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Abstract Theaus(Oryza sativaL.) 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 inausrice remain poorly understood. To address this knowledge gap, we investigated the genetic structure of 181ausaccessions 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 identifiedOsSAC1on Chromosome 7 as a significant gene influencing multiple agronomic traits. PC2-based GWAS highlighted the importance ofOsGLT1and OsPUP4/ Big Grain 3 in determining grain yield. Haplotype analysis of these genes in the 3,000 Rice Genome Panel revealed distinct genetic variations inausrice. In summary, this study offers valuable insights into the genetic structure and phenotypic diversity ofausrice accessions. We have identified significant loci associated with essential agronomic traits, withGLT1, PUP4, andSAC1genes emerging as key players in yield determination.
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This content will become publicly available on September 12, 2026
Origin, domestication, and diversity of the climate resilient Ethiopian cereal teff
Abstract Teff (Eragrostis tef) is a climate-resilient cereal and staple crop in the Horn of Africa, cultivated by millions of smallholder farmers. Despite its cultural and nutritional significance, teff has limited genomic tools, constraining progress in yield improvement and trait optimization. Here, we assembled and resequenced the Teff Association Panel (TAP), a diverse set of 265 landraces and cultivars, to investigate the domestication history, genetic diversity, and agronomic traits of teff. Phylogenetic and population genetic analyses confirmEragrostis pilosaas the direct progenitor of teff, with domestication likely occurring in the Tigray region of Ethiopia. We generated a high-quality reference genome forE. pilosaand found extensive chromosomal collinearity and minimal gene loss compared to teff, with teff-specific genes enriched in functions related to domestication traits. We identified signatures of selection across the teff genome and used genome-wide association studies (GWAS) to map loci associated with seed color and panicle architecture. Integrated GWAS, expression, metabolic, and comparative genomic analyses pinpoint a major seed color locus containing orthologs of theTT7cytochrome P450 gene involved in flavonoid hydroxylation and theTT2MYB transcription factor regulating proanthocyanidin biosynthesis. For panicle architecture, we identified a strong association near a teff ortholog of Dense and Erect Panicle 1 (DEP1), a key regulator of inflorescence structure in rice and sorghum. This suggests convergent selection on shared genetic pathways controlling panicle morphology across cereals. Our findings confirm the evolutionary origin of teff, identify key domestication loci, and highlight untapped genetic diversity among Ethiopian breeding lines. These genomic resources provide a foundation for accelerating teff improvement through molecular breeding and genome editing to enhance yield, resilience, and nutrition.
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- Award ID(s):
- 2419923
- PAR ID:
- 10687949
- Publisher / Repository:
- bioRxiv
- Date Published:
- Format(s):
- Medium: X
- Institution:
- bioRxiv
- Sponsoring Org:
- National Science Foundation
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