Molecular insight into cotton leaf curl geminivirus disease resistance in cultivated cotton (Gossypium hirsutum)

Cultivated cotton (Gossypium hirsutum) is the most important fibre crop in the world. Cotton leaf curl disease (CLCuD) is the major limiting factor and a threat to textile industry in India and Pakistan. All the local cotton cultivars exhibit moderate to no resistance against CLCuD. In this study, we evaluated an exotic cotton accession Mac7 as a resistance source to CLCuD by challenging it with viruliferous whiteflies and performing qPCR to evaluate the presence/absence and relative titre of CLCuD‐associated geminiviruses/betasatellites. The results indicated that replication of pathogenicity determinant betasatellite is significantly attenuated in Mac7 and probably responsible for resistance phenotype. Afterwards, to decipher the genetic basis of CLCuD resistance in Mac7, we performed RNA sequencing on CLCuD‐infested Mac7 and validated RNA‐Seq data with qPCR on 24 independent genes. We performed co‐expression network and pathway analysis for regulation of geminivirus/betasatellite‐interacting genes. We identified nine novel modules with 52 hubs of highly connected genes in network topology within the co‐expression network. Analysis of these hubs indicated the differential regulation of auxin stimulus and cellular localization pathways in response to CLCuD. We also analysed the differential regulation of geminivirus/betasatellite‐interacting genes in Mac7. We further performed the functional validation of selected candidate genes via virus‐induced gene silencing (VIGS). Finally, we evaluated the genomic context of resistance responsive genes and found that these genes are not specific to A or D sub‐genomes of G. hirsutum. These results have important implications in understanding CLCuD resistance mechanism and developing a durable resistance in cultivated cotton.     

Population genomics reveals a fine‐scale recombination landscape for genetic improvement of cotton

Recombination breaks up ancestral linkage disequilibrium, creates combinations of alleles, affects the efficiency of natural selection, and plays a major role in crop domestication and improvement. However, there is little knowledge regarding the variation in the population‐scaled recombination rate in cotton. We constructed recombination maps and characterized the difference in the genomic landscape of the population‐scaled recombination rate between Gossypium hirsutum and G. arboreum and sub‐genomes based on the 381 sequenced G. hirsutum and 215 G. arboreum accessions. Comparative genomics identified large structural variations and syntenic genes in the recombination regions, suggesting that recombination was related to structural variation and occurred preferentially in the distal chromosomal regions. Correlation analysis indicated that recombination was only slightly affected by geographical distribution and breeding period. A genome‐wide association study (GWAS) was performed with 15 agronomic traits using 267 cotton accessions and identified 163 quantitative trait loci (QTL) and an important candidate gene (Ghir_COL2) for early maturity traits. Comparative analysis of recombination and a GWAS revealed that the QTL of fibre quality traits tended to be more common in high‐recombination regions than were those of yield and early maturity traits. These results provide insights into the population‐scaled recombination landscape, suggesting that recombination contributed to the domestication and improvement of cotton, which provides a useful reference for studying recombination in other species.     

Expansion of MIR482/2118 by a class‐II transposable element in cotton

Some plant microRNA (miRNA) families contain multiple members generating identical or highly similar mature miRNA variants. Mechanisms underlying the expansion of miRNA families remain elusive, although tandem and/or segmental duplications have been proposed. In this study of two tetraploid cottons, Gossypium hirsutum and Gossypium barbadense, and their extant diploid progenitors, Gossypium arboreum and Gossypium raimondii, we investigated the gain and loss of members of the miR482/2118 superfamily, which modulates the expression of nucleotide‐binding site leucine‐rich repeat (NBS‐LRR) disease resistance genes. We found significant expansion of MIR482/2118d in G. barbadense, G. hirsutum and G. raimondii, but not in G. arboreum. Several newly expanded MIR482/2118d loci have mutated to produce different miR482/2118 variants with altered target‐gene specificity. Based on detailed analysis of sequences flanking these MIR482/2118 loci, we found that this expansion of MIR482/2118d and its derivatives resulted from an initial capture of an MIR482/2118d by a class‐II DNA transposable element (TE) in G. raimondii prior to the tetraploidization event, followed by transposition to new genomic locations in G. barbadense, G. hirsutum and G. raimondii. The ‘GosTE’ involved in the capture and proliferation of MIR482/2118d and its derivatives belongs to the PIF/Harbinger superfamily, generating a 3‐bp target site duplication upon insertion at new locations. All orthologous MIR482/2118 loci in the two diploids were retained in the two tetraploids, but mutation(s) in miR482/2118 were observed across all four species as well as in different cultivars of both G. barbadense and G. hirsutum, suggesting a dynamic co‐evolution of miR482/2118 and its NBS‐LRR targets. Our results provide fresh insights into the mechanisms contributing to MIRNA proliferation and enrich our knowledge on TEs.     

Long noncoding RNAs involve in resistance to Verticillium dahliae,a fungal disease in cotton

Long noncoding RNAs (lncRNAs) have several known functions in plant development, but their possible roles in responding to plant disease remain largely unresolved. In this study, we described a comprehensive disease‐responding lncRNA profiles in defence against a cotton fungal disease Verticillium dahliae. We further revealed the conserved and specific characters of disease‐responding process between two cotton species. Conservatively for two cotton species, we found the expression dominance of induced lncRNAs in the Dt subgenome, indicating a biased induction pattern in the co‐existing subgenomes of allotetraploid cotton. Comparative analysis of lncRNA expression and their proposed functions in resistant Gossypium barbadense cv. ‘7124’ versus susceptible Gossypium hirsutum cv. ‘YZ1’ revealed their distinct disease response mechanisms. Species‐specific (LS) lncRNAs containing more SNPs displayed a fiercer inducing level postinfection than the species‐conserved (core) lncRNAs. Gene Ontology enrichment of LS lncRNAs and core lncRNAs indicates distinct roles in the process of biotic stimulus. Further functional analysis showed that two core lncRNAs, GhlncNAT‐ANX2‐ and GhlncNAT‐RLP7‐silenced seedlings, displayed an enhanced resistance towards V. dahliae and Botrytis cinerea, possibly associated with the increased expression of LOX1 and LOX2. This study represents the first characterization of lncRNAs involved in resistance to fungal disease and provides new clues to elucidate cotton disease response mechanism.     

Brassinosteroid‐mediated reactive oxygen species are essential for tapetum degradation and pollen fertility in tomato

Phytohormone brassinosteroids (BRs) are essential for plant growth and development, but the mechanisms of BR‐mediated pollen development remain largely unknown. In this study, we show that pollen viability, pollen germination and seed number decreased in the BR‐deficient mutant d^{^im}, which has a lesion in the BR biosynthetic gene DWARF (DWF), and in the bzr1 mutant, which is deficient in BR signaling regulator BRASSINAZOLE RESISTANT 1 (BZR1), compared with those in wild‐type plants, whereas plants overexpressing DWF or BZR1 exhibited the opposite effects. Loss or gain of function in the DWF or BZR1 genes altered the timing of reactive oxygen species (ROS) production and programmed cell death (PCD) in tapetal cells, resulting in delayed or premature tapetal degeneration, respectively. Further analysis revealed that BZR1 could directly bind to the promoter of RESPIRATORY BURST OXIDASE HOMOLOG 1 (RBOH1), and that RBOH1‐mediated ROS promote pollen and seed development by triggering PCD and tapetal cell degradation. In contrast, the suppression of RBOH1 compromised BR signaling‐mediated ROS production and pollen development. These findings provide strong evidence that BZR1‐dependent ROS production plays a critical role in the BR‐mediated regulation of tapetal cell degeneration and pollen development in Solanum lycopersicum (tomato) plants.     

Identification and functional analysis of two P450 enzymes of Gossypium hirsutum involved in DMNT and TMTT biosynthesis

The homoterpenes (3E)‐4,8‐dimethyl‐1,3,7‐nonatriene (DMNT) and (E,E)‐4,8,12‐trimethyl‐1,3,7,11‐tridecatetraene (TMTT) are major herbivore‐induced plant volatiles that can attract predatory or parasitic arthropods to protect injured plants from herbivore attack. In this study, DMNT and TMTT were confirmed to be emitted from cotton (Gossypium hirsutum) plants infested with chewing caterpillars or sucking bugs. Two CYP genes (GhCYP82L1 and GhCYP82L2) involved in homoterpene biosynthesis in G. hirsutum were newly identified and characterized. Yeast recombinant expression and enzyme assays indicated that the two GhCYP82Ls are both responsible for the conversion of (E)‐nerolidol to DMNT and (E,E)‐geranyllinalool to TMTT. The two heterologously expressed proteins without cytochrome P450 reductase fail to convert the substrates to homoterpenes. Quantitative real‐time PCR (qPCR) analysis suggested that the two GhCYP82L genes were significantly up‐regulated in leaves and stems of G. hirsutum after herbivore attack. Subsequently, electroantennogram recordings showed that electroantennal responses of Microplitis mediator and Peristenus spretus to DMNT and TMTT were both dose dependent. Laboratory behavioural bioassays showed that females of both wasp species responded positively to DMNT and males and females of M. mediator could be attracted by TMTT. The results provide a better understanding of homoterpene biosynthesis in G. hirsutum and of the potential influence of homoterpenes on the behaviour of natural enemies, which lay a foundation to study genetically modified homoterpene biosynthesis and its possible application in agricultural pest control.     

A peptide hormone gene,GhPSK promotes fibre elongation and contributes to longer and finer cotton fibre

Cotton fibres, the single‐celled trichomes derived from the ovule epidermis, provide the most important natural material for the global textile industry. A number of studies have demonstrated that regulating endogenous hormone levels through transgenic approaches can improve cotton fibre qualities. Phytosulfokine‐α (PSK‐α) is a novel peptide hormone in plants that is involved in regulating cell proliferation and elongation. However, its potential applications in crop genetic improvement have not been evaluated. In this study, we describe how exogenous PSK‐α application promotes cotton fibre cell elongation in vitro. Chlorate, an effective inhibitor of peptide sulfation, suppressed fibre elongation in ovule culture. Exogenously applied PSK‐α partly restored the chlorate‐induced suppression. A putative PSK gene (GhPSK) was cloned from Gossypium hirsutum. Expression pattern analysis revealed that GhPSK is preferentially expressed in rapidly elongating fibre cells (5–20 days postanthesis). Overexpression of GhPSK in cotton increased the endogenous PSK‐α level and promoted cotton fibre cell elongation, resulting in longer and finer fibres. Further results from electrophysiological and physiological analyses suggest that GhPSK affects fibre development through regulation of K⁺ efflux. Digital gene expression (DGE) profile analysis of GhPSK overexpression lines indicates that PSK signalling may regulate the respiratory electron‐transport chain and reactive oxygen species to affect cotton fibre development. These results imply that peptide hormones are involved in cotton fibre growth and suggest a new strategy for the biotechnological improvement of cotton fibre quality.     

Impacts of elevated CO2 on Bemisia tabaci infesting Bt cotton and its parasitoid Encarsia formosa

Atmospheric carbon dioxide concentration is expected to rise in the coming decades. Rising atmospheric CO₂ levels may alter plant‐insect‐parasitoid associations due to the indirect effects of CO₂ enrichment on phytochemicals important for herbivore and parasitoid nutrition. Tritrophic effects of elevated CO₂ on Bt cotton (GK‐12) and non‐transgenic (Simian‐3, or S3) cotton [Gossypium hirsutum L. (Malvaceae)], Bemisia tabaci (Gennadius) biotype B (Hemiptera: Aleyrodidae), and its parasitoid Encarsia formosa Gahan (Hymenoptera: Aphelinidae), were examined in open‐top chambers. Significantly, longer egg‐adult developmental duration and higher mortality of nymphs were observed under elevated CO₂ concentrations on both cotton cultivars during three successive generations. However, no significant differences were found in adult longevity, offspring sex ratio, and the number of eggs laid per female adult of B. tabaci fed on transgenic (GK‐12) or non‐transgenic cotton (S3) grown under elevated CO₂. Abundance of B. tabaci adults increased from 10 to 120 per plant and then decreased to 40 per plant through the growing season, but no significant differences in density occurred between CO₂ treatments and between cultivar treatments. Similarly, no significant differences were found in the developmental duration, parasitization rate, and adult emergence rate of E. formosa after parasitizing B. tabaci for three successive generations. Our results showed that the effects of transgenic Bt cotton did not significantly affect the development, survivorship, life span, or fecundity of B. tabaci and its parasitoids. Moreover, interactions between B. tabaci and E. formosa were not significantly affected by elevated CO₂. These results suggest that the biological control of B. tabaci by E. formosa would not be influenced by transgenic Bt cotton and/or elevated CO₂, indicating that the current risk management strategy regarding B. tabaci outbreaks and biocontrol by E. formosa will remain effective if the atmospheric CO₂ level continues to rise.     

CYTOPLASMIC EFFECTS ON THE DIFFERENTIATION OF ANTHERS AND OVULES OF COTTON

Reciprocal crosses of Upland cotton with a hybrid derived from (Gossypium anomalum × G. thurberi) × G. hirsutum produced progenies differing significantly in anther development and in the production of supernumerary ovules outside the ovary. Plants with G. anomalum cytoplasm produced fewer anthers than the reciprocal hybrids with G. hirsutum cytoplasm, had a higher percentage of sterile anthers, and were far more likely to form external ovules on an abnormally thickened tip of the staminal tube. The number of locules and ovules within the ovary was not significantly affected by cytoplasm.     

Population structure and genetic basis of the agronomic traits of upland cotton in China revealed by a genome‐wide association study using high‐density SNPs

Gossypium hirsutum L. represents the largest source of textile fibre, and China is one of the largest cotton‐producing and cotton‐consuming countries in the world. To investigate the genetic architecture of the agronomic traits of upland cotton in China, a diverse and nationwide population containing 503 G. hirsutum accessions was collected for a genome‐wide association study (GWAS) on 16 agronomic traits. The accessions were planted in four places from 2012 to 2013 for phenotyping. The CottonSNP63K array and a published high‐density map based on this array were used for genotyping. The 503 G. hirsutum accessions were divided into three subpopulations based on 11 975 quantified polymorphic single‐nucleotide polymorphisms (SNPs). By comparing the genetic structure and phenotypic variation among three genetic subpopulations, seven geographic distributions and four breeding periods, we found that geographic distribution and breeding period were not the determinants of genetic structure. In addition, no obvious phenotypic differentiations were found among the three subpopulations, even though they had different genetic backgrounds. A total of 324 SNPs and 160 candidate quantitative trait loci (QTL) regions were identified as significantly associated with the 16 agronomic traits. A network was established for multieffects in QTLs and interassociations among traits. Thirty‐eight associated regions had pleiotropic effects controlling more than one trait. One candidate gene, Gh_D08G2376, was speculated to control the lint percentage (LP). This GWAS is the first report using high‐resolution SNPs in upland cotton in China to comprehensively investigate agronomic traits, and it provides a fundamental resource for cotton genetic research and breeding.     

Interaction of Anthonomus grandis and cotton genotypes: biological and behavioral responses

The boll weevil, Anthonomus grandisBoheman (Coleoptera: Curculionidae), is a key pest of cotton, Gossypium hirsutumL. (Malvaceae). Knowledge about boll weevil feeding and oviposition behavior and its response to plant volatiles can underpin our understanding of host plant resistance, and contribute to improved monitoring and mass capture of this pest. Boll weevil oviposition preference and immature development in four cotton genotypes (CNPA TB90, TB85, TB15, and BRS Rubi) were investigated in the laboratory and greenhouse. Volatile organic compounds (VOCs) produced by TB90 and Rubi genotypes were obtained from herbivore‐damaged and undamaged control plants at two phenological stages – vegetative (prior to squaring) and reproductive (during squaring) – and four collection times – 24, 48, 72, and 96 h following herbivore damage. The boll weevil exhibited similar feeding and oviposition behavior across the four tested cotton genotypes. The chemical profiles of herbivore‐damaged plants of both genotypes across the two phenological stages were qualitatively similar, but differed in the amount of volatiles produced. Boll weevil response to VOC extracts was studied using a Y‐tube olfactometer. The boll weevil exhibited similar feeding and oviposition behavior at the four tested cotton genotypes, although delayed development and production of smaller adults was found when fed TB85. The chemical profile of herbivore‐damaged plants of both genotypes at the two phenological stages and time periods (24–96 h) was similar qualitatively, with 30 identified compounds, but differed in the amount of volatiles produced. Additionally, boll weevil olfactory response was positive to herbivory‐induced volatiles. The results help to understand the interaction between A. grandis and cotton plants, and why it is difficult to obtain cotton genotypes possessing constitutive resistance to this pest.     

Genetic transformation of cotton with a harpin-encoding gene <Emphasis Type="Italic">hpa</Emphasis><Subscript><Emphasis Type="Italic">Xoo</Emphasis></Subscript> confers an enhanced defense response against different pathogens through a priming mechanism

Background  

The soil-borne fungal pathogen Verticillium dahliae Kleb causes Verticillium wilt in a wide range of crops including cotton (Gossypium hirsutum). To date, most upland cotton varieties are susceptible to V. dahliae and the breeding for cotton varieties with the resistance to Verticillium wilt has not been successful.     

Stay or move: how Bt‐susceptible Helicoverpa armigera neonates behave on Bt cotton plants

Helicoverpa armigera (Hübner) (Lepidoptera: Noctuidae) larvae occasionally have been reported to survive at management threshold levels in fields of Bollgard II^® cotton, Gossypium hirsutum L. (Malvaceae). The pattern and degree of larval survival is not easily predicted but depends on the ability of first instars to establish on host plants. Experiments were conducted with Bacillus thuringiensis Berliner (Bt)‐susceptible and Bt‐resistant larvae of H. armigera to understand how physiologically Bt‐susceptible H. armigera survive on Bt cotton plants, and examine how their first meal influences survival rates. In assays using cotton plant parts, both strains of larvae displayed similar tendencies to drop‐off specific plant parts of Bt and non‐Bt cotton. However, significantly more Bt‐susceptible larvae dropped off young leaves, mature leaves, and squares of Bt cotton compared to non‐Bt cotton plants. Egg cannibalism significantly improved the survival of Bt‐susceptible H. armigera larvae on Bt cotton plants. Larvae were more likely to eat live aged eggs, than newly laid or dead eggs. Survival significantly improved when larvae cannibalized eggs before feeding on Bt leaves. The behavior of Bt‐susceptible larvae with respect to drop‐off and egg cannibalism may help enhance their survival on Bt cotton plants.     

Abnormal Vacuolization of the Tapetum During the Tetrad Stage is Associated with Male Sterility in the Recessive Genic Male Sterile <Emphasis Type="Italic">Brassica napus</Emphasis> L. Line 9012A

In the recessive genic male sterile line 9012A of Brassica napus, pollen development is affected during the tetrad stage. According to the light and electron microscopy analysis of tapetal cells and tetrads, the sterile tapetal cells swelled with expanded vacuoles at the early tetrad stage and finally filled the center of the locules where a majority of tetrads encased with the thick callose wall collapsed and degraded. We suggested that an absence of callase, which is a wall-degrading enzyme stored in the vacuoles of tapetal cells before secretion, resulted in the failure of tetrad separation. Moreover, transmission electron microscopy analysis showed that the secretory tapetal cells were not observed in sterile anthers, which indicated that the transition of the tapetum from the parietal type to the secretory type was probably aberrant. In plants, degeneration of the tapetum is thought to be the result of programmed cell death (PCD). PCD of tapetal cells was investigated by terminal deoxynucleotidyl transferase-mediated dUTP nick-end labeling assay and signals indicative of deoxyribonucleic acid fragmentation were detected much earlier in sterile anther than in fertile anther. This suggests that tapetal breakdown does not occur by the normal procession of PCD and might be following an alternative mechanism of unscheduled apoptosis in line 9012A. This research supports the hypothesis that premature PCD is associated with male sterility in B. napus.