aim 2, To understand the physiological basis of BER, a pair of nearly isogenic lines, differing for alleles at the BER11.1 locus (resistant allele from BGV007900 resistant accession and susceptible allele derived from BGV007936 susceptible accession) have been used. Soil and leaf calcium analysis suggested that calcium translocation from soil to vegetative tissues were similar in both the susceptible and resistant genotypes. These results were further confirmed using reciprocal grafts. The BER phenotype was independent of the genotype of the rootstock, but was dependent on the scion used. Using a resistant rootstock did not confer resistance to susceptible scion suggesting that calcium translocation through the roots is not the limiting factor for BER susceptibility. Fruit calcium concentration at 14 days post anthesis was higher in the resistant genotype compared to the susceptible genotype. If differences in fruit calcium concentration are due to differences in fruit growth rate or vascular development between the two genotypes are currently being investigated. For Aim 3, currently, we are developing NILs and advancing the generation to reduce genetic variability for the rest of the genome. An F6 family (22S218) for BER4.1 is being grown now and will be phenotyped in two months. After we have seeds from these plants, the planned experiments will be conducted in the fall 2022.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2022
Citation:
Topcu, Y., Nambeesan, S.U. & van der Knaap, E. Blossom-end rot: a century-old problem in tomato (Solanum lycopersicum L.) and other vegetables. Mol Horticulture 2, 1 (2022). https://doi.org/10.1186/s43897-021-00022-9
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
https://pag.confex.com/pag/xxix/meetingapp.cgi/Paper/45248
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Progress 06/01/20 to 05/31/21
Outputs
Target Audience:Target audience include the scientific community and growers. Efforts include publication of scientific researcharticles, presentations in international and national conferences. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?This has led to the training of two graduate students and one undergraduate student. Activities for professional development for one of the students included publication of a manuscript in Theoretical Applied Genetics journal, presentations in national and international meetings such as the Plant Biology 2020, Worldwide summit powered by the American Society of Plant Biologists and SOL International Meeting. How have the results been disseminated to communities of interest?1- The knowledge derived from these studies was published in one of the top journals in the plant breeding area.(Topcu, Y., Sapkota, M., Illa-Berenguer, E.et al.Identification of blossom-end rot loci using joint QTL-seq and linkage-based QTL mapping in tomato.Theor Appl Genet(2021). https://doi.org/10.1007/s00122-021-03869-0). 2-The University of Georgia Research Foundation (UGARF) Cultivar Development Research Program was soliciting proposals for The John Ingle Innovation in Plant Breeding Award. This Awardtargets novel plant breeding approaches to overcome cultivar development challenges. Our initial findings for BER3.2andBER11.1were found to be valuable for crop improvement by the Award committee. Therefore, Ph.D. student Yasin Topcubecame a recipient of this award. BER3.2 and BER11.1 fine-mapping results were just submitted to UGARF Cultivar Development Research Program in August 2021. What do you plan to do during the next reporting period to accomplish the goals?In order to further fine map and identify the candidate genes (Aim 1), progeny tests of selected recombinants and recombinant screening approaches will be taken. Further fine mapping populations and families will be grown and evaluated for the BER. The lines will be used to evaluate developmental basis of BER development for Aim 2.Calcium distribution, fruit growth and xylem development will be investigated. Simultaneously,Near Isogenic Lines (NILs) will be developed to accomplish Aim 3.NILs that will be generated will begenetically identical except for the BER loci.
Impacts
What was accomplished under these goals?
?The major goal was to identify causal genes and their mechanisms that will ultimately lead to fundamental knowledge about BER development. For Aim 1, we have developed two main F2 mapping populations, 17S28 (n = 192) and 20S166 (n = 192), by crossing BER-resistant accessions BGV007900 (Solanum lycopersicum var. cerasiforme) and BGV008224 (S. lycopersicum var. lycopersicum), respectively, with BER-susceptible accession BGV007936 (S. lycopersicum var. lycopersicum). From these mapping populations in total, four BER QTLs were mapped on chromosome 3 (chr03), ch04, and ch11. QTLs BER3.1 and BER3.2 were mapped on ch03 whereas BER4.1 and BER11.1 were mapped on ch04 and ch11, respectively. Further progeny tests of selected recombinant plants and recombinant screening approaches were taken to fine map BER QTLs and identify candidate genes. QTL mapping in F4 and F5 populations composed of only recombinant F3:4 and F4:5 plants showed that BER3.2 was located between two markers, 20EP1033 (SL4.0ch3 58,308,917) and 18EP730 (SL4.0ch3 59,891,210), narrowing the locus down from 5.68 to 1.58 Mbp with a 1.5-LOD SI. This 1.58 Mbp SI consists of 209 candidate genes including the fruit weight locus FW3.2/SlKLUH, an ortholog of cytochrome P450 KLUH in Arabidopsis. Furthermore, BER11.1, the major BER QTL on ch11, was narrowed down from 3.99 to 1.13 Mbp with a 1.5-LOD SI interval. This interval comprises of 141 candidate genes including two pectin methylesterase genes (PMEs) (Solyc11g070175 and Solyc11g070187). The role of PMEs in BER development has been studied previously, and suppression of PMEs decreases fruit susceptibility to BER. To further fine map BER4.1, two F2 populations for recombinant screening, two F6 and nine F7 families for progeny testing were grown and phenotypic analyses were performed for BER in 2020 and 2021. Combined progeny testing and recombinant screening led to the reduction of the interval from 5.56 to approximately 190 kbp flanked by markers 18EP616 SL4.0ch04 5428456. Currently we continue to fine map the four BER QTL, identify potential candidate genes, functionally validate their function and characterize their role in BER development. These will lead to new fundamental information in causal genes that are responsible for BER development. For Aim 2, we are currently developing BER NILs from Aim 1 to generate information on calcium distribution and xylem development. For Aim 3, currently, we are developing NILs and advancing the generation to reduce genetic variability for the rest of the genome. After, we have the NILs, the planned experiments will be conducted.
Publications
- Type:
Journal Articles
Status:
Accepted
Year Published:
2021
Citation:
Topcu, Y., M. Sapkota, E. Illa-Berenguer, S.U. Nambeesan, and E. van der Knaap. 2021. Identification of blossom-end rot loci using joint QTL-seq and linkage-based QTL mapping in tomato. Theor Appl Genet. 134: 2931-2945 https://doi.org/10.1007/s00122-021-03869-0
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2020
Citation:
Topcu, Y., E. Illa-Berenguer, S. Nambeesan, and E. van der Knaap. 2020. The Molecular and genetic basis of blossom-end rot in tomato. SOL International Meeting-virtual
- Type:
Conference Papers and Presentations
Status:
Accepted
Year Published:
2020
Citation:
Topcu, Y., E. Illa-Berenguer, S. Nambeesan, and E. van der Knaap. 2020. The Molecular and genetic basis of blossom-end rot in tomato. Plant Biology 2020, Worldwide summit-virtual
- Type:
Other
Status:
Accepted
Year Published:
2020
Citation:
Topcu, Y., E. Illa-Berenguer, S. Nambeesan, and E. van der Knaap. 2020. The Molecular and genetic basis of blossom-end rot in tomato. Institute of Plant Breeding, Genetics & Genomics; Virtual Retreat 2020.
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