Progress 05/01/24 to 04/30/25
Outputs
Target Audience:The target audience of the project are chile pepper growers and consumers, and undergraduate and graduate students. Among the efforts related to the project include formal classroom instruction and development of innovative teaching methodologies to teach genomics in the GENE 452 (Applied Bioinformatics) class offered at the Department of Plant and Environmental Sciences, NMSU, in Fall semester 2024. Changes/Problems:Metabolomics will be integrated with a genome-wide association study (GWAS) to determine genomic regions affecting variation for metabolite content in New Mexican chile pepper. A metabolite-based GWAS (mGWAS) approach is expected to strengthen our current understanding of the genetics of the different health-promoting metabolites present in chile pepper. Our results would be relevant in performing more robust and informed breeding and selection decisions towards the development of chile pepper cultivars with improved nutritional value for consumers. The mGWAS will be implemented in Summer/Fall 2025 using a diverse panel of chile pepper that will be planted at the Fabian Garcia Science Center field plots, Las Cruces, NM. What opportunities for training and professional development has the project provided?Two PhD students have been trained to perform association mapping for fruit morphology, yield, and quality traits in chile pepper. Training in conducting genomewide prediction, high-performance liquid chromatography, and molecular marker design and validation is currently being conducted. The project also involves four undergraduate students who assist on processing samples and collecting phenotypic data in the field and in the lab. A PhD student funded through the project will be attending the American Society for Horticultural Science Conference which will provide opportunities for networking and professional development this Fall 2025. How have the results been disseminated to communities of interest?Results of the project have been disseminated in scientific conference (American Society for Horticultural Science Conference 2024 (Honolulu, HI) and International Pepper Conference 2024 (Ithaca, NY)), growers' meeting (New Mexico Chile Conference 2024 (Las Cruces, NM)), and field day (Fabian Garcia Science Center Field Day 2024, Las Cruces, NM) through three oral and one poster presentations. What do you plan to do during the next reporting period to accomplish the goals?A metabolite-based genomewide association study (mGWAS) for nutritional quality traits (see Changes/Problems) will be implemented to pinpoint the genetic determinants of these traits. Marker development and validation using information derived from mGWAS will be performed for marker-assisted breeding and selection. A GWAS for capsaicinoid content is currently under review for publication (Khan et al. 2025; under review).
Impacts
What was accomplished under these goals?
A multi-locus genome-wide association study (GWAS) was previously implemented on 123 chile pepper genotypes grown in field conditions in Las Cruces, New Mexico, USA (Objective 1; Khan et al. 2025, under review). High-performance liquid chromatography (HPLC) analysis was conducted to determine capsaicinoid contents and Scoville heat units (SHU). Significant phenotypic variation has been observed for the evaluated traits. The 'Superhots' '7 Pot Primo' and 'Trinidad Moruga Scorpion', belonging to C. chinense, showed SHU of 1.45 million and 1.09 million, respectively. A total of 30 GBS-SNP markers distributed across 12 chromosomes were associated with capsaicinoid production. Candidate genes including putative acyl-activating enzyme 2, ethylene transcription factor, and histone-lysine N-methyltransferase were identified for the associated SNP markers. Allele specific markers will be developed to validate these results for molecular breeding for capsaicinoid content in New Mexican chile pepper.
Publications
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Progress 05/01/23 to 04/30/24
Outputs
Target Audience:The target audience of the project are chile pepper growers and consumers, and undergraduate and graduate students. Efforts related to the project include formal classroom instruction and development of innovative teaching methodologies to teach association mapping, genomewide selection, and marker development and validation in GENE 452 (Applied Bioinformatics; Fall 2023) offered at the Department of Plant and Environmental Sciences, NMSU. Changes/Problems:Metabolomics will be integrated with a genome-wide association study (GWAS) to identify genomic regions affecting variation for metabolite content in New Mexican chile pepper. A metabolite-based GWAS (mGWAS) approach is anticipated to strengthen and expand our current understanding of the genetics of the different metabolites present in chile pepper that related to human health and nutrition. Furthermore, our results would be beneficial in performing more robust and informed breeding and selection decisions towards the development of chile pepper cultivars with improved nutritive value for consumers. The mGWAS will be implemented in Summer/Fall 2024 using a diverse panel of chile pepper that was planted at the Leyendecker Plant Science Research Center, Las Cruces, NM in the 2023 growing season. What opportunities for training and professional development has the project provided?Two PhD students have been trained to perform association mapping for yield and quality traits in chile pepper. Training in conducting genomewide prediction and molecular marker design and validation is currently being conducted. The project also involves four undergraduate students who assist on processing samples and collecting phenotypic data in the field and in the lab. A PhD student funded through the project will be attending the American Society for Horticultural Science Conference which will provide opportunities for networking and professional development this Fall 2024. Another PhD student was trained in analyzing metabolomics data derived from chile pepper fruit samples. How have the results been disseminated to communities of interest?Results have been disseminated through peer-reviewed journals (two published articles) and attendance in scientific conferences and growers' meetings (American Society for Horticultural Science Conference and New Mexico Chile Conference) through two oral and two poster presentations. What do you plan to do during the next reporting period to accomplish the goals?A metabolite-based genomewide association study for nutritional quality traits (see Changes/Problems) and an association study for capsaicinoid and carotenoid content (Objective 1) is currently being performed to identify important genomic regions associated with these traits. Marker development and validation using information derived from association mapping will be performed for marker-assisted breeding and selection.
Impacts
What was accomplished under these goals?
Genomic selection (GS) through cross-validations using various ridge regression and deep learning models has been implemented for yield and agronomic traits, and the utility of these approaches in the context of chile pepper breeding and improvement has been demonstrated (Lozada et al., 2023b; Objective 2). It was observed that under a relatively small size of the training population, genomic and ridge regression BLUP models were appropriate for optimal accuracies. Furthermore, integrating phenotypic selection and GS resulted in increased selection response to selection for yield-related traits, indicating that combining different approaches can render improved gains through selection (Lozada et al., 2023b). Untargeted metabolomics approaches also demonstrated the diversity of important health and nutrition-related metabolites in jalapeno and serrano peppers, indicating that pepper fruits are significant sources of vitamins and minerals for the human diet (Lozada et al., 2023a).
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2023
Citation:
Lozada, D. N., Pulicherla, S, Holguin, O. 2023a. Widely targeted metabolomics reveals metabolite diversity in jalape�o and serrano chile peppers (Capsicum annuum L.) Metabolites 13(2): 288 https://doi.org/10.3390/metabo13020288
- Type:
Journal Articles
Status:
Published
Year Published:
2023
Citation:
Lozada, D.N., Sandhu, K.S.S., Bhatta, M. 2023b. Ridge regression and deep learning models for genomewide selection of complex traits in New Mexican chile peppers. BMC Genomic Data 24(80). https://doi.org/10.1186/s12863-023-01179-6
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Progress 05/01/22 to 04/30/23
Outputs
Target Audience:The target audience of the project are chile pepper growers and consumers, and undergraduate and graduate students. Efforts related to the project include formal classroom instruction and development of innovative teaching methodologies to teach association mapping, genomewide selection, and marker development and validation in AGRO/HORT 610 (Advanced Crop Breeding; Spring 2022) and GENE 452 (Applied Bioinformatics; Fall 2022) offered at the Department of Plant and Environmental Sciences, NMSU. Changes/Problems:Metabolomics will be integrated with a genome-wide association study (GWAS) to identify genomic regions affecting variation for metabolite content in New Mexican chile pepper. A metabolite-based GWAS (mGWAS) approach is anticipated to strengthen and expand our current understanding of the genetics of the different metabolites present in chile pepper that related to human health and nutrition. Furthermore, our results would be beneficial in performing more robust and informed breeding and selection decisions towards the development of chile pepper cultivars with improved nutritive value for consumers. The mGWAS will be implemented in the Fall using a diverse population of chile pepper that will be planted at the Leyendecker Plant Science Research Center, Las Cruces, NM and at the NMSU Los Lunas Agricultural Science Center, Los Lunas, NM. What opportunities for training and professional development has the project provided?Two PhD students have been trained to perform association mapping for fruit morphology, yield, and quality traits in chile pepper. Training in conducting genomewide prediction and molecular marker design and validation is currently being conducted. The project also involves four undergraduate students who assist on processing samples and collecting phenotypic data in the field and in the lab. A PhD student funded through the project will be attending a conference which will provide opportunities for networking and professional development this Summer 2023. How have the results been disseminated to communities of interest?Results have been disseminated through peer-reviewed journals (two published articles) and attendance in scientific conferences and growers' meetings (American Society for Horticultural Science Conference, International Pepper Conference, and New Mexico Chile Conference) through various oral and poster presentations (total of six, three oral and three posters). What do you plan to do during the next reporting period to accomplish the goals?Association mapping for fruit morphology and quality traits in chile pepper using various multi-locus models is currently being performed (Objective 1). In addition, we plan to implement genomewide prediction to determine breeding values and selection accuracy for the evaluated traits (Objective 2) and a metabolite-based genomewide association mapping for nutritional quality traits (see Changes/Problems).
Impacts
What was accomplished under these goals?
Single nucleotide polymorphism markers associated with yield and yield components in chile peppers have been identified using multi-locus association mapping models (Lozada et al. 2022). These results will be used as a basis for future genomewide selection and marker development and validation for these traits. Diversity in terms of fruit morphology and architecture in New Mexican chile peppers has also been characterized using the Tomato Analyzer, a high-throughput phenotyping platform (Khokhar et al. 2022).
Publications
- Type:
Journal Articles
Status:
Published
Year Published:
2022
Citation:
Khokhar, E., Lozada, D.N., Nankar, A., Hernandez, S., Coon, D., Kaur, N., Nourbakhsh, S. 2022. High-throughput digital tool characterized fruit phenotypic diversity among New Mexican chile pepper. HortScience. https://doi.org/10.21273/HORTSCI16815-22 (Featured on the Cover Page of the December 2022 issue of the Journal)
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2023
Citation:
Khan, M.I., Lozada, D.N., Khokhar E. Identification of quantitative trait loci associated with heat content in chile pepper using genome-wide association study. New Mexico Chile Conference, February 7, 2023, Las Cruces, NM (Poster)
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Lozada, D. N., Bhatta, M., Coon, D., Bosland, P.W. Multi-locus association mapping for chile pepper breeding and genetics. American Society for Horticultural Science Conference, July 31, 2022, Chicago, IL (Oral)
- Type:
Journal Articles
Status:
Published
Year Published:
2022
Citation:
Lozada, D N., Barchenger, D.W., Coon, D., Bhatta, M., Bosland, P.W. 2022a. Multi-locus association mapping uncovers the genetic basis of yield and agronomic traits in chile pepper (Capsicum spp.). Crop Breeding, Genetics, and Genomics. 4(2):e220002; https://doi.org/10.20900/cbgg20220002.
- Type:
Conference Papers and Presentations
Status:
Other
Year Published:
2023
Citation:
Khokhar E., Lozada, D. N., Kaur, N., Khan, M. I., Nourbakhsh, S. S. High-throughput characterization of fruit phenotypic diversity among New Mexican chile pepper (Capsicum spp.) using the Tomato Analyzer software. NMSU Research and Creativity Week, February 23, 2023, Las Cruces, NM (Poster)
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Khokhar, E. S., Lozada, D.N., Kaur, N., Nourbakhsh, S. Genome-wide association mapping of fruit morphology traits in New Mexican chile pepper (Capsicum spp.). International Pepper Conference, September 28, 2022, Tucson, AZ (Oral)
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2023
Citation:
Khokhar E., Lozada, D. N., Kaur, N., Khan, M. I., Nourbakhsh, S. S. Genome-wide association mapping of fruit morphology traits in New Mexican chile pepper (Capsicum spp.). New Mexico Chile Conference, February 7, 2023, Las Cruces, NM (Awarded 1st Place, New Mexico Chile Conference Student Poster Competition 2023) (Poster)
- Type:
Conference Papers and Presentations
Status:
Published
Year Published:
2022
Citation:
Lozada, D.N., Bosland, P.W., Barchenger, D. W., Haghshenas-Jaryani, M., Sanogo, S., Walker, S. Omics approaches for chile pepper breeding and improvement. International Pepper Conference, September 28, 2022, Tucson, AZ (Oral)
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