BACKGROUND:Cotton is an important economic crop and a host of Liriomyza sativae. Pectin methylesterase (PME)-mediated pectin metabolism plays an indispensable role in multiple biological processes in planta. However, the pleiotropic functions of PME often lead to unpredictable effects on crop resistance to pests. Additionally, whether and how PME affects susceptibility to Liriomyza sativae remain unclear. RESULTS:Here, we isolated GhPME36, which is located in the cell wall, from upland cotton (Gossypium hirsutum L.). Interestingly, the overexpression of GhPME36 in cotton caused severe susceptibility to Liriomyza sativae but increased leaf biomass in Arabidopsis. Cytological observations revealed that the cell wall was thinner with more demethylesterified pectins in GhPME36-OE cotton leaves than in WT leaves, whereas the soluble sugar content of GhPME36-OE cotton leaf cell walls was accordingly higher; both factors attracted Liriomyza sativae to feed on GhPME36-OE cotton leaves. Metabolomic analysis demonstrated that glucose was significantly differentially accumulated. Transcriptomic analysis further revealed DEGs enriched in glucose metabolic pathways when GhPME36 was overexpressed, suggesting that GhPME36 aggravates susceptibility to Liriomyza sativae by affecting both the structure and components of cell wall biosynthesis. Moreover, GhPME36 interacts with another pectin-modifying enzyme, GhC/VIF1, to maintain the dynamic stability of pectin methyl esterification. CONCLUSIONS:Taken together, our results reveal the cytological and molecular mechanisms by which GhPME36 aggravates susceptibility to Liriomyza sativae. This study broadens the knowledge of PME function and provides new insights into plant resistance to pests and the safety of genetically modified plants.

Upland cotton accounts for a high percentage (95%) of the world’s cotton production. Plant height (PH) and branch number (BN) are two important agronomic traits that have an impact on improving the level of cotton mechanical harvesting and cotton yield. In this research, a recombinant inbred line (RIL) population with 250 lines developed from the variety CCRI70 was used for constructing a high-density genetic map and identification of quantitative trait locus (QTL). The results showed that the map harbored 8298 single nucleotide polymorphism (SNP) markers, spanning a total distance of 4876.70 centimorgans (cMs). A total of 69 QTLs for PH (9 stable) and 63 for BN (11 stable) were identified and only one for PH was reported in previous studies. The QTLs for PH and BN harbored 495 and 446 genes, respectively. Combining the annotation information, expression patterns and previous studies of these genes, six genes could be considered as potential candidate genes for PH and BN. The results could be helpful for cotton researchers to better understand the genetic mechanism of PH and BN development, as well as provide valuable genetic resources for cotton breeders to manipulate cotton plant architecture to meet future demands.

Introduction:Upland cotton (Gossypium hirsutum) is the main source of natural fiber in the global textile industry, and thus its fiber quality and yield are important parameters. In this study, comparative transcriptomics was used to analyze differentially expressed genes (DEGs) due to its ability to effectively screen candidate genes during the developmental stages of cotton fiber. However, research using this method is limited, particularly on fiber development. The aim of this study was to uncover the molecular mechanisms underlying the whole period of fiber development and the differences in transcriptional levels.Methods:Comparative transcriptomes are used to analyze transcriptome data and to screen for differentially expressed genes. STEM and WGCNA were used to screen for key genes involved in fiber development. qRT-PCR was performed to verify gene expression of selected DEGs and hub genes.Results:Two accessions of upland cotton with extreme phenotypic differences, namely EZ60 and ZR014121, were used to carry out RNA sequencing (RNA-seq) on fiber samples from different fiber development stages. The results identified 704, 376, 141, 269, 761, and 586 genes that were upregulated, and 1,052, 476, 355, 259, 702, and 847 genes that were downregulated at 0, 5, 10, 15, 20, and 25 days post anthesis, respectively. Similar expression patterns of DEGs were monitored using short time-series expression miner (STEM) analysis, and associated pathways of DEGs within profiles were investigated. In addition, weighted gene co-expression network analysis (WGCNA) identified five key modules in fiber development and screened 20 hub genes involved in the development of fibers.Discussion:Through the annotation of the genes, it was found that the excessive expression of resistance-related genes in the early fiber development stages affects the fiber yield, whereas the sustained expression of cell elongation-related genes is critical for long fibers. This study provides new information that can be used to improve fibers in newly developed upland cotton genotypes.

[Objective] The aim of this study is to explore the elite gene/quantitative trait loci（QTL） resources of yield and fiber quality, and to provide useful information for developing cotton varieties with high yield and excellent fiber quality.[Methods] A superior chromosome segment substitution line MBI9626, and a high-yield and wide-adaptability upland cotton CCRI 36 were selected to construct a secondary segregation population BC 6 F 2 which contained 152 individuals. And 109 selected simple sequence repeat（SSR） markers were used to genotyping parents and the population, and QTL mapping for yield and fiber quality traits was conducted based on genotype data and phenotype data. [Results] Genotyping resutts showed MBI9626 recovered to 94.8% of the genetic background of CCRI 36. A total of 28 QTLs related to yield and fiber quality traits were detected in BC 6 F 2 , BC 6 F 2:3 , and BC 6 F 2:4 populations, which were distributed on 6 chromosomes. Among them, there are 16 QTLs related to yield, accounting for 2.25%-6.14% of the phenotypic variation, including 6 stable QTLs; 12 QTLs related to quality traits, accounting for 2.49%-12.30% of the phenotypic variation, including 2 stable QTLs. There were 19 newly discovered QTLs, including 5 stable QTLs. And 233 genes were identified in a QTL cluster with 6 QTLs on D3 chromosome. Based on gene ontology（GO） cluster and Kyoto encyclopedia of genes and genomes（KEGG）analysis and TM-1 transcriptome data, 6 candidate genes were screened to be involved in fiber development, namely GH＿D03G1428、GH＿D03G1466, GH＿D03G1518, GH＿D03G1570, GH＿D03G1586, and GH＿D03G1640. [Conclusion] Twentyeight stable QTLs related to cotton yield and fiber quality were identified and would lay a solid foundation for fine mapping and cloning of candidates genes and marker assisted selection.

Cotton is the fifth-largest oil crop in the world. A high kernel oil content (KOC) and high stability are important cottonseed attributes for food security. In this study, the phenotype of KOC and the genotype-by-environment interaction factors were collectively dissected using 250 recombinant inbred lines, their parental cultivars sGK156 and 901-001, and CCRI70 across multi-environments. ANOVA and correlation analysis showed that both genotype and environment contributed significantly to KOC accumulation. Analyses of additive main effect multiplicative interaction and genotype-by-environment interaction biplot models presented the effects of genotype, environment, and genotype by environment on KOC performance and the stability of the experimental materials. Interaction network analysis revealed that meteorological and geographical factors explained 38% of the total KOC variance, with average daily rainfall contributing the largest positive impact and cumulative rainfall having the largest negative impact on KOC accumulation. This study provides insight into KOC accumulation and could direct selection strategies for improved KOC and field management of cottonseed in the future.

Upland cotton is an important allotetraploid crop that provides both natural fiber for the textile industry and edible vegetable oil for the food or feed industry. To better understand the genetic mechanism that regulates the biosynthesis of storage oil in cottonseed, we identified the genes harbored in the major quantitative trait loci/nucleotides (QTLs/QTNs) of kernel oil content (KOC) in cottonseed via both multiple linkage analyses and genome-wide association studies (GWAS). In ‘CCRI70′ RILs, six stable QTLs were simultaneously identified by linkage analysis of CHIP and SLAF-seq strategies. In ‘0-153′ RILs, eight stable QTLs were detected by consensus linkage analysis integrating multiple strategies. In the natural panel, thirteen and eight loci were associated across multiple environments with two algorithms of GWAS. Within the confidence interval of a major common QTL on chromosome 3, six genes were identified as participating in the interaction network highly correlated with cottonseed KOC. Further observations of gene differential expression showed that four of the genes, LtnD, PGK, LPLAT1, and PAH2, formed hub genes and two of them, FER and RAV1, formed the key genes in the interaction network. Sequence variations in the coding regions of LtnD, FER, PGK, LPLAT1, and PAH2 genes may support their regulatory effects on oil accumulation in mature cottonseed. Taken together, clustering of the hub genes in the lipid biosynthesis interaction network provides new insights to understanding the mechanism of fatty acid biosynthesis and TAG assembly and to further genetic improvement projects for the KOC in cottonseeds.

In this study, a total of 66 UDP-glucose pyrophosphorylase (UGP) (EC 2.7.7.9) genes were identified from the genomes of four cotton species, which are the members of Pfam glycosyltransferase family (PF01702) and catalyze the reaction between glucose-1-phosphate and UTP to produce UDPG. The analysis of evolutionary relationship, gene structure, and expression provides the basis for studies on function of UGP genes in cotton. The evolutionary tree and gene structure analysis revealed that the UGP gene family is evolutionarily conserved. Collinearity and Ka/Ks analysis indicated that amplification of UGP genes is due to repetitive crosstalk generating between new family genes, while being under strong selection pressure. The analysis of cis-acting elements exhibited that UGP genes play important role in cotton growth, development, abiotic and hormonal stresses. Six UGP genes that were highly expressed in cotton fiber at 15 DPA were screened by transcriptome data and qRT-PCR analysis. The addition of low concentrations of IAA and GA3 to ovule cultures revealed that energy efficiency promoted the development of ovules and fiber clusters, and qRT-PCR showed that expression of these six UGP genes was differentially increased. These results suggest that the UGP gene may play an important role in fiber development, and provides the opportunity to plant researchers to explore the mechanisms involve in fiber development in cotton.

In this study, a total of 66 UDP-glucose pyrophosphorylase (UGP) (EC 2.7.7.9) genes were identified from the genomes of four cotton species, which are the members of Pfam glycosyltransferase family (PF01702) and catalyze the reaction between glucose-1phosphate and UTP to produce UDPG.The analysis of evolutionary relationship, gene structure, and expression provides the basis for studies on function of UGP genes in cotton.The evolutionary tree and gene structure analysis revealed that the UGP gene family is evolutionarily conserved.Where, collinearity and Ka/Ks analysis indicated that amplification of UGP genes is due to repetitive crosstalk generating between new family genes, while being under strong selection pressure.The analysis of cis-acting elements exhibited that UGP genes play important role in cotton growth, development, abiotic and hormonal stresses.Six UGP genes that were highly expressed in cotton fiber at 15 DPA were screened by transcriptome data and qRT-PCR analysis.The addition of low concentrations of IAA and GA3 to ovule cultures revealed that energy efficiency promoted the development of ovules and fiber clusters, and qRT-PCR showed that expression of these six UGP genes was differentially increased.These results suggest that the UGP gene may play an important role in fiber development, and provides the opportunity to plant researchers to explore the mechanisms involve in fiber development in cotton.

中棉所135在四川省植棉区生育期132 d,株型松散,呈塔形,铃长卵圆形;抗枯萎病、耐黄萎病;抗棉铃虫、高抗红铃虫.2018―2019年四川省棉花品种区域试验中,该品种平均籽棉和皮棉产量分别为3797.88 kg·hm-2和1541.19 kg·hm-2.介绍了中棉所135的选育过程、特征特性、纤维品质及其栽培技术要点.

Peroxiredoxin (PRX) is a ubiquitous thioredoxin-dependent peroxidase that can eliminate excessive free radicals produced by stress and protect cells from oxidative damage. PRX s are also involved in reactive oxygen species (ROS)- and redox-dependent signaling by performing redox interactions with other proteins and modify their redox status. At present, PRX family identification, evolution and regulation research has been conducted in some plants; however, systematic research about this family is lacking in cotton. In this study, a total of 44 PRX s were identified in the cotton genome. Phylogenetic and conserved active site analyses showed that the PRX s were divided into six subfamilies according to the conserved site (PxxxTxxC…S…W/F) and conserved cysteinyl residues positions. Segmental duplication and polyploid events were the main methods for PRX family expansion, and the PRXs of diploid G. arboreum were the donors of PRX s in the D subgenomes of allotetraploid G. hirsutum and G. barbadense during the evolution of the PRX family. qRT-PCR analysis confirmed that cis-acting elements play important roles in regulating the expression of PRX s. Alternative splicing events occurred in GhPRX14-D that can increased the complexity of transcripts in G. hirsutum . Subcellular localization showed that most PRX members were located in chloroplasts, the cytoplasmic membrane and the nucleus. Our results provide systematic support for a better understanding of PRX s in cotton and a starting point for further studies of the specific functions of PRX s in cotton.

UDP-glucose dehydrogenase (UGD; EC1.1.1.22) is a NAD + -dependent enzyme that catalyzes the two-fold oxidation of UDP-glucose (UDP-Glc) to produce UDP-glucuronic acid and plays an important role in plant cell wall synthesis. A total of 42 UGD genes from four Gossypium genomes including G . hirsutum , G . arboretum , G . barbadense , and G . raimondii were identified and found that the UGD gene family has conservative evolution patterns in gene structure and protein domain. The growth of fibers can be effectively promoted after adding the UDP-Glc to the medium, and the GhUGD gene expression enhanced. In addition, the transgenic Arabidopsis lines over-expressing GH_D12G1806 had longer root lengths and higher gene expression level than the wild-type plants of Columbia-0 . These results indicated that UGD may play important roles in cotton fiber development and has a guiding significance for dissecting fiber development mechanism.

在湖南省植棉区,中棉所131夏播生育期为103.9 d,植株塔形,叶片中等大小,花药白色,吐絮畅,对脱叶剂敏感,耐枯萎病,耐黄萎病,抗棉铃虫.在2019―2020年湖南省机采棉区域试验中,该品种平均籽棉和皮棉产量分别为3814.43 kg·hm-2和1501.38 kg·hm-2,纤维品质为Ⅱ型.本文介绍了中棉所131的选育过程及其特征特性、产量、纤维品质表现和栽培要点.

介绍中棉所127的选育过程及其特征特性、产量、纤维品质以及栽培要点.

Background Pectin is a key substance involved in cell wall development, and the galacturonosyltransferases (GAUTs) gene family is a critical participant in the pectin synthesis pathway. Systematic and comprehensive research on GAUTs has not been performed in cotton. Analysis of the evolution and expression patterns of the GAUT gene family in different cotton species is needed to increase knowledge of the function of pectin in cotton fiber development. Results In this study, we have identified 131 GAUT genes in the genomes of four Gossypium species ( G. raimondii , G. barbadense , G. hirsutum , and G. arboreum ), and classified them as GAUT-A , GAUT-B and GAUT-C , which coding probable galacturonosyltransferases. Among them, the GAUT genes encode proteins GAUT1 to GAUT15. All GAUT proteins except for GAUT7 contain a conserved glycosyl transferase family 8 domain (H-DN-A-SVV-S-V-H-T-F). The conserved sequence of GAUT7 is PLN (phospholamban) 02769 domain. According to cis -elemet analysis, GAUT genes transcript levels may be regulated by hormones such as JA, GA, SA, ABA, Me-JA, and IAA. The evolution and transcription patterns of the GAUT gene family in different cotton species and the transcript levels in upland cotton lines with different fiber strength were analyzed. Peak transcript level of GhGAUT genes have been observed before 15 DPA. In the six materials with high fiber strength, the transcription of GhGAUT genes were concentrated from 10 to 15 DPA; while the highest transcript levels in low fiber strength materials were detected between 5 and 10 DPA. These results lays the foundation for future research on gene function during cotton fiber development. Conclusions The GAUT gene family may affect cotton fiber development, including fiber elongation and fiber thickening. In the low strength fiber lines, GAUTs mainly participate in fiber elongation, whereas their major effect on cotton with high strength fiber is related to both elongation and thickening.

Upland cotton (Gossypium hirsutum) is widely planted around the world for its natural fiber, and producing high-quality fiber is essential for the textile industry. CCRI70 is a hybrid cotton plant harboring superior yield and fiber quality, whose recombinant inbred line (RIL) population was developed from two upland cotton varieties (sGK156 and 901-001) and were used here to investigate the source of high-quality related alleles. Based on the material of the whole population, a high-density genetic map was constructed using specific locus-amplified fragment sequencing (SLAF-seq). It contained 24,425 single nucleotide polymorphism (SNP) markers, spanning a distance of 4,850.47 centimorgans (cM) over 26 chromosomes with an average marker interval of 0.20 cM. In evaluating three fiber quality traits in nine environments to detect multiple environments stable quantitative trait loci (QTLs), we found 289 QTLs, of which 36 of them were stable QTLs and 18 were novel. Based on the transcriptome analysis for two parents and two RILs, 24,941 unique differentially expressed genes (DEGs) were identified, 473 of which were promising genes. For the fiber strength (FS) QTLs, 320 DEGs were identified, suggesting that pectin synthesis, phenylpropanoid biosynthesis, and plant hormone signaling pathways could influence FS, and several transcription factors may regulate fiber development, such as GAE6, C4H, OMT1, AFR18, EIN3, bZIP44, and GAI. Notably, the marker D13_56413025 in qFS-chr18-4 provides a potential basis for enhancing fiber quality of upland cotton via marker-assisted breeding and gene cloning of important fiber quality traits.

Upland cotton is the most widely planted for natural fiber around the world, and either lint percentage (LP) or fiber length (FL) is the crucial component tremendously affecting cotton yield and fiber quality, respectively. In this study, two lines MBZ70-053 and MBZ70-236 derived from G. hirsutum CCRI70 recombinant inbred line (RIL) population presenting different phenotypes in LP and FL traits were chosen to conduct RNA sequencing on ovule and fiber samples, aiming at exploring the differences of molecular and genetic mechanisms during cotton fiber initiation and elongation stages. As a result, 249/128, 369/206, 4296/1198 and 3547/2129 up-/down- regulated differentially expressed genes (DGEs) in L2 were obtained at −3, 0, 5 and 10 days post-anthesis (DPA), respectively. Seven gene expression profiles were discriminated using Short Time-series Expression Miner (STEM) analysis; seven modules and hub genes were identified using weighted gene co-expression network analysis. The DEGs were mainly enriched into energetic metabolism and accumulating as well as auxin signaling pathway in initiation and elongation stages, respectively. Meanwhile, 29 hub genes were identified as 14-3-3ω, TBL35, GhACS, PME3, GAMMA-TIP, PUM-7, etc., where the DEGs and hub genes revealed the genetic and molecular mechanisms and differences during cotton fiber development.

为了进一步揭示棉花优质品种的纤维产量和品质性状之间的遗传关系,筛选纤维品质突出的优异材料,本研究以优质品种中棉所127为父本,与高产品系sGK中156为母本杂交,构建F2和F2∶3分离大群体,对分离群体的纤维产量与品质进行初步评价分析.结果表明F2和F2∶3世代中铃重、衣分、纤维上半部平均长度、断裂比强度、马克隆值、伸长率和整齐度性状均呈正态分布,表现双向超亲分离,群体内存在丰富的遗传变异,纤维上半部平均长度的超高亲比例分别为61.38％和69.55％,断裂比强度的超高亲比例分别为42.12％和61.00％,铃重的超高亲比例分别为41.31％和28.43％.2个分离世代纤维上半部平均长度和断裂比强度呈现出极显著正相关,衣分与纤维上半部平均长度和断裂比强度这2个主要纤维品质性状呈极显著负相关,表明同步对纤维产量和品质进行改良具有一定的难度.筛选出同时在F2和F2∶3中断裂比强度大于38.00 cN/tex的优异材料10个,且纤维上半部平均长度均大于31.00 mm.本研究为棉花纤维产量和品质QTL挖掘及分子聚合育种等储备了大量的基础材料.

Table S1. ANOVA and broad-sense heritability analysis for cottonseed oil content. Table S2. QTLs related to cottonseed oil content identified in eight environments. Table S3. 832 genes in the five stable QTL regions. Table S4. KEGG pathway enrichment analysis of 832 genes around stable QTLs. Table S5. Genes list identified by BLAST with Arabidopsis thaliana oil-related genes. Table S6. The expression level (FPKM values) of candidate oil genes during developing ovules of G. hirsutum L. Table S7. Four transcription factors related to cottonseed lipid content. Table S8. The microRNA-target gene regulatory network of G. hirsutum L. Table S9. The designed primers of genes encoding the key enzymes involved in lipid biosynthesis for qRT-PCR.

[目的]使用傅里叶变换红外显微光谱(Micro-Fourier transform infrared spectroscopy,micro-FTIR)结合X射线衍射(X-ray diffraction,XRD)方法研究2个不同品系发育中棉纤维的纤维素结晶度(Crystalline index,CI)变化,验证micro-FTIR法测定发育中棉花纤维素CI的可行性,并用此方法对成熟棉花纤维素CI进行分析.[方法]以陆地棉0-153和海岛棉S-6为研究材料.分别获取这2个品系开花后5～30 d的棉纤维样本,取样间隔为5 d.样本清洗烘干后,获取FTIR和XRD光谱.选择4种不同FTIR结晶度(FTIR-CI)计算方法,分析2个品系棉花纤维不同发育阶段的纤维素结晶度变化,并对FTIR-CI与XRD结晶度(XRD-CI)分析结果进行回归拟合相关性分析.[结果]采用FTIR-CCI(Carrillo-Colom index)法得到的CI与XRD-CI的回归拟合相关性较高,0-153和S-6的决定系数R2均高于0.9.将基于FTIR-CCI法的CI与XRD-CI的拟合模型用于计算随机选取的18种成熟纤维的CI(IR-CI),结果显示IR-CI虽然准确度较高,XRD-CI也在IR-CI结果的误差范围内,但是其精密度不够理想.[结论]micro-FTIR可以用于棉花纤维发育过程中结晶态纤维素累积变化研究.对FTIR-CCI法计算得到的CI与XRD-CI进行拟合建立的红外显微光谱结晶度模型可用于评估发育中棉纤维的结晶度,但是对于成熟纤维的结晶度,还需要后期使用大量的样品建立优化的研究模型.

Cotton (Gossypium hirsutum) is an important cash crop, providing people with high quality natural fiber. Lignin is the main component of cotton fiber, second only to cellulose. As a main substance filled in the cellulose framework during the secondary wall thickening process, lignin plays a key role in the formation of cotton fiber quality. However, the mechanism behind it is still unclear. In this research, we screened candidate genes involved in lignin biosynthesis based on analysis of cotton genome and transcriptome sequence data. The authenticity of the transcriptome data was verified by qRT-PCR assay. Total 62 genes were identified from nine gene families. In the process, we found the key gene GhCAD7 that affects the biosynthesis of S-lignin and the ratio of syringyl/guaiacyl (S/G). In addition, in combination with the metabolites and transcriptome profiles of the line 0-153 with high fiber quality and the line sGK9708 with low fiber quality during cotton fiber development, we speculate that the ratio of syringyl/guaiacyl (S/G) is inseparable from the quality of cotton fiber. Finally, the S-type lignin synthesis branch may play a more important role in the formation of high-quality fiber. This work provides insights into the synthesis of lignin in cotton and lays the foundation for future research into improving fiber quality.