Phenomics and transcriptomics analyses reveal deposition of suberin and lignin in the short fiber cell walls produced from a wild cotton species and two mutants

Kim, Hee Jin; Liu, Yongliang; Thyssen, Gregory N.; Naoumkina, Marina; Frelichowski, James

doi:10.1371/journal.pone.0282799

Cited by 3 publications

(1 citation statement)

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“…Analysis of saps in developing fibers revealed that the concentrations of sugars were less, while malic acid and ions higher in the Li 1 – Li 2 than in the wild‐type (Naoumkina et al., 2015). The fibers of Li 1 and Li 2 mutants contain a greater amount of lignin and suberin than the wild‐type fibers that reduce plant cell wall extensibility and water transport (Kim et al., 2023). RNAseq analysis revealed that aquaporins were significantly downregulated in both short‐fiber mutants, which correlated with reduced osmotic pressure and most likely contributed to the cessation of fiber elongation (Naoumkina et al., 2015).…”

Section: Recent Advances In Understanding Of Cotton Fiber Developmentmentioning

confidence: 99%

Bridging molecular genetics and genomics for cotton fiber quality improvement

Naoumkina

Kim

2023

Crop Science

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Upland cotton (Gossypium hirsutum L.) is the main source of natural fiber for the textile industry. Cotton fibers are unicellular trichomes that emerge from the epidermal cells of the seed. In cultivated cotton species, seed trichomes differentiate into two distinct types, spinnable lint, and short fuzz. The main priority for cotton growers is fiber yield, whereas the textile industry also demands better fiber quality characteristics, such as length, uniformity, strength, maturity, and optimal fineness. However, it is a major challenge for breeders to improve fiber quality while maintaining yield, because of the observed negative correlation between yield and fiber quality traits. Recent technical advances in sequencing and bioinformatics have facilitated the assembly of reference quality genomes of multiple cotton species, bringing a new era for cotton genomics. Available genomic resources will help genetically dissect the agronomic and fiber quality traits of cotton and identify gene variants that can be used for cotton improvement through breeding or biotechnology. Here, we review recent progress in the sequencing of genomes of cotton species and approaches in molecular genetics and genomics for the improvement of cotton fiber quality traits.We discuss progress in the understanding of each stage of cotton fiber development and the remaining challenges.

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Section: Recent Advances In Understanding Of Cotton Fiber Developmentmentioning

confidence: 99%

Bridging molecular genetics and genomics for cotton fiber quality improvement

Naoumkina

Kim

2023

Crop Science

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A cell fractionation and quantitative proteomics pipeline to enable functional analyses of cotton fiber development

Lee,

Rani,

Mallery

et al. 2024

Preprint

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Cotton fibers are aerial trichoblasts that employ a highly polarized diffuse growth mechanism to emerge from the developing ovule epidermis. After executing a complicated morphogenetic program, the cells reach lengths over 2 cm and serve as the foundation of a multi-billion-dollar textile industry. Important traits such as fiber diameter, length, and strength are defined by the growth patterns and cell wall properties of individual cells. At present, the ability to engineer fiber traits is limited by our lack of understanding regarding the primary controls governing the rate, duration, and patterns of cell growth. To gain insights into the compartmentalized functions of proteins in cotton fiber cells, we developed a label-free liquid chromatography mass spectrometry method for systems level analyses of fiber proteome. Purified fibers from a single locule were used to fractionate the fiber proteome into apoplast (APOT), membrane-associated (p200), and crude cytosolic (s200) fractions. Subsequently, proteins were identified, and their localizations and potential functions were analyzed using combinations of size exclusion chromatography, statistical and bioinformatic analyses. This method had good coverage of the p200 and apoplast fractions, the latter of which was dominated by proteins associated with particulate membrane-enclosed compartments. The apoplastic proteome was diverse, the proteins were not degraded, and some displayed distinct multimerization states compared to their cytosolic pool. This quantitative proteomic pipeline can be used to improve coverage and functional analyses of the cotton fiber proteome as a function of developmental time or differing genotypes.

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Homoeologs in Allopolyploids: Navigating Redundancy as Both an Evolutionary Opportunity and a Technical Challenge—A Transcriptomics Perspective

Aufiero,

Fruggiero,

D’Angelo

et al. 2024

Genes

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Allopolyploidy in plants involves the merging of two or more distinct parental genomes into a single nucleus, a significant evolutionary process in the plant kingdom. Transcriptomic analysis provides invaluable insights into allopolyploid plants by elucidating the fate of duplicated genes, revealing evolutionary novelties and uncovering their environmental adaptations. By examining gene expression profiles, scientists can discern how duplicated genes have evolved to acquire new functions or regulatory roles. This process often leads to the development of novel traits and adaptive strategies that allopolyploid plants leverage to thrive in diverse ecological niches. Understanding these molecular mechanisms not only enhances our appreciation of the genetic complexity underlying allopolyploidy but also underscores their importance in agriculture and ecosystem resilience. However, transcriptome profiling is challenging due to genomic redundancy, which is further complicated by the presence of multiple chromosomes sets and the variations among homoeologs and allelic genes. Prior to transcriptome analysis, sub-genome phasing and homoeology inference are essential for obtaining a comprehensive view of gene expression. This review aims to clarify the terminology in this field, identify the most challenging aspects of transcriptome analysis, explain their inherent difficulties, and suggest reliable analytic strategies. Furthermore, bulk RNA-seq is highlighted as a primary method for studying allopolyploid gene expression, focusing on critical steps like read mapping and normalization in differential gene expression analysis. This approach effectively captures gene expression from both parental genomes, facilitating a comprehensive analysis of their combined profiles. Its sensitivity in detecting low-abundance transcripts allows for subtle differences between parental genomes to be identified, crucial for understanding regulatory dynamics and gene expression balance in allopolyploids.

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Phenomics and transcriptomics analyses reveal deposition of suberin and lignin in the short fiber cell walls produced from a wild cotton species and two mutants

Cited by 3 publications

References 79 publications

Bridging molecular genetics and genomics for cotton fiber quality improvement

Bridging molecular genetics and genomics for cotton fiber quality improvement

A cell fractionation and quantitative proteomics pipeline to enable functional analyses of cotton fiber development

Homoeologs in Allopolyploids: Navigating Redundancy as Both an Evolutionary Opportunity and a Technical Challenge—A Transcriptomics Perspective

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