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Sar P, Gupta S, Behera M, Chakraborty K, Ngangkham U, Verma BC, Banerjee A, Hanjagi PS, Bhaduri D, Shil S, Kumar J, Mandal NP, Kole PC, Purugganan MD, Roy S. Exploring Genetic Diversity within aus Rice Germplasm: Insights into the Variations in Agro-morphological Traits. Rice (N Y) 2024; 17:20. [PMID: 38526679 DOI: 10.1186/s12284-024-00700-4] [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] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 03/12/2024] [Indexed: 03/27/2024]
Abstract
The aus (Oryza sativa L.) varietal group comprises of aus, boro, ashina and rayada seasonal and/or field ecotypes, and exhibits unique stress tolerance traits, making it valuable for rice breeding. Despite its importance, the agro-morphological diversity and genetic control of yield traits in aus rice remain poorly understood. To address this knowledge gap, we investigated the genetic structure of 181 aus accessions using 399,115 SNP markers and evaluated them for 11 morpho-agronomic traits. Through genome-wide association studies (GWAS), we aimed to identify key loci controlling yield and plant architectural traits.Our population genetic analysis unveiled six subpopulations with strong geographical patterns. Subpopulation-specific differences were observed in most phenotypic traits. Principal component analysis (PCA) of agronomic traits showed that principal component 1 (PC1) was primarily associated with panicle traits, plant height, and heading date, while PC2 and PC3 were linked to primary grain yield traits. GWAS using PC1 identified OsSAC1 on Chromosome 7 as a significant gene influencing multiple agronomic traits. PC2-based GWAS highlighted the importance of OsGLT1 and OsPUP4/ Big Grain 3 in determining grain yield. Haplotype analysis of these genes in the 3,000 Rice Genome Panel revealed distinct genetic variations in aus rice.In summary, this study offers valuable insights into the genetic structure and phenotypic diversity of aus rice accessions. We have identified significant loci associated with essential agronomic traits, with GLT1, PUP4, and SAC1 genes emerging as key players in yield determination.
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Affiliation(s)
- Puranjoy Sar
- Central Rainfed Upland Rice Research Station, ICAR-National Rice Research Institute, Hazaribag, Jharkhand, 825 301, India
| | - Sonal Gupta
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Motilal Behera
- Crop Physiology and Biochemistry Division, ICAR-National Rice Research Institute, Cuttack, Odisha, 753 006, India
| | - Koushik Chakraborty
- Crop Physiology and Biochemistry Division, ICAR-National Rice Research Institute, Cuttack, Odisha, 753 006, India
| | - Umakanta Ngangkham
- Manipur Center, ICAR Research Complex for NEH Region, Imphal, Manipur, 795 004, India
| | - Bibhash Chandra Verma
- Central Rainfed Upland Rice Research Station, ICAR-National Rice Research Institute, Hazaribag, Jharkhand, 825 301, India
| | - Amrita Banerjee
- Central Rainfed Upland Rice Research Station, ICAR-National Rice Research Institute, Hazaribag, Jharkhand, 825 301, India
| | - Prashantkumar S Hanjagi
- Crop Physiology and Biochemistry Division, ICAR-National Rice Research Institute, Cuttack, Odisha, 753 006, India
| | - Debarati Bhaduri
- Crop Production Division, ICAR-National Rice Research Institute, Cuttack, Odisha, 753 006, India
| | - Sandip Shil
- Research Centre - Mohitnagar, ICAR-Central Plantation Crops Research Institute, Jalpaiguri, West Bengal, 735 101, India
| | - Jitendra Kumar
- Central Rainfed Upland Rice Research Station, ICAR-National Rice Research Institute, Hazaribag, Jharkhand, 825 301, India
| | - Nimai Prasad Mandal
- Central Rainfed Upland Rice Research Station, ICAR-National Rice Research Institute, Hazaribag, Jharkhand, 825 301, India
| | - Paresh Chandra Kole
- Palli Siksha Bhavana (Institute of Agriculture), Visva-Bharati, Sriniketan, West Bengal, 731236, India
| | | | - Somnath Roy
- Central Rainfed Upland Rice Research Station, ICAR-National Rice Research Institute, Hazaribag, Jharkhand, 825 301, India.
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