Genome-wide analyses of member identification, expression pattern, and protein-protein interaction of EPF/EPFL gene family in Gossypium.

BACKGROUND: Epidermal patterning factor / -like (EPF/EPFL) gene family encodes a class of cysteine-rich secretory peptides, which are widelyfound in terrestrial plants.Multiple studies has indicated that EPF/EPFLs might play significant roles in coordinating plant development and growth, especially as the morphogenesis processes of stoma, awn, stamen, and fruit skin. However, few research on EPF/EPFL gene family was reported in Gossypium. RESULTS: We separately identified 20 G. raimondii, 24 G. arboreum, 44 G. hirsutum, and 44 G. barbadense EPF/EPFL genes in the 4 representative cotton species, which were divided into four clades together with 11 Arabidopsis thaliana, 13 Oryza sativa, and 17 Selaginella moellendorffii ones based on their evolutionary relationships. The similar gene structure and common motifs indicated the high conservation among the EPF/EPFL members, while the uneven distribution in chromosomes implied the variability during the long-term evolutionary process. Hundreds of collinearity relationships were identified from the pairwise comparisons of intraspecifc and interspecific genomes, which illustrated gene duplication might contribute to the expansion of cotton EPF/EPFL gene family. A total of 15 kinds of cis-regulatory elements were predicted in the promoter regions, and divided into three major categories relevant to the biological processes of development and growth, plant hormone response, and abiotic stress response. Having performing the expression pattern analyses with the basic of the published RNA-seq data, we found most of GhEPF/EPFL and GbEPF/EPFL genes presented the relatively low expression levels among the 9 tissues or organs, while showed more dramatically different responses to high/low temperature and salt or drought stresses. Combined with transcriptome data of developing ovules and fibers and quantitative Real-time PCR results (qRT-PCR) of 15 highly expressed GhEPF/EPFL genes, it could be deduced that the cotton EPF/EPFL genes were closely related with fiber development. Additionally, the networks of protein-protein interacting among EPF/EPFLs concentrated on the cores of GhEPF1 and GhEPF7, and thosefunctional enrichment analyses indicated that most of EPF/EPFLs participate in the GO (Gene Ontology) terms of stomatal development and plant epidermis development, and the KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways of DNA or base excision repair. CONCLUSION: Totally, 132 EPF/EPFL genes were identified for the first time in cotton, whose bioinformatic analyses of cis-regulatory elements and expression patterns combined with qRT-PCR experiments to prove the potential functions in the biological processes of plant growth and responding to abiotic stresses, specifically in the fiber development. These results not only provide comprehensive and valuable information for cotton EPF/EPFL gene family, but also lay solid foundation for screening candidate EPF/EPFL genes in further cotton breeding.

Ecotoxicity of Cadmium along the Soil-Cotton Plant-Cotton Bollworm System: Biotransfer, Trophic Accumulation, Plant Growth, Induction of Insect Detoxification Enzymes, and Immunocompetence.

Cadmium (Cd) is a hazardous element that may jeopardize environmental safety and human health through biotransfer and trophic accumulation. Here, we tested Cd toxicity on cotton plants, cotton bollworms, and their responses. Results demonstrated that Cd accumulated in plant roots, aerial parts, insect larvae, pupae, and frass in a dose-dependent pattern. The ∼9.35 mg kg-1 of Cd in plant aerial parts, ∼3.68 in larvae, ∼6.43 in pupae, and high transfer coefficient (∼5.59) indicate significant mobility. The ∼19.61 mg kg-1 of Cd in larvae frass suggests an effective detoxification strategy, while BAFcotton (∼1.14) and BAFworm (∼0.54) indicated low bioaccumulation. Cadmium exposure resulted in compromised plant growth and yield as well as alterations in photosynthetic pigment contents, antioxidant enzyme activities, and certain life history traits of cotton bollworms. Furthermore, carboxylesterase activity and encapsulation rates of insect larvae decreased with increasing Cd concentrations, whereas acetylcholinesterase, phenol oxidase, glutathione S-transferase, and multifunctional oxidase exhibited hormesis responses.

A Genome-Wide Analysis of the CEP Gene Family in Cotton and a Functional Study of GhCEP46-D05 in Plant Development.

C-TERMINALLY ENCODED PEPTIDEs (CEPs) are a class of peptide hormones that have been shown in previous studies to play an important role in regulating the development and response to abiotic stress in model plants. However, their role in cotton is not well understood. In this study, we identified 54, 59, 34, and 35 CEP genes from Gossypium hirsutum (2n = 4x = 52, AD1), G. barbadense (AD2), G. arboreum (2n = 2X = 26, A2), and G. raimondii (2n = 2X = 26, D5), respectively. Sequence alignment and phylogenetic analyses indicate that cotton CEP proteins can be categorized into two subgroups based on the differentiation of their CEP domain. Chromosomal distribution and collinearity analyses show that most of the cotton CEP genes are situated in gene clusters, suggesting that segmental duplication may be a critical factor in CEP gene expansion. Expression pattern analyses showed that cotton CEP genes are widely expressed throughout the plant, with some genes exhibiting specific expression patterns. Ectopic expression of GhCEP46-D05 in Arabidopsis led to a significant reduction in both root length and seed size, resulting in a dwarf phenotype. Similarly, overexpression of GhCEP46-D05 in cotton resulted in reduced internode length and plant height. These findings provide a foundation for further investigation into the function of cotton CEP genes and their potential role in cotton breeding.

Cotton (Gossypium hirsutum) VIRMA as an N6-Methyladenosine RNA Methylation Regulator Participates in Controlling Chloroplast-Dependent and Independent Leaf Development.

N6-methyladenosine (m6A) is one of the most abundant internal modifications of mRNA, which plays important roles in gene expression regulation, and plant growth and development. Vir-like m6A methyltransferase associated (VIRMA) serves as a scaffold for bridging the catalytic core components of the m6A methyltransferase complex. The role of VIRMA in regulating leaf development and its related mechanisms have not been reported. Here, we identified and characterized two upland cotton (Gossypium hirsutum) VIRMA genes, named as GhVIR-A and GhVIR-D, which share 98.5% identity with each other. GhVIR-A and GhVIR-D were ubiquitously expressed in different tissues and relatively higher expressed in leaves and main stem apexes (MSA). Knocking down the expression of GhVIR genes by the virus-induced gene silencing (VIGS) system influences leaf cell size, cell shape, and total cell numbers, thereby determining cotton leaf morphogenesis. The dot-blot assay and colorimetric experiment showed the ratio of m6A to A in mRNA is lower in leaves of GhVIR-VIGS plants compared with control plants. Messenger RNA (mRNA) high-throughput sequencing (RNA-seq) and a qRT-PCR experiment showed that GhVIRs regulate leaf development through influencing expression of some transcription factor genes, tubulin genes, and chloroplast genes including photosystem, carbon fixation, and ribosome assembly. Chloroplast structure, chlorophyll content, and photosynthetic efficiency were changed and unsuitable for leaf growth and development in GhVIR-VIGS plants compared with control plants. Taken together, our results demonstrate GhVIRs function in cotton leaf development by chloroplast dependent and independent pathways.

Exogenous application of bio-stimulant and growth retardant improved the productivity of cotton cultivars under different planting arrangement / A aplicação exógena de bioestimulante e regulador de crescimento na melhoria da produtividade de cultivares de algodão sob diferentes configurações de plantio

Optimum planting arrangement is an important attribute for efficient utilization of available resources and to obtain high yield of cotton. Application of plant growth promoter and retardant on cotton in improved planting density are the innovative techniques in the establishment of more productive cotton crop. Therefore, we planned a field study to assess the role of bio-stimulant and growth retardant in the resource utilization efficiency of cotton cultivars planted under variable row spacing at Agronomic Research Area Bahauddin Zakariya University and Usmania Agricultural Farm Shujabad during Kharif 2012. Experimental treatments consisted of cotton genotypes viz. CIM-573 and CIM-598, cultivated under conventional (75 cm), medium (50 cm) and ultra-narrow row spacing (25 cm) with foliar spray of bio-stimulant (moringa leaf extract) and growth retardant (mepiquate chloride), either sole or in combination, keeping distilled water as a control. Exogenously applied MLE alone and MLE + MC significantly enhanced the number of squares, flowers and green bolls per plant leading to higher cotton seed and lint yield of CIM 598 cultivar cultivated under conventional row spacing. While application of MC alone and MLE + MC produced maximum micronaire value, fiber strength and fiber uniformity ratio of CIM 573 cultivar cultivated under conventional row spacing. The results suggested that application of MLE is a possible approach to enhance the cotton productivity and the use of MC to enhance the fiber quality attributes under conventional row spacing.

A configuração ideal de plantio é um atributo importante para a utilização eficiente dos recursos disponíveis e para obter alto rendimento de algodão. A aplicação de promotores de crescimento de plantas e reguladores de crescimento no algodão em uma densidade de plantio adequada são técnicas inovadoras na obtenção de safras de algodão mais produtivas. Portanto, foi planejado um estudo de campo para avaliar o papel de um bioestimulante e um regulador de crescimento na eficiência da utilização de recursos de cultivares de algodão plantadas com espaçamento variável entre linhas na Área de Pesquisa Agronômica Universidade Bahauddin Zakariya e Usmania Agricultural Farm Shujabad durante Kharif 2012. Os tratamentos experimentais consistiram em genótipos de algodão viz. CIM-573 e CIM-598, cultivadas sob espaçamento convencional (75 cm), médio (50 cm) e ultraestreito (25 cm) e pulverização foliar de bioestimulante (extrato de folha de moringa) e regulador de crescimento (cloreto de mepiquato)), sozinho ou combinado, mantendo a água destilada como controle. O MLE aplicado exogenamente sozinho e o MLE + MC aumentaram significativamente o número de quadrados, flores e cápsulas verdes por planta, levando a um maior rendimento de sementes e fibra de algodão da cultivar CIM 598 cultivada sob espaçamento convencional entre fileiras. Enquanto a aplicação de MC sozinho e MLE + MC produziu valor máximo de micronaire, resistência da fibra e razão de uniformidade da fibra da cultivar CIM 573 cultivada sob espaçamento convencional entre linhas. Os resultados sugeriram que a aplicação do MLE é uma abordagem possível para aumentar a produtividade do algodão e o uso de MC para aprimorar os atributos de qualidade da fibra no espaçamento convencional entre linhas.

The application of ammonium sulphate and amino acid on cotton: effects on can improve growth, yield, quality and nitrogen absorption / Aplicação de sulfato de amônio e aminoácido no algodão: efeitos sobre o crescimento, o rendimento, a qualidade e a absorção de nitrogênio

A field study was carried out to determine the influence of foliage applied plant growth promoter and retardant in improving soil applied sulphur fertilizer use efficiency in cotton during two consecutive summers 2014 and 2015. Experimental trial comprised of three different sources of sulphur (ammonium sulphate, potassium sulphate and elemental sulphur) and foliar spray of plant growth promoter and growth retardant including tap water was taken as control. Among treatments soil applied ammonium sulphate with foliage applied amino acid produced maximum plant height, sympodial branches, pods per plant, seed cotton yield, fiber yield, biological yield, protein contents, oil contents and leaf nitrogen uptake as compared to the other treatments. Whereas, soil applied potassium sulphate with foliar spray of mepiquat chloride on cotton significantly improved the boll weight and leaf potassium uptake. We conclude that soil applied ammonium sulphate and foliage spray of amino acid was more effective in improving the productivity and quality attributes of cotton.

Foi realizado um estudo de campo para determinar a influência do promotor de crescimento das plantas e retardador da folhagem em algodão, para melhora da eficiência do uso de fertilizantes à base de enxofre aplicados no solo durante dois verões consecutivos (2014 e 2015). O ensaio experimental foi composto de três fontes diferentes de enxofre (sulfato de amônio, sulfato de potássio e enxofre elementar) e pulverização foliar do promotor de crescimento de plantas e retardador de crescimento, incluindo água da torneira que foi tomada como controle. Entre os tratamentos, o sulfato de amônio aplicado no solo com aminoácido aplicado na folhagem produziu o máximo na altura da planta, ramos simodiais, capulhos por planta, rendimento de algodão em caroço, rendimento de fibra, rendimento biológico, conteúdo de proteínas, conteúdo de óleo e absorção de nitrogênio nas folhas quando comparado a outros tratamentos. Enquanto o solo fertilizado com sulfato de potássio e aplicação foliar de cloreto de mepiquat no algodão melhorou, significativamente, o peso do capulho e a absorção de potássio nas folhas. Sulfato de amônio aplicado no solo e a aplicação foliar de aminoácidos foram mais eficazes na melhora dos atributos de produtividade e qualidade do algodão.

Identification of Raf-Like Kinases B Subfamily Genes in Gossypium Species Revealed GhRAF42 Enhanced Salt Tolerance in Cotton.

Salinity is a critical abiotic factor that significantly reduces agricultural production. Cotton is an important fiber crop and a pioneer on saline soil, hence genetic architecture that underpins salt tolerance should be thoroughly investigated. The Raf-like kinase B-subfamily (RAF) genes were discovered to regulate the salt stress response in cotton plants. However, understanding the RAFs in cotton, such as Enhanced Disease Resistance 1 and Constitutive Triple Response 1 kinase, remains a mystery. This study obtained 29, 28, 56, and 54 RAF genes from G. arboreum, G. raimondii, G. hirsutum, and G. barbadense, respectively. The RAF gene family described allopolyploidy and hybridization events in allotetraploid cotton evolutionary connections. Ka/Ks analysis advocates that cotton evolution was subjected to an intense purifying selection of the RAF gene family. Interestingly, integrated analysis of synteny and gene collinearity suggested dispersed and segmental duplication events involved in the extension of RAFs in cotton. Transcriptome studies, functional validation, and virus-induced gene silencing on salt treatments revealed that GhRAF42 is engaged in salt tolerance in upland cotton. This research might lead to a better understanding of the role of RAFs in plants and the identification of suitable candidate salt-tolerant genes for cotton breeding.

Genome-wide characterization and expression analysis of cystathionine ß-synthase genes in plant development and abiotic stresses of cotton (Gossypium spp.).

Cystathionine ß-synthase (CBS) domains containing proteins (CDCPs) form a large family and play roles in development via regulation of the thioredoxin system as well as abiotic and biotic stress responses of plant. However, the comprehensive study of CBS genes remained elusive in cotton. Here, we identified 237 CBS genes in 11 plant species and the phylogenetic analysis categorized CBS genes into four groups. Whole-genome or segmental with dispersed duplication events contributed to GhCBS gene family expansion. Moreover, orthologous/paralogous genes among three cotton species (G. hirsutum, G. arboreum, and G. raimondii) were detected from the syntenic map among eight plant species. Strong purifying selection for dicotyledonous and monocotyledonous CBS genes, and cis-elements related to plant growth and development, abiotic and hormonal response were observed. Transcriptomic data and qRT-PCR validation of 12 GhCBS genes indicated their critical role in ovule development as most of the genes showed high enrichment. Further, some of GhCBS (GhCBS5, GhCBS16, GhCBS17, GhCBS24, GhCBS25, GhCBS26, and GhCBS52) genes were regulated under various abiotic and hormonal treatments for different time points and involve in ovule and fiber development which provided key genes for future cotton breeding programs. In addition, transgenic tobacco plants overexpressing GhCBS4 transiently exhibited higher water and chlorophyll content indicating improved tolerance toward drought stress. Overall, this study provides the characterization of GhCBS genes for plant growth, abiotic and hormonal stresses, thereby, intimating their significance in cotton molecular breeding for resistant cultivars.

Identification and characteristics of a novel gland-forming gene in cotton.

The cotton (Gossypium hirsutum) pigment gland is a distinctive structure that functions as the main deposit organ of gossypol and its derivatives. It is also an ideal system in which to study cell differentiation and organogenesis. However, only a few genes that determine the process of gland formation have been reported, including GoPGF, CGP1, and CGFs; the molecular mechanisms underlying gland initiation are still largely unclear. Here, we report the discovery of the novel stem pigment gland-forming gene GoSPGF by map-based cloning; annotated as a GRAS transcription factor, this gene is responsible for the glandless trait specifically on the stem. In the stem glandless mutant T582, a point mutation (C to A) was found to create a premature stop codon and truncate the protein. Similarly, virus-induced gene silencing of GoSPGF resulted in glandless stems and dramatically reduced gossypol content. Comparative transcriptomic data showed that loss of GoSPGF significantly suppressed expression of many genes involved in gossypol biosynthesis and altered expression of genes involved in gibberellic acid signaling/biosynthesis. Overall, these findings provide more insight into the networks regulating glandular structure differentiation and formation in cotton, which will be helpful for understanding other plants bearing special gland structures such as tobacco (Nicotiana benthamiana), artemisia annua, mint (Mentha spp.), and rubber (Hevea brasiliensis).

Cotton Fiber Development Requires the Pentatricopeptide Repeat Protein GhIm for Splicing of Mitochondrial nad7 mRNA.

Pentatricopeptide repeat (PPR) proteins encoded by nuclear genomes can bind to organellar RNA and are involved in the regulation of RNA metabolism. However, the functions of many PPR proteins remain unknown in plants, especially in polyploidy crops. Here, through a map-based cloning strategy and Clustered regularly interspaced short palindromic repeats/cas9 (CRISPR/cas9) gene editing technology, we cloned and verified an allotetraploid cotton immature fiber (im) mutant gene (GhImA) encoding a PPR protein in chromosome A03, that is associated with the non-fluffy fiber phenotype. GhImA protein targeted mitochondrion and could bind to mitochondrial nad7 mRNA, which encodes the NAD7 subunit of Complex I. GhImA and its homolog GhImD had the same function and were dosage-dependent. GhImA in the im mutant was a null allele with a 22 bp deletion in the coding region. Null GhImA resulted in the insufficient GhIm dosage, affected mitochondrial nad7 pre-mRNA splicing, produced less mature nad7 transcripts, and eventually reduced Complex I activities, up-regulated alternative oxidase metabolism, caused reactive oxygen species (ROS) burst and activation of stress or hormone response processes. This study indicates that the GhIm protein participates in mitochondrial nad7 splicing, affects respiratory metabolism, and further regulates cotton fiber development via ATP supply and ROS balance.

Functional analysis of the cotton CLE polypeptide signaling gene family in plant growth and development.

The CLAVATA3 (CLV3)/EMBRYO SURROUNDING REGION (ESR)-RELATED (CLE) gene family encodes a large number of polypeptide signaling molecules involved in the regulation of shoot apical meristem division and root and vascular bundle development in a variety of plants. CLE family genes encode important short peptide hormones; however, the functions of these signaling polypeptides in cotton remain largely unknown. In the current work, we studied the effects of the CLE family genes on growth and development in cotton. Based on the presence of a conserved CLE motif of 13 amino acids, 93 genes were characterized as GhCLE gene family members, and these were subcategorized into 7 groups. A preliminary analysis of the cotton CLE gene family indicated that the activity of its members tends to be conserved in terms of both the 13-residue conserved domain at the C-terminus and their subcellular localization pattern. Among the 14 tested genes, the ectopic overexpression of GhCLE5::GFP partially mimicked the phenotype of the clv3 mutant in Arabidopsis. GhCLE5 could affect the endogenous CLV3 in binding to the receptor complex, comprised of CLV1, CLV2, and CRN, in the yeast two-hybrid assay and split-luciferase assay. Silencing GhCLE5 in cotton caused a short seedling phenotype. Therefore, we concluded that the cotton GhCLE gene family is functionally conserved in apical shoot development regulation. These results indicate that CLE also plays roles in cotton development as a short peptide hormone.

The cellulose synthase (CesA) gene family in four Gossypium species: phylogenetics, sequence variation and gene expression in relation to fiber quality in Upland cotton.

Cellulose synthases (CesAs) are multi-subunit enzymes found on the plasma membrane of plant cells and play a pivotal role in cellulose production. The cotton fiber is mainly composed of cellulose, and the genetic relationships between CesA genes and cotton fiber yield and quality are not fully understood. Through a phylogenetic analysis, the CesA gene family in diploid Gossypium arboreum and Gossypium raimondii, as well as tetraploid Gossypium hirsutum ('TM-1') and Gossypium barbadense ('Hai-7124' and '3-79'), was divided into 6 groups and 15 sub-groups, with each group containing two to five homologous genes. Most CesA genes in the four species are highly collinear. Among the five cotton genomes, 440 and 1929 single nucleotide polymorphisms (SNPs) in the CesA gene family were identified in exons and introns, respectively, including 174 SNPs resulting in amino acid changes. In total, 484 homeologous SNPs between the A and D genomes were identified in diploids, while 142 SNPs were detected between the two tetraploids, with 32 and 82 SNPs existing within G. hirsutum and G. barbadense, respectively. Additionally, 74 quantitative trait loci near 18 GhCesA genes were associated with fiber quality. One to four GhCesA genes were differentially expressed (DE) in ovules at 0 and 3 days post anthesis (DPA) between two backcross inbred lines having different fiber lengths, but no DE genes were identified between these lines in developing fibers at 10 DPA. Twenty-seven SNPs in above DE CesA genes were detected among seven cotton lines, including one SNP in Ghi_A08G03061 that was detected in four G. hirsutum genotypes. This study provides the first comprehensive characterization of the cotton CesA gene family, which may play important roles in determining cotton fiber quality.

Effects of biochar and biofertilizer on cadmium-contaminated cotton growth and the antioxidative defense system.

Consistent use of large amounts of fertilizers, pesticides, and mulch can cause the accumulation of harmful substances in cotton plants. Among these harmful substances, cadmium (Cd), an undegradable element, stands out as being particularly highly toxic to plants. The objective of this study was to evaluate the ability of biochar (3%) and biofertilizer (1.5%) to decrease Cd uptake, increase cotton dry weight, and modulate the activities of photosynthetic and peroxidase (POD), superoxide dismutase (SOD), catalase enzyme (CAT) in cotton (Gossypium hirsutum L.) grown in Cd-contaminated soil (0, 1, 2, or 4 mg Cd kg-1 soil) in pots. These studies showed that, as expected, exogenous Cd adversely affects cotton chlorophyll and photosynthesis. However, biochar and biofertilizer increased cotton dry weight by an average of 16.82% and 32.62%, respectively. Meanwhile, biochar and biofertilizer decreased the accumulation of Cd in cotton organs, and there was a significant reduction in the amount of Cd in bolls (P < 0.05). Biochar and biofertilizer have a positive impact on cotton chlorophyll content, net photosynthesis, stomatal conductance, transpiration rate, and intercellular CO2 concentration. Thus, the addition of biochar and biofertilizer promote cotton growth. However, biochar and biofertilizer increased the SOD activity of leaves (47.70% and 77.21%), CAT activity of leaves (35.40% and 72.82%), SOD activity of roots (33.62% and 39.37%), and CAT activity of roots (36.91% and 60.29%), respectively, and the addition of biochar and biofertilizer decreased the content of MDA and electrolyte leakage rate. Redundancy analyses showed that biochar and biofertilizer also improved SOD and POD activities by reducing the heavy metal-induced oxidative stress in cotton and reducing Cd uptake in cotton organs. Therefore, biochar and biofertilizer have a positive effect on the growth of cotton.

NST- and SND-subgroup NAC proteins coordinately act to regulate secondary cell wall formation in cotton.

Secondary cell wall (SCW) has a strong impact on plant growth and adaptation to the environments. Previous studies have shown that NAC (NAM, ATAF1/2, and CUC2) transcription factors act as key regulators of SCW biosynthesis. However, the regulatory network triggered by NAC proteins is largely unknown, especially in cotton, a model plant for SCW development studies. Here, we show that several cotton NAC transcription factors are clustered in the same group with Arabidopsis secondary wall NACs (SWNs), including secondary wall-associated NAC domain protein1 (SND1) and NAC secondary wall thickening promoting factor1/2 (NST1/2), so we name these cotton orthologs as SND1s and NST1s. We found that simultaneous silencing of SND1s and NST1s led to severe xylem and phloem developmental defect in cotton stems, however silencing either SND1s or NST1s alone had no visible phenotype. Silencing both SND1s and NST1s but not one subgroup caused decreased expression of a set of SCW-associated genes, while over-expression of cotton SWNs in tobacco leaves resulted in SCW deposition. SWNs could bind the promoter of MYB46 and MYB83, which are highly expressed in SCW-rich tissues of cotton. In total, our data provide evidence that cotton SWNs positively and coordinately regulate SCW formation.

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.

Phenotypical evidence of effective amelioration of ammonium-inhibited plant (root) growth by exogenous low urea.

Ammonium and nitrate are major soil inorganic-nitrogen sources for plant growth, but many species cultivated with even low millimolar NH4+ as a sole N form display a growth retardation. To date, critical biological components and applicable approaches involved in the effective enhancement of NH4+ tolerance remain to be thoroughly explored. Here, we report phenotypical traits of urea-dependent improvement of NH4+-suppressed plant/root growth. Urea at 0.1 mM was sufficient to remarkably stimulate NH4+ (3 mM)-fed cotton growth, showing a 2.5∼4-fold increase in shoot- and root-biomass and total root-length, 20 % higher GS activity, 18 % less NH4+-accumulation in roots, and a comparable plant total-N content compared to the control, implying a novel role for urea in cotton NH4+detoxification. A similar phenomenon was observed in tobacco and rice. Moreover, comparisons between twelve NH4+-grown Arabidopsis accessions revealed a great degree of natural variation in their root-growth response to low urea, with WAR and Blh-1 exhibiting the most significant increase in primary- and lateral-root length and numbers, and Sav-0 and Edi-0 being the most insensitive. Such phenotypical evidence suggests a common ability of plants to accommodate NH4+-stress by responding to exogenous urea, providing a novel aspect for further understanding the process of urea-dependent plant NH4+ tolerance.

Determination of Cotton as a Larval Feeding Source for Lepidopteran Moths Using a Derivative from Cotton Metabolites as a Marker by LC-MS/MS Method.

Determination of the feeding history of polyphagous insect pests, such as noctuid moths (Lepidoptera: Noctuidae), is a critical element in developing population and resistance management strategies for such pests. To identify reliable markers for larval host plant determination and to develop simple extraction and detection methods, a metabolomics approach was implemented after acid hydrolysis of adult moth samples. We identified a derivative from cotton metabolites as a marker in adult moths that were fed cotton tissues as a larval diet, and we propose that the marker is tricycloheliocide H4 based on NMR and mass fragmentation analysis. Using this derivative from cotton metabolites as a marker, a targeted LC-MS/MS method reliably identified cotton as a larval diet in extracts of three noctuid moth species: Helicoverpa zea (cotton bollworm), Chloridea (Heliothis) virescens (tobacco budworm) and Chrysodeixis includens (soybean looper). We are using similar approaches to identify markers for other host plants including soybean.

Sanitary quality improvement of fish produced in the northern Benin cotton basin water reservoirs by cage culture and fish transfer in agricultural contaminant-free water: human health implications.

Northern Benin water reservoirs may remain valuable resources for fish production if the ecotoxicological risks related to agricultural pesticides are eradicated. The present work was undertaken (i) to evaluate sanitary quality and human health implications of fish (Clarias gariepinus and Oreochromis niloticus) reared in cages compared with those produced in pens installed in a contaminated water reservoir (Batran) and a reference water reservoir (Songhaï) and (ii) to test the efficacy of fish transferring to water without agricultural contaminants on fish health status. Pathogenic bacteria and pesticide residues were analyzed by phenotypic and biochemical identification and gas chromatography coupled with mass spectrometry, respectively. For both species, Aeromonas species occur in fish reared in pens at Batran. In Batran, regardless of infrastructure and species, residues of 4,4'-DDE (Dichlorodiphenyldichloroethylene) (1.4-4.9 µg/kg) and Chlorpyriphos (ethyl) (2.8-12.1 µg/kg) were measured, while only the last molecule was found in C. gariepinus from Songhaï (8.9-8.10 µg/kg). Irrespective of the species in the Batran water reservoir, Chlorpyriphos (ethyl) concentration was higher in cages and lower in pens, while 4, 4'-DDE was more concentrated in fish farmed in pens. Levels of these pesticide residues were well below World Health Organization/Food and Agriculture Organization permissible limits and the risk analyzed indicates no potential adverse health implications in consumption of these fish. Also, fish bacteriological quality was in compliance with the international standards. The fish decontamination approach used herein results in a reduction of the splenic macrophage phagocytic activity in both studied fish species.

A high density SLAF-seq SNP genetic map and QTL for seed size, oil and protein content in upland cotton.

BACKGROUND: Cotton is a leading natural fiber crop. Beyond its fiber, cottonseed is a valuable source of plant protein and oil. Due to the much higher value of cotton fiber, there is less consideration of cottonseed quality despite its potential value. Though some QTL controlling cottonseed quality have been identified, few of them that warrant further study are known. Identifying stable QTL controlling seed size, oil and protein content is necessary for improvement of cottonseed quality. RESULTS: In this study, a recombinant inbred line (RIL) population was developed from a cross between upland cotton cultivars/lines Yumian 1 and M11. Specific locus amplified fragment sequencing (SLAF-seq) technology was used to construct a genetic map that covered 3353.15 cM with an average distance between consecutive markers of 0.48 cM. The seed index, together with kernel size, oil and protein content were further used to identify QTL. In total, 58 QTL associated with six traits were detected, including 13 stable QTL detected in all three environments and 11 in two environments. CONCLUSION: A high resolution genetic map including 7033 SNP loci was constructed through specific locus amplified fragment sequencing technology. A total of 13 stable QTL associated with six cottonseed quality traits were detected. These stable QTL have the potential for fine mapping, identifying candidate genes, elaborating molecular mechanisms of cottonseed development, and application in cotton breeding programs.

Over-expression of the red plant gene R1 enhances anthocyanin production and resistance to bollworm and spider mite in cotton.

Anthocyanins are a class of pigments ubiquitously distributed in plants and play roles in adoption to several stresses. The red plant gene (R1) promotes light-induced anthocyanin accumulation and red/purple pigmentation in cotton. Using 11 markers developed via genome resequencing, the R1 gene was located in an interval of approximately 136 kb containing three annotated genes. Among them, a PAP1 homolog, GhPAP1D (Gohir.D07G082100) displayed differential transcript level in the red- and green-plant leaves. GhPAP1D encoded a R2R3-MYB transcription factor and its over-expression resulted in increased anthocyanin accumulation in transgenic tobaccos and cottons. Dual luciferase assay indicated that GhPAP1D activated the promoters of several cotton anthocyanin structural genes in tobacco leaves. Importantly, we found that the GhPAP1D-overexpressing cotton leaves had increased resistance to both bollworm and spite mite. Our data demonstrated that GhPAP1D was the controlling gene of the red plant phenotype in cotton, and as the major anthocyanin regulator, this gene was potential to create transgenic cottons with resistance to a broad spectrum of herbivores.