Correlation analysis of the transcriptome and metabolome reveals the role of the flavonoid biosynthesis pathway in regulating axillary buds in upland cotton (Gossypium hirsutum L.).

MAIN CONCLUSION: Flavonoids are involved in axillary bud development in upland cotton. The phenylpropanoid and flavonoid biosynthesis pathways regulate axillary bud growth by promoting the transport of auxin in upland cotton. In cotton production, simplified cultivation and mechanical harvesting are emerging trends that depend on whether the cotton plant type meets production requirements. The axillary bud is an important index of cotton plant-type traits, and the molecular mechanism of axillary bud development in upland cotton has not yet been completely studied. Here, a combined investigation of transcriptome and metabolome analyses in G. hirsutum CCRI 117 at the fourth week (stage 1), fifth week (stage 2) and sixth week (stage 3) after seedling emergence was performed. The metabolome results showed that the total lipid, amino acid and organic acid contents in the first stalk node decreased during axillary bud development. The abundance of 71 metabolites was altered between stage 2 and stage 1, and 32 metabolites exhibited significantly altered abundance between stage 3 and stage 2. According to the correlation analysis of metabolome and transcriptome profiles, we found that phenylpropanoid and flavonoid biosynthesis pathways exhibit high enrichment degrees of both differential metabolites and differential genes in three stages. Based on the verification of hormone, soluble sugar and flavonoid detection, we propose a model for flavonoid-mediated regulation of axillary bud development in upland cotton, revealing that the decrease in secondary metabolites of phenylpropanoid and flavonoid biosynthesis is an essential factor to promote the transport of auxin and subsequently promote the growth of axillary buds. Our findings provide novel insights into the regulation of phenylpropanoid and flavonoid biosynthesis in axillary bud development and could prove useful for cultivating machine-harvested cotton varieties with low axillary buds.

Transcriptome analyses provide insights into the homeostatic regulation of axillary buds in upland cotton (G. hirsutum L.).

BACKGROUND: The axillary bud is an important index of cotton plant-type traits, and the molecular mechanism of axillary bud development in upland cotton has not yet been reported. We obtained a mutant (designated mZ571) with a high-budding phenotype in axillary bud development from the low-budding phenotype variety G. hirsutum Z571 (CCRI 9A02), which provided ideal materials for the study of complex regulatory networks of axillary bud development. In this study, RNA sequencing was carried out to detect gene expression levels during three stages of axillary buds in Z571 (LB, low budding) and mZ571 mutant (HB, high budding). RESULTS: A total of 7162 DEGs were identified in the three groups (HB-E vs. LB-E, HB-G1 vs. LB-G1, HB-G2 vs. LB-G2), including 4014 downregulated and 3184 upregulated DEGs. Additionally, 221 DEGs were commonly identified in all three groups, accounting for approximately 3.09% of the total DEGs. These DEGs were identified, annotated and classified. A significant number of DEGs were related to hormone metabolism, hormone signal transduction, and starch and sucrose metabolism. In addition, 45, 22 and 9 DEGs involved in hormone metabolic pathways and 67, 22 and 19 DEGs involved in hormone signal transduction pathwayspathway were identified in HB-E vs. LB-E, HB-G1 vs. LB-G1, and HB-G2 vs. LB-G2, respectively, suggesting that endogenous hormones are the primary factors influencing cotton axillary bud growth. Hormone and soluble sugar content measurements revealed that mZ571 exhibited higher concentrations of zeatin, gibberellins and soluble sugar in all three stages, which confirmed that these hormone metabolism-, hormone signal transduction- and starch metabolism-related genes showed interaction effects contributing to the divergence of axillary bud growth between mZ571 and Z571. CONCLUSIONS: Our results confirmed the importance of endogenous hormones and sugars in the development of axillary buds, and we found that mZ571 plants, with a high-budding phenotype of axillary buds, exhibited higher endogenous hormone and sugar concentrations. Overall, we present a model for the emergence and development of cotton axillary buds that provides insights into the complexity and dynamic nature of the regulatory network during axillary bud emergence and development.

The role of gibberellin synthase gene GhGA2ox1 in upland cotton (Gossypium hirsutum L.) responses to drought and salt stress.

Gibberellins (GAs) is one kind of important endogenous hormone in plants that regulates vegetative and reproductive growth of plants. GA2ox is a class of oxidase that plays a regulatory role in the third stage of GAs synthesis. In this paper, we cloned the GhGA2ox1 gene from an upland cotton (Gossypium hirsutum L. var. CCRI49). The results showed that the CDS of GhGA2ox1 is 996 bp, which encode 331 amino acids, which has high homology with GhGA2ox2 and NtGA2ox1. The quantitative real-time PCR showed that under the conditions of salt and drought stress, the expression of GhGA2ox1 had a higher upregulation in root, stem, and leaf of transgenic plant, compared with non-transgenic plant. Cotton plant that overexpressed the GhGA2ox1 gene showed higher drought and salt tolerance than non-transgenic cotton plant, and these results were supported by data of higher free proline, chlorophyll, and relative water content in transgenic plant compared with control plant. The expression level of antiretroviral genes, including GhEREB2, GhDREB1, GhWRKY5, and GhP5CS, was upregulated to varying degrees in transgenic plant. The above results indicate that overexpressed GhGA2ox1 gene can increases the tolerance to respond to drought and salt stress in upland cotton.

Global analysis of the developmental dynamics of Gossypium hirsutum based on strand-specific transcriptome.

Cotton is an economically important crop that provides both natural fiber and by-products such as oil and protein. Its global gene expression could provide insight into the biological processes underlying growth and development, which involve suites of genes expressed with temporal and spatial control by regulatory networks. Generally, the goal for cotton breeding is improvement of the fiber; thus, most previous research has focused on identifying genes specific to the fiber. However, seeds may also play an important role in fiber development. In this study, we constructed and systematically analyzed 21 strand-specific RNA-Seq libraries for Gossypium hirsutum, covering different tissues, organs and development stages, from which approximately 970 million reads were generated to provide a global view of gene expression during cotton development. The organ (tissue)-specific gene expression patterns were investigated, providing further insight into the dynamic programming associated with developmental processes and a way to study the coordination of development between fiber cells and ovules. Series of transcription factors and seed-specific genes have been identified as candidate genes that could elucidate key mechanisms and regulatory networks in nutrient accumulation during ovule development and in fiber development. This study reports comprehensive transcriptome dynamics at various stages of cotton development and will serve as a valuable genome-wide transcriptome resource for initial gene discovery and functional characterization of genes in cotton.

Development and identification of molecular markers of GhHSP70-26 related to heat tolerance in cotton.

Heat stress significantly affect plant growth and development, which is an important factor contributing to crop yield loss. However, heat shock proteins (HSPs) in plants can effectively alleviate cell damage caused by heat stress. In order to rapidly and accurately cultivate heat-tolerant cotton varieties, this study conducted correlation analysis between heat tolerance index and insertion/deletion (In/Del) sites of GhHSP70-26 promoter in 39 cotton materials, so as to find markers related to heat tolerance function of cotton, which can be used in molecular marker-assisted breeding. The results showed the natural variation allele (Del22 bp) type at -1590 bp upstream of GhHSP70-26 promoter (haplotype2, Hap2) in cotton (Gossypium spp.) promoted GhHSP70-26 expression under heat stress. The relative expression level of GhHSP70-26 of M-1590-Del22 cotton materials were significantly higher than that of M-1590-In type cotton materials under heat stress (40 ℃). Also, M-1590-Del22 material had lower conductivity and less cell damage after heat stress, indicating that it is a heat resistant cotton material. The Hap1 (M-1590-In) promoter was mutated into Hap1del22, and Hap1 and Hap1del22 were fused with GUS to transform Arabidopsis thaliana. Furthermore, Hap1del22 promoter had higher induction activity than Hap1 under heat stress and abscisic acid (ABA) treatment in transgenic Arabidopsis thaliana. Further analysis confirmed that M-1590-Del22 was the dominant heat-resistant allele. In summary, these results identify a key and previously unknown natural variation in GhHSP70-26 with respect to heat tolerance, providing a valuable functional molecular marker for genetic breeding of cotton and other crops with heat tolerance.

Overexpression of StGA2ox1 Gene Increases the Tolerance to Abiotic Stress in Transgenic Potato (Solanum tuberosum L.) Plants.

It has been known that GA2ox is one kind of key enzyme gene in the gibberellin synthesis pathway, which plays important regulatory roles throughout plant whole growth and development. In this article, one of the GA2ox family genes, designated StGA2ox1, was isolated from potato (Solanum tuberosum L.). The full length of cDNA is 1005 bp, and the cDNA corresponds to a protein of 334 amino acids; this protein was classified in a group with NtGA2ox3 based on multiple sequence alignments and phylogenetic characterization. A plant expression vector pCAEZ1383-StGA2ox1 was established. qRT-PCR showed that the expression of RD28, DREB1, WRKY1, and SnRK2 genes in StGA2ox1 transgenic plant is higher than that in non-transformed control under dehydration, low temperature conditions, and abscisic acid treatments. Overexpression of StGA2ox1 cDNA in transgenic potato plants exhibited an improved salt, drought, exogenous hormone, and low temperature stress tolerance in comparison to the non-transformed plant. The enhanced stress tolerance may be associated with the subsequent accumulation of proline osmoprotectant in addition to a better control of chlorophyll, carotenoids, and water loss. These data suggest that the StGA2ox1 is involved in the regulation of plant growth and tolerance in potato by regulating the synthesis of gibberellin.

Relative contribution of Na+/K+ homeostasis, photochemical efficiency and antioxidant defense system to differential salt tolerance in cotton (Gossypium hirsutum L.) cultivars.

In this study, the role of specific components of different coping strategies to salt load were identified. A pot experiment was conducted with four cotton (Gossypium hirsutum L.) cultivars (differing in salt-sensitivity) under salinity stress. Based on observed responses in growth performance and physiological characteristics, CZ91 was the most tolerant of the four cultivars, followed by cultivars CCRI44 and CCRI49, with Z571 being much more sensitive to salt stress. To perform this tolerant response, they implement different adaptative mechanisms to cope with salt-stress. The superior salt tolerance of CZ91 was conferred by at least three complementary physiological mechanisms: its ability to regulate K+ and Na+ transport more effectively, its higher photochemical efficiency and better antioxidant defense capacity. However, only one or a few specific components of these defense systems play crucial roles in moderately salt tolerant CCRI44 and CCRI49. Lower ROS load in CCRI44 may be attributed to simultaneous induction of antioxidant defenses by maintaining an unusually high level of SOD, and higher activities of CAT, APX, and POD during salt stress. CCRI49 could reduce the excess generation of ROS not only by maintaining a higher selective absorption of K+ over Na+ in roots across the membranes through SOS1, AKT1, and HAK5, but also by displaying higher excess-energy dissipation (e.g., higher ETR, PR and qN) during salt stress. Overall, our data provide a mechanistic explanation for differential salt stress tolerance among these cultivars and shed light on the different strategies employed by cotton cultivars to minimize the ill effects of stress.