Understanding the genetic function of the forage quality-related traits, including crude protein (CP), neutral detergent fiber (NDF), acid detergent fiber (ADF), hemicellulose (HC), and cellulose (CL) contents, is essential for the identification of forage quality genes and selection of effective molecular markers in sorghum. In this study, we genotyped 245 sorghum accessions by 85,585 single-nucleotide polymorphisms (SNPs) and obtained the phenotypic data from four environments. The SNPs and phenotypic data were applied to multi-locus genome-wide association studies (GWAS) with the mrMLM software. A total of 42 SNPs were identified to be associated with the five forage quality-related traits. Moreover, three and two quantitative trait nucleotides (QTNs) were simultaneously detected among them by three and two multi-locus methods, respectively. One QTN on chromosome 5 was found to be associated simultaneously with CP, NDF, and ADF. Furthermore, 3, 2, 2, 5, and 2 candidate genes were identified to be responsible for CP, NDF, ADF, HC, and CL contents, respectively. These results provided insightful information of the forage quality-related traits and would facilitate the genetic improvement of sorghum forage quality in the future.

Introduction: Water is essential for plant growth, and drought is one of the most predominant constraints on crop yield. Sorghum is a well-known drought-tolerant crop model, and sorghum landraces possess novel alleles for local adaptation.Methods: In this study, we evaluated a sorghum mini core panel of 239 landraces sampled globally for shoot and root growth under simulated drought conditions using 10% and 20% polyethylene glycol (PEG) in 2020 and 2024, and measured drought tolerance using the seedling tolerance coefficient (STC).Results and discussion: Phenotypic analysis showed that more accessions produced more roots than longer roots when exposed to 10% PEG; however, at 20% PEG, more accessions produced longer roots than more roots, reflecting the adaptability of some accessions to drought stress. However, PEG reduced shoot growth in all accessions in both years. A genome-wide association study (GWAS) on 32 growth and 19 STC traits identified 22 loci, 19 of which were mapped to the STC traits, and 17 of these 19 were associated with STC of shoot weight. Eleven of the 22 loci were collocated with 23 previously identified mapped drought-related quantitative trait loci (QTLs); 15 of these 23 QTLs were mapped to green leaf area, total number of green leaves, or chlorophyll content. We also found 19 candidate genes for 12 of the 22 loci. Five of those genes showed either preferential or specific expression in the roots according to GeneAtlas v2. One candidate gene from a locus colocated with a previously mapped chlorophyll fluorescence QTL has been shown to increase chlorophyll fluorescence in maize in another study. The results of this study lay the foundation for further characterizing the sorghum mini core panel for novel drought-tolerant genes.

Introduction: Salt stress is a major abiotic factor restricting sorghum seed germination and early seedling establishment, particularly in saline-affected soils. Understanding the genetic architecture underlying salt tolerance during germination is essential for improving sorghum adaptation to saline environments. Genome-wide association studies (GWAS) based on high-density genomic variants provide an effective approach for uncovering loci and genes controlling complex stress-response traits. However, the genetic basis of sorghum salt tolerance at the seedling stage remains insufficiently characterized. Methods: To dissect the genetic architecture of salt tolerance during germination, we conducted a genome-wide association study (GWAS) using a panel of 245 sorghum mini core accessions and 6,094,317 high-quality SNPs obtained through whole genome resequencing. Seedlings were evaluated under five NaCl concentrations (0, 50, 100, 150, and 200 mmol/L) in 2019 and three (0, 50, and 200 mmol/L) in 2020 for shoot/root length, shoot/root fresh weight, and shoot/root dry weight, resulting in 84 trait/treatment/year combinations for GWAS. Results and Discussion: GWAS mapped 35 salt tolerance loci and 39 candidate genes were identified for salt tolerance from 29 of the 35 loci. Majority of these candidate genes (29 of the 39) have orthologs in other species that have been shown to play roles in salt tolerance in plants. These candidate genes potentially involved in ion transport, stress signaling, and growth regulation were identified in genomic regions in or adjacent to the location of associated markers. These findings provide valuable insights into the genetic basis of salt tolerance in sorghum and offer potential targets for marker-assisted selection and genetic improvement of salt-tolerant cultivars.

Coleoptile is a sheath-like structure unique to monocots and is easily observed in sorghum. Colored coleoptiles have been shown to protect plants against abiotic and biotic stresses. The purpose of this study was to identify factors controlling coleoptile color in sorghum. We phenotyped the sorghum mini core accessions for coleoptile color in two environments, determined the anthocyanin content of each color of selected accessions, carried out a genome-wide association analysis and identified a candidate gene. The phenotypic analysis showed that 95 (40% of 235) accessions were green, 28 (12%) were purple and 42 (18%) were red in both 2022 and 2023. About 12% of the accessions changed from green to red due to environmental conditions. The anthocyanin content analysis showed a positive correlation between intensity of coleoptile color and anthocyanin levels. A genome-wide association analysis identified two candidate genes, Sobic.006G175700 and Sobic.006G175500, mapped to this trait in a single locus on chromosome 6. An orthologous comparison, together with mapping, sequence analysis and qPCR, identified Sobic.006G175700 as Rs1, the gene determining the sorghum coleoptile color. The haplotype analysis with SNPs from both coding and upstream regions of Sobic.006G175700 indicates that the predominant haplotypes can differentiate between green and colored coleoptile colors. This information can be used for marker-assisted selection of desired coleoptile colors in sorghum.

Grain size is a crucial agronomic trait that significantly impacts yield potential in sorghum (Sorghum bicolor), making it a key focus for genetic improvement. In this study, we investigated the genetic basis of grain size variation using two contrasting sorghum accessions, PI302232 (small grain, Sg) and PI563512 (large grain, Lg). The 1000-grain weight, grain length, and grain width of Lg were 3.63-fold, 1.22-fold, and 1.65-fold higher than Sg, respectively. The 1000-grain weight in the F₂ segregating population derived from the cross Sg and Lg parents exhibited the highest phenotypic variation and followed a normal distribution in the three traits. Using bulked segregant analysis sequencing (BSA-seq) with small- and large-grain bulks from the F₂ population, two major quantitative trait loci (QTLs) for grain size were identified on chromosomes 1 and 3. Fine mapping with SSR markers narrowed the qGS1 locus to a 1.03 Mb region on chromosome 1 (Chr01: 22,001,448–23,035,593), containing 49 candidate genes. To narrow down potential candidate genes, transcriptome analysis of spike tissues from Sg and Lg at 0 and 14 days after heading revealed 3719 differentially expressed genes (DEGs), primarily enriched in “starch and sucrose metabolism” and “phenylpropanoid biosynthesis” pathways. Integrating fine mapping intervals and RNA-seq data, 6 DEGs were identified within the qGS1 region. Quantitative real-time PCR confirmed that 6 genes exhibited different expression at two stages. The expression and bioinformatics analysis showed Sobic.001G230700 was the most likely candidate gene for the qGS1 locus. This study provides new insights into the genetic regulation of grain size and a new target to improve grain size in sorghum.

The complete chloroplast genome of Sorghum bicolor subsp. drummondii cultivar Sa (a modern Sudan grass cultivar) was sequenced and analyzed in the present study. The chloroplast genome is 140,754 bp in length and includes a large single-copy region 82,688 bp in length, a small single-copy region 12,503 bp, and two inverted repeat regions 22,782 bp each. The genome contains 104 unique genes, including 4 rRNAs, 29 tRNAs, and 71 protein-coding genes. The phylogenetic analysis showed that Sudan grass cultivar Sa in a clade with five other complete chloroplast genomes of S. bicolor. The work facilitates studies on population genetic structure and phylogenetic relationships in genus Sorghum.