DNA methylation is a stable epigenetic modification with essential roles in plant drought response. It is known that methyltransferase mutant is necessary for the regulation of methylation variations, but this epigenetic molecular mechanism based on methyltransferase mutant in responding to drought stress was still unclear in cotton. In this study, we aim to decipher the epigenetic code of drought response regulated by methyltransferase gene GhDMT9 in cotton, providing valuable information for the molecular research of drought resistance in cotton. We successfully created the first cotton methyltransferase mutant ghdmt9 using CRISPR/Cas9 method and performed methylation variations analysis with whole-genome bisulfite sequencing (WGBS) and transcriptome analysis based on ghdmt9 mutant. In addition, specific antibody of methyltransferase GhDMT9 was prepared and used for Chromatin Immunoprecipitation (ChIP-seq) analysis. The results indicated that ghdmt9 mutant interpreted approximately 2.06% methylation variations under drought stress. Demethylation variations, mainly derived from the CHG and CHH contexts, were closely correlated with drought response. Whether at normal growth stage or under drought stress, the number of up-regulated genes induced by demethylation variations was apparently higher than the number of down-regulated genes, especially genes regulating lipids and lipid-like molecules and hormone-related genes. In addition, fiber quality of ghdmt9 mutant was obviously better than that of wild type (WT). Interestingly, a transcription factor lsh (lysine-specific histone) was found to interact with methyltransferase gene GhDMT9 to activate its hyper-methylation function of target genomic regions by ChIP-seq analysis. Overall, our results extend our understanding of the epigenetic regulation of methyltransferase GhDMT9 in drought response and contribute to further investigations of the epigenetic mechanisms underlying abiotic stresses in cotton.

INTRODUCTION:Soil salinization and alkalization are major challenges to global agricultural productivity and food security. Ascorbic acid (AsA) is an essential antioxidant that helps plants mitigate various abiotic stresses. However, the genetic mechanisms underlying AsA's role in enhancing alkaline stress tolerance remain poorly understood. OBJECTIVES:The objective of this study was to determine whether GhIMP10D, a gene involved in AsA biosynthesis, enhances alkaline stress tolerance in cotton and Arabidopsis by modulating AsA accumulation and cell wall integrity. METHODS:We performed gene identification and functional analysis using overexpression and silencing techniques in Arabidopsis, rice, and cotton. GhIMP10D, a gene involved in the AsA biosynthesis pathway, was studied for its response to alkaline stress. The role of the bHLH transcription factor GhbHLH48 in regulating GhIMP10D was also explored. RESULTS:Our findings showed that overexpression of GhIMP10D resulted in increased AsA production, reduced reactive oxygen species (ROS), and enhanced cell wall integrity in the tested plants. In contrast, silencing GhIMP10D compromised alkaline stress adaptation. We further identified that GhbHLH48 directly activates GhIMP10D by binding to its promoter's G-box element. Manipulating GhbHLH48 levels altered AsA, lignin, and cellulose content, which affected ROS balance and cell wall biosynthesis. CONCLUSION:The GhbHLH48-GhIMP10D regulatory module plays a crucial role in AsA biosynthesis and the maintenance of cell wall integrity under alkaline stress. These findings contribute to a better understanding of AsA signaling pathways and cell wall formation in response to alkaline stress, offering potential strategies for enhancing plant stress tolerance.

Alkaline stress causes significant adverse effects that slows down the growth of plants and lowers the yield of crops; hence, it is a major challenge in cotton farming. Spermidine (Spd), a vital polyamine, plays a significant role in enhancing plant resistance to stress caused by various abiotic factors. The molecular mechanism of Spd biosynthesis and especially the role of spermidine synthase (SPDS) in tolerance of alkaline stress in cotton is, however, little known. In this study, a systematic comparative analysis of SPDS-associated genes was performed across four representative cotton cultivars (Gossypium spp.), followed by preliminary functional characterization through promoter cis-acting element profiling. Virus-induced gene silencing (VIGS) was utilized to disrupt GhSPDS11-mediated Spd biosynthesis. Under alkaline stress, GhSPDS11-silenced seedlings exhibited 29.14% and 11.12% reductions in superoxide dismutase (SOD) and catalase (CAT) activities, 31.57% and 15.16% decreases in soluble sugar and proline (Pro) content, along with 42.38% and 38.66% increases in malondialdehyde (MDA) and hydrogen peroxide (H₂O₂) compared to controls. Concurrently, silenced plants showed 44.87% fewer open stomata and significant declines in Spd content, relative water content, and biomass. These results indicate the key importance of Spd, which is composed of GhSPDS11, in improving alkali tolerance in cotton. This research gives good information regarding the molecular processes that take part in the tolerance of cotton to the saline-alkaline soils, and that GhSPDS11 could be a good genetic target in cotton enhancement in this tough agro-climatic condition.

Citrate synthase (CS) catalyzes the biosynthesis of citrate (CA), a tricarboxylic acid metabolite that serves as a pivotal biochemical regulator in plant cellular metabolism. This investigation conducted systematic genome-wide identification of CS family, integrating structural, phylogenetic relationships, collinearity analysis, cis-acting elements and expression analysis. GhCS6 protein is localized in the mitochondria. The pivotal cadmium-responsive regulatory candidate gene GhCS6 was identified, followed by its silencing mediation through virus-induced gene silencing (VIGS), silenced plants displaying phenotypic evidence of enhanced Cd2+ susceptibility. Simultaneously, CA content in the silenced plants was also significantly decreased, which reduced the chelating capacity for Cd2+ and consequently exacerbates the accumulation of Cd2+. The silenced plants showed an imbalance in the reactive oxygen species (ROS) scavenging system, as evidenced by lower superoxide dismutase (SOD) activity and a marked increase in H2O2 content, causing increased oxidative damage. This oxidative stress further compromised the integrity of cellular membranes, resulting in elevated malondialdehyde (MDA) content and compromised cellular structure. These changes ultimately impaired photosynthetic efficiency and plant growth and development. This study contributes significantly to understanding the function of the GhCS6 in plant Cd2+ tolerance, and identifies potential gene targets for breeding Cd2+ tolerant cotton varieties.

This study provides a comprehensive analysis of the impact of DNA methylation in cotton under salt stress conditions, elucidating its effects on gene expression and biological processes. Here, we determined the structures of the DNA methylation landscape across the cotton genome subjected to salt stress using whole-genome bisulfite sequencing (WGBS) and RNA-seq methodologies. We identified 4938 differentially methylated regions (DMRs) correlated with alterations in gene expression. Salt stress induced significant shifts in DNA methylation patterns, particularly in CHH contexts, suggesting context-dependent epigenetic regulation. DMRs were found to be implicated in diverse biological processes and pathways, encompassing protein metabolism, cellular homeostasis, starch and sucrose metabolism, and plant hormone signaling, all pivotal for cotton's adaptation to salt stress. Furthermore, RNA-seq analysis confirmed the impact of DNA methylation on gene expression, uncovering 9642 salt stress-responsive differentially expressed genes (DEGs). These DEGs exhibited enrichment in pathways such as carbohydrate metabolism, cell wall synthesis, and defense response, underscoring the intricate interplay between methylation and gene regulation in stress response. Moreover, the study investigated the role of the key DNA methyltransferase gene GhDMT7 in modulating cotton's response to salt stress, revealing that its downregulation enhanced cotton's salt tolerance, potentially attributed to decreased DNA methylation levels, reduced membrane damage, and enhanced antioxidant capacity. These findings elucidate the role of DNA methylation in abiotic stress resilience and provide insights for crop improvement.

Introduction: Ascorbic acid (AsA) is involved in plant responses to various abiotic stresses. However, its specific function in alkaline stress tolerance remains poorly understood. The L-galactono-1,4-lactone dehydrogenase (GLDH) gene is crucial for AsA synthesis, yet the precise role of GLDH in modulating plant resistance to alkaline stress has not been comprehensively characterized. Objectives: To investigate the role of GLDH genes in enhancing tolerance to alkaline stress. Methods: Bioinformatics analysis of the GLDH gene family members was conducted, and an evolutionary tree was constructed using MEGA software. Cis-acting elements and gene structures were analyzed using TBtools. Gene expression levels were quantified by qRT-PCR, while the function of the GhGLDH35A gene was validated through VIGS (Virus-induced gene silencing) in cotton, heterologous overexpression in Arabidopsis thaliana, and complementation assays in yeast. Results: Our study investigated the effects of salt-alkaline stress on cotton and found that alkaline stress caused significantly more severe damage than salt stress. The GLDH family genes were identified and analyzed, revealing a high degree of evolutionary conservation. Most GhGLDH genes exhibited a positive response to alkaline stress and were regulated by light. Among them, GhGLDH35A, which is highly expressed within the GLDH family, was found to play a key role in conferring tolerance to alkaline stress. Subcellular localization analysis indicated that GhGLDH35A is localized in the mitochondria. Silencing of GhGLDH35A in cotton resulted in reduced tolerance to alkaline stress, disruption of ROS homeostasis, and impairment of photosynthesis and stomatal function. Conversely, overexpression of GhGLDH35A in Arabidopsis enhanced alkaline stress resistance by elevating AsA levels, increasing antioxidant enzyme activities to enhance ROS scavenging, sustaining photosynthesis, and promoting stomatal closure. Furthermore, heterologous expression of GhGLDH35A in yeast also improved its tolerance to alkaline stress. Conclusions: GhGLDH35A positively regulates alkaline stress tolerance by enhancing antioxidant defenses and regulating stomatal movement.

Tryptophan decarboxylase (TDC) is the rate-limiting enzyme in the biosynthesis of melatonin and plays a crucial role in melatonin production in plants. Melatonin (MT), a multifunctional indoleamine compound, plays a pivotal role in plant responses to abiotic stress. Substantial evidence has demonstrated that MT can significantly enhance plant tolerance to drought stress. However, the molecular mechanisms underlying MT-mediated drought stress responses in plants remain unclear. This study systematically analyzed the evolutionary relationships of the TDC gene family in four cotton species using bioinformatics approaches, including phylogenetic analysis, chromosomal localization, gene structure, conserved motifs, cis-acting elements, synteny, and expression patterns. Functional characterization of GhTDC5 in Gossypium hirsutum was performed using virus-induced gene silencing (VIGS), with the following key findings: gene silencing efficiency reached 67.5

Brassinazole resistant (BZR) transcription factors play important roles in brassinosteroids (BRs) signaling pathway of plants, which are involved in many developmental processes and the responses to abiotic stress by regulating the expression of related genes. In order to explore the molecular mechanism of BZR transcription factors in cotton in response to abiotic stress, the BZR transcription factors in four cotton genomes were identified and analyzed. A total of 67 BZR transcription factors were identified and divided into three subfamilies according to their genetic relationship. The expression levels of BZR under cold, heat, salt, and drought treatments were analyzed to predict their function under abiotic stress. Promoter analysis of BZR proteins showed that light signaling can enhance the BZR transcriptional activity. The subcellular localization experiment showed that GhBZR15 protein was mainly distributed in the nucleus. Arabidopsis thaliana L. overexpressing GhBZR15 gene showed stronger cold tolerance and salt tolerance than wild type. These results, combined with the GhBZR protein-interaction network, suggest that the interaction of GhBZR with phytochrome interacting factors (PIF4) plays an important role in abiotic stress responses. These findings provide a basis for further understanding the function of BZR in cotton.

IRE1 is an endoplasmic reticulum (ER)-resident sensor and performs as a crucial regulator in the response to adverse conditions. Previous studies have focused on the function of IRE under drought and heat stress, but how IRE1 participates in salt stress is not clear. In this study, silencing the IRE1a and IRE1b genes in Gossypium hirsutum exhibited increased tolerance to salt stress compared to WT plants. Moreover, Arabidopsis thaliana overexpressing two splice variants of GhIRE1a, s1 and s2, showed different phenotypes under salt stress conditions. The overexpression of s1, which contains two domains (kinase and endoribonuclease domains), negatively regulated salt tolerance, while s2, which contains one kinase domain, did not affect the salt tolerance of Arabidopsis thaliana, suggesting that IRE1 negatively regulated salt tolerance. Cotton seedlings treated with STF-083010, which is a chemical inhibitor of IRE1 endoribonuclease, displayed reduced H2O2 contents and increased activity of GST, TPX and TRXR, suggesting that inhibition of IRE1 endoribonuclease confers salt tolerance by decreasing H2O2 contents in Gossypium hirsutum. Collectively, our results revealed the essential function of GhIRE1 in the salt stress response, in which GhIRE1 plays a vital role by regulating ROS under salt stress.

The subtilisin-like proteases (SBTs) are a large family of serine peptidases that are unique to plants. Previous studies have shown that SBTs are associated with developmental processes and environmental responses. However, comprehensive identification and systematic analysis of the SBT family have not been conducted in cotton. We used bioinformatics methods to analyze the structural characteristics, phylogenetic relationships, gene structures, expression modes, evolutionary relationships, selection pressures and stress responses of SBT gene family members in upland cotton. In this study, we identified 120 and 112 SBTs in the tetraploid cotton species G. hirsutum and G. barbadense, while 67 and 69 SBTs were identified in the diploid species G. arboreum and G. raimondii, respectively; these SBTs were divided into five distinct subfamilies. We identified the SBT gene GhSBT27A, and explore its function through virus-induced gene silencing and transmission electron microscopy. These results suggested that the GhSBT27A gene was involved in the response to drought stress. These results lay a foundation for further study on the drought stress mechanism of cotton.

As a receptor for plant melatonin, CAND2/PMTR plays an important role in melatonin signaling. Most of the CANDs are membrane proteins and play indispensable roles in signal transduction. In this study, the CANDs from four cotton species were characterized, and the phylogenetic relationships, expression patterns, stress responses of cotton CANDs were analyzed by bioinformatics. Through the analysis of phylogenetic and protein structure, it was found that the CANDs in clade Ⅱ might function as cotton melatonin receptors, and most of the GhCANDs in clade Ⅱ were induced by melatonin. A putative cotton melatonin receptor, GhCAND2-D5, was functionally probed by gene silencing. The plants with silenced expression of this gene exhibited decreased salt tolerance. Protein interaction prediction identified that GhCAND2-D5 interacted with several membrane proteins and played an important role in melatonin signaling. This study provided a theoretical reference for further investigation of melatonin signaling in cotton.

衡棉HD008是河北省农林科学院旱作农业研究所培育的中早熟、宜机采的转基因抗虫常规棉品种,2019年通过河北省审定,适宜河北省中南部春播棉区种植.该品种株型较紧凑,叶片较小,单株结铃性好,疯杈赘芽少,吐絮畅、集中.在早熟性、抗逆性、丰产稳产性、品质、适采性等方面表现突出.生育期119 d,株高92 cm,第1果枝节位6.9节,高度24.0 cm,单株果枝数11.6个,果枝夹角66.4°,单株结铃数11.3个,吐絮率80.7％.铃重5.8 g,子指12.7g,衣分率39.2％.生产试验中亩籽棉、皮棉产量分别为257.3 kg、99.1 kg.农业部棉花品质监督检验测试中心检测,半部平均长度29.5 mm,断裂比强度31.3cN/tex,马克隆值5.2,整齐度指数85.2％,纺纱均匀指数142.0.经河北省农林科学院植物保护研究所抗病性鉴定,为高抗枯萎病、耐黄萎病.根据品种特征特性,结合近两年生产示范推广情况,总结出该品种的配套栽培技术.

IntroductionStarch metabolism is involved in the stress response. Starch synthase (SS) is the key enzyme in plant starch synthesis, which plays an indispensable role in the conversion of pyrophosphoric acid to starch. However, the SS gene family in cotton has not been comprehensively identified and systematically analyzed.ResultIn our study, a total of 76 SS genes were identified from four cotton genomes and divided into five subfamilies through phylogenetic analysis. Genetic structure analysis proved that SS genes from the same subfamily had similar genetic structure and conserved sequences. A cis-element analysis of the SS gene promoter showed that it mainly contains light response elements, plant hormone response elements, and abiotic stress elements, which indicated that the SS gene played key roles not only in starch synthesis but also in abiotic stress response. Furthermore, we also conducted a gene interaction network for SS proteins. Silencing GhSS9 expression decreased the resistance of cotton to drought stress. These findings suggested that SS genes could be related to drought stress in cotton, which provided theoretical support for further research on the regulation mechanism of SS genes on abiotic starch synthesis and sugar levels.

As an important cash crop, cotton is often affected by Soil-drought stress. Soil-drought is a common abiotic stress that seriously affects the growth and development of crops. Since soil moisture is not easy to control and prolonged treatment is required to cause water stress, polyethylene glycol (PEG) is often used to simulate drought stress and cause dehydration in plants. However, whether there is a difference in the effects of these two types of drought stresses on cotton remains unclear. In this study, cotton seedlings with the same water potential under two stresses were used as research materials, and the differences in molecular mechanisms of cotton resistance to the different drought stresses were explored through physiological and biochemical detection, chloroplast ultrastructure observations and transcriptomic sequencing. The results showed that both Soil-drought and PEG-drought can cause water stress effects on cotton seedlings, causing them to dehydrate and wilt. The contents of soluble protein (SP), Proline (Pro), and malondialdehyde (MDA) and the activity of superoxide dismutase (SOD) showed similar changes under the two stresses. However, by observing the chloroplast ultrastructure, we found that starch accumulated in chloroplasts under Soil-drought, but was not obvious under PEG-drought. Stress-induced differentially expressed genes (DEGs) under both types of drought showed similar changes in Gene Ontology (GO) functional enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, but Soil-drought induced more DEGs. The differential expression of sugar-related (sugar synthesis, sugar metabolism, sugar transport, etc.) genes in cotton seedlings under Soil-drought stress was higher than that under PEG-drought. In the case of consistent dehydration, there are clear differences in the sugar-pathway when cotton experiences Soil-drought and PEG-drought. PEG drought can simulate Soil drought in terms of the physiological effects of dehydration on cotton, but it is not applicable in terms of the effects of drought stress on the sugar pathway. This study enables us to better understand the response of cotton to different drought stress and provides a certain research basis for exploring cotton resistance to drought stress.

Serotonin N-acetyltransferase (SNAT) is a key enzyme in the biosynthesis of melatonin, and plays an important role in the regulation of melatonin synthesis. The study of SNAT is of great significance to understand the function of melatonin. In this study, we analyzed the structural characteristics, phylogenetic relationship, gene structure, expression pattern, evolutionary relationship and stress response of the members of the SNAT gene family in upland cotton through bioinformatics. A putative Serotonin n-acetyltransferase gene GhSNAT3D was identified, and preliminarily function of GhSNAT3D was verified by virus-induced gene silencing. We identified a total of 52 SNAT genes in the whole genome of G. hirsutum, and part of the GhSNATs were regulated by exogenous melatonin. The content of melatonin, antioxidant enzyme activity and Ca2+ content of GhSNAT3D gene silenced plants decreased, and the salt tolerance of GhSNAT3D gene silenced plants was reduced. Exogenous melatonin supplementation restored the salt tolerance of GhSNAT3D gene silenced plants. GhSNAT3D may interact with GhSNAT25D and ASMT to regulate melatonin synthesis. This study provided an important basis for further study on the regulation of melatonin in cotton against abiotic stress.

Plants are sessile organisms suffering severe environmental conditions. Drought stress is one of the major environmental issues that affect plant growth and productivity. Although complex regulatory gene networks of plants under drought stress have been analyzed extensively, the response mechanism in the early stage of drought stress is still rarely mentioned. Here, we performed transcriptome analyses on cotton samples treated for a short time (10 min, 30 min, 60 min, 180 min) using 10% PEG, which is used to simulate drought stress. The analysis of differently expressed genes (DEGs) showed that the number of DEGs in roots was obviously more than that in stems and leaves at the four time points and maintained > 2000 FDEGs (DEGs appearing for the first time) from 10 min, indicating that root tissues of plants respond to drought stress quickly and continuously strongly. Gene ontology (GO) analysis showed that DEGs in roots were mainly enriched in protein modification and microtubule-based process. DEGs were found significantly enriched in phosphatidylinositol signaling system at 10 min through Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, implying the great importance of phosphatidylinositol signal in the early stage of drought stress. What was more, two co-expression modules, which were significantly positively correlated with drought stress, were found by Weighted Gene Co-expression Network Analysis (WGCNA). From one of the co-expression modules, we identified a hub-gene Gohir. A07G058200, which is annotated as "phosphatidylinositol 3-and 4-kinase " in phosphatidylinositol signaling system, and found this gene may interact with auxin-responsive protein. This result suggested that Gohir. A07G058200 may be involved in the crosstalk of phosphatidylinositol signal and auxin signal in the early stage of drought stress. In summary, through transcriptome sequencing, we found that phosphatidylinositol signaling system is an important signal transduction pathway in early stage in response to drought stress, and it may interact with auxin signal transduction through phosphatidylinositol 3-and 4-kinase.

为定量评估华北山前平原多因子对地下水水位动态变化的影响,选取华北山前平原典型井灌区石家庄市栾城区为研究区,从水量平衡角度分析了影响该地区地下水水位动态变化的主要影响因子;利用主成分回归分析法排除主要影响因子间的相互作用,定量分析了各综合因子对地下水水位回升的贡献率;构建了栾城地下水水位主成分时间序列模型预测多因子影响下的华北山前平原地下水水位变化.结果表明:1994—2015年栾城地下水水位主要受本地气候因子、本地人类活动和上游人类活动三方面影响因子的共同作用,各因子对当地地下水水位回升的贡献率分别为11.7％、-50.9％和-37.4％,对这三方面影响因子起主导作用的影响因素分别为栾城降水量、栾城小麦和玉米的种植面积以及上游石家庄市区人口;1994—2015年栾城自然气候变化有利于该地区地下水资源的恢复,但人类活动对地下水资源的影响仍占主导作用.

BACKGROUND:Gossypium hirsutum L. is the most widely cultivated cotton species, and a high-quality reference genome would be a huge boost for researching the molecular mechanism of agronomic traits in cotton. FINDINGS:Here, Pacific Biosciences and Hi-C sequencing technologies were used to assemble a new upland cotton genome of the No. 1 Chinese cotton variety CRI-12. We generated a high-quality assembled CRI-12 genome of 2.31 Gb with a contig N50 of 19.65 Mb, which was superior to previously reported genomes. Comparisons between CRI-12 and other reported genomes revealed 7,966 structural variations and 7,378 presence/absence variations. The distribution of the haplotypes among A-genome (Gossypium arboreum), D-genome (Gossypium raimondii), and AD-genome (G. hirsutum and Gossypium barbadense) suggested that many haplotypes were lost and recombined in the process of polyploidization. More than half of the haplotypes that correlated with different tolerances were located on chromosome D13, suggesting that this chromosome may be important for wide adaptation. Finally, it was demonstrated that DNA methylation may provide advantages in environmental adaptation through whole-genome bisulfite sequencing analysis. CONCLUSIONS:This research provides a new reference genome for molecular biology research on Gossypium hirsutum L. and helps decode the broad environmental adaptation mechanisms in the No. 1 Chinese cotton variety CRI-12.

Drought stress is one of the abiotic stresses that limits crop production and greatly affects crop yield. Enhancement of plant stress resistance by NaCl pretreatment has been reported, but the mechanism by which NaCl pretreatment activates cotton stress resistance remains unclear. In this study, upland cotton ( Gossypium hirsutum cv H177 ) was used as the material to conducted the treatments with three replications: 0 Mm NaCl + 0% PEG6000 (Polyethylene glycol), 0 mM NaCl + 15% PEG6000, 50 mM NaCl + 15% PEG6000 to explore the molecular mechanism by which NaCl improves the drought tolerance of cotton. The results showed that pretreatment with 50 mM NaCl could alleviate the adverse effects of PEG on cotton seeds while promoting the elongation of root length. RNA-seq showed that NaCl specifically induced the expression of carotenoid-related genes. By silencing the upstream gene GHLUT2 of lutein synthesis, it was found that the chlorophyll of silenced plants decreased, and leaf wilting was more sensitive to drought. We found that NaCl enhanced the drought resistance of cotton by regulating genes related to the carotenoid and abscisic acid downstream synthesis pathways. This study provides a new reference for the study of drought resistance in cotton and a theoretical basis for the molecular breeding of cotton.

Abstract Background Hailstorm might damage cotton plants severely and cause heavy economic loss in field production. It hailed vehemently three times in 2015 and 2016 in Yellow River Basin Cotton Region and damaged cotton seedling and buds. The apical buds, leaves and stems were damaged as well as boll branches and few flower buds in our experiments. Serials strategies were performed to recover and rescue the cotton plants. Based on evaluating the hailstone damage, we fertilized 112.50 kg/ha Urea fertilizer (N content ≥ 46.4%) and intertilled the field timely. Results The recovery of plant individuals sprouted new buds and many new leaves after 12 DAH. Then the unnecessary shoots were pruned to adjust the development of fruit branches. Normally three new boll branches (NBB) in the major stem were reserved and eight subsequent emerging boll branches (EBB) in cotton plants. Five accessions with varied recovery ability and with different yield potential were sampled to compare the yield after hail damage, Sumian 20, 11–0710 and 11–0516 increased, while the other two accessions decreased relative to the normal production without hail damage. BC and RIL populations of upland cotton were used to evaluate the damage ratio of yield, which resulted in yield loss ranged 13.45%-20.27%. Fiber length, fibre elongation, fibre uniformity, and fiber elongation decreased slightly in the five accessions and in two populations. Conclusions The present study indicated that different accessions showed varied recovery ability for yield production, but all of them with a decreased ratio less than 20%. In addition, there was no significant effect on fiber quality in different cotton varieties. These results proved that the cotton plants can compensate by proper field managements, and remedial output could be obtained after hail damage.