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Chiteri KO, Rairdin A, Sandhu K, Redsun S, Farmer A, O'Rourke JA, Cannon SB, Singh A. Combining GWAS and comparative genomics to fine map candidate genes for days to flowering in mung bean. BMC Genomics 2024; 25:270. [PMID: 38475739 DOI: 10.1186/s12864-024-10156-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 02/22/2024] [Indexed: 03/14/2024] Open
Abstract
BACKGROUND Mung bean (Vigna radiata (L.) Wilczek), is an important pulse crop in the global south. Early flowering and maturation are advantageous traits for adaptation to northern and southern latitudes. This study investigates the genetic basis of the Days-to-Flowering trait (DTF) in mung bean, combining genome-wide association studies (GWAS) in mung bean and comparisons with orthologous genes involved with control of DTF responses in soybean (Glycine max (L) Merr) and Arabidopsis (Arabidopsis thaliana). RESULTS The most significant associations for DTF were on mung bean chromosomes 1, 2, and 4. Only the SNPs on chromosomes 1 and 4 were heavily investigated using downstream analysis. The chromosome 1 DTF association is tightly linked with a cluster of locally duplicated FERONIA (FER) receptor-like protein kinase genes, and the SNP occurs within one of the FERONIA genes. In Arabidopsis, an orthologous FERONIA gene (AT3G51550), has been reported to regulate the expression of the FLOWERING LOCUS C (FLC). For the chromosome 4 DTF locus, the strongest candidates are Vradi04g00002773 and Vradi04g00002778, orthologous to the Arabidopsis PhyA and PIF3 genes, encoding phytochrome A (a photoreceptor protein sensitive to red to far-red light) and phytochrome-interacting factor 3, respectively. The soybean PhyA orthologs include the classical loci E3 and E4 (genes GmPhyA3, Glyma.19G224200, and GmPhyA2, Glyma.20G090000). The mung bean PhyA ortholog has been previously reported as a candidate for DTF in studies conducted in South Korea. CONCLUSION The top two identified SNPs accounted for a significant proportion (~ 65%) of the phenotypic variability in mung bean DTF by the six significant SNPs (39.61%), with a broad-sense heritability of 0.93. The strong associations of DTF with genes that have orthologs with analogous functions in soybean and Arabidopsis provide strong circumstantial evidence that these genes are causal for this trait. The three reported loci and candidate genes provide useful targets for marker-assisted breeding in mung beans.
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Affiliation(s)
- Kevin O Chiteri
- Department of Agronomy, Iowa State University, Ames, IA, United States
| | - Ashlyn Rairdin
- Department of Agronomy, Iowa State University, Ames, IA, United States
| | | | - Sven Redsun
- National Center for Genome Resources, Santa Fe, NM, 87505, United States
| | - Andrew Farmer
- National Center for Genome Resources, Santa Fe, NM, 87505, United States
| | - Jamie A O'Rourke
- Department of Agronomy, Iowa State University, Ames, IA, United States
- USDA - Agricultural Research Service, Corn Insects, and Crop Genetics Research Unit, Ames, IA, United States
| | - Steven B Cannon
- Department of Agronomy, Iowa State University, Ames, IA, United States.
- USDA - Agricultural Research Service, Corn Insects, and Crop Genetics Research Unit, Ames, IA, United States.
| | - Arti Singh
- Department of Agronomy, Iowa State University, Ames, IA, United States.
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Fattel L, Psaroudakis D, Yanarella CF, Chiteri KO, Dostalik HA, Joshi P, Starr DC, Vu H, Wimalanathan K, Lawrence-Dill CJ. Standardized genome-wide function prediction enables comparative functional genomics: a new application area for Gene Ontologies in plants. Gigascience 2022; 11:6568997. [PMID: 35426911 PMCID: PMC9012101 DOI: 10.1093/gigascience/giac023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 12/28/2021] [Accepted: 01/25/2022] [Indexed: 11/25/2022] Open
Abstract
Background Genome-wide gene function annotations are useful for hypothesis generation and for prioritizing candidate genes potentially responsible for phenotypes of interest. We functionally annotated the genes of 18 crop plant genomes across 14 species using the GOMAP pipeline. Results By comparison to existing GO annotation datasets, GOMAP-generated datasets cover more genes, contain more GO terms, and are similar in quality (based on precision and recall metrics using existing gold standards as the basis for comparison). From there, we sought to determine whether the datasets across multiple species could be used together to carry out comparative functional genomics analyses in plants. To test the idea and as a proof of concept, we created dendrograms of functional relatedness based on terms assigned for all 18 genomes. These dendrograms were compared to well-established species-level evolutionary phylogenies to determine whether trees derived were in agreement with known evolutionary relationships, which they largely are. Where discrepancies were observed, we determined branch support based on jackknifing then removed individual annotation sets by genome to identify the annotation sets causing unexpected relationships. Conclusions GOMAP-derived functional annotations used together across multiple species generally retain sufficient biological signal to recover known phylogenetic relationships based on genome-wide functional similarities, indicating that comparative functional genomics across species based on GO data holds promise for generating novel hypotheses about comparative gene function and traits.
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Affiliation(s)
- Leila Fattel
- Department of Agronomy, 2104 Agronomy Hall, 716 Farm House Lane Ames, Iowa 50011-1051, USA
| | - Dennis Psaroudakis
- Department of Plant Pathology and Microbiology, 1344 Advanced Teaching & Research Bldg, 2213 Pammel Drive, Ames, Iowa 50011, USA
| | - Colleen F Yanarella
- Department of Agronomy, 2104 Agronomy Hall, 716 Farm House Lane Ames, Iowa 50011-1051, USA
| | - Kevin O Chiteri
- Department of Agronomy, 2104 Agronomy Hall, 716 Farm House Lane Ames, Iowa 50011-1051, USA
| | - Haley A Dostalik
- Department of Agronomy, 2104 Agronomy Hall, 716 Farm House Lane Ames, Iowa 50011-1051, USA
| | - Parnal Joshi
- Department of Veterinary Microbiology and Preventive Medicine, 1800 Christensen Drive, Ames, Iowa 50011-1134, USA
| | - Dollye C Starr
- Department of Agronomy, 2104 Agronomy Hall, 716 Farm House Lane Ames, Iowa 50011-1051, USA
| | - Ha Vu
- Department of Genetics, Development and Cell Biology, 1210 Molecular Biology Building, 2437 Pammel Drive, Ames, Iowa 50011-1079, USA
| | - Kokulapalan Wimalanathan
- Department of Genetics, Development and Cell Biology, 1210 Molecular Biology Building, 2437 Pammel Drive, Ames, Iowa 50011-1079, USA
| | - Carolyn J Lawrence-Dill
- Department of Agronomy, 2104 Agronomy Hall, 716 Farm House Lane Ames, Iowa 50011-1051, USA
- Department of Genetics, Development and Cell Biology, 1210 Molecular Biology Building, 2437 Pammel Drive, Ames, Iowa 50011-1079, USA
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Elango D, Rajendran K, Van der Laan L, Sebastiar S, Raigne J, Thaiparambil NA, El Haddad N, Raja B, Wang W, Ferela A, Chiteri KO, Thudi M, Varshney RK, Chopra S, Singh A, Singh AK. Raffinose Family Oligosaccharides: Friend or Foe for Human and Plant Health? Front Plant Sci 2022; 13:829118. [PMID: 35251100 PMCID: PMC8891438 DOI: 10.3389/fpls.2022.829118] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 01/26/2022] [Indexed: 05/27/2023]
Abstract
Raffinose family oligosaccharides (RFOs) are widespread across the plant kingdom, and their concentrations are related to the environment, genotype, and harvest time. RFOs are known to carry out many functions in plants and humans. In this paper, we provide a comprehensive review of RFOs, including their beneficial and anti-nutritional properties. RFOs are considered anti-nutritional factors since they cause flatulence in humans and animals. Flatulence is the single most important factor that deters consumption and utilization of legumes in human and animal diets. In plants, RFOs have been reported to impart tolerance to heat, drought, cold, salinity, and disease resistance besides regulating seed germination, vigor, and longevity. In humans, RFOs have beneficial effects in the large intestine and have shown prebiotic potential by promoting the growth of beneficial bacteria reducing pathogens and putrefactive bacteria present in the colon. In addition to their prebiotic potential, RFOs have many other biological functions in humans and animals, such as anti-allergic, anti-obesity, anti-diabetic, prevention of non-alcoholic fatty liver disease, and cryoprotection. The wide-ranging applications of RFOs make them useful in food, feed, cosmetics, health, pharmaceuticals, and plant stress tolerance; therefore, we review the composition and diversity of RFOs, describe the metabolism and genetics of RFOs, evaluate their role in plant and human health, with a primary focus in grain legumes.
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Affiliation(s)
- Dinakaran Elango
- Department of Agronomy, Iowa State University, Ames, IA, United States
| | - Karthika Rajendran
- VIT School of Agricultural Innovations and Advanced Learning, Vellore Institute of Technology, Vellore, India
| | - Liza Van der Laan
- Department of Agronomy, Iowa State University, Ames, IA, United States
| | - Sheelamary Sebastiar
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, India
| | - Joscif Raigne
- Department of Agronomy, Iowa State University, Ames, IA, United States
| | | | - Noureddine El Haddad
- International Center for Agricultural Research in the Dry Areas, Rabat, Morocco
- Faculty of Sciences, Mohammed V University of Rabat, Rabat, Morocco
| | - Bharath Raja
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - Wanyan Wang
- Ecosystem Science and Management, Penn State University, University Park, PA, United States
| | - Antonella Ferela
- Department of Agronomy, Iowa State University, Ames, IA, United States
| | - Kevin O. Chiteri
- Department of Agronomy, Iowa State University, Ames, IA, United States
| | - Mahendar Thudi
- Department of Agricultural Biotechnology and Molecular Biology, Dr. Rajendra Prasad Central Agricultural University, Pusa, India
- Centre for Crop Health, University of Southern Queensland, Toowoomba, QLD, Australia
| | - Rajeev K. Varshney
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, India
- State Agricultural Biotechnology Centre, Crop Research Innovation Centre, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
| | - Surinder Chopra
- Department of Plant Science, Penn State University, University Park, PA, United States
| | - Arti Singh
- Department of Agronomy, Iowa State University, Ames, IA, United States
| | - Asheesh K. Singh
- Department of Agronomy, Iowa State University, Ames, IA, United States
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Chiteri KO, Jubery TZ, Dutta S, Ganapathysubramanian B, Cannon S, Singh A. Dissecting the Root Phenotypic and Genotypic Variability of the Iowa Mung Bean Diversity Panel. Front Plant Sci 2022; 12:808001. [PMID: 35154202 PMCID: PMC8828542 DOI: 10.3389/fpls.2021.808001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/06/2021] [Indexed: 06/14/2023]
Abstract
Mung bean [Vigna radiata (L.) Wilczek] is a drought-tolerant, short-duration crop, and a rich source of protein and other valuable minerals, vitamins, and antioxidants. The main objectives of this research were (1) to study the root traits related with the phenotypic and genetic diversity of 375 mung bean genotypes of the Iowa (IA) diversity panel and (2) to conduct genome-wide association studies of root-related traits using the Automated Root Image Analysis (ARIA) software. We collected over 9,000 digital images at three-time points (days 12, 15, and 18 after germination). A broad sense heritability for days 15 (0.22-0.73) and 18 (0.23-0.87) was higher than that for day 12 (0.24-0.51). We also reported root ideotype classification, i.e., PI425425 (India), PI425045 (Philippines), PI425551 (Korea), PI264686 (Philippines), and PI425085 (Sri Lanka) that emerged as the top five in the topsoil foraging category, while PI425594 (unknown origin), PI425599 (Thailand), PI425610 (Afghanistan), PI425485 (India), and AVMU0201 (Taiwan) were top five in the drought-tolerant and nutrient uptake "steep, cheap, and deep" ideotype. We identified promising genotypes that can help diversify the gene pool of mung bean breeding stocks and will be useful for further field testing. Using association studies, we identified markers showing significant associations with the lateral root angle (LRA) on chromosomes 2, 6, 7, and 11, length distribution (LED) on chromosome 8, and total root length-growth rate (TRL_GR), volume (VOL), and total dry weight (TDW) on chromosomes 3 and 5. We discussed genes that are potential candidates from these regions. We reported beta-galactosidase 3 associated with the LRA, which has previously been implicated in the adventitious root development via transcriptomic studies in mung bean. Results from this work on the phenotypic characterization, root-based ideotype categories, and significant molecular markers associated with important traits will be useful for the marker-assisted selection and mung bean improvement through breeding.
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Affiliation(s)
- Kevin O. Chiteri
- Department of Agronomy, Iowa State University, Ames, IA, United States
| | - Talukder Zaki Jubery
- Department of Mechanical Engineering, Iowa State University, Ames, IA, United States
| | - Somak Dutta
- Department of Statistics, Iowa State University, Ames, IA, United States
| | | | - Steven Cannon
- Department of Agronomy, Iowa State University, Ames, IA, United States
- USDA—Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, IA, United States
| | - Arti Singh
- Department of Agronomy, Iowa State University, Ames, IA, United States
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