Sorghum
Sorghum bicolor ranks among the most important cereal crops globally and serves as a primary dietary component for millions of people, particularly in Asia and Africa. Its exceptional tolerance to drought, high temperatures and marginal soils has positioned sorghum as a strategic crop under climate change scenarios. However, its yield potential remains vulnerable to a broad spectrum of biotic stresses, including anthracnose (
Colletotrichum sublineola), downy mildew (
Peronosclerospora sorghi), stalk rot (
Fusarium spp.) and insect pests such as the sugarcane aphid (
Melanaphis sacchari) (
Kanaka, 2006;
Sajjan et al., 2011; Veerabadhiran and Deepalakshmi, 2003).
Plants have evolved sophisticated defence mechanisms involving constitutive barriers and inducible immune responses governed by complex gene networks. The annotation of defence genes is therefore a critical step in identifying resistance loci, understanding evolutionary dynamics and enabling genomics-assisted breeding. With the advent of high-throughput sequencing technologies and advanced computational tools, the resolution and accuracy of defence gene annotation in sorghum have improved considerably
(Boyles et al., 2021; Xu et al., 2022). This review aims to synthesize recent developments and highlight future directions in this rapidly evolving field.
This review study was conducted at the School of Technology, Department of Bioinformatics, SRTM University Sub Campus, Latur, India, during the period 2023-2025.
A systematic literature survey was performed using major scientific databases, including Scopus, Web of Science, PubMed and Google Scholar. Relevant publications were identified using targeted keywords such as “sorghum defence genes”, “NLR proteins”, “pan-genomics”, “GWAS” and “CRISPR in cereals”. Only peer-reviewed articles published between 2015 and 2025 were considered, with priority given to high-impact and recent studies.
The collected literature was critically evaluated and synthesized using established review methodologies, with emphasis on integrating genomic, transcriptomic and functional data to provide a comprehensive understanding of defence gene annotation in sorghum
(Kour et al., 2022; Puri et al., 2023).
Genomic resources and pan-genome landscape
The availability of high-quality reference genomes and pan-genomic assemblies has transformed sorghum genomics. These resources have revealed extensive structural variation, including presence/absence variations (PAVs), which play a pivotal role in shaping defence gene diversity. Pan-genome analyses have enabled the identification of novel resistance loci that are absent in single reference genomes, thereby offering a more comprehensive view of genetic variation underlying disease resistance
(Xu et al., 2022; Birhanu et al., 2024).
Resistance genes and NLR protein architecture
Nucleotide-binding leucine-rich repeat (NLR) proteins constitute the central components of plant innate immunity. These proteins typically possess conserved NB-ARC domains coupled with variable leucine-rich repeats that facilitate pathogen recognition
(Boyles et al., 2021).
Recent studies have identified key resistance loci such as ARG2, ARG4 and ARG5 associated with anthracnose resistance
(Mewa et al., 2023; Habte et al., 2024). Genome-wide analyses indicate the presence of a large repertoire of NLR genes in sorghum, many of which remain functionally uncharacterized. The expansion and diversification of NLR gene families through duplication events highlight their evolutionary significance in adaptive immunity
(Lee et al., 2022).
Transcriptomic reprogramming and regulatory networks
Transcriptomic analyses have provided valuable insights into the dynamic reprogramming of gene expression during pathogen challenge. Defence responses are characterized by the activation of key metabolic pathways, including phenylpropanoid and flavonoid biosynthesis
(Kour et al., 2022; Puri et al., 2023).
Transcription factors such as WRKY, MYB and NAC families play crucial roles in regulating these responses. Additionally, hormonal signaling pathways involving salicylic acid, jasmonic acid and ethylene orchestrate coordinated defence responses through intricate cross-talk mechanisms
(Yu et al., 2021; Zhang et al., 2021).
Insect resistance and adaptive challenges
The sugarcane aphid has emerged as a major constraint in sorghum cultivation. Resistance loci such as RMES1 and RMES2 have been successfully identified and utilized in breeding programs
(VanGessel et al., 2024). However, the rapid evolution of new aphid biotypes poses a significant challenge to the durability of resistance. This underscores the need for continuous exploration and incorporation of novel resistance genes.
Role of secondary metabolites in defence
Sorghum synthesizes a diverse array of secondary metabolites, including dhurrin, tannins, flavonoids and 3-deoxyanthocyanidins, which function as chemical deterrents against biotic stressors
(Satish et al., 2020).
The biosynthesis of these compounds is tightly regulated and often induced under stress conditions. Recent studies have demonstrated coordinated upregulation of these pathways in resistant genotypes, highlighting their importance in plant defence
(Zhang et al., 2021).
Epigenetic regulation of defence responses
Epigenetic modifications, including DNA methylation and histone modifications, are increasingly recognized as key regulators of defence gene expression. These mechanisms enable plants to rapidly respond to environmental stimuli and may contribute to stress memory and transgenerational resistance. Understanding epigenetic regulation offers new avenues for crop improvement
(Yu et al., 2021).
Emerging technologies and future directions
Recent technological advancements are reshaping defence gene annotation and functional validation:
• Pan-genomics provides insights into gene presence/absence variation and structural diversity (
Xu et al., 2022).
• GWAS and QTL mapping facilitate identification of resistance-associated loci
(Nida et al., 2020; Upadhyaya et al., 2021).
• CRISPR/Cas genome editing enables precise functional validation and targeted improvement of defence genes
(Liu et al., 2022).
• Systems biology and machine learning approaches allow integration of multi-omics datasets to identify key regulatory networks
(Meng et al., 2023; Yu et al., 2021).
Collectively, these tools are accelerating the development of next-generation sorghum cultivars with enhanced resistance and adaptability.
