Chapters authored
Recent Developments in Fiber Genomics of Tetraploid Cotton Species
Cotton (Gossypium spp.) produces naturally soft, single-celled trichomes as fiber on the seed coat supplying the main source of natural raw material for the textile industry. It is economically considered as one of the most leading cash crops in the world and evolutionarily very important as a model system for detailed scientific investigations. Cotton production is going through a big transition stage such as losing the market share in competition with the synthetic fibers, high popularity of Bt and herbicide resistance genes in cotton cultivars, and the recent shift of fiber demands to meet the standard fiber quality due to change of textile technologies to produce high superior quality of fibers in the global market. Recently, next-generation sequencing technologies through high-throughput sequencing at greatly reduced costs provided opportunities to sequence the diploid and tetraploid cotton genomes. With the availability of large volume of literatures on molecular mapping, new genomic resources, characterization of cotton genomes, discoveries of many novel genes, regulatory elements including small and microRNAs and new genetic tools such as gene silencing or gene editing technique for genome manipulation, this report attempted to provide the readers a comprehensive review on the recent advances of cotton fiber genomics research.
Part of the book: Past, Present and Future Trends in Cotton Breeding
Transcriptome Analysis Using RNA Sequencing for Finding Genes Related to Fiber in Cotton: A Review
The cotton crop is economically important and primarily grown for its fiber. Although the genus Gossypium consists of over 50 species, only four domesticated species produce spinnable fiber. However, the genes determine the molecular phenotype of fiber, and variation in their expression primarily contributes to associated phenotypic changes. Transcriptome analyses can elucidate the similarity or variation in gene expression (GE) among organisms at a given time or a circumstance. Even though several algorithms are available for analyzing such high-throughput data generated from RNA Sequencing (RNA-Seq), a reliable pipeline that includes a combination of tools such as an aligner for read mapping, an assembler for quantitating full-length transcripts, a differential gene expression (DGE) package for identifying differences in the transcripts across the samples, a gene ontology tool for assigning function, and enrichment and pathway mapping tools for finding interrelationships between genes based on their associated functions are needed. Therefore, this chapter first introduces the cotton crop, fiber phenotype, transcriptome, then discusses the basic RNA-Seq pipeline and later emphasizes various transcriptome analyses studies focused on genes associated with fiber quality and its attributes.
Part of the book: Cotton
Recent Studies on Fusarium Wilt in Cotton
Fusarium oxysporum has been a subject of intensive research since 1882, with over 200 studies published from key cotton-growing countries such as the United States, China, Uzbekistan, India, Pakistan, Australia, and Brazil. The present study has employed a diverse array of research methodologies and technological approaches, primarily emphasizing research publications disseminated within the past decade. It places specific emphasis on two key domains: Molecular Mapping and Genome-Wide Association Studies (GWAS), elucidating the evolutionary analysis transition from Simple Sequence Repeat (SSR) to Single Nucleotide Polymorphism (SNP) chip utilization. The creation of a comprehensive molecular map that incorporates Quantitative Trait Loci (QTLs) related to Fusarium and consolidates findings from several research groups, accompanied by figures and tables, serves to facilitate a more thorough understanding of the genetic architecture underlying Fusarium-related traits. An in-depth examination of recent advances in marker-assisted selection for traits conferring resistance to Fusarium oxysporum f. sp. vasinfectum (FOV), coupled with a comprehensive evaluation of the pertinent genes, offers valuable insights into the development of resistant cultivars and the underlying genetic mechanisms. This entails doing a critical review of recent relevant literature. Furthermore, this investigation examines the obstacles and potential associated with developing technologies.
Part of the book: Fusarium - Recent Studies [Working title]