Key message: Seventy-three QTL related to grain color and tannin content were identified in Chinese sorghum accessions, and a new recessive allelic variant of TAN2 gene was discovered. Sorghum is mainly used for brewing distilled liquors in China. Since grain tannins play an important role in liquor brewing, accurately understanding the relationship between grain color and tannin content can provide basis for selection standards of tannin sorghum. We resequenced a panel of 242 Chinese sorghum accessions and performed population structure and genome-wide association study (GWAS) to identify quantitative trait locus (QTL) affecting pericarp color, testa pigment, and tannin content. Phylogenetic analysis, principal component analysis (PCA), and admixture model were used to infer population structure. Two distinct genetic sub-populations were identified according to their corresponding northern and southern geographic origin. To investigate the genetic basis of natural variation in sorghum grain color, GWAS with 2,760,264 SNPs was conducted in four environments using multiple models (Blink, FarmCPU, GLM, and MLM). Seventy-three QTL were identified to be associated for the color of exocarp, mesocarp, testa, and tannin content on all chromosomes except chromosome 5, of which 47 might be novel QTL. Some important QTL were found to colocalize with orthologous genes in the flavonoid biosynthetic pathway from other plants, including orthologous of Arabidopsis (Arabidopsis thaliana) TT2, TT7, TT12, TT16 and AT5G41220 (GST), as well as orthologous of rice (Oryza sativa) MYB61 and OsbHLH025. Our investigation of the variation in grain color and tannin content in Chinese sorghum germplasm may help guide future sorghum breeding for liquor brewing.

Chinese sorghum (S. bicolor) has been a historically critical ingredient for brewing famous distilled liquors ever since Yuan Dynasty (749 ∼ 652 years BP). Incomplete understanding of the population genetics and domestication history limits its broad applications, especially that the lack of genetics knowledge underlying liquor-brewing properties makes it difficult to establish scientific standards for sorghum breeding. To unravel the domestic history of Chinese sorghum, we re-sequenced 244 Chinese sorghum lines selected from 16 provinces. We found that Chinese sorghums formed three distinct genetic sub-structures, referred as the Northern, the Southern, and the Chishui groups, following an obviously geographic pattern. These sorghum accessions were further characterized in liquor brewing traits and identified selection footprints associated with liquor brewing efficiency. An importantly selective sweep region identified includes several homologous genes involving in grain size, pericarp thickness, and architecture of inflorescence. Our result also demonstrated that pericarp strength rather than grain size determines the ability of the grains to resist repeated cooking during brewing process. New insight into the traits beneficial to the liquor-brewing process provides both a better understanding on Chinese sorghum domestication and a guidance on breeding sorghum as a multiple use crop in China.

Sorghum has a strong tolerance to multi-abiotic stresses such as drought, heat, poor soil fertility, and salinity, yet its growth and development are significantly affected by extreme abiotic stresses, ultimately reducing grain yield. Peroxidase (POD) proteins, which are members of the oxidoreductase enzyme family, play an important role in protecting plants against multi-abiotic stress. However, this gene family has rarely been studied in sorghum. In this study, 114 POD gene members (SbPODs) were identified in sorghum and distributed unevenly throughout 10 chromosomes. Phylogenetic analysis clustered these genes into 12 subgroups. Gene structure and motif analyses showed the structural and functional diversity among the subgroups. These genes have undergone 16 segmental duplication and 32 tandem duplication events, indicating that both segmental and tandem duplications are major contributors to the expansion of the SbPOD gene family. Most duplicated SbPODs have undergone purifying selection with limited functional divergence during duplication events. Compared with maize, rice, and Arabidopsis, SbPOD gene family not only occurred the duplication on the whole-genome level, but also existed independent duplication events. The qRT-PCR results showed twenty SbPOD genes exhibited differential expression patterns in leaves under NaCl, H₂O₂ and PEG stress treatments. Of twenty SbPOD genes, most SbPOD genes showed consistently significant downregulation under NaCl, H₂O₂, and 30% PEG6000 stress treatments, except for SbPOD81 and SbPOD26. Under NaCl stress, the expression level of SbPOD81 showed a down-up regulation trend. Under H₂O₂ stress, the expression level of SbPOD81 showed a down regulation trend. Under 30% PEG6000 stress, SbPOD81 maintained down-up regulation trend but quite different under NaCl stress. In contrast, the expression level of SbPOD26 showed consistent down-up regulation trend under both NaCl and H₂O₂ stress, while after 3 h of adaptation under 30% PEG6000 stress, the expression level of SbPOD26 continued to increase. The analysis of cis-elements and conserved domain showed that SbPOD81 contains one W-box, four MYB, and three MYC cis-elements, while SbPOD26 has two W-boxes, four MBS, four MYB, and eight MYC cis-elements. Additionally, SbPOD26 possesses one PAT1 domain, which is absent in SbPOD81 and other SbPOD genes. This structural distinction not only would explain the observed expression divergence but suggests SbPOD26 may perform specialized biological functions distinct from other SbPOD genes. Totally, 114 POD gene members were identified in sorghum by a series of bioinformatics analysis. The expression patterns of some members of SbPOD gene family exhibited significantly difference under various stress conditions. These findings not only provide valuable insights into the evolutionary dynamics of the SbPOD gene family, but also lay a foundation for further studies on the functions of POD genes.

The grain sorghum inbred line 654 serves as a parent for numerous Chinese commercial hybrids and recombinant inbred lines (RILs), which have played a pivotal role in the cloning of several agronomically important traits. In this study, we present a telomere-to-telomere (T2T) genome assembly of the inbred line 654 (728.81 Mb) using PacBio HiFi, ultra-long Oxford Nanopore Technology, and Hi-C sequencing data. The T2T genome assembly has high integrity (contains all of 10 centromeres and 20 telomeres without any gaps), high contiguity (contig N90: 52.02 Mb), high completeness (98.33% BUSCO completeness, 98.88% k-mer completeness, and LAI 24.38), and extremely low base error (3.37 × 10^-7, QV: 64.72). A total of 62.34% sequences were identified as repetitive, and rest region contained 44,399 protein-coding genes, of which 30,245 were functionally annotated. The gap-free T2T genome assembly enables the full picture of the potential translational genomics, and provides the highest resolution genetic map for future studies on genome evolution, structure variation, and the genetic control of agronomic traits in sorghum breeding.