Development and Applications of Single Nucleotide Polymorphisms (SNPs) for the Improvement of Fiber Traits in Cotton Crops.

Single-nucleotide polymorphisms (SNPs) are among the most stable and widely used molecular markers in plant genomics and breeding. Especially in cotton (Gossypium hirsutum L.), SNP markers play a critical role in identifying genetic variations associated with different development traits such as fiber length, strength, micronaire, and elongation. This chapter describes the workflow of SNP marker development in a comprehensive manner targeting fiber development in cotton. The process is initiated by high-quality genomic DNA isolation followed by sequencing carried out through high-throughput sequencing approaches such as Whole Genome Sequencing (WGS), Genotyping-by-Sequencing (GBS), and Restriction Site-Associated DNA Sequencing (RAD-seq). Using the reference genome Gossypium hirsutum L., the sequencing reads are subjected to various bioinformatics analyses such as quality control, alignment, and SNP calling to identify true SNPs. Functional SNPs associated with genes are prioritized for further analysis. Selected SNPs are validated through PCR amplification and sequencing, followed by conversion into markers for accurate genotyping of germplasm and breeding populations. Overall, this protocol provides the discovery and validation of SNP markers for fiber development in cotton. Consequently, the validated markers are effectively applied in genetic studies, QTL mapping, and marker-assisted breeding strategies aimed at improving fiber quality traits in cotton.