Progress 01/15/21 to 01/14/25
Outputs
Target Audience:The target audiences for this research project include rice producers in the southern United States, as well as applied and fundamental rice researchers and rice breeding programs. The goal of this project is to characterize and identify major qualitative and quantitative resistance towards narrow brown leaf spot in rice. Results from this project will directly impact rice producers by enabling the development of new cultivars with durable resistance stacks. Identification of the CRSP2.1 resistance gene, along with markers tightly linked to quantitative resistance loci, will enable the development of user-friendly marker assays to introgress these resistances into elite varieties. The use of resistance will lower disease management costs by reducing the need for fungicide applications or other management interventions. The fundamental research community will also be impacted by furthering our understanding of the host-pathogen interactions within this pathosystem, as this will be the first resistance gene identified for this disease. We have communicated these results to research audiences this past reporting period at conferences, stakeholder meetings, and farm visits. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?A postdoctoral research associate has been trained in disease phenotyping, classical genetics, next-generation sequencing, bioinformatics, and comparative genomics. The postdoctoral research associate has also had the opportunity to present and communicate research atnational conferences and stakeholder meetings. A graduate student has been trained in disease phenotyping and bioinformatics and has also had the opportunity to present research at national conferences. How have the results been disseminated to communities of interest?These results have been communicated to stakeholders annually at commodity board meetings and field days. These results have also been presented at national and international conferences, including Plant Health, Plant and Animal Genome, and the Rice Technical Working Group meeting. One manuscript has already been published in The Plant Genome describing marker set and population development. Four additional manuscripts describing the 1) fine mapping/comparative genomics, 2) transcriptional profiling of the C. janseana - rice interaction, 3) quantitative NBLS resistance and genomic selection,and 4) Cercospora net blotch phenotyping and resistance screening, are currently being prepared and will be submitted for publication in 2025. A manuscript describing Cercospora janseana population dynamics, which was also aided by the funding of this project, has been accepted with revisions in Molecular Plant-Microbe Interactions. What do you plan to do during the next reporting period to accomplish the goals?
Nothing Reported
Impacts
What was accomplished under these goals?
The main objective of this proposal was to fine map and identify candidate CRSP2.1 resistance genes. We initiated a high throughput genotyping experiment, in which we genotyped 10,046 F2:3 individuals derived from a LaGrue x Cypress cross. This genotyping screen identified 26 critical recombinants in the CRSP2.1 region. Phenotyping these critical recombinants mapped the CRSP2.1 region to ~240 kb on rice chromosome 2. Unfortunately, a large portion of the CRSP2.1 region appears to have highly suppressed recombination and therefore could not be delimited further. To identify candidate genes, we conducted Nanopore sequencing of rice variety LaGrue and PacBio sequencing of Cypress. Both sequencing efforts resulted in highly contiguous genome assemblies (LaGrue: N50=10.1 Mb, L50=14, Cypress: N50=23.8 Mb, L50=8) with each assembly containing contigs spanning the CRSP2.1 region. A comparative genomics approach identified six expressed candidate genes in LaGrue: 4 receptor-like kinases and 2 receptor-like proteins. Interestingly, this region in Cypress appears highly expanded via repetitive element proliferation, resulting in reduced gene content with only two of the six candidate genes being present. Allele comparisons among LaGrue, Cypress, and Nipponbare show high allelic divergence. We are currently targeting all six genes for disruption and validation. We have successfully validated a transformation protocol in the LaGrue genetic background by overexpressing yellow fluorescent protein. Gene disruption transformations are now underway via CRISPR/Cas9. We also attempted to validate our candidate genes by screening a mutant population. LaGrue was irradiated with gamma irradiation and M1 seeds were selfed in the field to generate an M2 population. Screening over 4000 M2 individuals identified 12 putative mutants. Nine of these mutants were found to have non-LaGrue genetic backgrounds via KASP assays. The whole genomes of the remaining three were sequenced, however, no mutations in the CRSP2.1 region were found, indicating that another gene in the resistance pathway may be disrupted. A manuscript describing the fine mapping and comparative genomics is being prepared and will be submitted by Fall 2025. We conducted an RNA sequencing experiment to characterize genome-wide changes in gene expression, as well as determine gene expression patterns in our CRSP2.1 candidate genes. LaGrue and Cypress were inoculated with C. janseana isolate RL373 and samples were collected at 1, 7, 13, and 19 days post-inoculation. Non-inoculated samples were collected as controls and three replicates were collected for each treatment. ~60 million paired-end reads were generated per sample. We observed host defense pathways expressed at 1 and 7 dpi in LaGrue indicating early pathogen recognition and activation of the hypersensitive response. Conversely, we observed a suppression of host immune responses in Cypress, indicating that the pathogen may be suppressing host defenses until its transition into necrotrophy after 13 dpi. These results provide much needed novel insight into host-pathogen interactions in this pathosystem and can provide future breeding targets to improve host resistance. Throughout the course of this project, we discovered that CRSP2.1-mediated resistance appears to only function in rice leaves, but not in the sheath/stem (Cercospora net blotch; CNB). Varieties such as LaGrue or PVL03, which have functional CRSP2.1 haplotypes, were observed to develop substantial CNB symptoms in the field. Due to the importance of this discovery, we decided to place an effort on examining the tissue-specificity of CRSP2.1 resistance. Due to the lack of available methods for screening CNB resistance, we first developed and tested controlled phenotyping protocols. Throughout our protocol testing, we examined the effects of using conidia or mycelia as the inoculum, as well as the impact of wounding prior to inoculation. Our results indicated that the methods using wounding prior to inoculation resulted in consistent and reproducible symptom formation, with mycelia as the inoculum produced larger lesions. Going forward, we began screening varieties using the mycelia/wounding method. A manuscript describing this protocol has been written and will be submitted to Plant Disease in Summer 2025. Our initial controlled resistance screen identified three rice lines that were highly resistant to C. janseana sheath infection, including rice variety DG263L. We next phenotyped an F2 population derived from a cross of DG263L (CNB resistant) to an advanced breeding line (CNB susceptible). Resistance did not segregate as a single major resistance gene and the phenotype distribution was near normal, indicating that resistance may be quantitative and/or additive in nature. Additionally, we phenotyped a rice breeding germplasm panel for CNB resistance in 2024 in the field (n=400). DG263L was by far the most resistant variety, however, 13 additional varieties also exhibited moderate levels of resistance. These findings are highly relevant for the rice industry because severe CNB infection can lead to lodging and substantial yield loss. Specifically, these results will be the basis of future genetic mapping projects to characterize the genetic architecture of this trait and improve resistance in elite rice varieties. Our novel screening protocol will help screen varieties of interest in the breeding program. We took several different approaches to identify and characterize quantitative resistance to NBLS. First, we focused our efforts on the MPC bi-parental RIL population derived from a Cypress and CL173 cross. Neither of these varieties have the CRSP2.1 gene. We phenotyped this population in the field for four years (2021-2024). We observed transgressive segregation within the population and the phenotype distribution was near normal, indicating quantitative resistance. Mapping analyses identified 6 loci with smaller effect sizes in association with NBLS resistance, however, there were inconsistencies in the loci detected among years. We hypothesize that this may be due to differences in the prevalent pathogen race from year to year, as well as environmental effects. We also phenotyped the MP6/8 populations, which are multi-parent advanced intercross populations. We used the CRSP2.1 locus as a covariate in our association mapping models to focus on the effects of other genomic loci. This analysis identified nine significant loci. Loci detected on chromosomes 6 and 7 appeared to have larger effects, with percent variation explained ranging from 19.48-34.04%. Taken together, this objective has identified multiple loci in addition to CRSP2.1 that will be highly beneficial for rice breeding programs to use to improve NBLS resistance in elite varieties. In addition to traditional mapping techniques, we also tested genomic selection (GS) models. We used the previously mentioned phenotypic data from the MPC and MP6/8 populations. Genomic estimated breeding values (GEBVs) were estimated using a genomic best linear unbiased prediction (GBLUP) model and prediction accuracy was assessed by calculating the Pearson correlation between predicted and observed values. We observed moderate to moderately high broad-sense heritability for NBLS resistance in the MPC, MP6, and MP8 populations (0.40-0.73). High prediction accuracies were observed when predicting phenotypes within the same population across years (0.56-0.75). However, prediction accuracies dropped when using the MPC population to predict phenotypes in the MP6/8 populations (0.18-0.23). However, when using the MP6/8 populations as training sets, higher prediction accuracies were observed in the MPC population (0.21-0.38). These analyses are still ongoing, but these results suggest that GS could be a viable method to improve quantitative NBLS resistance in rice breeding programs.
Publications
- Type:
Conference Papers and Presentations
Status:
Submitted
Year Published:
2025
Citation:
Gaire, S., Budot, B., Searight, J., Angira, B., Famoso, A., and Richards, J.K. 2025. A diverged receptor-like kinase cluster underlies the CRSP2.1 narrow brown leaf spot resistance locus in rice. Submitted for presentation at IS-MPMI Congress in Cologne, Germany.
- Type:
Conference Papers and Presentations
Status:
Awaiting Publication
Year Published:
2025
Citation:
Gaire, S., Budot, B., Searight, J., Angira, B., Famoso, A., and Richards, J.K. 2025. Dissecting genetic resistance to narrow brown leaf spot and Cercospora net blotch of rice. Rice Technical Working Group Meeting. New Orleans, LA.
- Type:
Other Journal Articles
Status:
Under Review
Year Published:
2025
Citation:
Searight, J., Famoso, A., Zhou, X., Doyle, V., and Richards, J.K. 2025. A population genomics approach to understand the diversity, migration, and reproduction of the rice pathogen Cercospora janseana. Under review at Molecular Plant-Microbe Interactions.
- Type:
Peer Reviewed Journal Articles
Status:
Published
Year Published:
2022
Citation:
Cerioli, T., Hernandez, C.O., Angira, B., McCouch, S.R., Robbins, K.R., and Famoso, A.N. 2022. Development and validation of an optimized marker set for genomic selection in southern U.S. rice breeding programs. The Plant Genome. 15(3):e20219
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Progress 01/15/23 to 01/14/24
Outputs
Target Audience:The target audiences for this research project include rice producers in the southern United States, as well as applied and fundamental rice researchers and rice breeding programs. The goal of this project is to characterize and identify major qualitative and quantitative resistance towards narrow brown leaf spot in rice. Results from this project will directly impact rice producers by enabling the development of new cultivars with durable resistance stacks. Identification of the CRSP2.1 resistance gene, along with markers tightly linked to quantitative resistance loci, will enable the development of user-friendly marker assays to introgress these resistances into elite varieties. The use of resistance will lower disease management costs by reducing the need for fungicide applications or other management interventions. The fundamental research community will also be impacted by furthering our understanding of the host-pathogen interactions within this pathosystem, as this will be the first resistance gene identified for this disease. We have communicated these results to research audiences this past reporting period at stakeholder meetings, field days, and farm visits. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?A postdoctoral research associate has been trained in disease phenotyping, classical genetics, next-generation sequencing, bioinformatics, and comparative genomics. The postdoctoral research associate has also had the opportunity to present and communicate research at a national conference. A graduate student has been trained in disease phenotyping and bioinformatics. How have the results been disseminated to communities of interest?These results have been communicated to the research community at the Rice Technical Working Group meeting and the Louisiana Agricultural Consultants Meeting. Additionally, results from this research were communicated to rice producers at annual stakeholder meetings and field days. Manuscripts describing the CRSP2.1 fine mapping and QTL/genomic prediction analyses are being prepared for submission in 2024. What do you plan to do during the next reporting period to accomplish the goals?Our main focus in 2024 will be on candidate gene validation. Transformation protocols are being tested and preliminarily appear successful in the Lagrue genetic background. CRISPR/Cas9 is being used to disrupt the candidate genes in Lagrue and we are using traditional overexpression transformation in the susceptible rice variety Mermentau. These experiments are underway and will confirm or reject these candidate genes as the CRSP2.1 resistance gene. Additionally, we will be capitalizing on the phenotypic data generated over the last three years by focusing on testing genomic prediction models for NBLS quantitative resistance. Candidate loci detected in the MPC population will also be investigated further in the MP6/8 population. We also plan on submitting two manuscripts (CRSP2.1 fine mapping and QTL identification) in the next reporting period.
Impacts
What was accomplished under these goals?
Due to previous difficulties identifying recombinants in the mapped ~240 kb region, we pursued another effort to screen F2:3 individuals. However, this screen only resulted in the identification of a single potential recombinant in this region, but the plant did not survive to produce seed. As this region appears to be highly suppressed in recombination and we had already screened over 10,000 individuals, we decided to end the recombinant screen portion of the project and focus our efforts on gene validation. Currently, we are validating the transformation protocol in the Lagrue genetic background. Preliminary results appear promising, with Lagrue calli positively expressing YFP. Following conclusion of the protocol testing, we will begin gene disruption experiments via CRISPR/Cas9. In 2023, we conducted an RNA sequencing experiment to characterize genome-wide changes in gene expression, as well as determine gene expression patterns in our CRSP2.1 candidate genes. Lagrue and Cypress were inoculated with C. janseana isolate RL373 and samples were collected at 1, 7, 13, and 19 days post-inoculation. Non-inoculated samples were collected as controls and three replicates were collected for each treatment. RNA was extracted and sequenced, generating ~60 million paired-end reads per sample. Our preliminary results show a lack of host differentially expressed genes in Cypress until 13 days post-inoculation, when a large shift in host gene expression occurs and persists through 19 days post-inoculation, indicating the pathogen began triggering programmed cell death between 7 and 13 days post-inoculation. On the contrary, a large host response was observed in inoculated Lagrue samples at 7 days post-inoculation, indicating that the resistance response was triggered before 7 days post-inoculation. Gene/pathway enrichment analyses are currently underway. We also used the RNAseq data to polish the Lagrue genome annotation, which further solidified our candidate gene list. Our top candidates are two receptor-like kinases (with predicted transmembrane domains) and one cytoplasmic receptor-like protein. We are currently analyzing candidate gene expression with the RNA sequencing data. To confirm candidate gene expression, we also conducted an independent gene expression experiment using rice lines Lagrue, Cypress, and Nipponbare. Samples were collected every two days post-inoculation. These samples will be used to confirm candidate gene expression patterns and gain a more fine-grained understanding of their temporal expression dynamics. In 2023, we also decided to place an effort on examining the tissue-specificity of CRSP2.1 resistance. We discovered that CRSP2.1 resistance appears to only function in rice leaves, but not in the sheath/stem. To investigate this further, we developed a phenotyping procedure and rating scale (0-5) for sheath/stem evaluation. Using this protocol, we identified three rice lines that were highly resistant to C. janseana sheath infection, including rice variety DG263L. This finding will be the basis of future genetic mapping projects to characterize the genetic architecture of this trait and improve resistance in elite rice varieties. We also continued our mapping efforts in the MPC and MP6/8 populations. Both populations were evaluated in the field and/or greenhouse in 2023. In the MP6/8 population, we identified seven loci associated with resistance, including CRSP2.1. The smaller effect, quantitative loci were located on chromosomes 1, 2, 3, 7, and 10. Two of the loci identified on chromosome 1 were also identified from field evaluations of the MPC population. The identification of quantitative resistance loci will be important for the development of rice varieties with durable resistance, especially when combined with the major gene CRSP2.1. We are currently preparing a manuscript describing these results, as continuing to test genomic prediction models.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2023
Citation:
Searight, J., Famoso, A.N., Zhou, X., Doyle, V.P., and Richards, J.K. 2023. A high-quality genome assembly for Cercospora janseana, causal agent of narrow brown leaf spot of rice. Mol. Plant Microbe Inter. 36(10):666-669
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Richards, J.K., Gaire, S., Angira, B., and Famoso, A.N. 2023. Fine mapping of the CRSP2.1 narrow brown leaf spot resistance locus. 39th Rice Technical Working Group Meeting Proceedings. https://rtwg.org/pdf/proceedings/39th%20RTWG%20Proceedings%20-%202023.pdf
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Progress 01/15/22 to 01/14/23
Outputs
Target Audience:The target audiences for this research project include rice producers in the southern United States, as well as applied and fundamental rice researchers and rice breeding programs. The goal of this project is to characterize and identify major qualitative and quantitative resistance towards narrow brown leaf spot in rice. Results from this project will directly impact rice producers by enabling the development of new cultivars with durable resistance stacks. Identification of the CRSP2.1 resistance gene, along with markers tightly linked to quantitative resistance loci, will enable the development of user-friendly marker assays to introgress these resistances into elite varieties. The use of resistance will lower disease management costs by reducing the need for fungicide applications or other management interventions. The fundamental research community will also be impacted by furthering our understanding of the host-pathogen interactions within this pathosystem, as this will be the first resistance gene identified for this disease. We have communicated these results to research audiences this past reporting period at stakeholder meetings and farm visits. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?A postdoctoral research associate has been trained in disease phenotyping, classical genetics, next-generation sequencing, bioinformatics, and comparative genomics. The postdoctoral research associate has also had the opportunity to present and communicate research at a national conference. A graduate student has been trained in disease phenotyping and bioinformatics. How have the results been disseminated to communities of interest?These results have been communicated to the research community at the Annual Meeting of the American Phytopathological Society. An abstract describing this research was published in Phytopathology. A manuscript describing marker development and genomic selection using the MP bi-parental populations was published in The Plant Genome. Additionally, results from this research were communicated to rice producers at annual stakeholder meetings. What do you plan to do during the next reporting period to accomplish the goals?Our main focus in 2023 will be on candidate gene validation. We will finish the recombinant screen which is aiming to identify at least one recombinant in the middle of the CRSP2.1 region. CRISPR/Cas9 will be used to knockout the candidate genes in LaGrue. We will also begin developing the overexpression transformants in the Cypress genetic background. We expect that these experiments will confirm or reject these candidate genes as the CRSP2.1 resistance gene. Additionally, we will be phenotyping the MPC population in the field and testing additional genomic selection models. The MPC population will also be phenotyped in the greenhouse. Genetic mapping analyses in the MP6/8 populations will be refined.
Impacts
What was accomplished under these goals?
During the last reporting period, we continued to place a major focus on identifying and phenotyping critical recombinants in the CRSP2.1 region. Previously, we had screened 7,289 F2:3 individuals, which led to the identification of 448 recombinants. However, the majority of these recombinants were in the very distal end of the region (~150 kb). We further characterized these recombinants by designing new SNP markers within that region to localize the recombination breakpoint and determine if there are unique recombinants or if they stem from the same recombination that occurred in the F2 generation. Our results indicated that these recombinants all likely represent the same recombination event. Therefore, we are retaining a single recombinant from this class for future mapping efforts. We screened an additional ~2500 F2:3 individuals and when combined with our previous genotyping screens, led to a total of 26 identified critical recombinants. Recombination appears to be uneven across the region and additional recombinant screening is ongoing to identify recombinants in underrepresented regions. The 26 recombinants were phenotyped which localized the CRSP2.1 gene to an approximately 240 kb interval. The newly generated LaGrue reference genome was annotated and compared to the Nipponbare reference genome. The center of the CRSP2.1 region appeared to be highly diverged between Nipponbare and LaGrue, which may explain why very little recombination was observed in this region. Three receptor-like cytoplasmic kinases were identified and are currently our top candidate genes. The four previously identified LaGrue mutants were used for whole-genome sequencing. Variant analysis did not identify any obvious mutations in the CRSP2.1 region, indicating that likely mutations elsewhere in the genome had compromised resistance. Several crosses were made with these mutants to further characterize genes that are involved in NBLS resistance. An additional 3000 mutants were screened in the greenhouse and 12 putative resistance-compromised mutants were identified. Primers that amplify our top candidate genes were designed and are currently being used to characterize the candidate genes from the mutants. The MPC population (Cypress x CL172) was planted in the field in 2022 and phenotyped for NBLS. QTL analysis revealed a QTL that was consistent with 2021 results and explained ~10% of the phenotypic variation. Additionally, genomic prediction models were tested and found to have relatively high (0.53) predictive values, indicating that genomic selection may be a viable method to improve quantitative NBLS resistance in rice varieties. The MP6 and MP8 populations were genotyped using DaRT-seq, which identified 14,028 SNP markers. Genetic mapping in these population identified the CRSP2.1 locus as the major locus involved in NBLS resistance. Using markers linked to CRSP2.1 as a covariate in the analyses identified additional small-effect loci, including a QTL that was identified in the MPC population.
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2022
Citation:
Cerioli, T., Hernandez, C.O., Angira, B., McCouch, S.R., Robbins, K.R., and Famoso, A.N. 2022. Development and validation of an optimized marker set for genomic selection in southern U.S. rice breeding programs. Plant Genome. e20219
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Gaire, S.P., Famoso, A., Angira, B., and Richards, J. 2022. Fine mapping of the narrow brown leaf spot disease resistance locus CRSP2.1 and candidate gene identification in rice. Annual Meeting of the American Phytopathological Society. Phytopathology. 112(11S): 84
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Progress 01/15/21 to 01/14/22
Outputs
Target Audience:The target audiences for this research project include rice producers in the southern United States, as well as applied and fundamental rice researchers and rice breeding programs. The goal of this project is to characterize and identify major qualitative and quantitative resistance towards narrow brown leaf spot in rice. Results from this project will directly impact rice producers by enabling the development of new cultivars with durable resistance stacks. Identification of the CRSP2.1 resistance gene, along with markers tightly linked to quantitative resistance loci, will enable the development of user-friendly marker assays to introgress these resistances into elite varieties. The use of resistance will lower disease management costs by reducing the need for fungicide applications or other management interventions. The fundamental research community will also be impacted by furthering our understanding of the host-pathogen interactions within this pathosystem, as this will be the first resistance gene identified for this disease. We have communicated these results to research audiences this past reporting period in seminars at the University of Kentucky and Kansas State University, as well as at a rice breeding workshop at the virtual Plant and Animal Genome Meeting. Changes/Problems:
Nothing Reported
What opportunities for training and professional development has the project provided?A postdoctoral research associate was hired and trained as part of this project. The postdoctoral research associate has led the fine mapping, mutant identification, and phenotyping efforts. He has received specific training in plant genetics, molecular biology, genomics, bioinformatics, and plant pathology. How have the results been disseminated to communities of interest?Results from this research has been disseminated via presentations at universities and international conferences. Specifically, two presentations were given to plant pathology departments (University of Kentucky and Kansas State University) and to the rice genetics community at the Plant and Animal Genome Conference (January 2022). What do you plan to do during the next reporting period to accomplish the goals?We plan to finish phenotyping the critical recombinants, which will lead to the precise mapping of the CRSP2.1 resistance gene and delimit the gene to a small physical interval. The LaGrue reference genome will be annotated andused to identify genes within the mapped region. Sequences from the LaGrue mutants will be mapped to the LaGrue reference genome and identify potentially causal deletions that led to a loss of resistance. F1 and F2 individuals from the mutant crosses (allelism/complementation tests) will be phenotyped to determine if the mutations are within the same gene, as well as confirm that the mutations map to the CRSP2.1 region. Once candidate genes are identified, functional validation through CRISPR/Cas9 and over-expression will be initiated. The MPC population, as well as other RIL/MAGIC populations will be phenotyped under controlled conditions and in the field.
Impacts
What was accomplished under these goals?
A large effort was placed on fine mapping of the CRSP2.1 resistance locus (Objective 1). A total of 7,289 F2:3 individuals were genotyped with 13 SNP markers spanning the entire CRSP2.1 region, resulting in the identification of 448 recombinants. A majority of the recombinants were in the distal end of the region (~150 kb), but sufficient recombinants were identified throughout the entire locus to enable fine mapping. Phenotyping of these critical recombinants is currently underway. We next wanted to confirm the dominant inheritance of the CRSP2.1 resistance gene. We phenotyped an F2 population consisting of 49 individuals. Segregation did not deviate from a 3 R : 1S ratio, indicating that CRSP2.1 is a dominant resistance gene. Rice cultivar LaGrue (resistant variety that harbors CRSP2.1) was irradiated with fast-neutron irradiation. M1 seeds were planted in the field in 2020 and M2 seeds were harvested. Individual M2 plants were phenotyped in a growth chamber assay to identify resistance compromised mutants. Three resistance-compromised mutants were identified from our initial screening and transplanted in the greenhouse for seed increases. Seeds harvested from these mutants were planted and re-phenotyped to confirm the susceptibility. All three mutants were susceptible in the second round of phenotyping. The mutants were also planted and crossed to each other, as well as to other rice lines with a different resistant CRSP2.1 haplotype to conduct allelism/complementation tests and to facilitate mapping of the mutations. DNA was extracted from the LaGrue WT and three LaGrue mutants and sent for Illumina sequencing. We are currently awaiting the sequencing results. Nuclei were isolated from LaGrue WT and high-molecular weight DNA was extracted for Nanopore sequencing. We sequenced the LaGrue WT genome on an Oxford Nanopore MinION, resulting in approximately 17 Gb of sequences with a read N50 of ~25 kb. These long sequencing reads were assembled into a draft genome with an N50 of 11.9 Mb and an L50 of 12 contigs. Importantly, a contig was assembled that spanned the complete CRSP2.1 locus, which will enable precise candidate gene identification. These results poise us to identify strong candidate genes in the short-term and proceed to functional validation. We also made progress in the characterization of quantitative resistance to NBLS. The MPC population (Cypress x CL172) was planted in the field in 2021 and phenotyped for NBLS. Transgressive segregation was observed and two novel quantitative trait loci (QTL) were identified. Each QTL explained ~9-10% of the phenotypic variation.
Publications
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Richards, J.K., Famoso, A., Angira, B., Addison, C.K., and Cerioli, T. 2022. Mapping narrow brown leaf spot resistance in modern U.S. rice breeding germplasm. Plant and Animal Genome XXIX. Rice as a Model for Genetics, Genomics, and Breeding Workshop. 01/12/2022. Virtual Presentation.
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