Deepening genomic sequences of 1081 Gossypium hirsutum accessions reveals novel SNPs and haplotypes relevant for practical breeding utility.

Fiber quality is a major breeding goal in cotton, but phenotypically direct selection is often hindered. In this study, we identified fiber quality and yield related loci using GWAS based on 2.97 million SNPs obtained from 10.65× resequencing data of 1081 accessions. The results showed that 585 novel fiber loci, including two novel stable SNP peaks associated with fiber length on chromosomes At12 and Dt05 and one novel genome regions linked with fiber strength on chromosome Dt12 were identified. Furthermore, by means of gene expression analysis, GhM_A12G0090, GhM_D05G1692, GhM_D12G3135 were identified and GhM_D11G2208 function was identified in Arabidopsis. Additionally, 14 consistent and stable superior haplotypes were identified, and 25 accessions were detected as possessing these 14 superior haplotype in breeding. This study providing fundamental insight relevant to identification of genes associated with fiber quality and yield will enhance future efforts toward improvement of upland cotton.

Pressure effects on both fluorescent emission and charge transport properties of organic semiconductors: a computational study.

External pressure can regulate the photophysical property and charge transport performance of organic semiconductors, however, the underlying mechanism at the microscopic level is still elusive. Using thermal vibrational correlation function coupled quantum mechanics/molecular mechanics and full quantum charge transfer rate theory, we systematically explore the influence of pressure on fluorescence emission and charge transport behaviours of representative cyclooctatetrathiophene (COTh). It is found that, upon pressurization, the intramolecular configurations of COTh became more twisted, leading to the blue-shifted emission. The fluorescence quantum efficiency (FQE) of COTh crystals decreases monotonically in a wide pressure range of 0-4.38 GPa, because the increase of intermolecular electronic energy transfer rate constant (keet) is larger than the decrease of internal conversion rate constant (kic), and the variation of keet is dominant. The decrease in kic is attributed to the decreasing reorganization energy, reflecting the suppression of the low-frequency flipping vibrations of four thiophene rings and the high-frequency stretching vibrations of central cyclooctatetraene, while the keet increase is due to the simultaneous increase in exciton coupling and spectra overlap. Moreover, we predicted that the hole mobility of COTh increases monotonically by nearly an order of magnitude from 0.39 to 3.00 cm2 V-1 s-1 upon compression, because of the increase in transfer integral and the decrease of charged reorganization energy. Furthermore, its hole mobility exhibits obvious anisotropy. Our work systematically builds the external pressure, molecular packing, luminescence and transport properties relationships of organic semiconductors and provides theoretical guidance for the rational design of pressure responsive organic semiconductors with excellent photoelectric performance.

The influence of heteroatoms on the circularly polarized luminescence performance of [7]helicene derivatives: aromatic vs. non-aromatic five-membered rings.

Helicenes are promising candidates for circularly polarized luminescence (CPL) materials, although the performance is poor due to the unsatisfactory dissymmetric factor (glum) and fluorescence quantum efficiency (ΦF). Herein, the influence of heteroatoms (C, Si, Ge, O, S and Se) on the electronic structures and chiroptical properties of [7]helicene derivatives is systematically investigated using density functional theory (DFT) and time-dependent DFT calculations combined with the thermal vibration correlation function theory. The results reveal that the non-radiative energy consumption processes for helicene systems are closely related to the variation of bond length upon electronic excitation. Moreover, by introducing five-membered rings and heteroatoms, the dipole-forbidden S1 → S0 emission of [7]helicene changes to dipole-allowed transition due to the rearrangement of occupied orbitals and lifting of the nearly degenerate orbitals, resulting in an enhancement of ΦF. As the heteroatomic radius increases, ΦF decreases while the glum increases. Compared with the derivatives containing aromatic five-membered rings ([7]H-O, [7]H-S, and [7]H-Se), the non-aromatic counterparts ([7]H-C, [7]H-Si, and [7]H-Ge) exhibit a balance in ΦF and glum values. The present study helps to clarify the relationship between structures and chiroptical properties and offers a feasible strategy for the future design of helicene-based CPL materials.

Genome-wide association study reveals novel SNPs and genes in Gossypium hirsutum underlying Aphis gossypii resistance.

KEY MESSAGE: A. gossypii resistance showed great variability in G. hirsutum varieties. One hundred and seventy-six SNPs associated with A. gossypii resistance were identified using GWAS. Four candidate resistance genes were functionally validated. Aphis gossypii is an economically important sap-feeding pest and is widely distributed in the world's cotton-producing regions. Identification of cotton genotypes and developing cultivars with improved A. gossypii resistance (AGR) is essential and desirable for sustainable agriculture. In the present study, A. gossypii was offered no choice but to propagate on 200 Gossypium hirsutum accessions. A relative aphid reproduction index (RARI) was used to evaluate the AGR, which showed large variability in cotton accessions and was classified into 6 grades. A significantly positive correlation was found between AGR and Verticillium wilt resistance. A total of 176 SNPs significantly associated with the RARI were identified using GWAS. Of these, 21 SNPs could be repeatedly detected in three replicates. Cleaved amplified polymorphic sequence, a restriction digestion-based genotyping assay, was developed using SNP1 with the highest observed -log10(P-value). Four genes within the 650 kb region of SNP1 were further identified, including GhRem (remorin-like), GhLAF1 (long after far-red light 1), GhCFIm25 (pre-mRNA cleavage factor Im 25 kDa subunit) and GhPMEI (plant invertase/pectin methylesterase inhibitor superfamily protein). The aphid infection could induce their expression and showed a significant difference between resistant and susceptible cotton varieties. Silencing of GhRem, GhLAF1 or GhCFIm25 could significantly increase aphid reproduction on cotton seedlings. Silencing of GhRem significantly reduced callose deposition, which is reasonably believed to be the cause for the higher AGR. Our results provide insights into understanding the genetic regulation of AGR in cotton and suggest candidate germplasms, SNPs and genes for developing cultivars with improved AGR.

Transcriptome, Ectopic Expression and Genetic Population Analysis Identify Candidate Genes for Fiber Quality Improvement in Cotton.

Comparative transcriptome analysis of fiber tissues between Gossypium barbadense and Gossypium hirsutum could reveal the molecular mechanisms underlying high-quality fiber formation and identify candidate genes for fiber quality improvement. In this study, 759 genes were found to be strongly upregulated at the elongation stage in G. barbadense, which showed four distinct expression patterns (I-IV). Among them, the 346 genes of group IV stood out in terms of the potential to promote fiber elongation, in which we finally identified 42 elongation-related candidate genes by comparative transcriptome analysis between G. barbadense and G. hirsutum. Subsequently, we overexpressed GbAAR3 and GbTWS1, two of the 42 candidate genes, in Arabidopsis plants and validated their roles in promoting cell elongation. At the secondary cell wall (SCW) biosynthesis stage, 2275 genes were upregulated and exhibited five different expression profiles (I-V) in G. barbadense. We highlighted the critical roles of the 647 genes of group IV in SCW biosynthesis and further picked out 48 SCW biosynthesis-related candidate genes by comparative transcriptome analysis. SNP molecular markers were then successfully developed to distinguish the SCW biosynthesis-related candidate genes from their G. hirsutum orthologs, and the genotyping and phenotyping of a BC3F5 population proved their potential in improving fiber strength and micronaire. Our results contribute to the better understanding of the fiber quality differences between G. barbadense and G. hirsutum and provide novel alternative genes for fiber quality improvement.

Tissue-specific expression of GhnsLTPs identified via GWAS sophisticatedly coordinates disease and insect resistance by regulating metabolic flux redirection in cotton.

Cotton (Gossypium hirsutum) is constantly attacked by pathogens and insects. The most efficient control strategy is to develop resistant varieties using broad-spectrum gene resources. Several resistance loci harboured by superior varieties have been identified through genome-wide association studies. However, the key genes and/or loci have not been functionally identified. In this study, we identified a locus significantly associated with Verticillium wilt (VW) resistance, and within a 145.5-kb linkage disequilibrium, two non-specific lipid transfer protein genes (named GhnsLTPsA10) were highly expressed under Verticillium pathogen stress. The expression of GhnsLTPsA10 significantly increased in roots upon Verticillium dahliae stress but significantly decreased in leaves under insect attack. Furthermore, GhnsLTPsA10 played antagonistic roles in positively regulating VW and Fusarium wilt resistance and negatively mediating aphid and bollworm resistance in transgenic Arabidopsis and silenced cotton. By combining transcriptomic, histological and physiological analyses, we determined that GhnsLTPsA10-mediated phenylpropanoid metabolism further affected the balance of the downstream metabolic flux of flavonoid and lignin biosynthesis. The divergent expression of GhnsLTPsA10 in roots and leaves coordinated resistance of cotton against fungal pathogens and insects via the redirection of metabolic flux. In addition, GhnsLTPsA10 contributed to reactive oxygen species accumulation. Therefore, in this study, we elucidated the novel function of GhnsLTP and the molecular association between disease resistance and insect resistance, balanced by GhnsLTPsA10. This broadens our knowledge of the biological function of GhnsLTPsA10 in crops and provides a useful locus for genetic improvement of cotton.

Novel insights into water-deficit-responsive mRNAs and lncRNAs during fiber development in Gossypium hirsutum.

BACKGROUND: The fiber yield and quality of cotton are greatly and periodically affected by water deficit. However, the molecular mechanism of the water deficit response in cotton fiber cells has not been fully elucidated. RESULTS: In this study, water deficit caused a significant reduction in fiber length, strength, and elongation rate but a dramatic increase in micronaire value. To explore genome-wide transcriptional changes, fibers from cotton plants subjected to water deficit (WD) and normal irrigation (NI) during fiber development were analyzed by transcriptome sequencing. Analysis showed that 3427 mRNAs and 1021 long noncoding RNAs (lncRNAs) from fibers were differentially expressed between WD and NI plants. The maximum number of differentially expressed genes (DEGs) and lncRNAs (DERs) was identified in fibers at the secondary cell wall biosynthesis stage, suggesting that this is a critical period in response to water deficit. Twelve genes in cotton fiber were differentially and persistently expressed at ≥ five time points, suggesting that these genes are involved in both fiber development and the water-deficit response and could potentially be used in breeding to improve cotton resistance to drought stress. A total of 540 DEGs were predicted to be potentially regulated by DERs by analysis of coexpression and genomic colocation, accounting for approximately 15.76% of all DEGs. Four DERs, potentially acting as target mimics for microRNAs (miRNAs), indirectly regulated their corresponding DEGs in response to water deficit. CONCLUSIONS: This work provides a comprehensive transcriptome analysis of fiber cells and a set of protein-coding genes and lncRNAs implicated in the cotton response to water deficit, significantly affecting fiber quality during the fiber development stage.

Synthesis and crystal structures of unsymmetrical wave-shaped heptathienoacenes.

Three unsymmetrical wave-shaped heptathienoacenes (UHT-1, UHT-2 and UHT-3) with sulfur atoms at different isomeric locations in the two terminal thiophene rings were designed and synthesized. The synthetic strategy contains two crucial steps, including the cross-coupling of two different dithienothiophene isomers (DTT) from dithieno[2,3-b:3',2'-d]thiophene (bb-DTT), dithieno[2,3-b:2',3'-d]thiophene (bt-DTT) and dithieno[2,3-b:3',4'-d]thiophene (bs-DTT) as building blocks through the Negishi coupling and intramolecular cyclization reactions with (SnBu3)2S. X-ray crystal structures of UHT-1, UHT-2 and UHT-3 show that the molecules adopt a wave-shaped geometry with multiple intermolecular interactions, such as S-S, S-C and S-H, which result in different crystal packing patterns. The isomeric location of the sulfur atoms of the two terminal thiophene rings of UHT-1, UHT-2 and UHT-3 plays an important role in tuning π-electronic conjugation and spectroscopic behaviors.

GhENODL6 Isoforms from the Phytocyanin Gene Family Regulated Verticillium Wilt Resistance in Cotton.

Verticillium wilt (VW), a fungal disease caused by Verticillium dahliae, currently devastates cotton fiber yield and quality seriously, yet few resistance germplasm resources have been discovered in Gossypium hirsutum. The cotton variety Nongda601 with suitable VW resistance and high yield was developed in our lab, which supplied elite resources for discovering resistant genes. Early nodulin-like protein (ENODL) is mainly related to nodule formation, and its role in regulating defense response has been seldom studied. Here, 41 conserved ENODLs in G. hirsutum were identified and characterized, which could divide into four subgroups. We found that GhENODL6 was upregulated under V. dahliae stress and hormonal signal and displayed higher transcript levels in resistant cottons than the susceptible. The GhENODL6 was proved to positively regulate VW resistance via overexpression and gene silencing experiments. Overexpression of GhENODL6 significantly enhanced the expressions of salicylic acid (SA) hormone-related transcription factors and pathogenicity-related (PR) protein genes, as well as hydrogen peroxide (H2O2) and SA contents, resulting in improved VW resistance in transgenic Arabidopsis. Correspondingly, in the GhENODL6 silenced cotton, the expression levels of both phenylalanine ammonia lyase (PAL) and 4-coumarate-CoA ligase (4CL) genes significantly decreased, leading to the reduced SA content mediating by the phenylalanine ammonia lyase pathway. Taken together, GhENODL6 played a crucial role in VW resistance by inducing SA signaling pathway and regulating the production of reactive oxygen species (ROS). These findings broaden our understanding of the biological roles of GhENODL and the molecular mechanisms underlying cotton disease resistance.

Longitudinal impact of caregiver transition and family caregiving on psychiatric symptoms and psychosocial functioning among persons with schizophrenia in rural China.

This study examines the 21-year longitudinal impacts and predictive effects of family caregiver transition and the presence of family caregiving on the clinical status of persons with schizophrenia (PwSs) in a rural area of China. Using panel data derived from the Chengdu Mental Health Project (CMHP), 250 dyads of PwSs and their family caregivers were investigated in 1994 and 2015. The Positive and Negative Syndrome Scale (PANSS) and the Global Assessment of Functioning (GAF) were utilized. The generalized linear model (GLM) approach was used. The results of this study showed that more severe symptoms in PwSs were found to be significantly predicted by older age and nonmarried status at baseline. Compared with "spousal caregiving in two waves," the PANSS score was significantly higher in the "transition into sibling caregiving" group. A higher degree of psychosocial functioning was found to be significantly predicted by marital status, shorter duration of illness, and better mental status. Compared with "spousal caregiving in two waves," the GAF score was significantly lower in the "transition into parental caregiving" group. The presence of family caregiving was not a significant predictor of the severity of symptoms or psychosocial functioning in the PwSs. In conclusion, this study shows the 21-year predictive effects of family caregiver transition on the mental status of PwSs but not the presence of family caregiving. Psychosocial interventions and specific guidance should be provided to family caregivers to enhance their quality of caregiving and improve the prognosis of PwSs during long periods of home care.

En este estudio se analizan los efectos longitudinales a 21 años y los efectos pronósticos de la transición de los cuidadores familiares y la presencia de cuidado familiar en el estado clínico de las personas con esquizofrenia en un área rural de China. Utilizando datos de panel extraídos del Proyecto de salud mental de Chengdu (Chengdu Mental Health Project, CMHP), se investigaron 250 díadas de personas con esquizofrenia y sus cuidadores familiares en 1994 y 2015. Se utilizó la Escala de síndrome positivo y negativo (Positive and Negative Syndrome Scale, PANSS) y la Evaluación global del funcionamiento (Global Assessment of Functioning, GAF). También se utilizó el método de modelo lineal generalizado. Los resultados de este estudio demostraron que los síntomas más intensos en las personas con esquizofrenia fueron pronosticados principalmente por la edad avanzada y el estado de soltería en el momento basal. En comparación con el grupo de "cuidado de los cónyuges en dos intervalos", el puntaje de la PANSS fue considerablemente más alto en el grupo de "transición al cuidado de los hermanos". Se descubrió que principalmente el estado civil, la duración más corta de la enfermedad y un mejor estado mental pronosticaron un grado más alto de funcionamiento psicosocial. En comparación con el grupo de "cuidado de los cónyuges en dos intervalos", el puntaje de la GAF fue considerablemente más bajo en el grupo de "transición al cuidado de los padres". La presencia de cuidado familiar no fue un factor pronóstico importante de la intensidad de los síntomas ni del funcionamiento psicosocial en las personas con esquizofrenia. En resumen, en este estudio se muestran los efectos pronósticos a 21 años de la transición de los cuidadores familiares en el estado mental de las personas con esquizofrenia, pero no la presencia de cuidado familiar. Deben ofrecerse intervenciones psicosociales y orientación específica a los cuidadores familiares para mejorar su calidad de cuidado y mejorar el pronóstico de las personas con esquizofrenia durante los periodos prolongados de cuidado en el hogar.

Thiophene/selenophene-based S-shaped double helicenes: regioselective synthesis and structures.

2,5-Di(trimethylsilanyl)dithieno[2,3-b:3',2'-d]thiophene ((TMS)2-bb-DTT), 2,5-di(trimethylsilanyl)diseleno[2,3-b:3',2'-d]thiophene ((TMS)2-bb-DST), and 2,5-di(trimethylsilanyl)diseleno[2,3-b:3',2'-d] selenophene ((TMS)2-bb-DSS) were used as starting materials to synthesize three S-shaped double helicenes (i.e., DH-1, DH-2, and DH-3) through monobromination, formylation, the Wittig reaction, and double oxidative photocyclization. The photocyclization was a highly regioselective process. The molecular structures of DH-1 and DH-2 were confirmed by X-ray single-crystal analysis. Multiple intermolecular interactions, such as C-S, C-Se, S-S, S-Se, and Se-Se, were observed in the crystal packing structures of these compounds. Spectroscopic results and our previous work showed that the combination of molecular structure change and heteroatom replacement from S to Se could precisely modulate molecular energy levels.

Genome-wide dissection of hybridization for fiber quality- and yield-related traits in upland cotton.

An evaluation of combining ability can facilitate the selection of suitable parents and superior F1 hybrids for hybrid cotton breeding, although the molecular genetic basis of combining ability has not been fully characterized. In the present study, 282 female parents were crossed with four male parents in accordance with the North Carolina II mating scheme to generate 1128 hybrids. The parental lines were genotyped based on restriction site-associated DNA sequencing and 306 814 filtered single nucleotide polymorphisms were used for genome-wide association analysis involving the phenotypes, general combining ability (GCA) values, and specific combining ability values of eight fiber quality- and yield-related traits. The main results were: (i) all parents could be clustered into five subgroups based on population structure analyses and the GCA performance of the female parents had significant differences between subgroups; (ii) 20 accessions with a top 5% GCA value for more than one trait were identified as elite parents for hybrid cotton breeding; (iii) 120 significant single nucleotide polymorphisms, clustered into 66 quantitative trait loci, such as the previously reported Gh_A07G1769 and GhHOX3 genes, were found to be significantly associated with GCA; and (iv) identified quantitative trait loci for GCA had a cumulative effect on GCA of the accessions. Overall, our results suggest that pyramiding the favorable loci for GCA may improve the efficiency of hybrid cotton breeding.

Identification of cell wall-associated kinases as important regulators involved in Gossypium hirsutum resistance to Verticillium dahliae.

BACKGROUND: Verticillium wilt, caused by the soil borne fungus Verticillium dahliae, is a major threat to cotton production worldwide. An increasing number of findings indicate that WAK genes participate in plant-pathogen interactions, but their roles in cotton resistance to V. dahliae remain largely unclear. RESULTS: Here, we carried out a genome-wide analysis of WAK gene family in Gossypium hirsutum that resulted in the identification of 81 putative GhWAKs, which were all predicated to be localized on plasma membrane. In which, GhWAK77 as a representative was further located in tobacco epidermal cells using transient expression of fluorescent fusion proteins. All GhWAKs could be classified into seven groups according to their diverse protein domains, indicating that they might sense different outside signals to trigger intracellular signaling pathways that were response to various environmental stresses. A lot of cis-regulatory elements were predicted in the upstream region of GhWAKs and classified into four main groups including hormones, biotic, abiotic and light. As many as 28 GhWAKs, playing a potential role in the interaction between cotton and V. dahliae, were screened out by RNA-seq and qRT-PCR. To further study the function of GhWAKs in cotton resistance to V. dahliae, VIGS technology was used to silence GhWAKs. At 20 dpi, VIGSed plants exhibited more chlorosis and wilting than the control plants. The disease indices of VIGSed plants were also significantly higher than those of the control. Furthermore, silencing of GhWAKs significantly affected the expression of JA- and SA-related marker genes, increased the spread of V. dahliae in the cotton stems, dramatically compromised V. dahliae-induced accumulation of lignin, H2O2 and NO, but enhanced POD activity. CONCLUSION: Our study presents a comprehensive analysis on cotton WAK gene family for the first time. Expression analysis and VIGS assay provided direct evidences on GhWAKs participation in the cotton resistance to V. dahliae.

Dynamic characteristics and functional analysis provide new insights into long non-coding RNA responsive to Verticillium dahliae infection in Gossypium hirsutum.

BACKGROUND: Verticillium wilt is a widespread and destructive disease, which causes serious loss of cotton yield and quality. Long non-coding RNA (lncRNA) is involved in many biological processes, such as plant disease resistance response, through a variety of regulatory mechanisms, but their possible roles in cotton against Verticillium dahliae infection remain largely unclear. RESULTS: Here, we measured the transcriptome of resistant G. hirsutum following infection by V. dahliae and 4277 differentially expressed lncRNAs (delncRNAs) were identified. Localization and abundance analysis revealed that delncRNAs were biased distribution on chromosomes. We explored the dynamic characteristics of disease resistance related lncRNAs in chromosome distribution, induced expression profiles, biological function, and these lncRNAs were divided into three categories according to their induced expression profiles. For the delncRNAs, 687 cis-acting pairs and 14,600 trans-acting pairs of lncRNA-mRNA were identified, which indicated that trans-acting was the main way of Verticillium wilt resistance-associated lncRNAs regulating target mRNAs in cotton. Analyzing the regulation pattern of delncRNAs revealed that cis-acting and trans-acting lncRNAs had different ways to influence target genes. Gene Ontology (GO) enrichment analysis revealed that the regulatory function of delncRNAs participated significantly in stimulus response process, kinase activity and plasma membrane components. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis indicated that delncRNAs participated in some important disease resistance pathways, such as plant-pathogen interaction, alpha-linolenic acid metabolism and plant hormone signal transduction. Additionally, 21 delncRNAs and 10 target genes were identified as being involved in alpha-linolenic acid metabolism associated with the biosynthesis of jasmonic acid (JA). Subsequently, we found that GhlncLOX3 might regulate resistance to V. dahliae through modulating the expression of GhLOX3 implicated in JA biosynthesis. Further functional analysis showed that GhlncLOX3-silenced seedlings displayed a reduced resistance to V. dahliae, with down-regulated expression of GhLOX3 and decreased content of JA. CONCLUSION: This study shows the dynamic characteristics of delncRNAs in multiaspect, and suggests that GhlncLOX3-GhLOX3-JA network participates in response to V. dahliae invasion. Our results provide novel insights for genetic improvement of Verticillium wilt resistance in cotton using lncRNAs.

Evolution, expression and functional analysis of cultivated allotetraploid cotton DIR genes.

BACKGROUND: Dirigent (DIR) proteins mediate regioselectivity and stereoselectivity during lignan biosynthesis and are also involved in lignin, gossypol and pterocarpan biosynthesis. This gene family plays a vital role in enhancing stress resistance and in secondary cell-wall development, but systematical understanding is lacking in cotton. RESULTS: In this study, 107 GbDIRs and 107 GhDIRs were identified in Gossypium barbadense and Gossypium hirsutum, respectively. Most of these genes have a classical gene structure without intron and encode proteins containing a signal peptide. Phylogenetic analysis showed that cotton DIR genes were classified into four distinct subfamilies (a, b/d, e, and f). Of these groups, DIR-a and DIR-e were evolutionarily conserved, and segmental and tandem duplications contributed equally to their formation. In contrast, DIR-b/d mainly expanded by recent tandem duplications, accompanying with a number of gene clusters. With the rapid evolution, DIR-b/d-III was a Gossypium-specific clade involved in atropselective synthesis of gossypol. RNA-seq data highlighted GhDIRs in response to Verticillium dahliae infection and suggested that DIR gene family could confer Verticillium wilt resistance. We also identified candidate DIR genes related to fiber development in G. barbadense and G. hirsutum and revealed their differential expression. To further determine the involvement of DIR genes in fiber development, we overexpressed a fiber length-related gene GbDIR78 in Arabidopsis and validated its function in trichomes and hypocotyls. CONCLUSIONS: These findings contribute novel insights towards the evolution of DIR gene family and provide valuable information for further understanding the roles of DIR genes in cotton fiber development as well as in stress responses.

A large-scale genomic association analysis identifies a fragment in Dt11 chromosome conferring cotton Verticillium wilt resistance.

Verticillium wilt (VW) is a destructive disease that results in great losses in cotton yield and quality. Identifying genetic variation that enhances crop disease resistance is a primary objective in plant breeding. Here we reported a GWAS of cotton VW resistance in a natural-variation population, challenged by different pathogenicity stains and different environments, and found 382 SNPs significantly associated with VW resistance. The associated signal repeatedly peaked in chromosome Dt11 (68 798 494-69 212 808) containing 13 core elite alleles undescribed previously. The core SNPs can make the disease reaction type from susceptible to tolerant or resistant in accessions with alternate genotype compared to reference genotype. Of the genes associated with the Dt11 signal, 25 genes differentially expressed upon Verticillium dahliae stress, with 21 genes verified in VW resistance via gene knockdown and/or overexpression experiments. We firstly discovered that a gene cluster of L-type lectin-domain containing receptor kinase (GhLecRKs-V.9) played an important role in VW resistance. These results proved that the associated Dt11 region was a major genetic locus responsible for VW resistance. The frequency of the core elite alleles (FEA) in modern varieties was significantly higher than the early/middle varieties (12.55% vs 4.29%), indicating that the FEA increased during artificial selection breeding. The current developmental resistant cultivars, JND23 and JND24, had fixed these core elite alleles during breeding without yield penalty. These findings unprecedentedly provided genomic variations and promising alleles for promoting cotton VW resistance improvement.

A stable QTL qSalt-A04-1 contributes to salt tolerance in the cotton seed germination stage.

KEY MESSAGE: A stable QTL qSalt-A04-1 for salt tolerance in the cotton seed germination stage, and two candidate genes, GhGASA1 and GhADC2, that play negative roles by modulating the GA and PA signalling pathways, respectively, were identified. The successful transition of a seed into a seedling is a prerequisite for plant propagation and crop yield. Germination is a vulnerable stage in a plant's life cycle that is strongly affected by environmental conditions, such as salinity. In this study, we identified a novel quantitative trait locus (QTL) qRGR-A04-1 associated with the relative germination rate (RGR) after salt stress treatment based on a high-density genetic map under phytotron and field conditions, with LOD values that ranged from 6.65 to 16.83 and 6.11-12.63% phenotypic variations in all five environmental tests. Two candidate genes with significantly differential expression between the two parents were finally identified through RNA-seq and qRT-PCR analyses. Further functional analyses showed that GhGASA1- and GhADC2-overexpression lines were more sensitive to salt stress than wild-type Arabidopsis based on the regulation of the transcript levels of gibberellic acid (GA)- and polyamine (PA)- related genes in GA and PA biosynthesis and the reduction in the accumulation of GA and PA, respectively, under salt stress. Virus-induced gene silencing analysis showed that TRV:GASA1 and TRV:ADC2 were more tolerant to salt stress than TRV:00 based on the increased expression of GA synthesis genes and decreased H2O2 content, respectively. Taken together, our results suggested that QTL qRGR-A04-1 and its two harboured genes, GhGASA1 and GhADC2, are promising candidates for salt tolerance improvement in cotton.

Synthesis of All Thiophene-Based [7]Helicenes and Trithienothiepines with Isomeric Location of Sulfur Atoms Based on Intramolecular Selectivity of Deprotonation.

Three unsymmetric thiophene-based [7]helicenes, namely, endo-exo-UH-1, endo-top-UH-2, and exo-top-UH-3, with different isomeric locations of sulfur atoms in two terminal thiophene rings were efficiently synthesized using dithieno[2,3-b:3',2'-d]thiophene (bb-DTT), dithieno[2,3-b:2',3'-d]thiophene (bt-DTT), and dithieno[2,3-b:3',4'-d]thiophene (bs-DTT) as building blocks via Suzuki cross-coupling and intramolecular cyclization reactions. Aside from these racemic [7]helicenes, two novel heterocyclic isomers, namely, trithienothiepines TTTP-1 and TTTP-2, were simultaneously obtained during the intramolecular cyclization. Two novel deprotonations of bi-DTTs and cyclization for synthesizing target compounds showed high selectivity and efficiently constructed both UHs and TTTPs. X-ray crystallographic analyses revealed that the UHs have typical helical molecular structures. The isomeric location of sulfur atoms in the two terminal thiophene rings in endo-exo-UH-1, endo-top-UH-2, exo-top-UH-3, and TTTP-1 allowed multiple intermolecular interactions, such as S···S, S···C, and S···H interactions, resulting in different crystal-packing patterns. Moreover, the absorption behaviors of these [7]helicenes, TTTP-1, and TTTP-2 were examined and theoretically calculated. Results indicated that the isomeric location of sulfur atoms plays a key role in tuning intramolecular π-electronic conjugation.

A newly identified cluster of glutathione S-transferase genes provides Verticillium wilt resistance in cotton.

As the largest cultivated fiber crop in the world, cotton (Gossypium hirsutum) is often exposed to various biotic stresses during its growth periods. Verticillium wilt caused by Verticillium dahliae is a severe disease in cotton, and the molecular mechanism of cotton resistance for Verticillium wilt needs to be further investigated. Here, we revealed that the cotton genome contains nine types of GST genes. An evolutionary analysis showed that a newly identified cluster (including Gh_A09G1508, Gh_A09G1509 and Gh_A09G1510) located on chromosome 09 of the A-subgenome was under positive selection pressure during the formation of an allotetraploid. Transcriptome analysis showed that this cluster participates in Verticillium wilt resistance. Because the Gh_A09G1509 gene showed the greatest differential expression in the resistant cultivar under V. dahliae stress, we overexpressed this gene in tobacco and found that its overexpression resulted in enhanced Verticillium wilt resistance. Suppression of the gene cluster via virus-induced gene silencing made cotton plants of the resistant cultivar Nongda601 significantly susceptible. These results demonstrated that the GST cluster played an important role in Verticillium wilt resistance. Further investigation showed that the encoded enzymes of the cluster were essential for the delicate equilibrium between the production and scavenging of H2 O2 during V. dahliae stress.

Genome-wide identification of the expansin gene family reveals that expansin genes are involved in fibre cell growth in cotton.

BACKGROUND: Expansins (EXPs), a group of proteins that loosen plant cell walls and cellulosic materials, are involved in regulating cell growth and diverse developmental processes in plants. However, the biological functions of this gene family in cotton are still unknown. RESULTS: In this paper, we identified a total of 93 expansin genes in Gossypium hirsutum. These genes were classified into four subfamilies, including 67 GhEXPAs, 8 GhEXPBs, 6 GhEXLAs, and 12 GhEXLBs, and divided into 15 subgroups. The 93 expansin genes are distributed over 24 chromosomes, excluding Ghir_A02 and Ghir_D06. All GhEXP genes contain multiple exons, and each GhEXP protein has multiple conserved motifs. Transcript profiling and qPCR analysis revealed that the expansin genes have distinct expression patterns among different stages of cotton fibre development. Among them, 3 genes (GhEXPA4o, GhEXPA1A, and GhEXPA8h) were highly expressed in the initiation stage, 9 genes (GhEXPA4a, GhEXPA13a, GhEXPA4f, GhEXPA4q, GhEXPA8f, GhEXPA2, GhEXPA8g, GhEXPA8a, and GhEXPA4n) had high expression during the fast elongation stage, and GhEXLA1c and GhEXLA1f were preferentially expressed in the transition stage of fibre development. CONCLUSIONS: Our results provide a solid basis for further elucidation of the biological functions of expansin genes in relation to cotton fibre development and valuable genetic resources for future crop improvement.