Upland Cotton Varieties Research Articles

Evaluation of the Genetic Diversity, Haplotype, and Virulence of Fusarium oxysporum f. sp. vasinfectum Field Isolates from Alabama.

The United States is the third largest producer of cotton and the largest exporter of cotton globally. Fusarium wilt, caused by the soilborne fungal pathogen Fusarium oxysporum f. sp. vasinfectum (Fov), was estimated to cause a $21 million cotton yield loss in 2022. Historically, Alabama was an important producer of cotton in the Southeastern United States and was the first state in which Fusarium wilt on cotton was described. To assess the genetic diversity of Fov field isolates in Alabama, 118 field isolates were collected from six counties across the state from 2014 to 2016. Phylogenetic analysis using TEF1 and RPB2 placed the Fov field isolates into 18 haplotypes. Upon profiling the Tfo1 transposon insertion in the NAT gene, it was determined that no race 4 isolates were recovered in Alabama. Representatives of all field isolate haplotypes caused disease on Upland cotton variety Rowden in a hydroponic test tube assay. Two haplotype A isolates were the most aggressive isolates recovered, and haplotype A isolate TF1 was more aggressive than the race 4 isolate 89-1A on Upland cotton and had similar symptom severity on Pima cotton. Karyotype profiling indicted an abundance of small chromosomes characteristic of karyotypes that include accessory chromosomes, with considerable variability between isolates. Collectively, our study indicates that Fov isolates from Alabama are genetically diverse, which may have been promoted by its persistence in cotton fields.

Effect of cold stress on photosynthetic physiological characteristics and molecular mechanism analysis in cold-resistant cotton (ZM36) seedlings.

Low temperature and cold damage seriously hinder the growth, development, and morphogenesis of cotton seedlings. However, the response mechanism of cotton seedlings under cold stress still lacks research. In this study, transcriptome sequencing, gas exchange parameters, and rapid chlorophyll fluorescence parameters were analyzed in leaves of cold-tolerant upland cotton variety "ZM36" under different temperature stress [25°C (T25, CK), 15°C (T15), 10°C (T10), and 4°C (T4)]. The results showed that the net photosynthetic rate (Pn), stomatal conductance (Gs), transpiration rate (Tr), PSII potential maximum photochemical efficiency (Fv/Fm), and performance index (PIabs) of cotton leaves significantly decreased, and the intercellular CO2 concentration (Ci) and Fo/Fm significantly increased under cold stress. The transcriptome sequencing analysis showed that a total of 13,183 DEGs were involved in the response of cotton seedlings at each temperature point (T25, T15, T10, and T4), mainly involving five metabolic pathways-the phosphatidylinositol signaling system, photosynthesis, photosynthesis antenna protein, carbon fixation in photosynthetic organisms, and carotenoid synthesis. The 1,119 transcription factors were discovered among all the DEGs. These transcription factors involve 59 families, of which 15.8% of genes in the NAC family are upregulated. Through network regulatory analysis, the five candidate genes GhUVR8 (GH_A05G3668), GhPLATZ (GH_A09G2161), GhFAD4-1 (GH_A01G0758), GhNFYA1 (GH_A02G1336), and GhFAD4-2 (GH_D01G0766) were identified in response to cold stress. Furthermore, suppressing the expression level of GhPLATZ by virus-induced gene silencing led to the reduction of low temperature resistance, implying GhPLATZ as a positive regulator of low temperature tolerance. The findings of the study revealed a piece of the complex response mechanism of the cold-tolerant variety "ZM36" to different cold stresses and excavated key candidate genes for low temperature response, which provided support for accelerating the selection and breeding of cotton varieties with low temperature tolerance.

Evaluation of cotton varieties resistant to Amrasca biguttula (Hemiptera: Ciccadelidae) in the Indonesian agroecosystem to mitigate climate change impacts

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.

Repression of GhTUBB1 Reduces Plant Height in Gossypium hirsutum.

The original 'Green Revolution' genes are associated with gibberellin deficiency. However, in some species, mutations in these genes cause pleiotropic phenotypes, preventing their application in dwarf breeding. The development of novel genotypes with reduced plant height will resolve this problem. In a previous study, we obtained two dwarf lines, L28 and L30, by introducing the Ammopiptanthus mongolicus (Maxim. ex Kom.) Cheng f. C-repeat-binding factor 1 (AmCBF1) into the upland cotton variety R15. We found that Gossypium hirsutum Tubulin beta-1 (GhTUBB1) was downregulated in L28 and L30, which suggested that this gene may have contributed to the dwarf phenotype of L28 and L30. Here, we tested this hypothesis by silencing GhTUBB1 expression in R15 and found that decreased expression resulted in a dwarf phenotype. Interestingly, we found that repressing AmCBF1 expression in L28 and L30 partly recovered the expression of GhTUBB1. Thus, AmCBF1 expression presented a negative relationship with GhTUBB1 expression in L28 and L30. Moreover, yeast one-hybrid and dual-luciferase assays suggest that AmCBF1 negatively regulates GhTUBB1 expression by directly binding to C-repeat/dehydration-responsive (CRT/DRE) elements in the GhTUBB1 promoter, potentially explaining the dwarf phenotypes of L28 and L30. This study elucidates the regulation of GhTUBB1 expression by AmCBF1 and suggests that GhTUBB1 may be a new target gene for breeding dwarf and compact cultivars.

Recycling of gas-to-liquid sludge as a potential organic amendment: Effect on soil and cotton properties under hyperarid conditions

Gas-to-liquid (GTL) sludge is a specific wastewater treatment by-product, which is generated during the industrial process of natural gas conversion to transportation fuels. This least studied sludge is pathogen-free and rich in organic carbon and plant nutrients. Therefore, it can be reused for soil enhancement as a sustainable management strategy to mitigate landfill gas emissions. In this field study, we compared the performance of soil treatments with GTL sludge to the more conventional chemical fertilizers and cow manure compost for the cultivation of cotton under hyperarid conditions. After a complete growing season, GTL sludge application resulted in the enhancement of soil properties and plant growth compared to conventional inputs. As such, there was a significant dose-dependent increase of soil organic matter (4.01% and 4.54%), phosphorus (534 and 1090 mg kg−1), and cumulative lint yield (4.68 and 5.67 t ha−1) for GTL sludge application rates of 1.5% and 3%, respectively. The produced fiber quality was adequate for an upland cotton variety (Gossypium hirsutum var. MAY 344) and appeared more dependent on the prevailing climate conditions than soil treatments. On the other hand, the adverse effects generally related to industrial sludge reuse were not significant and did not affect the designed agro-environmental system. Accordingly, plants grown on GTL sludge-amended soils showed lower antioxidant activity despite significant salinity increase. In addition, the concentrations of detected heavy metals in soil were within the standards’ limits, which did not pose environmental issues under the described experimental conditions. Leachate analysis revealed no risks for groundwater contamination with phytotoxic metals, which were mostly retained by the soil matrix. Therefore, recycling GTL sludge as an organic amendment can be a sustainable solution to improve soil quality and lower carbon footprint. To reduce any environmental concerns, an application rate of 1.5% could be provisionally recommended since a two-fold increase in sludge dose did not result in a significant yield improvement.

Modeling and Optimization of High-Capacity Experimental Reclaimers to Minimize the Seed and Lint Loss during Roller Ginning of Upland and Pima Cotton

In the present study, two high-capacity experimental roller gin reclaimers, (a) a modified 3-saw cylinder stick machine (three-saw) and (b) a modified 2-saw cylinder gin stand feeder (700), were optimized with respect to reclaimer saw cylinder speed and carryover/seed ratio to minimize the seed and lint loss for both Pima and Upland cotton varieties and were compared to a conventional roller gin reclaimer operated by the ginning industry under standard conditions. Developed regression models adequately described the seed and lint loss phenomena during the reclaiming process. Surface plots indicated that the reclaimer saw cylinder speed and carryover/seed ratio impacted the seed and lint loss for both the 3-saw and 700 reclaimers. Under optimized conditions, the 700 reclaimer resulted in lower lint and seed loss compared to the 3-saw reclaimer when using Upland cotton. In the case of Pima cotton, under optimized conditions, the 3-saw reclaimer had 38% lower lint loss and 24% higher seed loss compared to the 700 reclaimer. The regression equations of both 3-saw and 700 reclaimers were further used to optimize the reclaimers in parallel arrangement to minimize the seed and lint loss. With Upland cotton, the economic loss was about 2.5 times greater with the conventional reclaimer compared to the 3-saw and 700 reclaimers ($15.97/bale loss for the conventional, $8.63 for the 3-saw, and $6.44 for the 700 reclaimers). With Pima cotton, the conventional reclaimer resulted in a lower economic loss ($3.44/bale) compared to the 700 reclaimer which had a loss of about $3.59/bale.

Detection of epistasis interaction loci for fiber quality-related trait via 3VmrMLM in upland cotton.

Cotton fiber quality-related traits, such as fiber length, fiber strength, and fiber elongation, are affected by complex mechanisms controlled by multiple genes. Determining the QTN-by-QTN interactions (QQIs) associated with fiber quality-related traits is therefore essential for accelerating the genetic enhancement of cotton breeding. In this study, a natural population of 1,245 upland cotton varieties with 1,122,352 SNPs was used for detecting the main-effect QTNs and QQIs using the 3V multi-locus random-SNP-effect mixed linear model (3VmrMLM) method. A total of 171 significant main-effect QTNs and 42 QQIs were detected, of which 22 were both main-effect QTNs and QQIs. Of the detected 42 QQIs, a total of 13 significant loci and 5 candidate genes were reported in previous studies. Among the three interaction types, the AD interaction type has a preference for the trait of FE. Additionally, the QQIs have a substantial impact on the enhancement predictability for fiber quality-related traits. The study of QQIs is crucial for elucidating the genetic mechanism of cotton fiber quality and enhancing breeding efficiency.

RVE2, a new regulatory factor in jasmonic acid pathway, orchestrates resistance to Verticillium wilt.

Verticillium dahliae, one of the most destructive fungal pathogens of several crops, challenges the sustainability of cotton productivity worldwide because very few widely-cultivated Upland cotton varieties are resistant to Verticillium wilt (VW). Here, we report that REVEILLE2 (RVE2), the Myb-like transcription factor, confers the novel function in resistance to VW by regulating the jasmonic acid (JA) pathway in cotton. RVE2 expression was essentially required for the activation of JA-mediated disease-resistance response. RVE2 physically interacted with TPL/TPRs and disturbed JAZ proteins to recruit TPL and TPR1 in NINJA-dependent manner, which regulated JA response by relieving inhibited-MYC2 activity. The MYC2 then bound to RVE2 promoter for the activation of its transcription, forming feedback loop. Interestingly, a unique truncated RVE2 widely existing in D-subgenome (GhRVE2D) of natural Upland cotton represses the ability of the MYC2 to activate GhRVE2A promoter but not GausRVE2 or GbRVE2. The result could partially explain why Gossypium barbadense popularly shows higher resistance than Gossypium hirsutum. Furthermore, disturbing the JA-signalling pathway resulted into the loss of RVE2-mediated disease-resistance in various plants (Arabidopsis, tobacco and cotton). RVE2 overexpression significantly enhanced the resistance to VW. Collectively, we conclude that RVE2, a new regulatory factor, plays a pivotal role in fine-tuning JA-signalling, which would improve our understanding the mechanisms underlying the resistance to VW.

Histone H3 lysine 27 trimethylation suppresses jasmonate biosynthesis and signaling to affect male fertility under high temperature in cotton

High-temperature (HT) stress causes male sterility in crops, thus decreasing yields. To explore the possible contribution of histone modifications to male fertility under HT conditions, we defined the histone methylation landscape for the marks histone H3 lysine 27 trimethylation (H3K27me3) and histone H3 lysine 4 trimethylation (H3K4me3) by chromatin immunoprecipitation sequencing (ChIP-seq) in two differing upland cotton (Gossypium hirsutum) varieties. We observed a global disruption in H3K4me3 and H3K27me3 modifications, especially H3K27me3, in cotton anthers subjected to HT. HT affected the bivalent H3K4me3–H3K27me3 modification more than either monovalent modification. We determined that removal of H3K27me3 at the promoters of jasmonate-related genes increased their expression, maintaining male fertility under HT in the HT-tolerant variety at the anther dehiscence stage. Modulating jasmonate homeostasis or signaling resulted in an anther indehiscence phenotype under HT. Chemical suppression of H3K27me3 deposition increased jasmonic acid contents and maintained male fertility under HT. In summary, our study provides new insights into the regulation of male fertility by histone modifications under HT and suggests a potential strategy for improving cotton HT tolerance.

Crossability Relationship between Wild Cotton G. anomalum and G. aridum with Upland Cotton (G. hirsutum)

Background: Utilizing two wild cotton species, Gossypium anomalum [Wawra and Peyritsch (2n=2x=26) B1] and Gossypium aridum [Skovsted (2n=2x=26) D4], extensive wide hybridization event carried out with upland cotton to assess the feasibility and ease of delivering genetic variation responsible for resistance to various stresses. Methods: The crossing was carried out using the wild species and the cultivate varieties of upland cotton in 2021-2022 at TNAU, Coimbatore. Total of 12 crosses were attempted and the various aspect regarding the feasibility success of different crosses was studied. Result: In contrast to their reciprocals, viable offspring were generated in the direct crosses with tetraploid parents employed as seed parents with both wild species. A huge bulk of bolls dropped during the first seven days of pollination and no matured boll set was observed in reciprocals. Most G. anomalum hybrids produce F1 offspring with thick and long leaf hairs which help the plant attain resistance against sucking pests. Through successive backcrosses or chromosome duplication, such genetic material potentially can be utilized furthermore in plant breeding to provide new beneficial resistance traits apart from other significant and relevant features.

A mutant cotton fatty acid desaturase 2-1d allele causes protein mistargeting and altered seed oil composition

BackgroundCotton (Gossypium sp.) has been cultivated for centuries for its spinnable fibers, but its seed oil also possesses untapped economic potential if, improvements could be made to its oleic acid content.ResultsPrevious studies, including those from our laboratory, identified pima accessions containing approximately doubled levels of seed oil oleic acid, compared to standard upland cottonseed oil. Here, the molecular properties of a fatty acid desaturase encoded by a mutant allele identified by genome sequencing in an earlier analysis were analyzed. The mutant sequence is predicted to encode a C-terminally truncated protein lacking nine residues, including a predicted endoplasmic reticulum membrane retrieval motif. We determined that the mutation was caused by a relatively recent movement of a Ty1/copia type retrotransposon that is not found associated with this desaturase gene in other sequenced cotton genomes. The mutant desaturase, along with its repaired isozyme and the wild-type A-subgenome homoeologous protein were expressed in transgenic yeast and stably transformed Arabidopsis plants. All full-length enzymes efficiently converted oleic acid to linoleic acid. The mutant desaturase protein produced only trace amounts of linoleic acid, and only when strongly overexpressed in yeast cells, indicating that the missing C-terminal amino acid residues are not strictly required for enzyme activity, yet are necessary for proper subcellular targeting to the endoplasmic reticulum membrane.ConclusionThese results provide the biochemical underpinning that links a genetic lesion present in a limited group of South American pima cotton accessions and their rare seed oil oleic acid traits. Markers developed to the mutant desaturase allele are currently being used in breeding programs designed to introduce this trait into agronomic upland cotton varieties.

Genome-wide analysis of mutations induced by carbon ion beam irradiation in cotton.

Carbon ion beam (CIB) irradiation is a powerful way to create mutations in animals, plants, and microbes. Research on the mutagenic effects and molecular mechanisms of radiation is an important and multidisciplinary issue. However, the effect of carbon ion radiation on cotton is uncertain. In this study, five different upland cotton varieties and five CIB doses were used to identify the suitable irradiation dose for cotton. Three mutagenized progeny cotton lines from the wild-type Ji172 were re-sequenced. The effect of half-lethal dose on mutation induction indicated that 200 Gy with LETmax of 226.9 KeV/μm was the most effective heavy-ion dose for upland cotton and a total of 2,959-4,049 single-base substitutions (SBSs) and 610-947 insertion-deletion polymorphisms (InDels) were identified among the three mutants by resequencing. The ratio of transition to transversion in the three mutants ranged from 2.16 to 2.24. Among transversion events, G:C>C:G was significantly less common than three other types of mutations (A:T>C:G, A:T>T:A, and G:C>T:A). The proportions of six types of mutations were very similar in each mutant. The distributions of identified SBSs and InDels were similar with unevenly distributed across the genome and chromosomes. Some chromosomes had significantly more SBSs than others, and there were "hotspot" mutation regions at the ends of chromosomes. Overall, our study revealed a profile of cotton mutations caused by CIB irradiation, and these data could provide valuable information for cotton mutation breeding.

Transcriptome, proteome and functional characterization reveals salt stress tolerance mechanisms in upland cotton (Gossypium hirsutum L.).

Uncovering the underlying mechanism of salt tolerance is important to breed cotton varieties with improved salt tolerance. In this study, transcriptome and proteome sequencing were performed on upland cotton (Gossypium hirsutum L.) variety under salt stress, and integrated analysis was carried out to exploit salt-tolerance genes in cotton. Enrichment analysis using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) was performed on differentially expressed genes (DEGs) obtained from transcriptome and proteome sequencing. GO enrichment was carried out mainly in the cell membrane, organelle, cellular process, metabolic process, and stress response. The expression of 23,981 genes was changed in physiological and biochemical processes such as cell metabolism. The metabolic pathways obtained by KEGG enrichment included glycerolipid metabolism, sesquiterpene and triterpenoid biosynthesis, flavonoid production, and plant hormone signal transduction. Combined transcriptome and proteome analysis to screen and annotate DEGs yielded 24 candidate genes with significant differential expression. The quantitative real-time polymerase chain reaction (qRT-PCR) validation of the candidate genes showed that two genes (Gh_D11G0978 and Gh_D10G0907) responded significantly to the induction of NaCl, and these two genes were further selected as target genes for gene cloning and functional validation through virus-induced gene silencing (VIGS). The silenced plants exhibited early wilting with a greater degree of salt damage under salt treatment. Moreover, they showed higher levels of reactive oxygen species (ROS) than the control. Therefore, we can infer that these two genes have a pivotal role in the response to salt stress in upland cotton. The findings in this research will facilitate the breeding of salt tolerance cotton varieties that can be grown on saline alkaline lands.

Genetic polymorphism detection in brazilian perennial cottons (Gossypium spp.) using an ISSR marker system and its application for molecular interspecific differentiation.

The semi-domesticated Brazilian perennial cotton (Gossypium spp.) germplasm is considered a source of variability for creating modern upland cotton varieties. Here we used Inter-simple Sequence Repeat (ISSR) markers to detect intra and interspecific genetic polymorphism in Gossypium hirsutum L. r. marie-galante and Gossypium barbadense L. and to use molecular data to assessing genetic diversity and molecular discrimination of these species. The sets contained 12 G. barbadense genotypes and 16 G. hirsutum genotypes from a Brazilian collection. The 11 ISSR primers were used for genotyping yielded 101 bands (polymorphism = 47.5%) and were classified as moderately informative (PIC = 0.304). The ISSR markers exposed a greater diversity in G. hirsutum (P = 24.72%; HE =0.071 and I = 0.111) as compared to G. barbadense (P = 17.98%, HE = 0.043 and I = 0.070). The AMOVA analysis showed that 89.47% of the genetic variation was partitioned within species which is supported by Nei's genetic differentiation (Gst = 0.598) and gene flow (Nm = 0.338), suggesting that strong reproductive barriers between species. The UPGMA Cluster Analysis, Principal Coordinate Analysis and Bayesian Model-Based Structural Analysis divided the 28 genotypes into two main clades consistent with the taxonomical delimitation. The ISSR marker system offers a new approach to determining molecular differences between two cotton species (G. hirsutum L. r. marie-galante and G. barbadense L.). This study can expand the molecular marker resources for the identification and improvement of our knowledge about the genetic diversity and relationships between perennial cotton genotypes.

Water Use Efficiency of Long Staple Cotton Varieties in Southern Zone of Uzbekistan

Previous research established field capacity (Fc) based irrigation scheduling for upland cotton (Gossypium hirsutum L.) varieties in Uzbekistan. In this paper, the irrigation scheduling Fc for two long staple cotton (Gossypium barbadense L.) varieties and its effect on seed-lint yield and irrigation water use efficiency and water consumption of plants were reported. The field experiments were conducted in the condition of takyr soils with mechanical composition of silt loam in southern zone of Uzbekistan, at the Kashkadarya Experimental Station of Uzbekistan’s Cotton Breeding, Seed Production and Agrotechnologies Research Institute in 2018, 2019 and 2020. In research, cotton growth stages such as germination to flowering, flowering to boll formation, and maturation were considered for the development of irrigation scheduling with respect to field capacity water content (Fc). Irrigation scheduling based on percentages of Fc and mineral fertilizer application rate of N250P175K125 should be considered applicable practices for long staple cotton varieties on silt loam soils of the southern zone of Uzbekistan and for similar soil-climatic conditions of Central Asian countries.

Phylogeny, gene structures, and expression patterns of the auxin response factor (GhARF2) in upland cotton (Gossypium hirsutum L.).

Auxin response factors (ARFs) are a class of transcription factors that regulate the expression of auxin-responsive genes and play important functions in plant growth and development. To understand the biological functions of the auxin response factor GhARF2 gene in upland cotton, the coding sequence (CDS) of GhARF2 gene was cloned, and its protein sequence, evolutionary relationship, subcellular localization and expression pattern were analysed. The CDS sequence of GhARF2 gene was cloned from upland cotton variety Baimian No.1, and its protein sequence was analyzed by bioinformatics method. The subcellular localization of GhARF2 protein was detected by tobacco epidermal transient transformation system, and the tissue expression and stress expression pattern of GhARF2 were analyzed by quantitative Real‑Time PCR (qRT-PCR). The full-length CDS of GhARF2 gene was 2583bp, encoded 860 amino acids, and had a molecular weight and an isoelectric point of 95.46 KDa and 6.02, respectively. The GhARF2 protein had multiple phosphorylation sites, no transmembrane domain, and secondary structures dominated by random coils and alpha helix. The GhARF2 protein had 3 conserved typical domains of ARF gene family members, including the B3 DNA binding domain, the Auxin_resp domain, and the Aux/IAA domain. Phylogenetic analysis revealed that ARF2 proteins in different species were clustered in the Group A subgroup, in which GhARF2 was closely related to TcARF2 of Theobroma cacao L. (Malvaceae). The subcellular localization results showed that the GhARF2 protein was localized in the nucleus. Analysis of tissue expression pattern showed that the GhARF2 gene was expressed in all testedtissues, with the highest expression levels in sepal, followed by leaf, and the lowest expression levels in fiber. Further stress expression analysis showed that the GhARF2 gene was induced by drought, high-temperature, low-temperature and salt stress, and had different expression patterns under different stress conditions. These results established a foundation for understanding the functions of GhARF2 and breeding varieties with high-stress tolerance in cotton.

Retraction: Path analysis based on genetic association of yield components and insects pest in upland cotton varieties.

Retraction: Path analysis based on genetic association of yield components and insects pest in upland cotton varieties.

Genome-wide association study reveals that GhTRL1 and GhPIN8 affect cotton root development.

Two regions located at chromosome A05 and D04 were found to be significantly associated with 0-0.5mm and 0.5-2mm diameter roots, respectively, and two candidate genes related to root development were identified. Roots absorb water and nutrients, and play an important role in plant growth. However, there are few genetic developmental studies on cotton root structural traits. In this study, we used 200 upland cotton (Gossypium hirsutum L.) varieties to analyze the phenotypic variation of 43 traits. A total of 2001 related single-nucleotide polymorphism (SNP) sites located within or near 1046 genes were detected through a genome-wide association study (GWAS). The 32 root traits were linked to SNPs that corresponded to 317 nonrepetitive genes. For SNPs associated with root length and 0-0.5mm diameter root traits, a significant peak appeared on chromosome A05 (between 21.91 and 22.24Mb). For SNPs associated with root surface area, root volume and 0.5-2mm diameter root traits, a significant peak appeared on chromosome D04 (between 7.35 and 7.70Mb). Within these two key regions, SNPs were detected in the promoter and coding regions of two candidate genes, GhTRL1-A05 and GhPIN8-D04. The expression levels of these two genes also changed significantly according to transcriptome sequencing and quantitative real-time PCR (qRT-PCR). After silencing the GhTRL1 and GhPIN8 genes via virus-induced gene silencing (VIGS), we found that the plants expressing TRV2::GhTRL1 and TRV2::GhPIN8 had a reduced root length, surface area. Moreover, the contents of cis-12-oxo-phytodienoic acid (cis-OPDA), isopentenyl adenosine (iPR) and cis-zeatin (cZ) in the roots of the plants expressing TRV2::GhTRL1 decreased. This study contributes to the cultivation and improvement of cotton varieties.

Use of SSR Markers for the Exploration of Genetic Diversity and DNA Finger-Printing in Early-Maturing Upland Cotton (Gossypium hirsutum L.) for Future Breeding Program

DNA fingerprinting and genetic diversity analysis of 79 early-maturing upland cotton (Gossypium hirsutum L.) cultivars were performed using Simple Sequence Repeat (SSR) molecular markers. Out of 126 pairs of SSR primers, we selected 71 pairs that gave good polymorphisms and clear bands, had good stability, and showed even distribution on the cotton chromosomes, and 142 polymorphic genotypes were amplified. The average number of alleles amplified with the SSR primers was 2.01. The polymorphism information content (PIC) of the markers ranged from 0.1841 to 0.9043, with an average of 0.6494. The results of fingerprint analysis showed that nine varieties had characteristic bands, and at least six primer pairs could be used to completely distinguish all 79 cotton accessions. Using NTSYS-pc 2.11 cluster analysis, the genetic similarity coefficients between the cotton genotypes ranged from 0.3310 to 0.8705, with an average of 0.5861. All cotton accessions were grouped into five categories at a similarity coefficient of 0.57, which was consistent with the pedigree sources. At the same time, the average genetic similarity coefficients of early-maturing upland cotton varieties in China showed a low-high-low pattern of variation over time, revealing the development history of early-maturing upland cotton varieties from the 1980s to the present. This also indirectly reflects that in recent years, China’s cotton breeders have focused on innovation and have continuously broadened the genetic resources for early-maturing upland cotton.

Comparative performance of hybrid generations reveals the potential application of F2 hybrids in upland cotton

BackgroundThe utilization of heterosis has greatly improved the productivity of cotton worldwide. However, a major constraint for the large-scale promotion of F1 hybrid cotton is artificial emasculation and pollination. This study proposed the potential utilization of F2 hybrids to improve upland cotton production through a comparative evaluation of hybrid generations.ResultsEight upland cotton varieties were analyzed and crosses were made according to NCII incomplete diallel cross-breeding design in two cotton belts of China. Variance analysis revealed significant differences in agronomic, yield, and fiber quality in both generations and environments. The broad-sense heritability of agronomic and yield traits was relatively higher than quality traits. Furthermore, the narrow-sense heritability of some traits was higher in F2 than in the F1 generation in both cotton belts. Overall, parental lines Zhong901, ZB, L28, and Z98 were observed with maximum combining ability while combinations with strong special combining ability were ZB × DT, L28 × Z98, and ZB × 851. The yield traits heterosis was predominant in both generations. However, the level of heterosis was altered with trait, hybrid combination, generation, and environment. Interestingly, L28 × Z98 performed outstandingly in Anyang. Its lint yield (LY) was 24.2% higher in F1 and 11.6% in F2 than that of the control Ruiza 816. The performance of SJ48 × Z98 was excellent in Aral which showed 36.5% higher LY in F1 and 10.9% in F2 than control CCRI 49. Further results revealed most hybrid combinations had shown a low level of heterosis for agronomic and fiber quality traits in both generations. Comparatively, ZB × DT and L28 × Z98 showed hybrid vigor for multiple traits in both generations and cotton belts. It is feasible to screen strong heterosis hybrid combinations with fine fiber in early generations. In the two environments, the correlation of some traits showed the same trend, and the correlation degree of Anyang site was higher than that of Aral site, and the correlation of some traits showed the opposite trend. According to the performance of strong heterosis hybrid combinations in different environments, the plant type, yield and fiber traits associated with them can be improved according to the correlation.ConclusionsThrough comparative analysis of variance, combining ability, and heterosis in F1 and F2 hybrids in different cotton belts, this study proposed the potential utilization of F2 hybrids to improve upland cotton productivity in China.