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1.
Insects ; 15(7)2024 Jul 11.
Artigo em Inglês | MEDLINE | ID: mdl-39057255

RESUMO

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-1ß, 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-1ß 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-1ß 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-1ß 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.

2.
Front Plant Sci ; 15: 1320844, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38660439

RESUMO

Introduction: Sorghum 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. Results: In 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 Discussion: Eight 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.

3.
Huan Jing Ke Xue ; 45(3): 1428-1438, 2024 Mar 08.
Artigo em Chinês | MEDLINE | ID: mdl-38471858

RESUMO

To understand the water pollution status and environmental risks of Changshou Lake, the concentrations of heavy metals (Cr, Cu, Zn, As, Cd, and Pb) in the water were collected and analyzed during different seasons. The study investigated temporal and spatial variations, distribution characteristics, pollution levels, and health risks associated with heavy metals in Changshou Lake. The results showed that all six heavy metals were below than the Class Ⅰ standard of the Surface Water Environmental Quality Standard (GB 3838-2002), but recent years have witnessed an increasing trend, with Cu, As, and Pb showing a significant increase (P<0.05). The temporal and spatial distributions of these heavy metals were different. Temporally, Cr and Cd concentrations in surface water were higher in summer, As and Zn were higher in spring, and Pb and Cu were higher in autumn and winter. Spatially, the concentrations of Cr, As, Cu, Zn, and Pb showed higher concentrations in the southern outlet of the reservoir, the northwestern Longxi River inlet, and the central part of the reservoir, whereas Cd was higher in the northern stagnant area. The overall levels of heavy metals in the water body of Changshou Lake were low, with Cr and Cu slightly polluted, while other heavy metals were identified as having an insignificant pollution level. Drinking water was the primary exposure pathway to carcinogenic and non-carcinogenic heavy metals in surface water bodies. The health risk values of Cr and As in water bodies were high, ranging from 6.2×10-10 to 3.0×10-4 and 5.1×10-8 to 3.9×10-5, respectively. The corresponding contribution rates for children and adults to the total health risk were high, with Cr accounting for 87.18% and 87.20%, respectively, while As accounted for 12.73% and 12.71%, respectively. Therefore, it is crucial to prioritize environmental risks associated with Cr and Cu, as well as the health risks associated with Cr and As in Changshou Lake These findings provide a scientific foundation for water pollution control and environmental quality improvement in Changshou Lake, and rational development and utilization of water resources.


Assuntos
Água Potável , Metais Pesados , Poluentes Químicos da Água , Cádmio , China , Monitoramento Ambiental , Sedimentos Geológicos , Lagos/análise , Chumbo , Metais Pesados/análise , Medição de Risco , Poluentes Químicos da Água/análise , Humanos , Criança , Adulto
4.
Huan Jing Ke Xue ; 45(2): 1058-1068, 2024 Feb 08.
Artigo em Chinês | MEDLINE | ID: mdl-38471943

RESUMO

In order to explore the characteristics and sources of heavy metal pollution in cultivated soil around a red mud yard in Chongqing, the content and spatial distribution characteristics of eight heavy metal elements (Cd, Cr, Hg, Ni, Pb, As, Cu, and Zn) in the soil were analyzed, and the single factor pollution index method and Nemerow comprehensive pollution index method were used to evaluate the characteristics of heavy metal pollution in soil. On the basis of correlation analysis, the APCS-MLR and PMF models were used to quantitatively analyze the sources of heavy metals. The results showed that the average contents of the other seven heavy metal elements were higher than the background values of Chongqing soil, except for that of Cr. The heavy metals Cd, Hg, and As were moderately polluted, and Pb, Cu, Ni, and Zn were mildly polluted. The spatial distribution pattern of Cr, Ni, Pb, Cu, and Zn in the soil was similar, and there was a very significant positive correlation between them (P < 0.01). The spatial distribution characteristics of Cd, Hg, and As were significantly different, and there was no significant correlation between them (P > 0.05). The source apportionment showed that the sources of heavy metals in the soil in the study area were relatively complex, and the APCS-MLR and PMF models could identify the same four pollution sources, namely red mud yard percolation emission and natural sources, thermal power generation emission sources, agricultural activities and natural sources, and non-ferrous metal smelting emission sources. There was little difference in the results of source apportionment between the two models. The contribution rates of the four pollution sources in the APCS-MLR model were 51.8%, 18.0%, 15.9%, and 14.3%, respectively, whereas those in the PMF model were 45.9%, 12.8%, 21.5%, and 19.8%, respectively.

5.
Sci Total Environ ; 917: 170610, 2024 Mar 20.
Artigo em Inglês | MEDLINE | ID: mdl-38307271

RESUMO

The potential for heavy metal (HM) pollution in agricultural soils adjacent to industries with elevated HM emissions has long been recognized. However, industries with relatively lower levels of HM emissions, such as alumina smelting and glass production, may still contribute to the pollution of surrounding agricultural soils through continuous, albeit low-level, emissions. Despite this, this issue has not garnered adequate attention thus far. Therefore, this study aimed to assess the extent of HM pollution in agricultural soils adjacent to an alumina smelting and a glass production factory, identifying contamination levels and potential sources through the analysis of input fluxes, isotope fingerprints, and receptor models. Results showed moderate cadmium (Cd) contamination in surface soil, exceeding standards at a rate of 86.36 %. Further analysis revealed that atmospheric deposition was the primary route for Cd input in both paddy fields (89.20 %) and dryland soils (91.61 %). Additionally, the δ114/110Cd values in surface soils indicated that dust played a role in influencing Cd levels in distant surface soils, while raw materials and slags were identified as primary sources near the factory. Industrial sources were considered the primary contributors of Cd in soil accounting for approximately 73.38 % and 82.67 %, respectively, according to the positive matrix factorization model (PMF) and absolute principal component scores-multiple linear regression model (APCS-MLR). Overall, this study underscores the importance of monitoring HMs from industries with relatively low emissions and provides a scientific basis for effectively managing HMs pollution in agricultural soils, ensuring the preservation of agricultural soil quality.

6.
Theor Appl Genet ; 136(3): 60, 2023 Mar 13.
Artigo em Inglês | MEDLINE | ID: mdl-36912984

RESUMO

KEY MESSAGE: Sudangrass is more similar to US commercial sorghums than to cultivated sorghums from Africa sequence-wise and contain significantly lower dhurrin than sorghums. CYP79A1 is linked to dhurrin content in sorghum. Sudangrass [Sorghum sudanense (Piper) Stapf] is a hybrid between grain sorghum and its wild relative S. bicolor ssp. verticilliflorum and is grown as a forage crop due to its high biomass production and low dhurrin content compared to sorghum. In this study, we sequenced the sudangrass genome and showed that the assembled genome was 715.95 Mb with 35,243 protein-coding genes. Phylogenetic analysis with whole genome proteomes demonstrated that the sudangrass genome was more similar to US commercial sorghums than to its wild relatives and cultivated sorghums from Africa. We confirmed that at seedling stage, sudangrass accessions contained significantly lower dhurrin as measured by hydrocyanic acid potential (HCN-p) than cultivated sorghum accessions. Genome-wide association study identified a QTL most tightly associated with HCN-p and the linked SNPs were located in the 3' UTR of Sobic.001G012300 which encodes CYP79A1, the enzyme that catalyzes the first step of dhurrin biosynthesis. As in other grasses such as maize and rice, we also found that copia/gypsy long terminal repeat (LTR) retrotransposons were more abundant in cultivated than in wild sorghums, implying that crop domestication in the grasses was accompanied by increased copia/gypsy LTR retrotransposon insertions in the genomes.


Assuntos
Sorghum , Sorghum/genética , Filogenia , Estudo de Associação Genômica Ampla , Cromossomos , Evolução Molecular
7.
PeerJ ; 11: e15066, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-36935918

RESUMO

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.


Assuntos
Sorghum , Taninos , Taninos/metabolismo , Sorghum/genética , Transformação Genética , Transgenes , Plantas Geneticamente Modificadas/genética , Grão Comestível
8.
Artigo em Inglês | MEDLINE | ID: mdl-36834375

RESUMO

The particular condition of the water-level-fluctuation zone (WLFZ) in the Three Gorges Reservoir (TGR), the largest hydroelectric reservoir in China, raises great concerns about mercury (Hg) contamination and ecological risk. In addition, previous research found that soil organic carbon (SOC) plays an essential role in controlling Hg distribution and speciation. However, there is minimal information on the Hg storage distribution and their relationships with SOC in the WLFZ in TGR. This study investigated Hg distribution, storage, and their relationships with SOC in the surface soils in WLFZ. The results showed that the total Hg (THg) content in the surface soils ranged from 18.40 to 218.50 ng g-1, with an average value of 78.17 ± 41.92 ng g-1. About 89% of samples had THg content above the background value in Chongqing, showing specific enrichment of Hg in WLFZ due to contamination in the TGR. The surface soils have low SOC, with an average value of 8.10 ± 3.90 g kg-1. Moreover, THg content showed consistent distribution with the SOC in WLFZ, with a significantly positive correlation (R = 0.52, p < 0.01, n = 242). THg storage (201.82 ± 103.46 g ha-1) in the surface soils was also significantly positively correlated with the SOC storage (R = 0.47, p < 0.01, n = 242). The reduced SOC sequestration, due to the periodical alternative "flooding-draining" and frequent reclamation and utilization of WLFZ, decreased the Hg adsorption in soil. Those might result in the re-release of Hg into waters when WLFZ is flooded. Therefore, more attention should be directed towards Hg cycling and the consequent environmental risks in the TGR region.


Assuntos
Mercúrio , Compostos de Metilmercúrio , Poluentes Químicos da Água , Mercúrio/análise , Solo , Carbono , Água , Monitoramento Ambiental , Poluentes Químicos da Água/análise , China
9.
PeerJ ; 10: e14452, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-36518287

RESUMO

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.


Assuntos
Arabidopsis , Setaria (Planta) , Termotolerância , Arabidopsis/genética , Setaria (Planta)/genética , Proteínas de Plantas/genética , Termotolerância/genética , Biomassa , Melhoramento Vegetal
10.
J Exp Bot ; 73(11): 3584-3596, 2022 06 02.
Artigo em Inglês | MEDLINE | ID: mdl-35290448

RESUMO

Sorghum is a feed/industrial crop in developed countries and a staple food elsewhere in the world. This study evaluated the sorghum mini core collection for days to 50% flowering (DF), biomass, plant height (PH), soluble solid content (SSC), and juice weight (JW), and the sorghum reference set for DF and PH, in 7-12 testing environments. We also performed genome-wide association mapping with 6 094 317 and 265 500 single nucleotide polymorphism markers in the mini core collection and the reference set, respectively. In the mini core panel we identified three quantitative trait loci for DF, two for JW, one for PH, and one for biomass. In the reference set panel we identified another quantitative trait locus for PH on chromosome 6 that was also associated with biomass, DF, JW, and SSC in the mini core panel. Transgenic studies of three genes selected from the locus revealed that Sobic.006G061100 (SbSNF4-2) increased biomass, SSC, JW, and PH when overexpressed in both sorghum and sugarcane, and delayed flowering in transgenic sorghum. SbSNF4-2 encodes a γ subunit of the evolutionarily conserved AMPK/SNF1/SnRK1 heterotrimeric complexes. SbSNF4-2 and its orthologs will be valuable in genetic enhancement of biomass and sugar yield in plants.


Assuntos
Saccharum , Sorghum , Biomassa , Carboidratos , Grão Comestível/genética , Estudo de Associação Genômica Ampla , Fenótipo , Saccharum/genética , Sorghum/genética , Açúcares
11.
Mitochondrial DNA B Resour ; 6(12): 3456-3457, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34869873

RESUMO

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.

12.
Front Plant Sci ; 12: 743838, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34675951

RESUMO

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.

13.
PeerJ ; 9: e11849, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34430078

RESUMO

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.

14.
Front Plant Sci ; 12: 788433, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-35087554

RESUMO

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.

15.
Mitochondrial DNA B Resour ; 5(2): 1208-1209, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-33366915

RESUMO

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.

16.
PeerJ ; 8: e10077, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-33083135

RESUMO

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.

17.
Front Plant Sci ; 9: 1146, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-30186292

RESUMO

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.

18.
Plant J ; 95(3): 557-567, 2018 08.
Artigo em Inglês | MEDLINE | ID: mdl-29761864

RESUMO

Gene editing techniques are becoming powerful tools for modifying target genes in organisms. Although several methods have been developed to detect gene-edited organisms, these techniques are time and labour intensive. Meanwhile, few studies have investigated high-throughput detection and screening strategies for plants modified by gene editing. In this study, we developed a simple, sensitive and high-throughput quantitative real-time (qPCR)-based method. The qPCR-based method exploits two differently labelled probes that are placed within one amplicon at the gene editing target site to simultaneously detect the wild-type and a gene-edited mutant. We showed that the qPCR-based method can accurately distinguish CRISPR/Cas9-induced mutants from the wild-type in several different plant species, such as Oryza sativa, Arabidopsis thaliana, Sorghum bicolor, and Zea mays. Moreover, the method can subsequently determine the mutation type by direct sequencing of the qPCR products of mutations due to gene editing. The qPCR-based method is also sufficiently sensitive to distinguish between heterozygous and homozygous mutations in T0 transgenic plants. In a 384-well plate format, the method enabled the simultaneous analysis of up to 128 samples in three replicates without handling the post-polymerase chain reaction (PCR) products. Thus, we propose that our method is an ideal choice for screening plants modified by gene editing from many candidates in T0 transgenic plants, which will be widely used in the area of plant gene editing.


Assuntos
Edição de Genes/métodos , Ensaios de Triagem em Larga Escala/métodos , Plantas Geneticamente Modificadas/genética , Reação em Cadeia da Polimerase em Tempo Real/métodos , Arabidopsis/genética , Proteína 9 Associada à CRISPR , Sistemas CRISPR-Cas , Triagem de Portadores Genéticos , Homozigoto , Oryza/genética , Sorghum/genética , Zea mays/genética
19.
PeerJ ; 4: e2005, 2016.
Artigo em Inglês | MEDLINE | ID: mdl-27231650

RESUMO

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.

20.
PLoS One ; 11(5): e0154947, 2016.
Artigo em Inglês | MEDLINE | ID: mdl-27152648

RESUMO

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<1.0, indicating that these genes were influenced by purifying selection. The results from this study provide important information for molecular genetic research and a rich resource for marker development in sudangrass and other Sorghum species.


Assuntos
Marcadores Genéticos , Sorghum/genética , Transcriptoma , Expressão Gênica , Genes de Plantas , Mutação INDEL , Polimorfismo de Nucleotídeo Único
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