On March 7, 2025, a research team led by Dr. Qi Xie from the Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, in collaboration with Prof. Feifei Yu from China Agricultural University, published a study titled “A comprehensive omics resource and genetic tools for functional genomics research and genetic improvement of sorghum” in Molecular Plant (IF: 24.1).
In the experimental setup, seedlings were cultivated in Jiupo plant growth chambers, using a photoperiod of 16 hours (28°C) and a dark period of 8 hours (25°C).
This study, based on the sorghum inbred line E048, established an integrated research platform encompassing genome, transcriptome, mutant library, and transformation system—providing a systematic resource for sorghum functional genomics and molecular breeding.
Sorghum is the fifth-largest cereal crop globally, feeding over 500 million people in arid and semi-arid regions. Originating from the Sahel region of Africa, it exhibits strong tolerance to abiotic stresses such as drought, heat, nutrient deficiency, and salinity, making it an ideal model for studying stress response mechanisms. However, limited genetic tools and transformation techniques have restricted the progress of sorghum gene research.
Figure 1. Genome Assembly of E048
Using ONT ultra-long reads, PacBio HiFi sequencing, and Hi-C technologies, the team generated a gap-free T2T genome of E048 (729.5 Mb, 35,549 genes), including full telomere and centromere sequences. Comparative analysis identified a 2.9 Mb region unique to E048 with 187 genes, involved in signal transduction, immune response, and metabolism—offering insights into traits like disease resistance and high sugar content.
To explore transcriptional regulation, transcriptomic data from 13 tissues and stages were collected, forming a comprehensive gene expression atlas. Of the predicted genes, 93.39% were expressed in at least one tissue, and 57.59% in all tissues. Pre-flowering inflorescences had the most tissue-specific genes, mainly linked to reproductive processes.
A saturated EMS mutant library was also developed, including 13,226 M1 lines and resequencing of 179 M2 lines, identifying over 2.29 million SNPs and InDels, covering 97.54% of genes. Using the E048 genome and mutant lines, the team successfully mapped key genes using MutMap and MapMap+, and established an optimized Agrobacterium-mediated transformation system.
Figure 2. Homepage Snapshot of the SGMD Database
To enhance resource accessibility, the team created the SGMD database (https://sorghum.genetics.ac.cn/SGMD), integrating genomic, expression, phenotypic, and variant data—forming a “super toolkit” for sorghum research.
In conclusion, this work provides powerful genetic resources and omics tools for sorghum gene discovery and breeding, accelerating scientific breakthroughs in the field.