Cotton neps, entangled knots that form within raw cotton fibers, are biological and industrial challenges because they reduce fiber quality and interfere with downstream textile processing. Two distinct types of neps occur in upland cotton (Gossypium hirsutum): fiber neps (FN), which consist of entangled fiber strands, and seed coat neps (SCN), which arise when fragments of the seed coat become wrapped in developing fibers. Understanding the biological origins of FN and SCN is essential for improving fiber quality, as these structures differ in composition, developmental timing, and response to environmental conditions. Using a 550\u2011recombinant inbred line (RIL) multi\u2011parent advanced generation inter\u2011cross (MAGIC) population grown across three environments, we performed phenotyping and genome wide association studies (GWAS) to characterize FN and SCN formation.
The scripts archived in this GitHub release represent the code used to generate the genomic and statistical analytic workflow used in this study. It includes read alignment using bwa\u2011mem2 and BAM processing, BAM merging for multi\u2011lane samples, variant calling and chromosome\u2011wise VCF generation, VCF concatenation and preparation for imputation, genotype phasing and imputation using Beagle, descriptive statistics for multi\u2011environment phenotypes, GWAS using GAPIT across multiple models, Manhattan and QQ plot refinement, LD heatmap generation around significant SNPs, and expression profiling for candidate gene evaluation.
", "distribution": [{"@type": "dcat:Distribution", "downloadURL": "https://ndownloader.figshare.com/files/65403066", "format": "zip", "mediaType": "application/zip", "title": "GWAS-workflow-Cotton-1.1.0.zip"}, {"@type": "dcat:Distribution", "downloadURL": "https://ndownloader.figshare.com/files/65403072", "format": "gz", "mediaType": "application/x-gzip", "title": "GWAS-workflow-Cotton-1.1.0.tar.gz"}], "identifier": "10.15482/USDA.ADC/31400775.v1", "keyword": ["Fiber neps", "GWAS", "Gossipium hirsutum", "QTL", "Seed coat neps", "Variants", "source code"], "license": "https://www.usa.gov/publicdomain/label/1.0/", "modified": "2026-07-06", "programCode": ["005:040"], "publisher": {"@type": "org:Organization", "name": "Agricultural Research Service"}, "temporal": "2025-03-01/2026-03-31", "title": "Custom scripts supporting GWAS for the study of fiber neps (FN) and seed coat neps (SCN) in a 550\u2011line Gossypium hirsutum MAGIC population"}