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Ahn E, Botkin J, Ellur V, Lee Y, Poudel K, Prom LK, Magill C. Genome-Wide Association Study of Seed Morphology Traits in Senegalese Sorghum Cultivars. PLANTS (BASEL, SWITZERLAND) 2023; 12:2344. [PMID: 37375969 DOI: 10.3390/plants12122344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 06/13/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023]
Abstract
Sorghum is considered the fifth most important crop in the world. Despite the potential value of Senegalese germplasm for various traits, such as resistance to fungal diseases, there is limited information on the study of sorghum seed morphology. In this study, 162 Senegalese germplasms were evaluated for seed area size, length, width, length-to-width ratio, perimeter, circularity, the distance between the intersection of length & width (IS) and center of gravity (CG), and seed darkness and brightness by scanning and analyzing morphology-related traits with SmartGrain software at the USDA-ARS Plant Science Research Unit. Correlations between seed morphology-related traits and traits associated with anthracnose and head smut resistance were analyzed. Lastly, genome-wide association studies were performed on phenotypic data collected from over 16,000 seeds and 193,727 publicly available single nucleotide polymorphisms (SNPs). Several significant SNPs were found and mapped to the reference sorghum genome to uncover multiple candidate genes potentially associated with seed morphology. The results indicate clear correlations among seed morphology-related traits and potential associations between seed morphology and the defense response of sorghum. GWAS analysis listed candidate genes associated with seed morphologies that can be used for sorghum breeding in the future.
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Affiliation(s)
- Ezekiel Ahn
- USDA-ARS Plant Science Research Unit, St. Paul, MN 55108, USA
| | - Jacob Botkin
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN 55108, USA
| | - Vishnutej Ellur
- Molecular Plant Sciences, Washington State University, Pullman, WA 99164, USA
| | - Yoonjung Lee
- Department of Plant Pathology, University of Minnesota, Saint Paul, MN 55108, USA
| | - Kabita Poudel
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA
| | - Louis K Prom
- USDA-ARS Southern Plains Agricultural Research Center, College Station, TX 77845, USA
| | - Clint Magill
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77843, USA
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Luong AM, Adam H, Gauron C, Affortit P, Ntakirutimana F, Khong NG, Le QH, Le TN, Fournel M, Lebrun M, Tregear J, Jouannic S. Functional Diversification of euANT/PLT Genes in Oryza sativa Panicle Architecture Determination. FRONTIERS IN PLANT SCIENCE 2021; 12:692955. [PMID: 34305984 PMCID: PMC8302143 DOI: 10.3389/fpls.2021.692955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 06/15/2021] [Indexed: 05/13/2023]
Abstract
Grain yield, which is one of the most important traits in rice breeding, is controlled in part by panicle branching patterns. Numerous genes involved in the control of panicle architecture have been identified through mutant and QTL characterization. Previous studies suggested the importance of several AP2/ERF transcription factor-encoding genes in the control of panicle development, including the AINTEGUMENTA/PLETHORA-like (euANT/PLT) genes. The ANT gene was specifically considered to be a key regulator of shoot and floral development in Arabidopsis thaliana. However, the likely importance of paralogous euANT/PLT genes in the regulation of meristem identities and activities during panicle architecture development has not to date been fully addressed in rice. In this study, we observed that the rice euANT/PLT genes displayed divergent temporal expression patterns during the branching stages of early panicle development, with spatial localization of expression in meristems for two of these genes. Moreover, a functional analysis of rice ANT-related genes using genome editing revealed their importance in the control of panicle architecture, through the regulation of axillary meristem (AM) establishment and meristem fate transition. Our study suggests that the paralogous euANT/PLT genes have become partially diversified in their functions, with certain opposing effects, since they arose from ancestral gene duplication events, and that they act in regulating the branching of the rice panicle.
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Affiliation(s)
- Ai My Luong
- DIADE, University of Montpellier, IRD, CIRAD, Montpellier, France
| | - Hélène Adam
- DIADE, University of Montpellier, IRD, CIRAD, Montpellier, France
| | - Carole Gauron
- DIADE, University of Montpellier, IRD, CIRAD, Montpellier, France
| | - Pablo Affortit
- DIADE, University of Montpellier, IRD, CIRAD, Montpellier, France
| | | | - Ngan Giang Khong
- LMI RICE, National Key Laboratory for Plant CellBiotechnology, Agronomical Genetics Institute, University of Montpellier, IRD, CIRAD, University of Science and Technologyof Hanoi, Hanoi, Vietnam
| | - Quang Hoa Le
- School of Biotechnology and Food Technology, Hanoi University of Science and Technology, Hanoi, Vietnam
| | - Thi Nhu Le
- LMI RICE, National Key Laboratory for Plant CellBiotechnology, Agronomical Genetics Institute, University of Montpellier, IRD, CIRAD, University of Science and Technologyof Hanoi, Hanoi, Vietnam
| | - Marie Fournel
- DIADE, University of Montpellier, IRD, CIRAD, Montpellier, France
| | - Michel Lebrun
- LMI RICE, National Key Laboratory for Plant CellBiotechnology, Agronomical Genetics Institute, University of Montpellier, IRD, CIRAD, University of Science and Technologyof Hanoi, Hanoi, Vietnam
- LSTM, University of Montpellier, IRD, CIRAD, INRAE, SupAgro, Montpellier, France
| | - James Tregear
- DIADE, University of Montpellier, IRD, CIRAD, Montpellier, France
| | - Stefan Jouannic
- DIADE, University of Montpellier, IRD, CIRAD, Montpellier, France
- *Correspondence: Stefan Jouannic,
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