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Introduction: Defoliation by applying defoliants before machine picking is an important agricultural practice that enhances harvesting efficiency and leads to increased raw cotton purity. However, the fundamental characteristics of leaf abscission and the underlying genetic basis in cotton are not clearly understood. Objectives: In this study, we aimed to (1) reveal the phenotypic variations in cotton leaf abscission, (2) discover the whole-genome differentiation sweeps and genetic loci related to defoliation, (3) identify and verify the functions of key candidate genes associated with defoliation, and (4) explore the relationship between haplotype frequency of loci and environmental adaptability. Methods: Four defoliation-related traits of 383 re-sequenced Gossypium hirsutum accessions were investigated in four environments. The genome-wide association study (GWAS), linkage disequilibrium (LD) interval genotyping and functional identification were conducted. Finally, the haplotype variation related to environmental adaptability and defoliation traits was revealed. Results: Our findings revealed the fundamental phenotypic variations of defoliation traits in cotton. We showed that defoliant significantly increased the defoliation rate without incurring yield and fiber quality penalties. The strong correlations between defoliation traits and growth period traits were observed. A genome-wide association study of defoliation traits identified 174 significant SNPs. Two loci (RDR7 on A02 and RDR13 on A13) that significantly associated with the relative defoliation rate were described, and key candidate genes GhLRR and GhCYCD3;1, encoding a leucine-rich repeat (LRR) family protein and D3-type cell cyclin 1 protein respectively, were functional verified by expression pattern analysis and gene silencing. We found that combining of two favorable haplotypes (HapRDR7 and HapRDR13) improved sensitivity to defoliant. The favorable haplotype frequency generally increased in high latitudes in China, enabling adaptation to the local environment. Conclusion: Our findings lay an important foundation for the potentially broad application of leveraging key genetic loci in breeding machine-pickable cotton.

Abstract Background Cotton fiber is a model tissue for studying microtubule-associated proteins (MAPs). The Xklp2 (TPX2) proteins that belong to the novel MAPs member mainly participate in the formation and development of microtubule (MT). However, there is a lack of studies concerning the systematic characterization of the TPX2 genes family in cotton. Therefore, the identification and portrayal of G. hirsutum TPX2 genes can provide key targets for molecular manipulation in the breeding of cotton fiber improvement. Result In this study, TPX2 family genes were classified into two distinct subclasses TPXLs and MAP genes WAVE DAMPENED2-LIKE (WDLs) and quite conservative in quantity. GhWDL3 was significantly up-regulated in 15 days post anthesis fibers of ZRI-015 (an upland cotton with longer and stronger fiber). GhWDL3 promotes all stem hairs to become straight when overexpressed in Arabidopsis, which may indirectly regulate cotton fiber cell morphology during fiber development. Virus induced gene silencing (VIGS) results showed that GhWDL3 inhibited fiber cell elongation at fiber development periods through regulating the expression of cell wall related genes. Conclusion These results reveal that GhWDL3 regulated cotton fiber cell elongation and provide crucial information for the further investigation in the regulatory mechanisms/networks of cotton fiber length.

Abstract Background Photosystem II (PSII) constitutes an intricate assembly of protein pigments, featuring extrinsic and intrinsic polypeptides within the photosynthetic membrane. The low-molecular-weight transmembrane protein PsbX has been identified in PSII, which is associated with the oxygen-evolving complex. The expression of PsbX gene protein is regulated by light. PsbX's central role involves the regulation of PSII, facilitating the binding of quinone molecules to the Qb (PsbA) site, and it additionally plays a crucial role in optimizing the efficiency of photosynthesis. Despite these insights, a comprehensive understanding of the PsbX gene's functions has remained elusive. Results In this study, we identified ten PsbX genes in Gossypium hirsutum L. The phylogenetic analysis results showed that 40 genes from nine species were classified into one clade. The resulting sequence logos exhibited substantial conservation across the N and C terminals at multiple sites among all Gossypium species. Furthermore, the orthologous/paralogous, Ka/Ks ratio revealed that cotton PsbX genes subjected to positive as well as purifying selection pressure might lead to limited divergence, which resulted in the whole genome and segmental duplication. The expression patterns of GhPsbX genes exhibited variations across specific tissues, as indicated by the analysis. Moreover, the expression of GhPsbX genes could potentially be regulated in response to salt, intense light, and drought stresses. Therefore, GhPsbX genes may play a significant role in the modulation of photosynthesis under adverse abiotic conditions. Conclusion We examined the structure and function of PsbX gene family very first by using comparative genomics and systems biology approaches in cotton. It seems that PsbX gene family plays a vital role during the growth and development of cotton under stress conditions. Collectively, the results of this study provide basic information to unveil the molecular and physiological function of PsbX genes of cotton plants.

Abstract Background Gossypium hirsutum undergoes rapid clonal propagation to regenerate a mature plant through tissue culture. However, the correlation between cotton leaf regeneration, callus induction, and regeneration ability was still obscure. In this research, cotton leaf regeneration level for 21 accessions in the field (new leaves) was observed after the first harvest, and a comparison between field regeneration level and callus induction with its regeneration capacity (new shoots and roots) for the same 21 accessions was carried out. Agronomic traits, including plant height, leaf area, fresh leaf weight, dry leaf weight, the number of flowers and bolls, and biochemical (proline content) and physiological (chlorophyll and carotenoid content) traits during the flowering stage of 21 upland cotton accessions, were investigated. Result A significant correlation between physiological parameters and callus induction was discovered. Callus induction and regeneration capacity of roots and shoots for hypocotyl, cotyledons, and shoot tip tissues were used to validate field leaf regeneration level after the first harvest. CCRI 24 showed significant leaf regeneration in the field and callus induction capacity through callus induction and regeneration. Conclusion We found a substantial relationship between field regeneration capability and callus induction with its regeneration capacity for the hypocotyl, cotyledons, and shoot tip. The results showed that ZS061, Lumian 378, Jimian 863, and ZS065 have the highest moisture retention capacity, while CCRI 24, Liaoyang Duomaomian, and Beizhe Gongshemian have the lowest moisture retention capacity. CCRI 24 has the highest leaf regeneration capacity in the field, while Beizhe Gongshemian has the lowest leaf regeneration capacity. All our result provides a clue for checking the regeneration capacity through leaf regeneration level in the field.

Abstract Background Cotton production is adversely effected by drought stress. It is exposed to drought stress at various critical growth stages grown under a water scarcity environment. Roots are the sensors of plants; they detect osmotic stress under drought stress and play an important role in plant drought tolerance mechanisms. The seedling stage is very sensitive to drought stress, and it needed to explore the methods and plant characteristics that contribute to drought tolerance in cotton. Results Initially, seedlings of 18 genotypes from three Gossypium species: G. hirsutum, G. barbadense, and G. arboreum, were evaluated for various seedling traits under control (NS) and drought stress (DS). Afterward, six genotypes, including two of each species, one tolerant and one susceptible, were identified based on the cumulative drought sensitivity response index (CDSRI). Finally, growth rates (GR) were examined for shoot and root growth parameters under control and DS in experimental hydroponic conditions. A significant variation of drought stress responses was observed across tested genotypes and species. CDSRI allowed here to identify the drought-sensitive and drought-resistant cultivar of each investigated species. Association among root and shoots growth traits disclosed influential effects of enduring the growth under DS. The traits including root length, volume, and root number were the best indicators with significantly higher differential responses in the tolerant genotypes. These root growth traits, coupled with the accumulation of photosynthates and proline, were also the key indicators of the resistance to drought stress. Conclusion Tolerant genotypes have advanced growth rates and the capacity to cop with drought stress by encouraging characteristics, including root differential growth traits coupled with physiological traits such as chlorophyll and proline contents. Tolerant and elite genotypes of G. hirsutum were more tolerant of drought stress than obsolete genotypes of G. barbadense and G. arboreum. Identified genotypes have a strong genetic basis of drought tolerance, which can be used in cotton breeding programs.

Abstract Background The lateral root is one of the most important organs that constitute the root architecture system in plants. It can directly affect the contact area between plants and soil and plays an important role in plant structural support and nutrient absorption. Optimizing root architecture systems can greatly increase crop yields. This study was designed to identify the molecular markers and candidate genes associated with lateral root development in cotton and to evaluate correlations with yield and disease traits. Result The number of lateral roots for 14-day old seedlings was recorded for 215 Gossypium arboreum accessions. A correlation analysis showed that the number of lateral roots positively correlates with the sympodial branch node and seed index traits, but negatively correlates with lint percentage. A Genome-wide association study (GWAS) identified 18 significant SNPs with 19 candidate genes associated with the lateral root number. Expression analysis identified three genes (FLA12, WRKY29, and RBOHA) associated with lateral root development. Conclusion GWAS analysis identified key SNPs and candidate genes for lateral root number, and genes of FLA12, WRKY29, and RBOHA may play a pivotal role in lateral root development in Asian cotton.

Abstract Background Seedling stage plant biomass is usually used as an auxiliary trait to study plant growth and development or stress adversities. However, few molecular markers and candidate genes of seedling biomass-related traits were found in cotton. Result Here, we collected 215 Gossypium arboreum accessions, and investigated 11 seedling biomass-related traits including the fresh weight, dry weight, water content, and root shoot ratio. A genome-wide association study (GWAS) utilizing 142,5003 high-quality SNPs identified 83 significant associations and 69 putative candidate genes. Furthermore, the transcriptome profile of the candidate genes emphasized higher expression of Ga03G1298, Ga09G2054, Ga10G1342, Ga11G0096, and Ga11G2490 in four representative cotton accessions. The relative expression levels of those five genes were further verified by qRT-PCR. Conclusions The significant SNPs, candidate genes identified in this study are expected to lay a foundation for studying the molecular mechanism for early biomass development and related traits in Asian cotton.

Abstract Complex interactions between symbiotic bacteria and insects ultimately result in equilibrium in all aspects of life in natural insect populations. In this study, abundance of principal symbiotic bacteria was estimated using qPCR in 1553 individuals of aphids, Aphis gossypii. Aphids were sampled from primary and secondary host plants—hibiscus and cotton. Hibiscus aphids were collected from 24 different locations in April, September, and November, whereas cotton aphids were collected between 2015 and 2017 from areas with wide variations in climatic conditions. About 30%–45% aphids were recorded with the most dominant symbiont, Arsenophonus. The other symbionts were in low frequency, and about 7% of aphids were noted with Hamiltonella, Acinetobacter, and Microbacterium, and 3% of aphids were verified with Serratia and Pseudomonas. Aphids infected with Hamiltonella, Arsenophonus, and Serratia can influence Buchnera densities. Hamiltonella has positive interaction with densities of Arsenophonus and Serratia. Almost 100% coinfection of Hamiltonella and Arsenophonus was detected in Xinxiang aphids and 50% coinfection was reported in aphids from North China, while no coinfection was detected in Hainan aphids. These findings describe the prevalence pattern and richness of core community of symbiotic bacteria in naturally occurring populations of A. gossypii and provide new insights for the study of symbiotic bacteria.

Abstract Background Stem hardness is one of the major influencing factors for plant architecture in upland cotton (Gossypium hirsutum L.). Evaluating hardness phenotypic traits is very important for the selection of elite lines for resistance to lodging in Gossypium hirsutum L. Cotton breeders are interested in using diverse genotypes to enhance fiber quality and high-yield. Few pieces of research for hardness and its relationship with fiber quality and yield were found. This study was designed to find the relationship of stem hardness traits with fiber quality and yield contributing traits of upland cotton. Results Experiments were carried out to measure the bending, acupuncture, and compression properties of the stem from a collection of upland cotton genotypes, comprising 237 accessions. The results showed that the genotypic difference in stem hardness was highly significant among the genotypes, and the stem hardness traits (BL, BU, AL, AU, CL, and CU) have a positive association with fiber quality traits and yield-related traits. Statistical analyses of the results showed that in descriptive statistics result bending (BL, BU) has a maximum coefficient of variance, but fiber length and fiber strength have less coefficient of variance among the genotypes. Principal component analysis (PCA) trimmed quantitative characters into nine principal components. The first nine principal components (PC) with Eigenvalues > 1 explained 86% of the variation among 237 accessions of cotton. Both 2017 and 2018, PCA results indicated that BL, BU, FL, FE, and LI contributed to their variability in PC1, and BU, AU, CU, FD, LP, and FWPB have shown their variability in PC2. Conclusion We describe here the systematic study of the mechanism involved in the regulation of enhancing fiber quality and yield by stem bending strength, acupuncture, and compression properties of G. hirsutum.

Growth-regulating factors-interacting factors (GIFs) are a type of transcription co-activators in plants, playing crucial roles in plants’ growth, development, and stress adaptation. Here, a total of 35 GIF genes were identified and clustered into two groups by phylogenetic analysis in four cotton genus. The gene structure and conserved domain analysis proved the conservative characteristics of GIF genes in cotton. The function of GIF genes was evaluated in two cotton accessions, Ji A-1-7 (33xi) and King, which have larger and smaller lateral root numbers, respectively. The results showed that the expression of GhGIF4 in Ji A-1-7 (33xi) was higher than that in King. The enzyme activity and microstructure assay showed a higher POD activity, lower MDA content, and more giant cells of the lateral root emergence part phenotype in Ji A-1-7 (33xi) than in King. A mild waterlogging assay showed the GIF genes were down-regulated in the waterlogged seedling. Further confirmation of the suppression of GhGIF4 in cotton plants further confirmed that GhGIF4 could reduce the lateral root numbers in cotton. This study could provide a basis for future studies of the role of GIF genes in upland cotton.

Cotton is an important agro-industrial crop across the globe. Improving the fiber quality and yield potential of cotton are major commercial targets for cotton breeders. The cotton lint yield is computed by multiplying three fundamental yield constituents: average boll weight, boll number per unit ground area, and lint percentage. The cotton species Gossypium arboreum exhibits a wide range of desirable traits, which are absent in the congener Gossypium hirsutum. Four parental lines of G. hirsutum and G. arboreum, with significant differences in boll-related traits, were used to develop the following four F2 populations: Mei Zhongmian × Chimu Heizi (MC), Mei Zhongmian × L-02292-3 (ML), Dixie king × Suyuan 04-44 (DS), and Dixie king × Pamuk (DP), in order to study complex traits, such as boll weight (BW) (g), lint percentage (LP) (%), boll upper width (BUW), boll medium width (BMW), boll lower width (BLU), and boll length (BL) (mm). In segregation populations, extensive phenotypic differences and transgressive segregation were observed. The results show that most of the correlation clusters were negatively associated with boll weight and lint percentage. The positive correlation clusters were observed among boll upper width (BUW), boll medium width (BMW), boll lower width (BLW), and boll length (BL). Seven of the twenty-four extracted principal components had eigenvalues > 1. This accounted for 62.2% of the difference between the four F2 populations. Principal component 1 accounted for 15.1% of the overall variability. The variation in principal component 1 was mainly attributed to boll lower width (BLW), boll medium width (BMW), boll upper width (BUW), boll length (BL), and boll weight (BW) of the ML population. The heritability estimates varied between high, medium, and low for various traits among the studied F2 populations. Interestingly, all traits demonstrated low genetic advance, which indicates that non-additive genes controlled these characters and that direct selection for these traits is not beneficial. The outcome of the present investigation will help to develop cotton cultivars with improved boll weight and lint percentage.

Obesity, a serious and growing issue, is associated with metabolic complications like dyslipidemia, non-alcoholic fatty liver disease, oxidative stress, and systemic inflammation. These complications pose a severe threat to human health. Fucoidan, a bioactive polysaccharide extracted from brown algae and certain marine invertebrates, holds the potential to ameliorate obesity and its associated diseases, thus becoming a current research hotspot. As a dietary supplement, fucoidan enhances obesity by modulating fat synthesis and breakdown, adipocyte differentiation and basal energy metabolism, as well as the abundance and beneficial bacteria ratio of intestinal microbiota. Additionally, fucoidan alleviates obesity-related diseases by reducing liver fat accumulation and lipotoxicity, lowering blood lipid levels and insulin resistance, promoting macrophage M1 to M2 polarization and the release of anti-inflammatory cytokines, and eliminating reactive oxygen species and lipid peroxidation products. This article presents some of the current applications of fucoidan in the food, medicine, and medical fields, and discusses the existing limitations, providing references for further research on fucoidan efficacy and new product development.

AbstractThe proportion of different lithofacies is essential to determine the net-gross ratio, which directly affects the calculation of oil and gas reserves. Under the condition of few wells, the reliability of different lithofacies proportions obtained using well data is poor because it is difficult to estimate the uncertainty variation range of different lithofacies proportions. The present study overcomes this problem using an uncertainty evaluation method for reservoir lithofacies proportion. First, different lithofacies proportions of the reservoir are determined using the well and seismic data and are considered as the most likely estimated. Based on the lithofacies proportion, the lithofacies models of the study area are developed. Second, uniform and random methods are applied to sample the lithofacies models, and then, the probability distribution functions of different lithofacies proportions are derived. Third, the three levels of lithofacies proportions in the study area are calculated using the method of quantile and discretization of the probability distribution. Finally, we take M gas field as a sample and compare the test results of the fixed and random well structures. The results show that the sampling results of the fixed well structure model significantly deviate under the influence of the extension direction of the channel and well pattern distribution. Therefore, it is suggested to use random well structure to determine the uncertainty distribution range of lithofacies proportion.

Bar top hollows (BTHs) are morphological elements recognized in modern braided rivers; however, information regarding their depositional features and types of filling units in ancient strata is unclear. This is an important reason behind why it is difficult to identify BTH units in subsurface reservoirs. A Middle Jurassic dryland sandy braided river outcrop in northwestern China is characterized in this study through the application of an unmanned aerial vehicle (UAV) surveying and mapping, and ground penetrating radar (GPR). A workflow of UAV data processing has been established, and a 3D digital outcrop model has been built. By observation and measurement of the outcrop model and GPR profiles, two types of BTH filled units were found: (a) sandstone-filled, and (b) mudstone-filled hollows. Both of these units were located between two adjacent bar units in an area that is limited to a compound bar, and were developed in the upper part of a braided bar depositional sequence. The ellipse-shaped, sandstone-filled unit measures 10 m × 27 m in map view and reaches a maximum thickness of 5 m. The transversal cross-section across the BTHs displays a concave upward basal surface, while the angle of the inclined structures infilling the BTHs decreases up-section. The GPR data show that, in the longitudinal profile, the basal surface is relatively flat, and low-angle, inclined layers can be observed in the lower- and middle part of the sandstone-filled BTHs. In contrast, no obvious depositional structures were observed in the mudstone-filled BTH in outcrop. The new understanding of BTH has a wide application, including the optimization of CO2 storage sites, fresh water aquifers exploration, and oil and gas reservoir characterization.