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Carotenoid cleavage oxygenases (CCOs) cleave carotenoid molecules to produce bioactive products that influence the synthesis of hormones such as abscisic acid (ABA) and strigolactones (SL), which regulate plant growth, development, and stress adaptation. Here, to explore the molecular characteristics of all members of the OsCCO family in rice, fourteen OsCCO family genes were identified in the genome-wide study. The results revealed that the OsCCO family included one OsNCED and four OsCCD subfamilies. The OsCCO family was phylogenetically close to members of the maize ZmCCO family and the Sorghum SbCCO family. A collinearity relationship was observed between OsNCED3 and OsNCED5 in rice, as well as OsCCD7 and OsNCED5 between rice and Arabidopsis, Sorghum, and maize. OsCCD4a and OsCCD7 were the key members in the protein interaction network of the OsCCO family, which was involved in the catabolic processes of carotenoids and terpenoid compounds. miRNAs targeting OsCCO family members were mostly involved in the abiotic stress response, and RNA-seq data further confirmed the molecular properties of OsCCO family genes in response to abiotic stress and hormone induction. qRT-PCR analysis showed the differential expression patterns of OsCCO members across various rice organs. Notably, OsCCD1 showed relatively high expression levels in all organs except for ripening seeds and endosperm. OsNCED2a, OsNCED3, OsCCD1, OsCCD4a, OsCCD7, OsCCD8a, and OsCCD8e were potentially involved in plant growth and differentiation. Meanwhile, OsNCED2a, OsNCED2b, OsNCED5, OsCCD8b, and OsCCD8d were associated with reproductive organ development, flowering, and seed formation. OsNCED3, OsCCD4b, OsCCD4c, OsCCD8b, and OsCCD8c were related to assimilate transport and seed maturation. These findings provide a theoretical basis for further functional analysis of the OsCCO family.

IntroductionSorghum plant color is the leaf sheath/leaf color and is associated with seed color, tannin and phenol content, head blight disease incidence, and phytoalexin production.ResultsIn this study, we evaluated plant color of the sorghum mini core collection by scoring leaf sheath/leaf color at maturity as tan, red, or purple across three testing environments and performed genome-wide association mapping (GWAS) with 6,094,317 SNPs markers.Results and DiscussionEight loci, one each on chromosomes 1, 2, 4, and 6 and two on chromosomes 5 and 9, were mapped. All loci contained one to three candidate genes. In qPC5-1, Sobic.005G165632 and Sobic.005G165700 were located in the same linkage disequilibrium (LD) block. In qPC6, Sobic.006G149650 and Sobic.006G149700 were located in the different LD block. The single peak in qPC6 covered one gene, Sobic.006G149700, which was a senescence regulator. We found a loose correlation between the degree of linkage and tissue/organ expression of the underlying genes possibly related to the plant color phenotype. Allele analysis indicated that none of the linked SNPs can differentiate between red and purple accessions whereas all linked SNPs can differentiate tan from red/purple accessions. The candidate genes and SNP markers may facilitate the elucidation of plant color development as well as molecular plant breeding.

Appropriate reference genes must be selected for accurate qRT-PCR data to conduct a thorough gene expression analysis in the sorghum aphid (Melanaphis sacchari, Hemiptera, Aphididae). This approach will establish a foundation for gene expression analysis and determines the efficacy of RNA interference in the sorghum aphid. Nine potential reference genes, including Actin, 18S, GAPDH, RPL7, EF-1α, EF-1β, 28S, HSP70, and TATA, were assessed under various experimental conditions to gauge their suitability based on qRT-PCR Ct values. The stability of these candidate reference genes in diverse experimental setups was analyzed employing several techniques, including the ΔCt comparative method, geNorm, Normfinder, BestKeeper, and RefFinder. The findings revealed that the quantity of ideal reference genes ascertained by the geNorm method for diverse experimental conditions remained consistent. For the developmental stages of the sorghum aphid, RPL7 and 18S proved to be the most dependable reference genes, whereas GAPDH and EF-1β were recommended as the most stable reference genes for different tissues. In experiments involving wing dimorphism, EF-1α and GAPDH were identified as the optimal reference gene pair. Under varying temperatures, EF-1α and EF-1β were found to be the most dependable gene pair. For studies focusing on insecticide susceptibility, 18S and TATA emerged as the most stable candidate reference genes. Across all experimental conditions, EF-1α and EF-1β was the optimal combination of reference genes in the sorghum aphid. This research has pinpointed stable reference genes that can be utilized across various treatments, thereby enhancing gene expression studies and functional genomics research on the sorghum aphid.

Callose is widely present in higher plants and plays a significant role in plant growth, development, and response to various stresses. Although numerous studies have highlighted the importance of the callose synthase (CalS) genes, their role in the resistance of sorghum (Sorghum bicolor) to aphids (Melanaphis sacchari) remains limitedly understood. This study identified 11 sorghum callose synthase genes (SbCalS), unevenly distributed across four chromosomes of sorghum. All SbCalS proteins contain glucan synthase and Fks1 domains, with segmental duplication playing a major role in gene diversification. Cis-element prediction revealed the presence of numerous stress-responsive elements, indicating that this gene family is primarily involved in stress resistance. Using published RNA-seq data, we discovered the differential expression of the SbCalS5 gene between resistant and susceptible sorghum varieties. Real-time quantitative PCR (qPCR) analysis confirmed the relative expression levels of all SbCalS members under aphid stress. To further verify the role of callose in sorghum, we measured the callose content in both resistant and susceptible sorghum varieties. The results indicated that callose plays a critical role in aphid resistance in sorghum, particularly the SbCalS5 gene. This study provides a reference for further investigation into the role of callose synthase genes in sorghum aphid resistance.

Background Tannins are the main bottlenecks restricting the transformation efficiency of plants. Hongyingzi is a special tannin-containing sorghum cultivar used in brewing. Methods In this study, a highly efficient microprojectile transformation system for tannin-containing sorghum was successfully exploited using immature embryos (IEs) of Hongyingzi as explants. Results Hongyingzi presented two types of calli. Type II calli were found to be the most suitable and effective explants for transformation. After optimization of the geneticin (G418) concentration and tissue culture medium, an average transformation frequency of 27% was achieved. Molecular analyzis showed that all transgenic plants were positive and showed transgenes expression. The inheritance analyzis confirmed that the transgenes could be inherited into the next generation. Thus, we successfully established an efficient transformation system for tannin-containing sorghum and demonstrated the possibility of breaking the restriction imposed by tannins in plants.

Foxtail millet is commonly used as a food and forage grass. ERECTA (ER) is a receptor-like kinase that can improve plant biomass and stress resistance. The sorghum SbER10_X1 gene was used as a probe to identify ER family genes on the Setaria italica genomes (SiERs), and determine the characteristics of the SiERs family. Herein, the structural features, expression patterns, and thermotolerance of SiERs function were identified by bioinformatics analysis, real-time PCR and transgenesis estimation. Results showed that SiERs had four members: two members were located on chromosome 1 with a total of six copies (SiER1_X1, SiER1_X2, SiER1_X3, SiER1_X4, SiER1_X5, and SiER1_X6), and two were on chromosome 4, namely, SiER4 (SiER4_X1 and SiER4_X2) and SiERL1. Among them, SiER1_X4 and SiER4_X1 were expressed highest in above-ground organs of foxtail millet, and actively responded to treatments with abscisic acid, brassinolide, gibberellin, and indole acetic acid. After overexpression of SiER1_X4 and SiER4_X1 in Arabidopsis, the plant height and biomass of the transgenic Arabidopsis significantly increased. Following high-temperature treatment, transgenic seedlings survived better compared to wild type. Transgenic lines showed higher SOD and POD activities, and expression level of AtHSF1 and AtBl1 genes significantly increased. These results indicated that SiER1_X4 and SiER4_X1 played important regulatory roles in plant growth and thermotolerance. The two genes provide potential targets for conventional breeding or biotechnological intervention to improve the biomass of forage grass and thermotolerance of field crops.

Cobalt blue pigments, which mainly comprise CoAl2O4, are widely synthesized as nano-scale particles using the coprecipitation method. Such ultrafine powders are necessary for the ceramics industry because of their significant effect on the color of glaze and bulk tiles. In this paper, cobalt blue pigments have been prepared using the coprecipitation method and then subjected to supercritical fluid drying. The differences in their physicochemical and optical properties are characterized using a series of analysis including X-ray diffraction (XRD), field emission scanning electron microscopy (FESEM), energy-dispersive spectrometer (EDS), and CIE-L*a*b*colorimetry analysis. The results indicate that the CoAl2O4 pigments subjected to supercritical fluid drying exhibit a fine-scale structure, a crystallite size of approximately 52 nm at 1400°C, and an excellent stability at high temperatures. They also present a vivid blue color, with improved brightness and hue than those of other cobalt blue pigments. Furthermore, this study elucidates the promising potential of supercritical fluid drying for fabricating nano-sized CoAl2O4 pigments with excellent optical and physicochemical properties.

Genetic dissection of forage yield traits is critical to the development of sorghum as a forage crop. In the present study, association mapping was performed with 85,585 SNP markers on four forage yield traits, namely plant height (PH), tiller number (TN), stem diameter (SD), and fresh weight per plant (FW) among 245 sorghum accessions evaluated in four environments. A total of 338 SNPs or quantitative trait nucleotides (QTNs) were associated with the four traits, and 21 of these QTNs were detected in at least two environments, including four QTNs for PH, ten for TN, six for SD, and one for FW. To identify candidate genes, dynamic transcriptome expression profiling was performed at four stages of sorghum development. One hundred and six differentially expressed genes (DEGs) that were enriched in hormone signal transduction pathways were found in all stages. Weighted gene correlation network analysis for PH and SD indicated that eight modules were significantly correlated with PH and that three modules were significantly correlated with SD. The blue module had the highest positive correlation with PH and SD, and the turquoise module had the highest negative correlation with PH and SD. Eight candidate genes were identified through the integration of genome-wide association studies (GWAS) and RNA sequencing. Sobic.004G143900, an indole-3-glycerol phosphate synthase gene that is involved in indoleacetic acid biosynthesis, was down-regulated as sorghum plants grew in height and was identified in the blue module, and Sobic.003G375100, an SD candidate gene, encoded a DNA repair RAD52-like protein 1 that plays a critical role in DNA repair-linked cell cycle progression. These findings demonstrate that the integrative analysis of omics data is a promising approach to identify candidate genes for complex traits.

Panicle morphology is an important trait in racial classification and can determine grain yield and other agronomic traits in sorghum. In this study, we performed association mapping of panicle length, panicle width, panicle compactness, and peduncle recurving in the sorghum mini core panel measured in multiple environments with 6,094,317 single nucleotide polymorphism (SNP) markers. We mapped one locus each on chromosomes 7 and 9 to recurving peduncles and eight loci for panicle length, panicle width, and panicle compactness. Because panicle length was positively correlated with panicle width, all loci for panicle length and width were colocalized. Among the eight loci, two each were on chromosomes 1, 2, and 6, and one each on chromosomes 8 and 10. The two loci on chromosome 2, i.e., Pm 2-1 and Pm 2-2, were detected in 7 and 5 out of 11 testing environments, respectively. Pm 2-2 colocalized with panicle compactness. Candidate genes were identified from both loci. The rice Erect Panicle2 (EP2) ortholog was among the candidate genes in Pm 2-2. EP2 regulates panicle erectness and panicle length in rice and encodes a novel plant-specific protein with unknown functions. The results of this study may facilitate the molecular identification of panicle morphology-related genes and the enhancement of yield and adaptation in sorghum.

Significant progress has been made on sorghum transformation in the last decades; however, the transformation process has been constrained by the availability of immature embryos because most of the researchers have utilized immature embryos as favorable explants. Although immature embryos have been proven to be optimal for tissue culture and transformation, isolation of immature embryos is time-consuming, labor-intensive, and limited by warm weather. In this study, we developed an efficient genetic transformation system using mature seeds as explants. The nptII and gus gene, used as the selective marker and report gene respectively, have been co-transformed by particle bombardment. After optimization of tissue culture, the G418 concentration, and transgenic, the average transformation frequency at 13.33% was achieved routinely. The transgenic events and transgene copy numbers were determined by PCR and RT-PCR, respectively. The geneticin selection and GUS staining on T1 seedlings confirmed that the transgenic plants were heritable. Our results demonstrated that the efficient sorghum transformation system has been established using mature seeds as explants. This transformation system will promote sorghum research on genetic engineering and genome editing without seasonal weather conditions restriction and explant resources restriction.

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.

Protoplasts are commonly used in genetic and breeding research. In this study, the isolation of sorghum protoplasts was optimized and applied to transient gene expression and editing by CRISPR/Cas9. The protoplast was most viable in 0.5 M mannitol, which was the highest of three concentrations after 48- and 72-hours treatments. Using this method we can derive an average of 1.6×106 cells which vary from 5 to 22 nm in size. The average transfection of the protoplasts was 68.5% using the PEG-mediated method. The subcellular assays located Sobic.002G279100-GFP and GFP proteins in the cell compartments as predicted bioinformatically. Two CRISPR/Cas9 plasmids were transfected into sorghum protoplasts to screen for an appropriate sgRNA for gene editing. One plasmid can correctly edit the target region using a single protoplast cell as template DNA. Our results indicated that the protoplast assays as optimized are suitable for transient gene expression and sgRNA screening in CRISPR/Cas9 gene editing procedures.

Megaselia spiracularis and Dohrniphora cornuta were two forensically important flies in relatively sealed environments. Their mitochondrial genomes were first sequenced, annotated, and phylogenetic analyses were performed with other 8 species of the Asehiza in this study. Maximum-likelihood phylogenetic tree revealed that Phoridae is closer to Platypezidae and Lonchopteridae within Diptera. This work increases the databases of Phoridae species, and contributes to the further study of species identification and phylogenetics of this family.

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.

Cinnamoyl-CoA reductase (CCR) is the first enzyme in the monolignol-specific branch of the lignin biosynthetic pathway. In this research, three sorghum CCR genes including SbCCR1, SbCCR2-1 and SbCCR2-2 were cloned and characterized. Analyses of the structure and phylogeny of the three CCR genes showed evolutionary conservation of the functional domains and divergence of function. Transient expression assays in Nicotiana benthamiana leaves demonstrated that the three CCR proteins were localized in the cytoplasm. The expression analysis showed that the three CCR genes were induced by drought. But in 48 h, the expression levels of SbCCR1 and SbCCR2-2 did not differ between CK and the drought treatment; while the expression level of SbCCR2-1 in the drought treatment was higher than in CK. The expression of the SbCCR1 and SbCCR2-1 genes was not induced by sorghum aphid [Melanaphis sacchari (Zehntner)] attack, but SbCCR2-2 was significantly induced by sorghum aphid attack. It is suggested that SbCCR2-2 is involved in the process of pest defense. Absolute quantitative real-time PCR revealed that the three CCR genes were mainly expressed in lignin deposition organs. The gene copy number of SbCCR1 was significantly higher than those of SbCCR2-1 and SbCCR2-2 in the tested tissues, especially in stem. The results provide new insight into the functions of the three CCR genes in sorghum.

Sudangrass, Sorghum sudanense, is an important forage in warm regions. But little is known about its genome. In this study, the transcriptomes of sudangrass S722 and sorghum Tx623B were sequenced by Illumina sequencing. More than 4Gb bases were sequenced for each library. For Tx623B and S722, 88.79% and 83.88% reads, respectively were matched to the Sorghum bicolor genome. A total of 2,397 differentially expressed genes (DEGs) were detected by RNA-Seq between the two libraries, including 849 up-regulated genes and 1,548 down-regulated genes. These DEGs could be divided into three groups by annotation analysis. A total of 44,495 single nucleotide polymorphisms (SNPs) were discovered by aligning S722 reads to the sorghum reference genome. Of these SNPs, 61.37% were transition, and this value did not differ much between different chromosomes. In addition, 16,928 insertion and deletion (indel) loci were identified between the two genomes. A total of 5,344 indel markers were designed, 15 of which were selected to construct the genetic map derived from the cross of Tx623A and Sa. It was indicated that the indel markers were useful and versatile between sorghum and sudangrass. Comparison of synonymous base substitutions (Ks) and non-synonymous base substitutions (Ka) between the two libraries showed that 95% orthologous pairs exhibited Ka/Ks

Interspecific grafting is limited by graft-incompatibility but regeneration of hybrid plants from grafting of genetically distinct scions and rootstocks has been reported in tobaccos. Here we report the regeneration of a hybrid plant via grafting between cross-incompatible sorghum and maize. By grafting maize and sorghum plants and regenerating hybrid from the graft junction in selection media, we generated a plant that was phenotypically a hybrid between sorghum and maize, i.e., the hybrid produced a seed-bearing "ear" toward the top of the stalk. To our knowledge, this is the first report of successful hybrid from grafting between two monocot plants. [ABSTRACT FROM AUTHOR]

Two sudangrass varieties, Sa and S722, were sequenced using restriction site-associated DNA sequencing (RAD-seq) on the Illumina Miniseq platform. After quality control, 920 542 and 892 626 clean reads were obtained for Sa and S722, respectively. Compared with the sorghum reference genome, 2341 and 2123 single nucleotide polymorphisms (SNPs) were obtained from Sa and S722, respectively. A total of 543 and 472 insertion-deletion (InDel) loci were obtained by sequence analysis in Sa and S722, respectively. From these InDel loci, 100 InDels were randomly selected to design InDel markers from Sa and S722. Polymorphism analyses were performed between sorghum Tx623B and Sa and between Tx623B and S722 using the InDel markers. The results showed that the polymorphism between Tx623B and Sa was 85%, and that between Tx623B and S722 was 87%. Diversity analysis was performed using 39 InDel markers for 42 sorghum and 6 sudangrass germplasms. Statistical analyses showed that the Shannon information index was 0.10–1.09 with an average value of 0.54. The polymorphism information content of the InDel markers ranged from 0.04 to 0.66 with an average of 0.35. Two genetic maps of chromosomes 1 and 2 of the Wancao No. 2 recombinant inbred line population were constructed using 16 InDel markers. Thus, it is an effective method to develop InDel markers for sorghum and sudangrass using sudangrass RAD-seq data. [ABSTRACT FROM AUTHOR]

Sorghum is considered a recalcitrant crop based on genetic transformation. The main technical problem is callus browning in culture tissue and genetic transformation for sorghum. In this study, we developed a simple and effective method for sorghum transformation excluding tissue culture process. Sorghum mature embryos were pierced by a needle and then soaked in an Agrobacterium inoculum with acetosyringone. The best-performing concentration of acetosyringone was 100 µM in inoculation with pierced seeds. When these inoculated seeds grew to three leaves, a 1? hygromycin solution was used to brush the second and third leaf of inoculated seedlings to identify transformants. The identification results showed that the highest efficiency of transformation was 4% in the study. Molecular analysis for T0 and T1 plants identified that target gene was integrated into sorghum genomic DNA. And target gene can normally express in transformants' leaves. Genetic analysis of T1 transformants showed that most of T1 transformants fitted to 3:1 Mendelian inheritance. All these results showed that the presented method is an easy and successful method for sorghum transformation. In the future, the method will be used for broad functional genomics studies and for biotechnological application of sorghum. [ABSTRACT FROM AUTHOR]