Recent advances and future perspectives in early-maturing cotton research

Sphingolipid inhibitor response gene GhMYB86 controls fiber elongation by regulating microtubule arrangement

Although the cell membrane and cytoskeleton play essential roles in cellular morphogenesis, the interaction between the membrane and cytoskeleton is poorly understood. Cotton fibers are extremely elongated single cells, which makes them an ideal model for studying cell development. Here, we used the sphingolipid biosynthesis inhibitor, fumonisin B1 (FB1), and found that it effectively suppressed the myeloblastosis (MYB) transcription factor GhMYB86, thereby negatively affecting fiber elongation. A direct target of GhMYB86 is GhTUB7, which encodes the tubulin protein, the major component of the microtubule cytoskeleton. Interestingly, both the overexpression of GhMYB86 and GhTUB7 caused an ectopic microtubule arrangement at the fiber tips, and then leading to shortened fibers. Moreover, we found that GhMBE2 interacted with GhMYB86 and that FB1 and reactive oxygen species induced its transport into the nucleus, thereby enhancing the promotion of GhTUB7 by GhMYB86. Overall, we established a GhMBE2-GhMYB86-GhTUB7 regulation module for fiber elongation and revealed that membrane sphingolipids affect fiber elongation by altering microtubule arrangement.

GhRCD1 promotes cotton tolerance to cadmium by regulating the GhbHLH12-GhMYB44-GhHMA1 transcriptional cascade

Heavy metal pollution poses a significant risk to human health and wreaks havoc on agricultural productivity. Phytoremediation, a plant-based, environmentally benign, and cost-effective method, is employed to remove heavy metals from contaminated soil, particularly in agricultural or heavy metal-sensitive lands. However, the phytoremediation capacity of various plant species and germplasm resources display significant genetic diversity, and the mechanisms underlying these differences remain hitherto obscure. Given its potential benefits, genetic improvement of plants is essential for enhancing their uptake of heavy metals, tolerance to harmful levels, as well as overall growth and development in contaminated soil. In this study, we uncover a molecular cascade that regulates cadmium (Cd2+) tolerance in cotton, involving GhRCD1, GhbHLH12, GhMYB44, and GhHMA1. We identified a Cd2+-sensitive cotton T-DNA insertion mutant with disrupted GhRCD1 expression. Genetic knockout of GhRCD1 by CRISPR/Cas9 technology resulted in reduced Cd2+ tolerance in cotton seedlings, while GhRCD1 overexpression enhanced Cd2+ tolerance. Through molecular interaction studies, we demonstrated that, in response to Cd2+ presence, GhRCD1 directly interacts with GhbHLH12. This interaction activates GhMYB44, which subsequently activates a heavy metal transporter, GhHMA1, by directly binding to a G-box cis-element in its promoter. These findings provide critical insights into a novel GhRCD1-GhbHLH12-GhMYB44-GhHMA1 regulatory module responsible for Cd2+ tolerance in cotton. Furthermore, our study paves the way for the development of elite Cd2+-tolerant cultivars by elucidating the molecular mechanisms governing the genetic control of Cd2+ tolerance in cotton.

Integrative Transcriptomics and Proteomics Analysis of a Cotton Mutant yl1 with a Chlorophyll-Reduced Leaf

Leaf color mutants serve as ideal materials for studying photosynthesis, chlorophyll metabolism, and other physiological processes. Here, we identified a spontaneous yellow-leaf mutant (yl1) with chlorophyll-reduced leaves from G. hirsutum L. cv ZM24. Compare to wild type ZM24 with green leaves, yl1 exhibited patchy yellow leaves and reduced chlorophyll content. To further explore the mechanisms of the patchy yellow phenotype of the mutant plant, the transcriptomics and proteomics profiles were conducted for the mutant and wild types. A total of 9247 differentially expressed genes (DEGs) and 1368 differentially accumulated proteins (DAPs) were identified. Following gene ontology (GO) annotation and KEGG enrichment, the DEGs/DAPs were found to be significantly involved in multiple important pathways, including the obsolete oxidation-reduction process, photosynthesis, light-harvesting, the microtubule-based process, cell redox homeostasis, and the carbohydrate metabolic process. In photosynthesis and the light-harvesting pathway, a total of 39 DAPs/DEGs were identified, including 9 genes in the PSI, 7 genes in the PS II, 9 genes in the light-harvesting chlorophyll protein complex (LHC), 10 genes in the PsbP family, and 4 genes in the cytochrome b6/f complex. To validate the reliability of the omics data, GhPPD1, a DAPs in the PsbP family, was knocked down in cotton using the TRV-based VIGS system, and it was observed that the GhPPD1-silenced plants exhibited patchy yellow color, accompanied by a significant decrease in chlorophyll content. In conclusion, this study integrated transcriptomic and proteomic approaches to gain a deeper understanding of the mechanisms underlying the chlorophyll-reduced leaf phenotype.

GhGASA14 regulates the flowering time of upland cotton in response to GA3

KEY MESSAGE

The silencing of GhGASA14 and the identification of superior allelic variation in its coding region indicate that GhGASA14 may positively regulate flowering and the response to GA3. Gibberellic acid-stimulated Arabidopsis (GASA), a member of the gibberellin-regulated short amino acid family, has been extensively investigated in several plant species and found to be critical for plant growth and development. However, research on this topic in cotton has been limited. In this study, we identified 38 GhGASAs that were dispersed across 18 chromosomes in upland cotton, and all of these genes had a GASA core domain. Transcriptome expression patterns and qRT-PCR results revealed that GhGASA9 and GhGASA14 exhibited upregulated expression not only in the floral organs but also in the leaves of early-maturing cultivars. The two genes were functionally characterized by virus-induced gene silencing (VIGS), and the budding and flowering times after silencing the target genes were later than those of the control (TRV:00). Compared with that in the water-treated group (MOCK), the flowering period of the different fruiting branches in the GA3-treated group was more concentrated. Interestingly, allelic variation was detected in the coding sequence of GhGASA14 between early-maturing and late-maturing accessions, and the frequency of this favorable allele was greater in high-latitude cotton cultivars than in low-latitude ones. Additionally, a significant linear relationship was observed between the expression level of GhGASA14 and flowering time among the 12 upland cotton accessions. Taken together, these results indicated that GhGASA14 may positively regulate flowering time and respond to GA3. These findings could lead to the use of valuable genetic resources for breeding early-maturing cotton cultivars in the future.

Overexpression of GhGSTF9 Enhances Salt Stress Tolerance in Transgenic Arabidopsis

Soil salinization is a major abiotic stress factor that negatively impacts plant growth, development, and crop yield, severely limiting agricultural production and economic development. Cotton, a key cash crop, is commonly cultivated as a pioneer crop in regions with saline-alkali soil due to its relatively strong tolerance to salt. This characteristic renders it a valuable subject for investigating the molecular mechanisms underlying plant salt tolerance and for identifying genes that confer salt tolerance. In this study, focus was placed on examining a salt-tolerant variety, E991, and a salt-sensitive variety, ZM24. A combined analysis of transcriptomic data from these cotton varieties led to the identification of potential salt stress-responsive genes within the glutathione S-transferase (GST) family. These versatile enzyme proteins, prevalent in animals, plants, and microorganisms, were demonstrated to be involved in various abiotic stress responses. Our findings indicate that suppressing GhGSTF9 in cotton led to a notably salt-sensitive phenotype, whereas heterologous overexpression in Arabidopsis plants decreases the accumulation of reactive oxygen species under salt stress, thereby enhancing salt stress tolerance. This suggests that GhGSTF9 serves as a positive regulator in cotton's response to salt stress. These results offer new target genes for developing salt-tolerant cotton varieties.

A cotton mitochondrial alternative electron transporter, GhD2HGDH, induces early flowering by modulating GA and photoperiodic pathways

D-2-hydroxyglutarate dehydrogenase (D2HGDH) is a mitochondrial enzyme containing flavin adenine dinucleotide FAD, existing as a dimer, and it facilitates the specific oxidation of D-2HG to 2-oxoglutarate (2-OG), which is a key intermediate in the tricarboxylic acid (TCA) cycle. A Genome-wide expression analysis (GWEA) has indicated an association between GhD2HGDH and flowering time. To further explore the role of GhD2HGDH, we performed a comprehensive investigation encompassing phenotyping, physiology, metabolomics, and transcriptomics in Arabidopsis thaliana plants overexpressing GhD2HGDH. Transcriptomic and qRT-PCR data exhibited heightened expression of GhD2HGDH in upland cotton flowers. Additionally, early-maturing cotton exhibited higher expression of GhD2HGDH across all tissues than delayed-maturing cotton. Subcellular localization confirmed its presence in the mitochondria. Overexpression of GhD2HGDH in Arabidopsis resulted in early flowering. Using virus-induced gene silencing (VIGS), we investigated the impact of GhD2HGDH on flowering in both early- and delayed-maturing cotton plants. Manipulation of GhD2HGDH expression levels led to changes in photosynthetic pigment and gas exchange attributes. GhD2HGDH responded to gibberellin (GA3) hormone treatment, influencing the expression of GA biosynthesis genes and repressing DELLA genes. Protein interaction studies, including yeast two-hybrid, luciferase complementation (LUC), and GST pull-down assays, confirmed the interaction between GhD2HGDH and GhSOX (Sulfite oxidase). The metabolomics analysis demonstrated GhD2HGDH's modulation of the TCA cycle through alterations in various metabolite levels. Transcriptome data revealed that GhD2HGDH overexpression triggers early flowering by modulating the GA3 and photoperiodic pathways of the flowering core factor genes. Taken together, GhD2HGDH positively regulates the network of genes associated with early flowering pathways.

Multistage temporal transcriptomic atlas unveils major contributor to reproductive phase in upland cotton

Flowering is a major developmental transition in plants, but asynchronous flowering hinders the utilization of wild cotton relatives in breeding programs. We performed comparative transcriptomic profiling of early- and late-flowering Gossypium hirsutum genotypes to elucidate genetic factors influencing reproductive timing. Shoot apices were sampled from the photoperiod-sensitive landrace G. hirsutum purpurascens (GhP) and early-maturing variety ZhongMianSuo (ZMS) at five time points following the emergence of sympodial nodes. RNA-sequencing revealed extensive transcriptional differences during floral transition. Numerous flowering-associated genes exhibited genotype-specific expression, including FLOWERING LOCUS T (FT) homologs upregulated in ZMS. FT-interacting factors like SOC1 and CO-like also showed higher expression in ZMS, implicating florigen pathways in early flowering. Additionally, circadian clock and light signalling components were misregulated between varieties, suggesting altered photoperiod responses in GhP. Weighted co-expression network analysis specifically linked a module enriched for circadian-related genes to GhP's late flowering. Through an integrated transcriptome analysis, we defined a regulatory landscape of reproductive phase change in cotton. Differentially expressed genes related to photoperiod, circadian clock, and light signalling likely contribute to delayed flowering in wild cottons. Characterization of upstream flowering regulators will enable modifying photoperiod sensitivity and expand germplasm use for cotton improvement. This study provides candidate targets for elucidating interactive mechanisms that control cotton flowering time across diverse genotypes.

GhCOL2 Positively Regulates Flowering by Activating the Transcription of GhHD3A in Upland Cotton (Gossypium hirsutum L.)

Plants have evolved sophisticated signaling networks to adjust flowering time, ensuring successful reproduction. Two crucial flowering regulators, FLOWERING LOCUS T (FT) and CONSTANS (CO), play pivotal roles in regulating flowering across various species. Previous studies have indicated that suppressing Gossypium hirsutum CONSTANS-LIKE 2 (GhCOL2), a homolog of Arabidopsis CO, leads to delayed flowering in cultivated cotton. However, the underlying regulatory mechanisms remain unknown. In this study, a yeast one-hybrid and dual-LUC expression assays were used to elucidate the molecular mechanism through which GhCOL2 regulates the transcription of GhHD3A. RT-qPCR was used to examine the expression of GhCOL2 and GhHD3A. Our findings reveal that GhCOL2 directly binds to CCACA cis-elements and atypical CORE (TGTGTATG) cis-elements in the promoter regions of HEADING DATE 3 A (HD3A), thereby activating GhHD3A transcription. Notably, GhCOL2 and GhHD3A exhibited high expression levels in the adult stage and low levels in the juvenile stage. Interestingly, the expression of GhCOL2 and GhHD3A varied significant between the two cotton varieties (Tx2094 and Maxxa). In summary, our study enhances the understanding of the molecular mechanism by which cotton GhCOL2-GhHD3A regulates flowering at the molecular level. Furthermore, it contributes to a broader comprehension of the GhCOL2-GhHD3A model in G. hirsutum.

Morphological and physio-biochemical responses under heat stress in cotton: Overview

Cotton is an important cash crop in addition to being a fiber commodity, and it plays an essential part in the economies of numerous nations. High temperature is the most critical element affecting its yield from fertilization to harvest. The optimal temperature for root formation is 30 C -35 °C; however, root development ends around 40 °C. Increased temperature, in particular, influences different biochemical and physiological processes associated with cotton plant, resulting in low seed cotton production. Many studies in various agroecological zones used various agronomic strategies and contemporary breeding techniques to reduce heat stress and improve cotton productivity. To attain desired traits, cotton breeders should investigate all potential possibilities, such as generating superior cultivars by traditional breeding, employing molecular techniques and transgenic methods, such as using genome editing techniques. The main objective of this review is to provide the recent information on the environmental factors, such as temperature, heat and drought, influence the growth and development, morphology and physio-chemical alteration associated with cotton. Furthermore, recent advancement in cotton breeding to combat the serious threat of drought and heat stress.

Synergistic optimization of crops by combining early maturation with other agronomic traits

Many newly created early maturing varieties exhibit poor stress resistance and low yield, whereas stress-resistant varieties are typically late maturing. For this reason, the polymerization of early maturity and other desired agronomic qualities requires overcoming the negative connection between early maturity, multi-resistance, and yield, which presents a formidable challenge in current breeding techniques. We review the most salient constraints of early maturity breeding in current crop planting practices and the molecular mechanisms of different maturation timeframes in diverse crops from their origin center to production areas. We explore current breeding tactics and the future direction of crop breeding and the issues that must be resolved to accomplish the polymerization of desirable traits in light of the current obstacles and limitations.

QTL mapping and BSA-seq map a major QTL for the node of the first fruiting branch in cotton

Understanding the genetic basis of the node of the first fruiting branch (NFFB) improves early-maturity cotton breeding. Here we report QTL mapping on 200 F₂ plants and derivative F_2:3 and F_2:4 populations by genotyping by sequencing (GBS). BC₁F₂ population was constructed by backcrossing one F_2:4 line with the maternal parent JF914 and used for BSA-seq for further QTL mapping. A total of 1,305,642 SNPs were developed between the parents by GBS, and 2,907,790 SNPs were detected by BSA-seq. A high-density genetic map was constructed containing 11,488 SNPs and spanning 4,202.12 cM in length. A total of 13 QTL were mapped in the 3 tested populations. JF914 conferred favorable alleles for 11 QTL, and JF173 conferred favorable alleles for the other 2 QTL. Two stable QTL were repeatedly mapped in F_2:3 and F_2:4, including qNFFB-D3-1 and qNFFB-D6-1. Only qNFFB-D3-1 contributed more than 10% of the phenotypic variation. This QTL covered about 24.7 Mb (17,130,008-41,839,226 bp) on chromosome D3. Two regions on D3 (41,779,195-41,836,120 bp, 41,836,768-41,872,287 bp) were found by BSA-seq and covered about 92.4 Kb. This 92.4 Kb region overlapped with the stable QTL qNFFB-D3-1 and contained 8 annotated genes. By qRT-PCR, Ghir_D03G012430 showed a lower expression level from the 1- to 2-leaf stage and a higher expression level from the 3- to 6-leaf stage in the buds of JF173 than that of JF914. Ghir_D03G012390 reached the highest level at the 3- and 5-leaf stages in the buds of JF173 and JF914, respectively. As JF173 has lower NFFB and more early maturity than JF914, these two genes might be important in cell division and differentiation during NFFB formation in the seedling stage. The results of this study will facilitate a better understanding of the genetic basis of NFFB and benefit cotton molecular breeding for improving earliness traits.