Exploring agro-morphological and fiber traits diversity in cotton (G. barbadense L.).

Cotton (Gossypium barbadense L.) is a leading fiber and oilseed crop globally, but genetic diversity among breeding materials is often limited. This study analyzed genetic variability in 14 cotton genotypes from Egypt and other countries, including both cultivated varieties and wild types, using agro-morphological traits and genomic SSR markers. Field experiments were conducted over two seasons to evaluate 12 key traits related to plant growth, yield components, and fiber quality. Molecular diversity analysis utilized 10 SSR primers to generate DNA profiles. The Molecular diversity analysis utilized 10 SSR primers to generate DNA profiles. Data showed wide variation for the morphological traits, with Egyptian genotypes generally exhibiting higher means for vegetative growth and yield parameters. The top-performing genotypes for yield were Giza 96, Giza 94, and Big Black Boll genotypes, while Giza 96, Giza 92, and Giza 70 ranked highest for fiber length, strength, and fineness. In contrast, molecular profiles were highly polymorphic across all genotypes, including 82.5% polymorphic bands out of 212. Polymorphism information content was high for the SSR markers, ranging from 0.76 to 0.86. Genetic similarity coefficients based on the SSR data varied extensively from 0.58 to 0.91, and cluster analysis separated genotypes into two major groups according to geographical origin. The cotton genotypes displayed high diversity in morphology and genetics, indicating sufficient variability in the germplasm. The combined use of physical traits and molecular markers gave a thorough understanding of the genetic diversity and relationships between Egyptian and global cotton varieties. The SSR markers effectively profiled the genotypes and can help select ideal parents for enhancing cotton through hybridization and marker-assisted breeding.

Gene Expression Correlation Analysis Reveals MYC-NAC Regulatory Network in Cotton Pigment Gland Development.

Plant NAC (NAM, ATAF1/2, and CUC2) family is involved in various development processes including Programmed Cell Death (PCD) associated development. However, the relationship between NAC family and PCD-associated cotton pigment gland development is largely unknown. In this study, we identified 150, 153 and 299 NAC genes in newly updated genome sequences of G. arboreum, G. raimondii and G. hirsutum, respectively. All NAC genes were divided into 8 groups by the phylogenetic analysis and most of them were conserved during cotton evolution. Using the vital regulator of gland formation GhMYC2-like as bait, expression correlation analysis screened out 6 NAC genes which were low-expressed in glandless cotton and high-expressed in glanded cotton. These 6 NAC genes acted downstream of GhMYC2-like and were induced by MeJA. Silencing CGF1(Cotton Gland Formation1), another MYC-coding gene, caused almost glandless phenotype and down-regulated expression of GhMYC2-like and the 6 NAC genes, indicating a MYC-NAC regulatory network in gland development. In addition, predicted regulatory mechanism showed that the 6 NAC genes were possibly regulated by light, various phytohormones and transcription factors as well as miRNAs. The interaction network and DNA binding sites of the 6 NAC transcription factors were also predicted. These results laid the foundation for further study of gland-related genes and gland development regulatory network.

Biochar induced improvement in root system architecture enhances nutrient assimilation by cotton plant seedlings.

BACKGROUND: Raising nitrogen use efficiency of crops by improving root system architecture is highly essential not only to reduce costs of agricultural production but also to mitigate climate change. The physiological mechanisms of how biochar affects nitrogen assimilation by crop seedlings have not been well elucidated. RESULTS: Here, we report changes in root system architecture, activities of the key enzymes involved in nitrogen assimilation, and cytokinin (CTK) at the seedling stage of cotton with reduced urea usage and biochar application at different soil layers (0-10 cm and 10-20 cm). Active root absorption area, fresh weight, and nitrogen agronomic efficiency increased significantly when urea usage was reduced by 25% and biochar was applied in the surface soil layer. Glutamine oxoglutarate amino transferase (GOGAT) activity was closely related to the application depth of urea/biochar, and it increased when urea/biochar was applied in the 0-10 cm layer. Glutamic-pyruvic transaminase activity (GPT) increased significantly as well. Nitrate reductase (NR) activity was stimulated by CTK in the very fine roots but inhibited in the fine roots. In addition, AMT1;1, gdh3, and gdh2 were significantly up-regulated in the very fine roots when urea usage was reduced by 25% and biochar was applied. CONCLUSION: Nitrogen assimilation efficiency was significantly affected when urea usage was reduced by 25% and biochar was applied in the surface soil layer at the seedling stage of cotton. The co-expression of gdh3 and gdh2 in the fine roots increased nitrogen agronomic efficiency. The synergistic expression of the ammonium transporter gene and gdh3 suggests that biochar may be beneficial to amino acid metabolism.

Morphological description of a novel synthetic allotetraploid(A1A1G3G3) of Gossypium herbaceum L.and G.nelsonii Fryx. suitable for disease-resistant breeding applications.

Wild species of Gossypium ssp. are an important source of traits for improving commercial cotton cultivars. Previous reports show that Gossypium herbaceum L. and Gossypium nelsonii Fryx. have better disease resistance characteristics than commercial cotton varieties. However, chromosome ploidy and biological isolation make it difficult to hybridize diploid species with the tetraploid Gossypium hirsutum L. We developed a new allotetraploid cotton genotype (A1A1G3G3) using a process of distant hybridization within wild cotton species to create new germplasms. First of all, G. herbaceum and G. nelsonii were used for interspecific hybridization to obtain F1 generation. Afterwards, apical meristems of the F1 diploid cotton plants were treated with colchicine to induce chromosome doubling. The new interspecific F1 hybrid and S1 cotton plants originated from chromosome duplication, were tested via morphological and molecular markers and confirmed their tetraploidy through flowrometric and cytological identification. The S1 tetraploid cotton plants was crossed with a TM-1 line and fertile hybrid offspring were obtained. These S2 offsprings were tested for resistance to Verticillium wilt and demonstrated adequate tolerance to this fungi. The results shows that the new S1 cotton line could be used as parental material for hybridization with G. hirsutum to produce pathogen-resistant cotton hybrids. This new S1 allotetraploid genotype will contributes to the enrichment of Gossypium germplasm resources and is expected to be valuable in polyploidy evolutionary studies.

Genetic analysis of some morphological traits in synthetic x naturally polyploid cotton derivatives.

Cotton has received attention of geneticists since more than a century. Gossypium hirsutum, the predominantly cultivated cotton species worldwide, has a narrow genetic base. It is important to broaden its genetic base through introgression of novel alleles from related species. Here, we report the development and characterization of a backcross population derived from the hybridization of a 'synthetic' (derived by crossing and chromosomal doubling of nonprogenitor Gossypium species) and natural tetraploid upland cotton. 'Synthetic' was observed to be male-sterile and thus, was used as the female parent. A total of 7434 flowers were pollinated to obtain 1868 BC1F1 seeds by direct and reciprocal crosses. Characterization of the experimental plant material was conducted in the field for several morphological traits such as pubescence on the stem, leaf, petiole and bract, presence/absence of petal spot, petal margin colouration and stamen filament colouration. Genetic analysis revealed that petal margin colouration phenotype was governed by a single dominant gene, whereas the petal spot and filament colouration phenotypes manifested segregation distortion. None of the BC1F1 plants was devoid of trichomes thus demonstrating that presence of trichomes is dominant over their absence. Modern upland cotton cultivars are usually devoid of petal spot, petal margin colouration and stamen filament colouration. These floral anthocyanin pigmentation characteristics, if fixed in the cotton germplasm, may serve as diagnostic features for the identification of cultivars during DUS testing as well as in the maintenance breeding programmes.

Genome-wide association study reveals the genetic basis of fiber quality traits in upland cotton (Gossypium hirsutum L.).

BACKGROUND: Fiber quality is an important economic trait of cotton, and its improvement is a major goal of cotton breeding. To better understand the genetic mechanisms responsible for fiber quality traits, we conducted a genome-wide association study to identify and mine fiber-quality-related quantitative trait loci (QTLs) and genes. RESULTS: In total, 42 single nucleotide polymorphisms (SNPs) and 31 QTLs were identified as being significantly associated with five fiber quality traits. Twenty-five QTLs were identified in previous studies, and six novel QTLs were firstly identified in this study. In the QTL regions, 822 genes were identified and divided into four clusters based on their expression profiles. We also identified two pleiotropic SNPs. The SNP locus i52359Gb was associated with fiber elongation, strength, length and uniformity, while i11316Gh was associated with fiber strength and length. Moreover, these two SNPs were nonsynonymous and located in genes Gh_D09G2376 and Gh_D06G1908, respectively. RT-qPCR analysis revealed that these two genes were preferentially expressed at one or more stages of cotton fiber development, which was consistent with the RNA-seq data. Thus, Gh_D09G2376 and Gh_D06G1908 may be involved in fiber developmental processes. CONCLUSIONS: The findings of this study provide insights into the genetic bases of fiber quality traits, and the identified QTLs or genes may be applicable in cotton breeding to improve fiber quality.

Fine-mapping and candidate gene analysis of qFS-Chr. D02, a QTL for fibre strength introgressed from a semi-wild cotton into Gossypium hirsutum.

Fibre strength (FS) is an important quality attribute in the modern textile industry, which is genetically controlled by quantitative trait loci (QTLs). Fine-mapping stable QTLs for FS to identify candidate genes would be valuable for uncovering the genetic basis of fibre quality traits in cotton. Here, a single segment introgression line, IL-D2-2, from the cross of (TM-1×TX-1046) reported in our previous studies, was found to have significantly improved FS compared with the recurrent parent TM-1. To fine-map the QTLs of the FS, we further crossed IL-D2-2 with its recurrent parent TM-1 to produce F2 and F2:3 populations. QTL analysis and substitution mapping showed qFS-Chr. D02 was anchored into a 550.66 kb-interval between two markers, INTR1027 and JESPR-231. This interval contained 67 genes, among which 27 genes related to cell-wall synthesis were selected to conduct qRT-PCR. The results revealed seven genes were expressed significantly differently during the fibre secondary-wall-thickening stage (10-25 days post-anthesis), three being upregulated and four downregulated in IL-D2-2. Both GH_D02G2269 (UDP-glucosyl transferase 84B1) and GH_D02G2289 (unknown function (DUF869)) with nonsynonymous SNPs in IL-D2-2 had significantly downregulated expression, suggesting they were candidates for qFS-Chr. D02. This research provides information about marker-assisted selection for cotton fibre strength improvement.

Genetic dissection of an allotetraploid interspecific CSSLs guides interspecific genetics and breeding in cotton.

BACKGROUND: The low genetic diversity of Upland cotton limits the potential for genetic improvement. Making full use of the genetic resources of Sea-island cotton will facilitate genetic improvement of widely cultivated Upland cotton varieties. The chromosome segments substitution lines (CSSLs) provide an ideal strategy for mapping quantitative trait loci (QTL) in interspecific hybridization. RESULTS: In this study, a CSSL population was developed by PCR-based markers assisted selection (MAS), derived from the crossing and backcrossing of Gossypium hirsutum (Gh) and G. barbadense (Gb), firstly. Then, by whole genome re-sequencing, 11,653,661 high-quality single nucleotide polymorphisms (SNPs) were identified which ultimately constructed 1211 recombination chromosome introgression segments from Gb. The sequencing-based physical map provided more accurate introgressions than the PCR-based markers. By exploiting CSSLs with mutant morphological traits, the genes responding for leaf shape and fuzz-less mutation in the Gb were identified. Based on a high-resolution recombination bin map to uncover genetic loci determining the phenotypic variance between Gh and Gb, 64 QTLs were identified for 14 agronomic traits with an interval length of 158 kb to 27 Mb. Surprisingly, multiple alleles of Gb showed extremely high value in enhancing cottonseed oil content (SOC). CONCLUSIONS: This study provides guidance for studying interspecific inheritance, especially breeding researchers, for future studies using the traditional PCR-based molecular markers and high-throughput re-sequencing technology in the study of CSSLs. Available resources include candidate position for controlling cotton quality and quantitative traits, and excellent breeding materials. Collectively, our results provide insights into the genetic effects of Gb alleles on the Gh, and provide guidance for the utilization of Gb alleles in interspecific breeding.

Ethyl methanesulfonate mutant library construction in Gossypium hirsutum L. for allotetraploid functional genomics and germplasm innovation.

As the gene pool is exposed to both strain on land resources and a lack of diversity in elite allotetraploid cotton, the acquisition and identification of novel alleles has taken on epic importance in facilitating cotton genetic improvement and functional genomics research. Ethyl methanesulfonate (EMS) is an excellent mutagen that induces genome-wide efficient mutations to activate the mutagenic potential of plants with many advantages. The present study established, determined and verified the experimental procedure suitable for EMS-based mutant library construction as the general reference guide in allotetraploid upland cotton. This optimized method and procedure are efficient, and abundant EMS mutant libraries (approximately 12 000) in allotetraploid cotton were successfully obtained. More than 20 mutant phenotypes were observed and screened, including phenotypes of the leaf, flower, fruit, fiber and plant architecture. Through the plants mutant library, high-throughput and high-resolution melting technology-based variation evaluation detected the EMS-induced site mutation. Additionally, based on overall genome-wide mutation analyses by re-sequencing and mutant library assessment, the examination results demonstrated the ideal quality of the cotton EMS-treated mutant library constructed in this study with appropriate high mutation density and saturated genome. What is more, the collection is composed of a broad repertoire of mutants, which is the valuable resource for basic genetic research and functional genomics underlying complex allotetraploid traits, as well as cotton breeding.

Benefits of organic manure combined with biochar amendments to cotton root growth and yield under continuous cropping systems in Xinjiang, China.

Organic manure and biochar amendments have been used in agriculture to improve soil fertility and enhance crop productivity. Plant roots play an important role in the functionality of individual plants, and although the addition of organic manure and biochar reportedly affect roots, it remains unclear how root morphology and physiology respond. We conducted a field experiment to test the hypothesis that organic manure combined with biochar amendment could also enhance the productivity of continuous cropping systems in Xinjiang cotton plantations. Different levels of organic manure and biochar were applied. Organic manure and biochar significantly affected root morphology and physiology by improving soil nutrients. In the absence of biochar, organic manure amendment increased Root TTC reducing capacity, glutamine synthetase and nitrate reductase activity. Furthermore, morphological and physiological parameters peaked with 6% organic manure combined with 1% biochar. A significant increase in root physiology was recognized with an increase in soil nutrient content at the bud stage and a negative relationship between root physiology and soil total K content at the harvesting stage. Thus, our results indicate that organic manure combined with biochar positively influenced cotton roots, and therefore should be used to improve root health in continuous cropping systems.

Insights obtained using different modules of the cotton uceA1.7 promoter.

MAIN CONCLUSION: The structure of the cotton uceA1.7 promoter and its modules was analyzed; the potential of their key sequences has been confirmed in different tissues, proving to be a good candidate for the development of new biotechnological tools. Transcriptional promoters are among the primary genetic engineering elements used to control genes of interest (GOIs) associated with agronomic traits. Cotton uceA1.7 was previously characterized as a constitutive promoter with activity higher than that of the constitutive promoter from the Cauliflower mosaic virus (CaMV) 35S gene in various plant tissues. In this study, we generated Arabidopsis thaliana homozygous events stably overexpressing the gfp reporter gene driven by different modules of the uceA1.7 promoter. The expression level of the reporter gene in different plant tissues and the transcriptional stability of these modules was determined compared to its full-length promoter and the 35S promoter. The full-length uceA1.7 promoter exhibited higher activity in different plant tissues compared to the 35S promoter. Two modules of the promoter produced a low and unstable transcription level compared to the other promoters. The other two modules rich in cis-regulatory elements showed similar activity levels to full-length uceA1.7 and 35S promoters but were less stable. This result suggests the location of a minimal portion of the promoter that is required to initiate transcription properly (the core promoter). Additionally, the full-length uceA1.7 promoter containing the 5'-untranslated region (UTR) is essential for higher transcriptional stability in various plant tissues. These findings confirm the potential use of the full-length uceA1.7 promoter for the development of new biotechnological tools (NBTs) to achieve higher expression levels of GOIs in, for example, the root or flower bud for the efficient control of phytonematodes and pest-insects, respectively, in important crops.

Genome-wide association reveals genetic variation of lint yield components under salty field conditions in cotton (Gossypium hirsutum L.).

BACKGROUND: Salinity is one of the most significant environmental factors limiting the productivity of cotton. However, the key genetic components responsible for the reduction in cotton yield in saline-alkali soils are still unclear. RESULTS: Here, we evaluated three main components of lint yield, single boll weight (SBW), lint percentage (LP) and boll number per plant (BNPP), across 316 G. hirsutum accessions under four salt conditions over two years. Phenotypic analysis indicated that LP was unchanged under different salt conditions, however BNPP decreased significantly and SBW increased slightly under high salt conditions. Based on 57,413 high-quality single nucleotide polymorphisms (SNPs) and genome-wide association study (GWAS) analysis, a total of 42, 91 and 25 stable quantitative trait loci (QTLs) were identified for SBW, LP and BNPP, respectively. Phenotypic and QTL analysis suggested that there was little correlation among the three traits. For LP, 8 stable QTLs were detected simultaneously in four different salt conditions, while fewer repeated QTLs for SBW or BNPP were identified. Gene Ontology (GO) analysis indicated that their regulatory mechanisms were also quite different. Via transcriptome profile data, we detected that 10 genes from the 8 stable LP QTLs were predominantly expressed during fiber development. Further, haplotype analyses found that a MYB gene (GhMYB103), with the two SNP variations in cis-regulatory and coding regions, was significantly correlated with lint percentage, implying a crucial role in lint yield. We also identified that 40 candidate genes from BNPP QTLs were salt-inducible. Genes related to carbohydrate metabolism and cell structure maintenance were rich in plants grown in high salt conditions, while genes related to ion transport were active in plants grown in low salt conditions, implying different regulatory mechanisms for BNPP at high and low salt conditions. CONCLUSIONS: This study provides a foundation for elucidating cotton salt tolerance mechanisms and contributes gene resources for developing upland cotton varieties with high yields and salt stress tolerance.

Genetic regulatory networks for salt-alkali stress in Gossypium hirsutum with differing morphological characteristics.

BACKGROUND: Cotton grows in altering environments that are often unfavorable or stressful for its growth and development. Consequently, the plant must cope with abiotic stresses such as soil salinity, drought, and excessive temperatures. Alkali-salt stress response remains a cumbersome biological process and is regulated via a multifaceted transcriptional regulatory network in cotton. RESULTS: To discover the molecular mechanisms of alkali-salt stress response in cotton, a comprehensive transcriptome analysis was carried out after alkali-salt stress treatment in three accessions of Gossypium hirsutum with contrasting phenotype. Expression level analysis proved that alkali-salt stress response presented significant stage-specific and tissue-specific. GO enrichment analysis typically suggested that signal transduction process involved in salt-alkali stress response at SS3 and SS12 stages in leaf; carbohydrate metabolic process and oxidation-reduction process involved in SS48 stages in leaf; the oxidation-reduction process involved at all three phases in the root. The Co-expression analysis suggested a potential GhSOS3/GhCBL10-SOS2 network was involved in salt-alkali stress response. Furthermore, Salt-alkali sensitivity was increased in GhSOS3 and GhCBL10 Virus-induced Gene Silencing (VIGS) plants. CONCLUSION: The findings may facilitate to elucidate the underlying mechanisms of alkali-salt stress response and provide an available resource to scrutinize the role of candidate genes and signaling pathway governing alkali-salt stress response.

Near-Infrared Hyperspectral Imaging Combined with Deep Learning to Identify Cotton Seed Varieties.

Cotton seed purity is a critical factor influencing the cotton yield. In this study, near-infrared hyperspectral imaging was used to identify seven varieties of cotton seeds. Score images formed by pixel-wise principal component analysis (PCA) showed that there were differences among different varieties of cotton seeds. Effective wavelengths were selected according to PCA loadings. A self-design convolution neural network (CNN) and a Residual Network (ResNet) were used to establish classification models. Partial least squares discriminant analysis (PLS-DA), logistic regression (LR) and support vector machine (SVM) were used as direct classifiers based on full spectra and effective wavelengths for comparison. Furthermore, PLS-DA, LR and SVM models were used for cotton seeds classification based on deep features extracted by self-design CNN and ResNet models. LR and PLS-DA models using deep features as input performed slightly better than those using full spectra and effective wavelengths directly. Self-design CNN based models performed slightly better than ResNet based models. Classification models using full spectra performed better than those using effective wavelengths, with classification accuracy of calibration, validation and prediction sets all over 80% for most models. The overall results illustrated that near-infrared hyperspectral imaging with deep learning was feasible to identify cotton seed varieties.

GhYGL1d, a pentatricopeptide repeat protein, is required for chloroplast development in cotton.

BACKGROUND: The pentatricopeptide repeat (PPR) gene family, which contains multiple 35-amino acid repeats, constitutes one of the largest gene families in plants. PPR proteins function in organelles to target specific transcripts and are involved in plant development and growth. However, the function of PPR proteins in cotton is still unknown. RESULTS: In this study, we characterized a PPR gene YELLOW-GREEN LEAF (GhYGL1d) that is required for cotton plastid development. The GhYGL1d gene has a DYW domain in C-terminal and is highly express in leaves, localized to the chloroplast fractions. GhYGL1d share high amino acid-sequence homology with AtECB2. In atecb2 mutant, overexpression of GhYGL1d rescued the seedling lethal phenotype and restored the editing of accD and ndhF transcripts. Silencing of GhYGL1d led to the reduction of chlorophyll and phenotypically yellow-green leaves in cotton. Compared with wild type, GhYGL1d-silenced cotton showed significant deformations of thylakoid structures. Furthermore, the transcription levels of plastid-encoded polymerase (PEP) and nuclear-encoded polymerase (NEP) dependent genes were decreased in GhYGL1d-silenced cotton. CONCLUSIONS: Our data indicate that GhYGL1d not only contributes to the editing of accD and ndhF genes, but also affects the expression of NEP- and PEP-dependent genes to regulate the development of thylakoids, and therefore regulates leaf variegation in cotton.

Multispectral imaging and unmanned aerial systems for cotton plant phenotyping.

This paper demonstrates the application of aerial multispectral images in cotton plant phenotyping. Four phenotypic traits (plant height, canopy cover, vegetation index, and flower) were measured from multispectral images captured by a multispectral camera on an unmanned aerial system. Data were collected on eight different days from two fields. Ortho-mosaic and digital elevation models (DEM) were constructed from the raw images using the structure from motion (SfM) algorithm. A data processing pipeline was developed to calculate plant height using the ortho-mosaic and DEM. Six ground calibration targets (GCTs) were used to correct the error of the calculated plant height caused by the georeferencing error of the DEM. Plant heights were measured manually to validate the heights predicted from the imaging method. The error in estimation of the maximum height of each plot ranged from -40.4 to 13.5 cm among six datasets, all of which showed strong linear relationships with the manual measurement (R2 > 0.89). Plot canopy was separated from the soil based on the DEM and normalized differential vegetation index (NDVI). Canopy cover and mean canopy NDVI were calculated to show canopy growth over time and the correlation between the two indices was investigated. The spectral responses of the ground, leaves, cotton flower, and ground shade were analyzed and detection of cotton flowers was satisfactory using a support vector machine (SVM). This study demonstrated the potential of using aerial multispectral images for high throughput phenotyping of important cotton phenotypic traits in the field.

Comparative physiological analysis in the tolerance to salinity and drought individual and combination in two cotton genotypes with contrasting salt tolerance.

Soil salinity and drought are the two most common and frequently co-occurring abiotic stresses limiting cotton growth and productivity. However, physiological mechanisms of tolerance to such condition remain elusive. Greenhouse pot experiments were performed to study genotypic differences in response to single drought (4% soil moisture; D) and salinity (200 mM NaCl; S) stress and combined stresses (D + S) using two cotton genotypes Zhongmian 23 (salt-tolerant) and Zhongmian 41 (salt-sensitive). Our results showed that drought and salinity stresses, alone or in combination, caused significant reduction in plant growth, chlorophyll content and photosynthesis in the two cotton genotypes, with the largest impact visible under combined stress. Interestingly, Zhongmian 23 was more tolerant than Zhongmian 41 under the three stresses and displayed higher plant dry weight, photosynthesis and antioxidant enzymes activities such as superoxide dismutase (SOD), peroxidase (POD) catalase (CAT) and ascorbate peroxidase (APX) activities compared to control, while those parameters were significantly decreased in salt-stresses Zhongmian 41 compared to control. Moreover, Na+ /K+ -ATPase activity was more enhanced in Zhongmian 23 than in Zhongmian 41 under salinity stress. However, under single drought stress and D + S stress no significant differences were observed between the two genotypes. No significant differences were detected in Ca2+ /Mg2+ -ATPase activity in Zhongmian 41, while in Zhongmian 23 it was increased under salinity stress. Furthermore, Zhongmian 23 accumulated more soluble sugar, glycine-betaine and K+ , but less Na+ under the three stresses compared with Zhongmian 41. Obvious changes in leaf and root tips cell ultrastructure was observed in the two cotton genotypes. However, Zhongmian 23 was less affected than Zhongmian 41 especially under salinity stress. These results give a novel insight into the mechanisms of single and combined effects of drought and salinity stresses on cotton genotypes.

Whole genome sequencing of a MAGIC population identified genomic loci and candidate genes for major fiber quality traits in upland cotton (Gossypium hirsutum L.).

KEY MESSAGE: Significant associations between candidate genes and six major cotton fiber quality traits were identified in a MAGIC population using GWAS and whole genome sequencing. Upland cotton (Gossypium hirsutum L.) is the world's major renewable source of fibers for textiles. To identify causative genetic variants that influence the major agronomic measures of cotton fiber quality, which are used to set discount or premium prices on each bale of cotton in the USA, we measured six fiber phenotypes from twelve environments, across three locations and 7 years. Our 550 recombinant inbred lines were derived from a multi-parent advanced generation intercross population and were whole-genome-sequenced at 3× coverage, along with the eleven parental cultivars at 20× coverage. The segregation of 473,517 single nucleotide polymorphisms (SNPs) in this population, including 7506 non-synonymous mutations, was combined with phenotypic data to identify seven highly significant fiber quality loci. At these loci, we found fourteen genes with non-synonymous SNPs. Among these loci, some had simple additive effects, while others were only important in a subset of the population. We observed additive effects for elongation and micronaire, when the three most significant loci for each trait were examined. In an informative subset where the major multi-trait locus on chromosome A07:72-Mb was fixed, we unmasked the identity of another significant fiber strength locus in gene Gh_D13G1792 on chromosome D13. The micronaire phenotype only revealed one highly significant genetic locus at one environmental location, demonstrating a significant genetic by environment component. These loci and candidate causative variant alleles will be useful to cotton breeders for marker-assisted selection with minimal linkage drag and potential biotechnological applications.

Drought-introduced variability of mesophyll conductance in Gossypium and its relationship with leaf anatomy.

Mesophyll conductance (gm ) is one of the major determinants of photosynthetic rate, for which it has an impact on crop yield. However, the regulatory mechanisms behind the decline in gm of cotton (Gossypium. spp) by drought are unclear. An upland cotton (Gossypium hirsutum) genotype and a pima cotton (Gossypium barbadense) genotype were used to determine the gas exchange parameters, leaf anatomical structure as well as aquaporin and carbonic anhydrase gene expression under well-watered and drought treatment conditions. In this study, the decrease of net photosynthetic rate (AN ) under drought conditions was related to a decline in gm and in stomatal conductance (gs ). gm and gs coordinate with each other to ensure optimum state of CO2 diffusion and achieve the balance of water and CO2 demand in the process of photosynthesis. Meanwhile, mesophyll limitations to photosynthesis are equally important to the stomatal limitations. Considering gm , its decline in cotton leaves under drought was mostly regulated by the chloroplast surface area exposed to leaf intercellular air spaces per leaf area (Sc /S) and might also be regulated by the expression of leaf CARBONIC ANHYDRASE (CA1). Meanwhile, cotton leaves can minimize the decrease in gm under drought by maintaining cell wall thickness (Tcw ). Our results indicated that modification of chloroplasts might be a target trait in future attempts to improve cotton drought tolerance.

Genome-wide analysis of cotton GH3 subfamily II reveals functional divergence in fiber development, hormone response and plant architecture.

BACKGROUND: Auxin-induced genes regulate many aspects of plant growth and development. The Gretchen Hagen 3 (GH3) gene family, one of three major early auxin-responsive families, is ubiquitous in the plant kingdom and its members function as regulators in modulating hormonal homeostasis, and stress adaptations. Specific Auxin-amido synthetase activity of GH3 subfamily II genes is reported to reversibly inactivate or fully degrade excess auxin through the formation of amino acid conjugates. Despite these crucial roles, to date, genome-wide analysis of the GH3 gene family has not been reported in cotton. RESULTS: We identified a total of 10 GH3 subfamily II genes in G. arboreum, 10 in G. raimondii, and 20 in G. hirsutum, respectively. Bioinformatic analysis showed that cotton GH3 genes are conserved with the established GH3s in plants. Expression pattern analysis based on RNA-seq data and qRT-PCR revealed that 20 GhGH3 genes were differentially expressed in a temporally and spatially specific manner, indicating their diverse functions in growth and development. We further summarized the organization of promoter regulatory elements and monitored their responsiveness to treatment with IAA (indole-3-acetic acid), SA (salicylic acid), GA (gibberellic acid) and BL (brassinolide) by qRT-PCR in roots and stems. These hormones seemed to regulate the expression of GH3 genes in both a positive and a negative manner while certain members likely have higher sensitivity to all four hormones. Further, we tested the expression of GhGH3 genes in the BR-deficient mutant pag1 and the corresponding wild-type (WT) of CCRI24. The altered expression reflected the true responsiveness to BL and further suggested possible reasons, at least in part, responsible for the dramatic dwarf and shriveled phenotypes of pag1. CONCLUSION: We comprehensively identified GH3 subfamily II genes in cotton. GhGH3s are differentially expressed in various tissues/organs/stages. Their response to IAA, SA, BL and GA and altered expression in pag1 suggest that some GhGH3 genes might be simultaneously involved in multiple hormone signaling pathways. Taken together, our results suggest that members of the GhGH3 gene family could be possible candidate genes for mechanistic study and applications in cotton fiber development in addition to the reconstruction of plant architecture.