Transcriptome Profiling of the Elongating Internode of Cotton (Gossypium hirsutum L.) Seedlings in Response to Mepiquat Chloride

The Roles of Mepiquate Chloride and Melatonin in the Morpho-Physiological Activity of Cotton under Abiotic Stress

Cotton growth and yield are severely affected by abiotic stress worldwide. Mepiquate chloride (MC) and melatonin (MT) enhance crop growth and yield by reducing the negative effects of abiotic stress on various crops. Numerous studies have shown the pivotal role of MC and MT in regulating agricultural growth and yield. Nevertheless, an in-depth review of the prominent performance of these two hormones in controlling plant morpho-physiological activity and yield in cotton under abiotic stress still needs to be documented. This review highlights the effects of MC and MT on cotton morpho-physiological and biochemical activities; their biosynthetic, signaling, and transduction pathways; and yield under abiotic stress. Furthermore, we also describe some genes whose expressions are affected by these hormones when cotton plants are exposed to abiotic stress. The present review demonstrates that MC and MT alleviate the negative effects of abiotic stress in cotton and increase yield by improving its morpho-physiological and biochemical activities, such as cell enlargement; net photosynthesis activity; cytokinin contents; and the expression of antioxidant enzymes such as catalase, peroxidase, and superoxide dismutase. MT delays the expression of NCED1 and NCED2 genes involved in leaf senescence by decreasing the expression of ABA-biosynthesis genes and increasing the expression of the GhYUC5, GhGA3ox2, and GhIPT2 genes involved in indole-3-acetic acid, gibberellin, and cytokinin biosynthesis. Likewise, MC promotes lateral root formation by activating GA20x genes involved in gibberellin catabolism. Overall, MC and MT improve cotton's physiological activity and antioxidant capacity and, as a result, improve the ability of the plant to resist abiotic stress. The main purpose of this review is to present an in-depth analysis of the performance of MC and MT under abiotic stress, which might help to better understand how these two hormones regulate cotton growth and productivity.

High-resolution genetic linkage map and height-related QTLs in an oil palm (Elaeis guineensis) family planted across multiple sites

A refined SNP array containing 92,459 probes was developed and applied for chromosome scanning, construction of a high-density genetic linkage map and QTL analysis in a selfed Nigerian oil palm family (T128). Genotyping of the T128 mapping family generated 76,447 good quality SNPs for detailed scanning of aberration and homozygosity in the individual pseudo-chromosomes. Of them, 25,364 polymorphic SNPs were used for linkage analysis resulting in an 84.4% mapping rate. A total of 21,413 SNPs were mapped into 16 linkage groups (LGs), covering a total map length of 1364.5 cM. This genetic map is 16X denser than the previous version used to establish pseudo-chromosomes of the oil palm reference genome published in 2013. The QTLs associated with height, height increment and rachis length were identified in LGs TT05, 06, 08, 15 and 16. The present QTLs as well as those published previously were tagged to the reference genome to determine their chromosomal locations. Almost all the QTLs identified in this study were either close to or co-located with those reported in other populations. Determining the QTL position on chromosomes was also helpful in mining for the underlying candidate genes. In total, 55 putative genes and transcription factors involved in the biosynthesis, conjugation and signalling of the major phytohormones, especially for gibberellins and cell wall morphogenesis were found to be present in the identified genomic QTL regions, and their potential roles in plant dwarfism are discussed.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-023-01360-2.

Analysis of morphological traits and regulatory mechanism of a semi-dwarf, albino, and blue grain wheat line

The plant height and leaf color are important traits in crops since they contribute to the production of grains and biomass. Progress has been made in mapping the genes that regulate plant height and leaf color in wheat (Triticum aestivum L.) and other crops. Wheat line DW-B (dwarfing, white leaves, and blue grains) with semi-dwarfing and albinism at the tillering stage and re-greening at the jointing stage was created using Lango and Indian Blue Grain. Transcriptomic analyses of the three wheat lines at the early jointing stages indicated that the genes of gibberellin (GA) signaling pathway and chlorophyll (Chl) biosynthesis were expressed differently in DW-B and its parents. Furthermore, the response to GA and Chl contents differed between DW-B and its parents. The dwarfing and albinism in DW-B were owing to defects in the GA signaling pathway and abnormal chloroplast development. This study can improve understanding of the regulation of plant height and leaf color.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-023-01379-z.

Mepiquat chloride inhibits soybean growth but improves drought resistance

Soybeans are an important economic crop. As the most widely used growth regulator globally, the molecular mechanism of mepiquat chloride (DPC) in soybean remains unknown. In this study, RNA sequencing technology combined with ultra-performance liquid chromatography and tandem mass spectrometry were used to analyze the changes in the leaf transcriptome and metabolomics of soybean leaves at the seedling stage under DPC stress. The results showed that differentially expressed genes related to photosynthesis and cell wall synthesis were significantly downregulated at the transcriptional level. In addition, the syntheses of gibberellin, zeatin, brassinolide, and other plant hormones were inhibited in the signal transduction pathway of plant hormones, thereby inhibiting plant growth. In contrast, at the metabolic level, the expression levels of flavonoid differential metabolites were significantly increased, and the proportions of flavonoids in the two varieties were 61.5 and 66%, respectively. The combined analysis of transcriptome and metabolomics showed that the differential expressed genes and metabolites were mainly enriched in the isoflavonoid biosynthesis and flavonoid biosynthesis pathways. Principally, DPC inhibited plant growth but improved drought resistance. Our study is the first to report the molecular mechanism of DPC regulation in soybean, providing useful insights into the rational application of DPC in soybean.

Genotyping-by-Sequencing Based Investigation of Population Structure and Genome Wide Association Studies for Seven Agronomically Important Traits in a Set of 346 Oryza rufipogon Accessions

Being one of the most important staple dietary constituents globally, genetic enhancement of cultivated rice for yield, agronomically important traits is of substantial importance. Even though the climatic factors and crop management practices impact complex traits like yield immensely, the contribution of variation by underlying genetic factors surpasses them all. Previous studies have highlighted the importance of utilizing exotic germplasm, landraces in enhancing the diversity of gene pool, leading to better selections and thus superior cultivars. Thus, to fully exploit the potential of progenitor of Asian cultivated rice for productivity related traits, genome wide association study (GWAS) for seven agronomically important traits was conducted on a panel of 346 O. rufipogon accessions using a set of 15,083 high-quality single nucleotide polymorphic markers. The phenotypic data analysis indicated large continuous variation for all the traits under study, with a significant negative correlation observed between grain parameters and agronomic parameters like plant height, culm thickness. The presence of 74.28% admixtures in the panel as revealed by investigating population structure indicated the panel to be very poorly genetically differentiated, with rapid LD decay. The genome-wide association analyses revealed a total of 47 strong MTAs with 19 SNPs located in/close to previously reported QTL/genic regions providing a positive analytic proof for our studies. The allelic differences of significant MTAs were found to be statistically significant at 34 genomic regions. A total of 51 O. rufipogon accessions harboured combination of superior alleles and thus serve as potential candidates for accelerating rice breeding programs. The present study identified 27 novel SNPs to be significantly associated with different traits. Allelic differences between cultivated and wild rice at significant MTAs determined superior alleles to be absent at 12 positions implying substantial scope of improvement by their targeted introgression into cultivars. Introgression of novel significant genomic regions into breeder's pool would broaden the genetic base of cultivated rice, thus making the crop more resilient.

Genome-wide Association Study for Yield and Yield-Related Traits in Diverse Blackgram Panel (Vigna mungo L. Hepper) Reveals Novel Putative Alleles for Future Breeding Programs

Blackgram (Vigna mungo L. Hepper) is an important tropical and sub-tropical short-duration legume that is rich in dietary protein and micronutrients. Producing high-yielding blackgram varieties is hampered by insufficient genetic variability, absence of suitable ideotypes, low harvest index and susceptibility to biotic-abiotic stresses. Seed yield, a complex trait resulting from the expression and interaction of multiple genes, necessitates the evaluation of diverse germplasm for the identification of novel yield contributing traits. Henceforth, a panel of 100 blackgram genotypes was evaluated at two locations (Ludhiana and Gurdaspur) across two seasons (Spring 2019 and Spring 2020) for 14 different yield related traits. A wide range of variability, high broad-sense heritability and a high correlation of grain yield were observed for 12 out of 14 traits studied among all environments. Investigation of population structure in the panel using a set of 4,623 filtered SNPs led to identification of four sub-populations based on ad-hoc delta K and Cross entropy value. Using Farm CPU model and Mixed Linear Model algorithms, a total of 49 significant SNP associations representing 42 QTLs were identified. Allelic effects were found to be statistically significant at 37 out of 42 QTLs and 50 known candidate genes were identified in 24 of QTLs.

Transcriptome Profiling Provides New Insights into the Molecular Mechanism Underlying the Sensitivity of Cotton Varieties to Mepiquat Chloride

Mepiquat chloride (MC) is a plant growth regulator widely used in cotton production to control vegetative overgrowth of cotton plants to achieve ideal plant architecture required for high yielding. Cotton varieties respond differently to MC application, but there is little information about the molecular mechanisms underlying the varietal difference. In this study, comparative transcriptome analysis was conducted by using two Upland cotton varieties with different sensitivity (XLZ74, insensitive; SD1068, sensitive) to MC treatment, aiming to understand the molecular mechanisms responsible for varietal difference of MC sensitivity. RNA-seq data were generated from the two varieties treated with MC or water at three time points, 1, 3 and 6 days post-spray (dps). Genes differentially expressed between the MC and mock treatments of XLZ74 (6252) and SD1068 (6163) were subjected to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses to compare the enriched GO terms and KEGG pathways between the two varieties. Signal transduction of phytohormones, biosynthesis of gibberellins (GAs) and brassinosteroids (BRs) and profiles of transcription factors (TFs) seemed to be differentially affected by MC in the two varieties. The transcriptomic results were further consolidated with the content changes of phytohormones in young stem. Several GA catabolic genes, GA2ox, were highly induced by MC in both varieties especially in SD1068, consistent with a more significant decrease in GA₄ in SD1068. Several AUX/IAA and SAUR genes and CKX genes were induced by MC in both varieties, but with a more profound effect observed in SD1068 that showed a significant reduction in indole-3-acetic acid (IAA) and a significant increase in cytokinin (CTK) at 6 days post-spray (dps). BR biosynthesis-related genes were downregulated in SD1068, but not in XLZ74. Additionally, more downregulated TFs were observed in MC-treated SD1068 than in MC-treated XLZ74, and the two varieties had very different profiles of genes involved in starch and sucrose metabolism, with those of SD1068 and XLZ74 being downregulated and upregulated by MC treatment, respectively. Together, these results indicate that although the same or similar biological pathways are affected by MC treatment in cotton varieties showing different MC sensitivity, the extent of effect is variable, leading to their different phenotypic outcomes. How the quantitative effect of MC on the biological processes associated with growth retardation is regulated is still an open question.

The effects of mepiquat chloride (DPC) on the soluble protein content and the activities of protective enzymes in cotton in response to aphid feeding and on the activities of detoxifying enzymes in aphids

BACKGROUND

Mepiquat chloride (DPC) enhances the resistance of cotton plants, and it is widely used as a growth regulator. DPC can stimulate photosynthesis, stabilize the structure of cotton leaves, and affect population reproduction and energy substances in Aphis gossypii Glover (cotton aphids), but interactions between DPC and cotton aphids remain unclear. In this study, we analyzed the physiological responses of cotton to DPC, and the toxicity of DPC toward cotton aphids, before and after feeding, to explore the DPC-induced defense mechanism against cotton aphids.

RESULTS

Measurements of protective enzyme activity in cotton showed that the soluble protein contents, peroxidase (POD) activity, and catalase (CAT) activity in cotton treated with different concentrations of DPC were higher than in the control. Superoxide dismutase (SOD) activity was higher than that of the control when the concentration of DPC was < 0.1 g/L. Under aphid feeding stress, POD activity in cotton treated with a low insect population density was significantly lower than in the controls, but the reverse was true for cotton treated with a high insect population density, and SOD activity was positively correlated with population density. The activities of detoxification enzymes in field and laboratory experiments showed that DPC promoted the specific activity of glutathione S-transferase (GST) in cotton aphids, while the specific activities of carboxylesterase (CarE) and acetylcholinesterase (AchE) were decreased.

CONCLUSIONS

DPC enhanced the aphid resistance in cotton by increasing the soluble protein content and the activity of protective enzymes. It also had a toxic effect on cotton aphids by increasing GST activity (the main DPC target). DPC increased the soluble protein content and protective enzymes activity in cotton under aphid stress, and thereby enhanced tolerance to cotton aphids. It conclude that DPC interferes with cotton aphids through indirect (DPC induced cotton defense responses) and direct (DPC toxicity to cotton aphids) ways, which plays a positive role in interfering with cotton aphids.

iTRAQ-based quantitative proteome analysis insights into cold stress of Winter Rapeseed (Brassica rapa L.) grown in the field

Winter rapeseed (Brassica rapa L.) is a major oilseed crop in Northern China, where its production was severely affected by chilling and freezing stress. However, not much is known about the role of differentially accumulated proteins (DAPs) during the chilling and freezing stress. In this study, isobaric tag for relative and absolute quantification (iTRAQ) technology was performed to identify DAPs under freezing stress. To explore the molecular mechanisms of cold stress tolerance at the cellular and protein levels, the morphological and physiological differences in the shoot apical meristem (SAM) of two winter rapeseed varieties, Longyou 7 (cold-tolerant) and Lenox (cold-sensitive), were explored in field-grown plants. Compared to Lenox, Longyou 7 had a lower SAM height and higher collar diameter. The level of malondialdehyde (MDA) and indole-3-acetic acid (IAA) content was also decreased. Simultaneously, the soluble sugars (SS) content, superoxide dismutase (SOD) activity, peroxidase (POD) activity, soluble protein (SP) content, and collar diameter were increased in Longyou 7 as compared to Lenox. A total of 6330 proteins were identified. Among this, 98, 107, 183 and 111 DAPs were expressed in L7 CK/Le CK, L7 d/Le d, Le d/Le CK and L7 d/L7 CK, respectively. Quantitative real-time PCR (RT-qPCR) analysis of the coding genes for seventeen randomly selected DAPs was performed for validation. These DAPs were identified based on gene ontology enrichment analysis, which revealed that glutathione transferase activity, carbohydrate-binding, glutathione binding, metabolic process, and IAA response were closely associated with the cold stress response. In addition, some cold-induced proteins, such as glutathione S-transferase phi 2(GSTF2), might play an essential role during cold acclimation in the SAM of Brassica rapa. The present study provides valuable information on the involvement of DAPs during cold stress responses in Brassica rapa L, and hence could be used for breeding experiments.

Overexpression of the maize WRKY114 gene in transgenic rice reduce plant height by regulating the biosynthesis of GA

WRKYs represent an important family of transcription factors that are widely involved in plant development, defense regulation and stress response. Transgenic rice that constitutively expressed ZmWRKY114 had shorter plant height and showed less sensitivity to gibberellic acid (GA₃). Further investigation proved that transgenic rice accumulated lower levels of bioactive GAs than that in wild-type plants. Application of exogenous GA₃ fully rescued the semi-dwarf phenotype of ZmWRKY114 transgenic plants. Transcriptome and qRT-PCR analyses indicated that the expression of OsGA2ox4, encoding the repressor of GA biosynthesis, was markedly increased. Electrophoretic mobility shift assay and dual-luciferase reporter assay indicated that ZmWRKY114 directly binds to a W-box motif in the OsGA2ox4 promoter. Taken together, these results confirm that ZmWRKY114 is a GA-responsive gene and is participated in the regulation of plant height in rice.

Profiling of MicroRNAs Involved in Mepiquat Chloride-Mediated Inhibition of Internode Elongation in Cotton (Gossypium hirsutum L.) Seedlings

Mepiquat chloride (MC) is the most important plant growth retardant that is widely used in cotton (Gossypium hirsutum L.) production to suppress excessive vegetative growth and improve plant architecture. MicroRNAs (miRNAs) are important gene expression regulators that control plant growth and development. However, miRNA-mediated post-transcriptional regulation in MC-induced growth inhibition remains unclear. In this study, the dynamic expression profiles of miRNAs responsive to MC in cotton internodes were investigated. A total of 508 known miRNAs belonging to 197 families and five novel miRNAs were identified. Among them, 104 miRNAs were differentially expressed at 48, 72, or 96 h post MC treatment compared with the control (0 h); majority of them were highly conserved miRNAs. The number of differentially expressed miRNAs increased with time after treatment. The expression of 14 known miRNAs was continuously suppressed, whereas 12 known miRNAs and one novel miRNA were continuously induced by MC. The expression patterns of the nine differentially expressed miRNAs were verified using qRT-PCR. The targets of the known and novel miRNAs were predicted. Four conserved and six novel targets were validated using the RLM-5' RACE assay. This study revealed that miRNAs play crucial regulatory roles in the MC-induced inhibition of internode elongation. It can improve our understanding of post-transcriptional gene regulation in MC-mediated growth inhibition and could potentially facilitate the breeding of dwarf cotton.