scholarly journals Comparative transcriptome analysis of fiber and nonfiber tissues to identify the genes preferentially expressed in fiber development in Gossypium hirsutum

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jiangtao Yang ◽  
Lihua Gao ◽  
Xiaojing Liu ◽  
Xiaochun Zhang ◽  
Xujing Wang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gossypium Hirsutum ◽  
Rna Sequencing ◽  
Transcriptome Analysis ◽  
Cotton Fiber ◽  
Upland Cotton ◽  
Fiber Quality ◽  
Fiber Development ◽  
Comparative Transcriptome

AbstractCotton is an important natural fiber crop and economic crop worldwide. The quality of cotton fiber directly determines the quality of cotton textiles. Identifying cotton fiber development-related genes and exploring their biological functions will not only help to better understand the elongation and development mechanisms of cotton fibers but also provide a theoretical basis for the cultivation of new cotton varieties with excellent fiber quality. In this study, RNA sequencing technology was used to construct transcriptome databases for different nonfiber tissues (root, leaf, anther and stigma) and fiber developmental stages (7 days post-anthesis (DPA), 14 DPA, and 26 DPA) of upland cotton Coker 312. The sizes of the seven transcriptome databases constructed ranged from 4.43 to 5.20 Gb, corresponding to approximately twice the genome size of Gossypium hirsutum (2.5 Gb). Among the obtained clean reads, 83.32% to 88.22% could be compared to the upland cotton TM-1 reference genome. By analyzing the differential gene expression profiles of the transcriptome libraries of fiber and nonfiber tissues, we obtained 1205, 1135 and 937 genes with significantly upregulated expression at 7 DPA, 14 DPA and 26 DPA, respectively, and 124, 179 and 213 genes with significantly downregulated expression. Subsequently, Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathway analyses were performed, which revealed that these genes were mainly involved in catalytic activity, carbohydrate metabolism, the cell membrane and organelles, signal transduction and other functions and metabolic pathways. Through gene annotation analysis, many transcription factors and genes related to fiber development were screened. Thirty-six genes were randomly selected from the significantly upregulated genes in fiber, and expression profile analysis was performed using qRT-PCR. The results were highly consistent with the gene expression profile analyzed by RNA-seq, and all of the genes were specifically or predominantly expressed in fiber. Therefore, our RNA sequencing-based comparative transcriptome analysis will lay a foundation for future research to provide new genetic resources for the genetic engineering of improved cotton fiber quality and for cultivating new transgenic cotton germplasms for fiber quality improvement.

scholarly journals Co-Expression Network Analysis and Hub Gene Selection for High-Quality Fiber in Upland Cotton (Gossypium hirsutum) Using RNA Sequencing Analysis

Genes ◽  
2019 ◽  
Vol 10 (2) ◽  
pp. 119 ◽  
Author(s):  
Xianyan Zou ◽  
Aiying Liu ◽  
Zhen Zhang ◽  
Qun Ge ◽  
Senmiao Fan ◽  
...  
Keyword(s):  
Network Analysis ◽  
Gossypium Hirsutum ◽  
Rna Sequencing ◽  
Differentially Expressed Genes ◽  
Upland Cotton ◽  
Fiber Quality ◽  
Fiber Development ◽  
Hub Genes ◽  
High Quality ◽  
Development Stages

Upland cotton (Gossypium hirsutum) is grown for its elite fiber. Understanding differential gene expression patterns during fiber development will help to identify genes associated with fiber quality. In this study, we used two recombinant inbred lines (RILs) differing in fiber quality derived from an intra-hirsutum population to explore expression profiling differences and identify genes associated with high-quality fiber or specific fiber-development stages using RNA sequencing. Overall, 72/27, 1137/1584, 437/393, 1019/184, and 2555/1479 differentially expressed genes were up-/down-regulated in an elite fiber line (L1) relative to a poor-quality fiber line (L2) at 10, 15, 20, 25, and 30 days post-anthesis, respectively. Three-hundred sixty-three differentially expressed genes (DEGs) between two lines were colocalized in fiber strength (FS) quantitative trait loci (QTL). Short Time-series Expression Miner (STEM) analysis discriminated seven expression profiles; gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation were performed to identify difference in function between genes unique to L1 and L2. Co-expression network analysis detected five modules highly associated with specific fiber-development stages, especially for high-quality fiber tissues. The hub genes in each module were identified by weighted gene co-expression network analysis. Hub genes encoding actin 1, Rho GTPase-activating protein with PAK-box, TPX2 protein, bHLH transcription factor, and leucine-rich repeat receptor-like protein kinase were identified. Correlation networks revealed considerable interaction among the hub genes, transcription factors, and other genes.

scholarly journals QUALIDADE DA FIBRA DO ALGODOEIRO BRS VERDE IRRIGADO COM ÁGUAS DE DIFERENTES NÍVEIS SALINOS

Irriga ◽  
2018 ◽  
Vol 1 (1) ◽  
pp. 209 ◽  
Author(s):  
Francisco Italo Gomes Paiva ◽  
Marcelo Tavares Gurgel ◽  
Francisco De Assis de Oliveira ◽  
Lucas Ramos Da Costa ◽  
Andygley Fernandes Mota ◽  
...  
Keyword(s):  
Electrical Conductivity ◽  
Gossypium Hirsutum ◽  
Irrigation Water ◽  
Cotton Fiber ◽  
Fiber Quality ◽  
Short Fiber ◽  
Gossypium Hirsutum L ◽  
Third Phase ◽  
Salinity Levels

QUALIDADE DA FIBRA DO ALGODOEIRO BRS VERDE IRRIGADO COM ÁGUAS DE DIFERENTES NÍVEIS SALINOS FRANCISCO ITALO GOME PAIVA1; MARCELO TAVARES GURGEL2; FRANCISCO DE ASSIS DE OLIVEIRA3 ANDYGLEY FERNANDES MOTA4;LUCAS RAMOS DA COSTA 5; HERMINIO SABINO DE OLIVEIRA JUNIOR6 1Engenheiro Agrônomo, Mestrando em Manejo de solo e agua – UFERSA/RN, [email protected];2 Engenheiro Agrônomo, Prof. Doutor, Manejo solo e agua – UFERSA/RN, [email protected];3Engenheiro Agrônomo, Prof. Doutor, Manejo solo e agua – UFERSA/RN, [email protected];4Engenheiro Agrônomo, Mestre, Doutorando, UFCG – Campina Grande/PB, [email protected];5Engenheiro Agrônomo, Mestre, Doutorando – UFERSA/RN, [email protected];6Gestor Ambiental, Mestre – UFERSA/RN, [email protected].  1 RESUMO As fibras de algodão representam em torno de 80% das fibras utilizadas nas fiações brasileiras. Nesse contexto, o objetivo do presente estudo foi avaliar a qualidade da fibra do algodoeiro BRS verde, usando níveis de salinidade da água de irrigação. O experimento foi realizado em condições de campo na Fazenda Experimental Rafael Fernandes, de propriedade da Universidade Federal Rural do Semiárido­–UFERSA no período 21/10/11 até 06/02/12. O delineamento experimental adotado foi em blocos casualizados com seis tratamentos e cinco repetições, totalizando 30 parcelas experimentais. Os tratamentos resultaram das combinações de três tipos de condutividade elétrica da água de irrigação (S1- 0,55; S2-2,16 e S3-3,53 dS m-1) de acordo com as fases de desenvolvimento da cultura (T1- S1S1S1; T2- S2S2S2; T3- S3S3S3; T4- S1S2S2; T5- S1S2S3 e T6- S1S3S3), sendo a primeira fase do semeio até 30 dias; a segunda fase inicia-se dos 31 aos 90 dias; e a terceira fase dos 91 a colheita. As variáveis analisadas foram: porcentagem de fibra, comprimento da fibra, uniformidade do comprimento, maturidade, resistência, índice micronaire, índice de fibras curtas, elongação de ruptura e índice de fiabilidade. No geral, não houve efeito da salinidade da água de irrigação sobre a qualidade de fibra do algodão BRS verde, exceto para a característica elongamento da ruptura (ELG). Deste modo, torna-se viável o uso de água com salinidade de (3,5 dS m-1) em todo o ciclo da cultura considerando as condições de realização do estudo. Palavras-chave: Gossypium hirsutum L.. Condutividade elétrica. Características tecnológicas da fibra.  PAIVA,F.I.G.;GURGEL,M.T.;OLIVEIRA,F.A.;MOTA,A.F.;COSTA,L.R.;JUNIOR,H.S.EQUALITY OF COTTON FIBER BRS GREEN IRRIGATED WITH DIFFERENT SALT LEVELS    2 ABSTRACT Cotton fibers represent around 80% of the fibers used in spinning mills in Brazil. In this context, the aim of this study was to evaluate the quality of the cotton fiber BRS green, using salinity levels of irrigation water. The experiment was conducted under field condition sat the Experimental Farm Rafael Fernandes, owned by Federal Rural University of the semiarid – UFERSA the period 21/10/11 to 06/02/12. The treatments consisted of combinations of three types of electrical conductivity of irrigation water (S1- 0,55; S2-2,16 and S3-3,53 dS m-1) according to the development stages of culture T1- S1S1S1; T2- S2S2S2; T3- S3S3S3; T4- S1S2S2; T5- S1S2S3; T6- S1S3S3, the first phase being 30 days from the sowing; the second stage starts from 31 to 90 days; and the third phase of the 91 harvest. The variables analyzed were: fiber percentage, fiber length, length uniformity, maturity, strength, micronaire, short fiber index, elongation at break and reliability index. Overall, there was no effect of irrigation water salinity on the fiber quality of cotton BRS green, except for the elongation characteristic of rupture (ELG). Thus, it becomes feasible to use water with salinity (3,5 dS m-1) throughout the crop cycle considering the conditions of the study. Keywords: Gossypium hirsutum L.. Electrical conductivity. technological characteristics of the fiber.

scholarly journals Identification of the Group III WRKY Subfamily and the Functional Analysis of GhWRKY53 in Gossypium hirsutum L.

Plants ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 1235
Author(s):  
Dongjie Yang ◽  
Yuanyuan Liu ◽  
Hailiang Cheng ◽  
Qiaolian Wang ◽  
Limin Lv ◽  
...  
Keyword(s):  
Gossypium Hirsutum ◽  
Cotton Fiber ◽  
Fiber Quality ◽  
Fiber Development ◽  
Amino Acid Sequences ◽  
Fiber Formation ◽  
Biotic And Abiotic Stress ◽  
Motif Analysis ◽  
Gossypium Hirsutum L ◽  
Group Iii

WRKY transcription factors had multiple functions in plant secondary metabolism, leaf senescence, fruit ripening, adaptation to biotic and abiotic stress, and plant growth and development. However, knowledge of the group III WRKY subfamily in fiber development in upland cotton (Gossypium hirsutum L.) is largely absent. Previous studies have shown that there were 21 putative group III WRKY members in G. hirsutum L. These putative amino acid sequences from the III WRKY group were phylogenetically clustered into three clades. Multiple alignment, conservative motif analysis, and gene structure analysis showed that the members clustered together in the phylogenetic tree had similar motifs and gene structures. Expression pattern analysis revealed that variation in the expression levels of these genes in different tissues and fiber development stages. To better understand the functions of putative group III WRKY genes in G. hirsutum L., we selected the cotton fiber initiation-related gene GhWRKY53 for cloning and functional identification. The subcellular localization experiment of GhWRKY53 in Nicotiana tabacum leaves showed that it was located in the nucleus. The heterologous expression of GhWRKY53 in Arabidopsis thaliana could significantly increase the density of trichomes. Twelve proteins that interacted with GhWRKY53 were screened from the cotton fiber cDNA library by yeast two-hybrid experiment. This study findings lay a foundation for further research on the role of the GhWRKY53 during cotton fiber development and provide a new insight for further studying putative group III WRKY genes in G. hirsutum L. Our research results also provide vital information for the genetic mechanism of high-quality cotton fiber formation and essential genetic resources for cotton fiber quality improvement.

scholarly journals Transcriptome analysis reveals gene expression associated with fuzz fiber initiation regulated by high-temperature in Gossypium barbadense

2020 ◽  
Author(s):  
Gongmin Cheng ◽  
Longyan Zhang ◽  
Hengling Wei ◽  
Hantao Wang ◽  
Jianhua Lu ◽  
...  
Keyword(s):  
Gene Expression ◽  
High Temperature ◽  
Candidate Genes ◽  
Transcriptome Analysis ◽  
Fiber Quality ◽  
Expression Patterns ◽  
Gossypium Barbadense ◽  
Fiber Development ◽  
Potential Candidate ◽  
Fiber Initiation

Abstract Background: Gossypium barbadense L. is the most important renewable source of textile fiber. Cotton fiber cell initiation and elongation are often affected by various environmental stimulus, such as high temperature. However, little is known about the underlying mechanisms of temperature regulating the fuzz fiber initiation.Results: In the present study, phenotypic observation revealed that high temperature (HT) accelerated the fiber development, improved fiber quality and induced fuzz fiber initiation. It has been proved that the fuzz fiber initiation was inhibited by low temperature (LT), and 4 days post-anthesis (DPA) was the key stage for fuzz fiber initiation. Based on comparative transcriptome analysis, a total of 43,826 differentially expressed genes (DEGs) were identified, of which 9,667 were involved in both fiber development and temperature response with 901 transcription factor genes and 189 genes related to plant hormone signal transduction. Further analysis of gene expression patterns revealed that 240 genes were involved in fuzz fiber initiation. Functional annotation revealed that the candidate genes related to fuzz initiation were significantly involved in asparagine biosynthetic process, cell wall biosynthesis and stress response. Furthermore, the expression trends of sixteen selected genes from the RNA-seq data were almost consistent with the results of qRT-PCR results.Conclusions: Our study revealed several potential candidate genes and pathways that related to fuzz fiber initiation induced by high-temperature and provided a new view of temperature-induced tissue and organ development in Gossypium barbadense.

scholarly journals Quantitative Trait Loci and Transcriptome Analysis Reveal Genetic Basis of Fiber Quality Traits in CCRI70 RIL Population of Gossypium hirsutum

2021 ◽  
Vol 12 ◽  
Author(s):  
Xiao Jiang ◽  
Juwu Gong ◽  
Jianhong Zhang ◽  
Zhen Zhang ◽  
Yuzhen Shi ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Gossypium Hirsutum ◽  
Transcriptome Analysis ◽  
Quantitative Trait ◽  
Upland Cotton ◽  
Fiber Quality ◽  
Quality Traits ◽  
High Quality ◽  
Fiber Quality Traits ◽  
Ril Population

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.

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