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Climate change employs substantial effects on agroecosystems, particularly the dynamics between plants and herbivores. In response, the adoption of pest-resistant varieties has emerged as a critical strategy within agroecosystems, notably in Indonesia’s cotton Integrated Pest Management (IPM). This research focused on evaluating the response of five cotton lines, which adapted to the Indonesian agroecosystem, to the cotton leafhopper ( Amrasca biguttula ) as a mitigating measure to climate change. Two upland cotton varieties, Tamcot SP 37 (susceptible) and LRA 5166 (resistant), served as standards for susceptibility and resistance to leafhoppers. The study examined leaf morphological characters, specifically trichome density, known to act as oviposition deterrents for leafhopper females, indicative of non-preference resistance. Low damage scores and high leaf trichome density comparable to the resistant variety (LRA 5166) were indicators of notable field resistance in lines 06062/3/3 and 06062/3/4 against A. biguttula during observations that spanned 35 to 105 days post-planting. These findings highlight the potential of these lines as promising cotton varieties, marked by their resilience to A. biguttula , fostering sustainable cultivation practices that address climate change impacts. This study underscores the intricate dynamics between plant-insect interactions and resilience strategies within agroecosystems.

Background Transgenic research in crops involves using genetic engineering techniques to introduce specific genes of interest from other organisms, or even entirely new genes into plant genomes to create crops with desirable traits that wouldn't be possible through conventional breeding methods. Transgenic crops have been developed for various traits globally. Whitefly, Bemisia tabaci (Gennadius) is one of the major sucking pests of cotton that cause significant damage to the cotton production. To combat whitefly infestations, researchers have developed four transgenic cotton lines expressing the fern protein. And those transgenic lines need to be evaluated for their performance against the target pest—whitefly. The evaluation was designed as controlled trials in polyhouse or muslin cloth cages under open-choice and no-choice conditions by comparing four transgenic cotton lines (A, B, C, and D) with three control groups, including untransformed cotton plants with a same genetic background of the transgenic line, conventionally bred whitefly-resistant cotton, and whitefly-susceptible cotton. In order to study the generational effect, the evaluation also involved studies on whitefly development in laboratory, muslin cloth cage, and polyhouse conditions. Results Both open-choice and no-choice experiments had shown that all the four transgenic cotton lines (A, B, C, and D) expressing the fern protein reduced adult whitefly numbers significantly compared with the control lines, except for the no-choice conditions in 2021, where the transgenic line C was non-significant different from the resistant control line. Notably, the nymphal population on the resistant control line was relatively low and non-significant different from the transgenic line C in 2021; and the transgenic lines A and C in 2022 under open-choice conditions. Under no-choice condition, the nymphal counts in the resistant control line was non-significant different from transgenic lines C and D in 2021; and transgenic line D in 2022. All transgenic lines showed significant decrease in egg hatching in 2021 and nymphal development in 2022, except for the transgenic line C which had no significant different in the nymphal development comparing with non-transgenic control lines in 2022. Adult emergence rates in both years of evaluation showed significant decrease in transgenic lines A and B comparing with the control lines. Additionally, the results showed a significant reduction in cotton leaf curl disease and sooty mold development in all the four transgenic lines compared with susceptible control under open-choice conditions, indicating potential benefits of transgenic lines beyond direct effect on whitefly control. Furthermore, the research explored the generational effects of the fern protein on whitefly which revealed the lowest fecundity in the transgenic line C across F 0 , F 1 and F 3 generations, lower egg hatching in F 1 and F 2 generations in transgenic lines A and B, shorter nymphal duration in F 1 and F 2 generations in transgenic line B, and the least total adult emergence in the transgenic line C in F 0 and F 3 generations. Conclusions These findings suggest that the transgenic cotton lines expressing fern protein disrupts whitefly populations and the life cycle to a certain extent. However, results are not consistent over generations and years of study, indicating these transgenic lines were not superior over control lines and need to be improved in future breeding.

Weed interference consistently poses a significant agronomic challenge in cotton production, leading to unfavorable direct and indirect consequences. Consequently, the predominant strategy employed to manage weeds is the application of synthetic herbicides. However, this extensive reliance has resulted in the development of herbicide-resistant weed populations due to the prolonged use of a single herbicide and the lack of rotation. This project focused on identifying weed-suppressive cotton chromosome substitution (CS) lines. These CS lines closely resemble the parent TM-1, an upland cotton derivative (Gossypium hirsutum). Each CS line carries a single chromosome or chromosome arm exchanged from G. barbadense, G. tomentosum, or G. mustelinum within the TM-1 background. In a greenhouse experiment utilizing a stepwise approach, five CS lines, along with two conventional varieties (Enlist and UA48) and the parent line (TM1), were assessed to determine their potential for suppressing Palmer amaranth growth. The plant height was measured 7, 14, and 21 days after establishment, and the chlorophyll content was measured 21 days after establishment. The results revealed varying levels of chlorophyll reduction in Palmer amaranth, with the Enlist variety displaying the lowest reduction (32%) and TM-1 exhibiting the highest (78%). Within 14 days of establishment, the CS lines T26lo, BNTN 1-15, and T11sh demonstrated substantial suppression of Palmer amaranth height, with reductions of 79, 70, and 71%, respectively. Conversely, Enlist displayed the least effective performance among the CS lines. Moreover, CS22, CS49, CS50, CS34, UA48, and CS23 displayed a decreasing trend in reducing Palmer amaranth height from 14 to 21 days after establishment. This research demonstrates the inherent herbicidal attributes within cotton CS lines against Palmer amaranth. In light of the versatile applications of cotton fibers and the unique characteristics of the G. hirsutum genome, this study investigates the potential of specific cotton lines in enhancing weed management practices. By elucidating the implications of our findings, we aim to contribute to promoting sustainability and developing alternatives to synthetic herbicides in agricultural systems.

Molecular markers associated with fiber development traits have the potential to play a key role in understanding of cotton fiber development. Seventeen SSRs out of 304 markers tested from MGHES (EST-SSR), JESPR (genomic SSR), and TMB (BAC-derived SSR) collections showed significant linkage associations (using a Kurskal-Wallis non-parametric test) with lint percentage QTL in a set of recombinant inbred cotton lines (RILs) segregating for lint percentage. The permutation test of these potential markers associated with lint percentage QTL(s) determined that 12 SSR markers have stable estimates, exceeding empirically chosen threshold significance values at or above α = 0.01. Interval mapping demonstrated that 9 SSRs with stable critical LOD threshold values at α = 0.01 have significant QTL effect. Multiple QTL-mapping (MQM) revealed that at least, two highly significant fiber development QTLs exist around regions TMB0471 and MGHES-31 (explained about 23-59% of the phenotypic variation of lint percentage) and around markers MGHES-31 and TMB0366 (accounted for 5.4-12.5% phenotypic variation of lint percentage). These markers, in particular fiber-specific EST-SSRs, might be the possible 'candidate' loci contributing for fiber development in cotton. BAC-derived SSRs associated with fiber trait are the possible markers that are useful for the identification of physical genomic contigs that contain fiber development genes. Several lint percentage trait associated SSR markers have been located to chromosomes 12, 18, 23, and 26 using deletion analysis in aneuploid chromosome substitution lines. Outcomes of the work may prove useful in understanding and revealing the molecular basis of the fiber development, and the utilization of these markers for development of superior cotton cultivars through marker-assisted selection (MAS) programs.

Nanofibers of natural cotton lines cellulose, with a degree of polymerization above 10000, were prepared by electrospinning. The effects of cellulose concentration, flow rate and electric field strength on the morphologies of the fibers were systematically investigated. Furthermore, two effective improvements on the electrospinning apparatus were made: heating the pathway between the tip of the needle and the collector instead of the needle or the collector, and covering the drum with activated cellulose flake. High quality cellulose nanofibers were obtained under the optimized spinning conditions combined with the apparatus improvements. Moreover, oriented cotton nanofibers were acquired by elevating the rotation speed of the drum collector. The wettability of the nonwoven was greatly improved compared with the original activated cellulose. The obtained nonwoven or nanofibers of the natural cotton cellulose could be potentially applied in tissue scaffolds, protective clothing and high efficient water absorbing materials etc.

Fiber length (FL) and strength (FS) are the core indicators for evaluating cotton fiber quality. The corresponding stages of fiber elongation and secondary wall thickening are of great significance in determining FL and FS formation, respectively. QTL mapping and high-throughput sequencing technology have been applied to dissect the molecular mechanism of fiber development. In this study, 15 cotton chromosome segment substitution lines (CSSLs) with significant differences in FL and FS, together with their recurrent parental Gossypium hirsutum line CCRI45 and donor parent G. barbadense line Hai1, were chosen to conduct RNA-seq on developing fiber samples at 10 days post anthesis (DPA) and 20 DPA. Differentially expressed genes (DEGs) were obtained via pairwise comparisons among all 24 samples (each one with three biological repeats). A total of 969 DEGs related to FL-high, 1285 DEGs to FS-high, and 997 DEGs to FQ-high were identified. The functional enrichment analyses of them indicated that the GO terms of cell wall structure and ROS, carbohydrate, and phenylpropanoid metabolism were significantly enriched, while the GO terms of glucose and polysaccharide biosynthesis, and brassinosteroid and glycosylphosphatidylinositol metabolism could make great contributions to FL and FS formation, respectively. Weighted gene co-expressed network analyses (WGCNA) were separately conducted for analyzing FL and FS traits, and their corresponding hub DEGs were screened in significantly correlated expression modules, such as EXPA8, XTH, and HMA in the fiber elongation and WRKY, TDT, and RAC-like 2 during secondary wall thickening. An integrated analysis of these hub DEGs with previous QTL identification results successfully identified a total of 33 candidate introgressive DEGs with non-synonymous mutations between the Gh and Gb species. A common DEG encoding receptor-like protein kinase 1 was reported to likely participate in fiber secondary cell thickening regulation by brassionsteroid signaling. Such valuable information was conducive to enlightening the developing mechanism of cotton fiber and also provided an abundant gene pool for further molecular breeding.

The objective of this study was to facilitate the selection in cotton breeding program and estimate the general combining ability (GCA) of the parents and specific combining ability (SCA) of hybrids considered for the development of high yielding and better fiber quality in early generations. The study was carried out at the Southeastern Anatolia Agricultural Research Institute during 2006 and 2007 cotton growing season. Seven cotton lines (which are known as high quality) and three testers (which are known as well adapted and high yielding) were crossed in a line x tester mating design in 2006. Ten genotypes and 21 F1 hybrids were planted in the randomized complete block design with three replications at the same experimental area in 2007. The variance due to GCA and SCA were highly significant for all the traits studied. This indicated that both additive and non-additive gene effects were responsible for the investigated characters. From the trial it was found that in the population, fiber length, fiber fineness and fiber elongation were influenced by additive gene effects while seed cotton yield, fiber yield, ginning percentage, fiber strength and fiber uniformity were influenced by non-additive gene effects. Among the parents FiberMax 832, Teks, Stoneville 453 and Maras 92 for seed cotton yield and fiber yield; Askabat 71 and Giza 45 for fiber length and fiber strength; Askabat 71 for fiber fineness and fiber uniformity were detected with higher general combining ability. Most of the parents except Askabat 71, Giza 45 and Maras 92 exhibited GCA for ginning percentage. SCA was significant for FiberMax 832 x Stoneville 453, Tam 94 L 25 x Maras 92 and Teks x Stoneville 453 hybrid combinations for yield with acceptable fiber quality.

Circular RNAs (circRNAs), a class of recently discovered non-coding RNAs, play a role in biological and developmental processes. A recent study showed that circRNAs exist in plants and play a role in their environmental stress responses. However, cotton circRNAs and their role in Verticillium wilt response have not been identified up to now. In this study, two CSSLs (chromosome segment substitution lines) of G.barbadense introgressed into G. hirsutum , CSSL-1 and CSSL-4 (a resistant line and a susceptible line to Verticillium wilt, respectively), were inoculated with V. dahliae for RNA-seq library construction and circRNA analysis. A total of 686 novel circRNAs were identified. CSSL-1 and CSSL-4 had similar numbers of circRNAs and shared many circRNAs in common. However, CSSL-4 differentially expressed approximately twice as many circRNAs as CSSL-1, and the differential expression levels of the common circRNAs were generally higher in CSSL-1 than in CSSL-4. Moreover, two C-RRI comparisons, C-RRI-vs-C-RRM and C-RRI-vs-C-RSI, possessed a large proportion (approximately 50%) of the commonly and differentially expressed circRNAs. These results indicate that the differentially expressed circRNAs may play roles in the Verticillium wilt response in cotton. A total of 280 differentially expressed circRNAs were identified. A Gene Ontology analysis showed that most of the ‘stimulus response’ term source genes were NBS family genes, of which most were the source genes from the differentially expressed circRNAs, indicating that NBS genes may play a role in Verticillium wilt resistance and might be regulated by circRNAs in the disease-resistance process in cotton.

Background Improving fiber quality and yield are the primary research objectives in cotton breeding for enhancing the economic viability and sustainability of Upland cotton production. Identifying the quantitative trait loci (QTL) for fiber quality and yield traits using the high-density SNP-based genetic maps allows for bridging genomics with cotton breeding through marker assisted and genomic selection. In this study, a recombinant inbred line (RIL) population, derived from cross between two parental accessions, which represent broad allele diversity in Upland cotton, was used to construct high-density SNP-based linkage maps and to map the QTLs controlling important cotton traits. Results Molecular genetic mapping using RIL population produced a genetic map of 3129 SNPs, mapped at a density of 1.41 cM. Genetic maps of the individual chromosomes showed good collinearity with the sequence based physical map. A total of 106 QTLs were identified which included 59 QTLs for six fiber quality traits, 38 QTLs for four yield traits and 9 QTLs for two morphological traits. Sub-genome wide, 57 QTLs were mapped in A sub-genome and 49 were mapped in D sub-genome. More than 75% of the QTLs with favorable alleles were contributed by the parental accession NC05AZ06. Forty-six mapped QTLs each explained more than 10% of the phenotypic variation. Further, we identified 21 QTL clusters where 12 QTL clusters were mapped in the A sub-genome and 9 were mapped in the D sub-genome. Candidate gene analyses of the 11 stable QTL harboring genomic regions identified 19 putative genes which had functional role in cotton fiber development. Conclusion We constructed a high-density genetic map of SNPs in Upland cotton. Collinearity between genetic and physical maps indicated no major structural changes in the genetic mapping populations. Most traits showed high broad-sense heritability. One hundred and six QTLs were identified for the fiber quality, yield and morphological traits. Majority of the QTLs with favorable alleles were contributed by improved parental accession. More than 70% of the mapped QTLs shared the similar map position with previously reported QTLs which suggest the genetic relatedness of Upland cotton germplasm. Identification of QTL clusters could explain the correlation among some fiber quality traits in cotton. Stable and major QTLs and QTL clusters of traits identified in the current study could be the targets for map-based cloning and marker assisted selection (MAS) in cotton breeding. The genomic region on D12 containing the major stable QTLs for micronaire, fiber strength and lint percentage could be potential targets for MAS and gene cloning of fiber quality traits in cotton.

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