Genome-wide association study and RNA sequencing identify candidate genes regulating nitrogen use efficiency and associated traits in sorghum (Sorghum bicolor (L.) Moench)

Authors: BOLLAM, SRIKANTH - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; RAYAPROLU, LAAVANYA - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; ROMANA, KIRANDEEP - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; RUPERAO, PRADEEP - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; SELVANAYAGAM, SIVASUBRAMANI - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; VEMULA, ANIL - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; ADAPALA, GOPIKRISHNA - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; VALLURI, VINOD - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; BAJAJ, PRASAD - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; Gupta, Rajeev; RATHORE, ABHISHEK - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; ODENY, DAMARIS - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; DESHPANDE, SANTOSH - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India; SRIVASTAVA, RAKESH - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India

Submitted to: Food and Energy Security
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/5/2025
Publication Date: 2/6/2026
Citation: Bollam, S., Rayaprolu, L., Romana, K., Ruperao, P., Selvanayagam, S., Vemula, A., Adapala, G., Valluri, V., Bajaj, P., Gupta, R., Rathore, A., Odeny, D., Deshpande, S., Srivastava, R. 2026. Genome-wide association study and RNA sequencing identify candidate genes regulating nitrogen use efficiency and associated traits in sorghum (Sorghum bicolor (L.) Moench). Food and Energy Security. 15(1). https://doi.org/10.1002/fes3.70174.
DOI: https://doi.org/10.1002/fes3.70174

Interpretive Summary: Sorghum (Sorghum bicolor (L.) Moench) is a vital cereal crop ranked fifth in importance worldwide, following wheat, rice, maize, and barley. It holds particular significance in Sub-Saharan Africa and South Asia, serving as a major food crop and staple for many food-insecure farming communities. Abiotic stresses including low nitrogen poses a significant challenge for crop production especially in climate change scenarios and marginal cropping systems. In this study, we screened a sorghum diversity panel comprising 186 lines for plant features associated with crop yield under both normal and low nitrogen conditions over multiple years. This study unveils key candidate genes and genomic regions associated with nitrogen use efficiency related traits in sorghum. The identification of promising accessions and key candidate genes offers promising avenues for further research and application in genomics-assisted breeding programs in sorghum.

Technical Abstract: Introduction: Sorghum (Sorghum bicolor L. Moench) is a vital cereal crop with remarkable adaptability to diverse environments. Nitrogen use efficiency (NUE) is critical for improving sorghum yields, resource utilization, livelihood security and fostering environmental sustainability in the target ecologies. Objectives: This study aimed to unravel the physio-genetic variability of sorghum for NUE/ N stress tolerance and identify candidate genes regulating NUE. Methods: A set of 186 diverse sorghum accessions were evaluated for agro-physiological (13) and NUE (2) related traits across three nitrogen regimes (N0, N50 and N100% of the recommended dose) for two seasons. Genotyping-by-sequencing (GbS) facilitated SNP data generation from the same individuals. Genome-wide association studies (GWAS) were carried out by integrating phenotypic and genotypic datasets. Additionally, transcriptome analysis of shoot and root samples from contrasting sorghum accessions for NUE was undertaken to identify differentially expressed genes (DEGs). Results: A total of 1369 marker-trait associations (MTAs) spanning sorghum chromosomes were identified, highlighting 69 candidate genes/genetic loci associated with N metabolism including Nitrate transporter, Early nodulin 75-like protein, Sucrose-phosphatase, Sucrose-phosphate synthase, Squamosa promoter-binding-like protein, Aquaporin NIP3-2 and various transcription factors like WRKY, Dehydrin and NAC domain. Transcriptome analysis detected 2229 (shoot) and 8661 (root) DEGs among contrasting sorghum accessions. Integration of GWAS and Transcriptome analysis pinpointed 106 genes, including F-box genes (Sobic.002G106200), ATP-binding Cassette (ABC) transporters (Sobic.007G095100), Amino acid transporters (Sobic.005G052500, Sobic.006G045400), Bi-directional sugar transporter (SWEET) (Sobic.004G133500), Xyloglucan endotransglucosylase (Sobic.004G1272000), Protein kinases (Sobic.002G172100), Leucine-rich repeats (LRR) (Sobic.002G343600), WRC proteins (Sobic.004G269900), APETALA2/ethylene response factor (AP2/ERF) (Sobic.009G111200) among others. Furthermore, this study also identified contrasting sorghum accessions for N stress tolerance. Conclusion: This study unveils key candidate genes associated with NUE in sorghum, shedding light on mechanisms underlying nitrogen stress tolerance. The identification of promising accessions and key candidate genes for NUE offers promising avenues for further research and application in genomics-assisted breeding programs aimed at enhancing NUE and sustainability in sorghum.