Transcriptome analysis revealed the possible contribution of chromosome introgression fragments from Sea Island cotton (Gossypium barbadense) to fiber strength in Upland cotton (Gossypium hirsutum)

AbstractCotton fiber strength is a critical property determining fiber qualities, and determined by the secondary cell wall development. Understanding the mechanism of fiber development will provide a way to improvement of fiber strength. In this study, the introgression lines of upland and sea island cotton, and have experience of four generations of backcross with upland parent, and have significant higher fiber strength than their upland parent, and the transcriptome were analyzed and compared between the introgression lines and their upland parent. There were 2201 differentially expressed genes (DEG) identified by comparing two introgression lines with their recurrent parent CCRI45, in different development stages from 15 days post-anthesis (DPA) to 28 DPA. The up-regulated genes regulated the polysaccharide metabolic process, single-organism localization, cell wall organization or biogenesis and so on. The down-regulated genes involved in the microtubule-based process, cellular response to stress, cell cycle process and so on. Further functional analysis revealed three significant functional genes, XLOC_036333 (mannosyl-oligosaccharide-alpha-mannosidase mns1), XLOC_029945 (FLA8) and XLOC_075372 (snakin-1), playing important roles in the regulation of cotton fiber strength. Our results provide important candidates genes and inspirations for the future investigation of the molecular mechanism of fiber quality formation, and improvement of cotton fiber quality in breeding.

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Transcriptome analysis reveals genes potentially related to high fiber strength in a Gossypium hirsutum line IL9 with Gossypium mustelinum introgression

Genome ◽

10.1139/gen-2020-0177 ◽

2021 ◽

pp. 1-11

Author(s):

Qi Chen ◽

Wei Wang ◽

Sameer Khanal ◽

Jinlei Han ◽

Mi Zhang ◽

...

Keyword(s):

Transcriptome Analysis ◽

Fiber Strength ◽

Fiber Quality ◽

Enrichment Analysis ◽

Introgression Line ◽

Recurrent Parent ◽

High Fiber ◽

Go Enrichment ◽

Annotation Information ◽

Cotton Fiber Quality

Cotton (Gossypium L.) is the most important fiber crop worldwide. Here, transcriptome analysis was conducted on developing fibers of a G. mustelinum introgression line, IL9, and its recurrent parent, PD94042, at 17 and 21 days post-anthesis (dpa). Differentially expressed genes (DEGs) of PD94042 and IL9 were identified. Gene Ontology (GO) enrichment analysis showed that the annotated DEGs were rich in two main biological processes and two main molecular functions. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis likewise showed that the annotated DEGs were mainly enriched in metabolic pathways and biosynthesis of secondary metabolites. In total, 52 DEGs were selected as candidate genes based on comparison of the DEGs and GO function annotation information. Quantitative real-time PCR (RT-qPCR) analysis results for 12 randomly selected DEGs were consistent with transcriptome analysis. SNP identification based on G. mustelinum chromatin segment introgression showed that 394 SNPs were identified in 268 DEGs, and two genes with known functions were identified within fiber strength quantitative trait loci (QTL) regions or near the confidence intervals. We identified 52 key genes potentially related to high fiber strength in a G. mustelinum introgression line and provided significant insights into the study of cotton fiber quality improvement.

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Genome-wide identification and characterization of TALE superfamily genes in cotton reveals their functions in regulating secondary cell wall biosynthesis

BMC Plant Biology ◽

10.1186/s12870-019-2026-1 ◽

2019 ◽

Vol 19 (1) ◽

Cited By ~ 3

Author(s):

Qiang Ma ◽

Nuohan Wang ◽

Pengbo Hao ◽

Huiru Sun ◽

Congcong Wang ◽

...

Keyword(s):

Cell Wall ◽

Cotton Fiber ◽

Secondary Cell Wall ◽

Fiber Strength ◽

Fiber Quality ◽

Expression Patterns ◽

Evolutionary Analysis ◽

Regulatory Relationship ◽

Genome Wide ◽

Regulation Functions

Abstract Background Cotton fiber length and strength are both key traits of fiber quality, and fiber strength (FS) is tightly correlated with secondary cell wall (SCW) biosynthesis. The three-amino-acid-loop-extension (TALE) superclass homeoproteins are involved in regulating diverse biological processes in plants, and some TALE members has been identified to play a key role in regulating SCW formation. However, little is known about the functions of TALE members in cotton (Gossypium spp.). Results In the present study, based on gene homology, 46, 47, 88 and 94 TALE superfamily genes were identified in G. arboreum, G. raimondii, G. barbadense and G. hirsutum, respectively. Phylogenetic and evolutionary analysis showed the evolutionary conservation of two cotton TALE families (including BEL1-like and KNOX families). Gene structure analysis also indicated the conservation of GhTALE members under selection. The analysis of promoter cis-elements and expression patterns suggested potential transcriptional regulation functions in fiber SCW biosynthesis and responses to some phytohormones for GhTALE proteins. Genome-wide analysis of colocalization of TALE transcription factors with SCW-related QTLs revealed that some BEL1-like genes and KNAT7 homologs may participate in the regulation of cotton fiber strength formation. Overexpression of GhKNAT7-A03 and GhBLH6-A13 significantly inhibited the synthesis of lignocellulose in interfascicular fibers of Arabidopsis. Yeast two-hybrid (Y2H) experiments showed extensive heteromeric interactions between GhKNAT7 homologs and some GhBEL1-like proteins. Yeast one-hybrid (Y1H) experiments identified the upstream GhMYB46 binding sites in the promoter region of GhTALE members and defined the downstream genes that can be directly bound and regulated by GhTALE heterodimers. Conclusion We comprehensively identified TALE superfamily genes in cotton. Some GhTALE members are predominantly expressed during the cotton fiber SCW thicking stage, and may genetically correlated with the formation of FS. Class II KNOX member GhKNAT7 can interact with some GhBEL1-like members to form the heterodimers to regulate the downstream targets, and this regulatory relationship is partially conserved with Arabidopsis. In summary, this study provides important clues for further elucidating the functions of TALE genes in regulating cotton growth and development, especially in the fiber SCW biosynthesis network, and it also contributes genetic resources to the improvement of cotton fiber quality.

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Genotype by Environment Interactions on Cotton Fiber Traits and Their Implications on Variety Recommendation

Journal of Agricultural Studies ◽

10.5296/jas.v5i2.10762 ◽

2017 ◽

Vol 5 (2) ◽

pp. 86

Author(s):

Vasileios Greveniotis ◽

Evangelia Sioki

Keyword(s):

Cotton Fiber ◽

Fiber Strength ◽

Fiber Quality ◽

Quality Traits ◽

Breeding Method ◽

Fiber Quality Traits ◽

Precise Knowledge ◽

Environmental Fluctuations ◽

Cotton Fiber Quality ◽

Fiber Traits

The objective of this study was to evaluate cotton fiber quality traits across diverse environments. This could lead to the selection of the best environment for cotton cultivations and the best adapted commercial cultivars. For this reason four main cotton regions were chosen as different environments: Thessaly, Thrace, Macedonia and Sterea Ellas. Five of the most commercial upland cotton cultivars (DP332, DP377, ST402, CELIA and ELSA) were used for evaluation of their fiber quality traits. Each cultivar was sown in 10 different fields (in order to exploit and evaluate different soil types) in each of the above mentioned regions and (in total) 200 fields were used in total. Four samples from each field were collected in order to analyze fiber quality traits: micronaire, maturity index (%), fiber length as the upper half mean length (mm), fiber strength (gram/tex), uniformity index (%), fiber elongation, short fiber index, yellowness (+b), reflectance index (Rd).Cultivation regions must also be selected in a way that they could promote fiber traits, in order to ensure the highest fiber quality. Cotton fiber quality traits were affected differently from environmental fluctuations, showing that the ranking of cultivars according to environmental fluctuations is important, if proper breeding methods should be applied. Each trait is affected differently by environmental fluctuations and requires precise knowledge of the degree of inheritance i.e., as to how much qualitative or quantitative is the trait, in order to choose and apply the proper breeding method.

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