Dynamic transcriptome profiling revealed a key gene ZmJMJ20 and pathways associated with cadmium stress in maize.

Cadmium (Cd) pollution in soil poses a global concern due to its serious impacts on human health and ecological security. In plants, tremendous efforts have been made to identify some key genes and pathways in Cd stress responses. However, studies on the roles of epigenetic factors in response to Cd stress were still limited. In the study, we first gain insight into the gene expression dynamics for maize seedlings under 0 h, 12 h, and 72 h Cd stress. As a result, six distinct groups of genes were identified by hierarchical clustering and principal component analysis. The key pathways associated with 12 h Cd stress were protein modifications including protein ubiquitination, signal transduction by protein phosphorylation, and histone modification. Whereas, under 72 h stress, main pathways were involved in biological processes including phenylalanine metabolism, response to oxygen-containing compounds and metal ions. Then to be noted, one of the most highly expressed genes at 12 h under Cd treatment is annotated as histone demethylases (ZmJMJ20). The evolutionary tree analysis and domain analysis showed that ZmJMJ20 belonged to the JmjC-only subfamily of the Jumonji-C (JmjC) family, and ZmJMJ20 was conserved in rice and Arabidopsis. After 72 h of Cd treatment, the zmjmj20 mutant created by EMS treatment manifested less severe chlorosis/leaf yellowing symptoms compared with wild-type plants, and there was no significant difference in Fv/Fm and φPSII value before and after Cd treatment. Moreover, the expression levels of several photosynthesis-related down-regulated genes in EMS mutant plants were dramatically increased compared with those in wild-type plants at 12 h under Cd treatment. Our results suggested that ZmJMJ20 plays an important role in the Cd tolerance response pathway and will facilitate the development of cultivars with improved Cd stress tolerance.

Development and validation of KASP markers for resistance to Phytophthora capsici in Capsicum annuum L.

Resistance of Capsicum annuum to Phytophthora blight is dependent on the genetic background of the resistance source and the Phytophthora capsici isolate, which poses challenges for development of generally applicable molecular markers for marker-assisted selection. In this study, the resistance to P. capsici of C. annuum was genetically mapped to chromosome 5 within a 1.68-Mb interval by genome-wide association study analysis of 237 accessions. In this candidate region, 30 KASP markers were developed using genome resequencing data for a P. capsici-resistant line (0601 M) and a susceptible line (77,013). Seven of these KASP markers, located in the coding region of a probable leucine-rich repeats receptor-like serine/threonine-protein kinase gene (Capana05g000704), were validated in the 237 accessions, which showed an average accuracy of 82.7%. The genotyping of the seven KASP markers strongly corresponded with the phenotype of 42 individual plants in a pedigree family (PC83-163) developed from the P. capsici-resistant line CM334. This research provides a set of efficient and high-throughput KASP markers for marker-assisted selection of resistance to P. capsici in C. annuum. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-023-01367-3.

Genome-Wide Investigation and Characterization of SWEET Gene Family with Focus on Their Evolution and Expression during Hormone and Abiotic Stress Response in Maize.

The sugar will eventually be exported transporters (SWEET) family is an important group of transport carriers for carbon partitioning in plants and has important functions in growth, development, and abiotic stress tolerance. Although the SWEET family is an important sugar transporter, little is known of the functions of the SWEET family in maize (Zea mays), especially in response to abiotic stresses. To further explore the response pattern of maize SWEET to abiotic stress, a bioinformatics-based approach was used to predict and identify the maize SWEET gene (ZmSWEET) family. Twenty-four ZmSWEET genes were identified using the MaizeGDB database. Phylogenetic analysis resolved these twenty-four genes into four clades. One tandem and five segmental duplication events were identified, which played a major role in ZmSWEET family expansion. Synteny analysis provided insight into the evolutionary characteristics of the ZmSWEET genes with those of three graminaceous crop species. A heatmap showed that most ZmSWEET genes responded to at least one type of abiotic stress. By an abscisic acid signaling pathway, among which five genes were significantly induced under NaCl treatment, eight were obviously up-regulated under PEG treatment and five were up-regulated under Cd stress, revealing their potential functions in response to abiotic stress. These findings will help to explain the evolutionary links of the ZmSWEET family and contribute to future studies on the functional characteristics of ZmSWEET genes, and then improve abiotic stress tolerance in maize through molecular breeding.

Genome-wide identification and characterization of lncRNAs in sunflower endosperm.

BACKGROUND: Long non-coding RNAs (lncRNAs), as important regulators, play important roles in plant growth and development. The expression and epigenetic regulation of lncRNAs remain uncharacterized generally in plant seeds, especially in the transient endosperm of the dicotyledons. RESULTS: In this study, we identified 11,840 candidate lncRNAs in 12 day-after-pollination sunflower endosperm by analyzing RNA-seq data. These lncRNAs were evenly distributed in all chromosomes and had specific features that were distinct from mRNAs including tissue-specificity expression, shorter and fewer exons. By GO analysis of protein coding genes showing strong correlation with the lncRNAs, we revealed that these lncRNAs potential function in many biological processes of seed development. Additionally, genome-wide DNA methylation analyses revealed that the level of DNA methylation at the transcription start sites was negatively correlated with gene expression levels in lncRNAs. Finally, 36 imprinted lncRNAs were identified including 32 maternally expressed lncRNAs and four paternally expressed lncRNAs. In CG and CHG context, DNA methylation levels of imprinted lncRNAs in the upstream and gene body regions were slightly lower in the endosperm than that in embryo tissues, which indicated that the maternal demethylation potentially induce the paternally bias expression of imprinted lncRNAs in sunflower endosperm. CONCLUSION: Our findings not only identified and characterized lncRNAs on a genome-wide scale in the development of sunflower endosperm, but also provide novel insights into the parental effects and epigenetic regulation of lncRNAs in dicotyledonous seeds.

Genome-Wide Identification and Characterization of the CCT Gene Family in Foxtail Millet (Setaria italica) Response to Diurnal Rhythm and Abiotic Stress.

The CCT gene family plays important roles in diurnal rhythm and abiotic stress response, affecting crop growth and development, and thus yield. However, little information is available on the CCT family in foxtail millet (Setaria italica). In the present study, we identified 37 putative SiCCT genes from the foxtail millet genome. A phylogenetic tree was constructed from the predicted full-length SiCCT amino acid sequences, together with CCT proteins from rice and Arabidopsis as representatives of monocotyledonous and dicotyledonous plants, respectively. Based on the conserved structure and phylogenetic relationships, 13, 5, and 19 SiCCT proteins were classified in the COL, PRR, and CMF subfamilies, respectively. The gene structure and protein conserved motifs analysis exhibited highly similar compositions within the same subfamily. Whole-genome duplication analysis indicated that segmental duplication events played an important role in the expansion of the CCT gene family in foxtail millet. Analysis of transcriptome data showed that 16 SiCCT genes had significant diurnal rhythm oscillations. Under abiotic stress and exogenous hormonal treatment, the expression of many CMF subfamily genes was significantly changed. Especially after drought treatment, the expression of CMF subfamily genes except SiCCT32 was significantly up-regulated. This work provides valuable information for further study of the molecular mechanism of diurnal rhythm regulation, abiotic stress responses, and the identification of candidate genes for foxtail millet molecular breeding.

Changes in antioxidant system and sucrose metabolism in maize varieties exposed to Cd.

Different maize varieties respond differentially to cadmium (Cd) stress. However, the physiological mechanisms that determine the response are not well defined. Antioxidant systems and sucrose metabolism help plants to cope with abiotic stresses, including Cd stress. The relationship of these two systems in the response to Cd stress is unclear. Seed is sensitive to Cd stress during germination. In this study, we investigated changes in the antioxidant system, sucrose metabolism, and abscisic acid and gibberellin concentrations in two maize varieties with low (FY9) or high (SY33) sensitivities to Cd under exposure to CdCl2 (20 mg L-1) at different stages of germination (3, 6, and 9 days).The seed germination and seedling growth were inhibited under Cd stress. The superoxide, malondialdehyde, and proline concentrations, and the superoxide dismutase, peroxidase, catalase, and lipoxygenase activities increased compared with those of the control (CK; without Cd). The expression levels of three genes (ZmOPR2, ZmOPR5, and ZmPP2C6) responsive to oxidative stress increased differentially in the two varieties under Cd stress. The activity of the antioxidant system and the transcript levels of oxidative stress-responsive genes were higher in the Cd-tolerant variety, FY9, than in the sensitive variety, SY33. Sucrose metabolism was increased under Cd stress compared with that of the CK and was more active in the Cd-sensitive variety, SY33. These results suggest that the antioxidant system is the first response to Cd stress in maize, and that sucrose metabolism is cooperative and complementary under exposure to Cd.

Epigenetic modifications potentially controlling the allelic expression of imprinted genes in sunflower endosperm.

BACKGROUND: Genomic imprinting is an epigenetic phenomenon mainly occurs in endosperm of flowering plants. Genome-wide identification of imprinted genes have been completed in several dicot Cruciferous plant and monocot crops. RESULTS: Here, we analyzed global patterns of allelic gene expression in developing endosperm of sunflower which belongs to the composite family. Totally, 691 imprinted loci candidates were identified in 12 day-after-pollination sunflower endosperm including 79 maternally expressed genes (MEG) and 596 paternally expressed genes (PEG), 6 maternally expressed noncoding RNAs (MNC) and 10 paternally expressed noncoding RNAs (PNC). And a clear clustering of imprinted genes throughout the rapeseed genome was identified. Generally, imprinting in sunflower is conserved within a species, but intraspecific variation also was detected. Limited loci in sunflower are imprinted in other several different species. The DNA methylation pattern around imprinted genes were investigated in embryo and endosperm tissues. In CG context, the imprinted genes were significantly associated with differential methylated regions exhibiting hypomethylation in endosperm and hypermethylation in embryo, which indicated that the maternal demethylation in CG context potentially induce the genomic imprinting in endosperm. CONCLUSION: Our study would be helpful for understanding of genomic imprinting in plants and provide potential basis for further research in imprinting in sunflower.

Development and application of KASP markers associated with Restorer-of-fertility gene in Capsicum annuum L.

Fertility restoration of cytoplasmic male sterility (CMS) in Capsicum annuum is controlled by multiple alleles of Restorer-of-fertility (Rf) genes. The isolation of additional Rf genes should therefore enrich the knowledge of CMS/Rf systems and accelerate their exploitation in hybrid seed production. In this study, the fertility restorer gene CaRfm of '0601 M', a non-pungent bell pepper, was genetically mapped to a 1.2-cM region flanked by KASP markers S761 and S183. CaRfm was then physically mapped to a 128.96-Kb interval predicted from 24 recombinants with two co-segregated markers, S423 and S424. CaPPR6 encoding a pentatricopeptide repeat (PPR) protein was suggested as the most likely candidate gene for the CaRfm locus on the basis of sequence alignment as well as genotyping of tightly linked markers. In addition, molecular markers S1597 and S1609, which are immediately adjacent to CaRfm at 15.7 and 57.8-Kb respectively, were developed and applied to marker-assisted selection. The results provided friendly markers for breeding pepper restorer lines and laid the foundation for elucidating the male fertility restoration mechanism. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12298-021-01109-9.

Changes in sucrose metabolism in maize varieties with different cadmium sensitivities under cadmium stress.

Sucrose metabolism contributes to the growth and development of plants and helps plants cope with abiotic stresses, including stress from Cd. Many of these processes are not well-defined, including the mechanism underlying the response of sucrose metabolism to Cd stress. In this study, we investigated how sucrose metabolism in maize varieties with low (FY9) and high (SY33) sensitivities to Cd changed in response to different levels of Cd (0 (control), 5, 10, and 20 mg L-1 Cd). The results showed that photosynthesis was impaired, and the biomass decreased, in both varieties of maize at different Cd concentrations. Cd inhibited the activities of sucrose phosphate synthase (SPS) and sucrose synthase (SS) (sucrose synthesis), and stimulated the activities of acid invertase (AI) and SS (sucrose hydrolysis). The total soluble sugar contents were higher in the Cd-treated seedlings than in the control. Also, Cd concentrations in the shoots were higher in SY33 than in FY9, and in the roots were lower in SY33 than in FY9. The decreases in the photosynthetic rate, synthesis of photosynthetic products, enzyme activity in sucrose synthesis direction, and increases in activity in hydrolysis direction were more obvious in SY33 (the sensitive variety) than in FY9 (the tolerant variety), and more photosynthetic products were converted into soluble sugar in SY33 than in FY9 as the Cd stress increased. The transcript levels of the sugar transporter genes also differed between the two varieties at different concentrations of Cd. These results suggest that sucrose metabolism may be a secondary response to Cd additions, and that the Cd-sensitive variety used more carbohydrates to defend against Cd stress rather than to support growth than the Cd-tolerant variety.

Fine mapping of the male fertility restoration gene CaRf032 in Capsicum annuum L.

KEY MESSAGE: A novel strong candidate gene CA00g82510 for the male fertility restoration locus CaRf032 in Capsicum annuum was identified by genome re-sequencing and recombination analysis. A single dominant locus (CaRf032) for fertility restoration of cytoplasmic male sterility was identified in the strong restorer inbred line IVF2014032 of chili pepper (Capsicum annuum L.). CaRf032 was localized within an 8.81-Mb candidate intervals on chromosome 6 using bulked segregant analysis based on high-throughput sequencing data. Subsequently, the candidate interval was genetically mapped and defined to a 249.41-kb region using an F2 population of 441 individuals generated by crossing the male-sterile line 77013A and the restorer line IVF2014032. To fine map CaRf032, eight newly developed KASP markers were used to genotype 23 recombinants screened from a larger F2 population of 2877 individuals. The CaRf032 locus was localized to a 148.05-kb region between the KASP markers S1402 and S1354, which was predicted to contain 22 open reading frames (ORFs). One ORF with an incomplete sequence was predicted to contain a PPR motif, and its physical position overlapped with the Rf candidate gene CaPPR6_46. The PPR ORF sequence before the gap showed 100% identity with the CA00g82510 locus of the CM334 reference genome. CA00g82510 encodes a protein of 583 amino acids, containing 14 PPR motifs, and shows significantly differential expression between the flower buds of the maintainer line 77013 and the restorer line IVF2014032. These results indicated that CA00g82510 is a strong candidate gene for CaRf032. Five KASP markers, which detected single-nucleotide polymorphisms in CA00g82510 of 77013 and IVF2014032, co-segregated with CaRf032 and showed 64.4% successful genotyping of 38 maintainer and 63 restorer lines.

Biosorption of heavy metals from aqueous solutions by chemically modified orange peel.

Equilibrium, thermodynamic and kinetic studies were carried out for the biosorption of Pb(2+), Cd(2+) and Ni(2+) ions from aqueous solution using the grafted copolymerization-modified orange peel (OPAA). Langmuir and Freundlich isotherm models were applied to describe the biosorption of the metal ions onto OPAA. The influences of pH and contact time of solution on the biosorption were studied. Langmuir model fitted the equilibrium data better than the Freundlich isotherm. According to the Langmuir equation, the maximum uptake capacities for Pb(2+), Cd(2+) and Ni(2+) ions were 476.1, 293.3 and 162.6 mg g(-1), respectively. Compared with the unmodified orange peel, the biosorption capacity of the modified biomass increased 4.2-, 4.6- and 16.5-fold for Pb(2+), Cd(2+) and Ni(2+), respectively. The kinetics for Pb(2+), Cd(2+) and Ni(2+) ions biosorption followed the pseudo-second-order kinetics. The free energy changes (ΔG°) for Pb(2+), Cd(2+) and Ni(2+) ions biosorption process were found to be -3.77, -4.99 and -4.22 kJ mol(-1), respectively, which indicates the spontaneous nature of biosorption process. FTIR demonstrated that carboxyl and hydroxyl groups were involved in the biosorption of the metal ions. Desorption of Pb(2+), Cd(2+) and Ni(2+) ions from the biosorbent was effectively achieved in a 0.05 mol L(-1) HCl solution.

[Effects of low light on photosynthetic characteristics of tomato at different growth stages].

Taking low light tolerance tomato strains 02S02 and 02S32 and sensitive strains 02S52 and 02S57 as test objects, this paper studied their leaf photosynthetic characteristics at seedling stage, flowering-fruit-setting stage, and fruit-inflating stage under effects of low light. The experiment was carried out in a low light environment, a plastic tunnel covered with black shading nets, with the light intensity being about 50% of that in normal plastic tunnel (average light intensity 800 micromol x m(-2) x s(-1) at sunny morning 9:00-11:00). For the four test tomato strains, their leaf photosynthetic rate in low light environment had a slight increase, but decreased greatly when the light intensity increased, with the change trends being similar but the change degree differed with strains and growth stages. The light compensation point and dark respiration rate decreased gradually with plant growth, and the decrement was larger for low light tolerance strains than for sensitive strains. The light saturation point, maximum photosynthetic rate, and apparent quantum yield decreased at all the growth stages, but the decrements differed with growth stages and were not consistent with the low light tolerability of test strains.