The National Plant Germplasm System cotton collection-a review of germplasm resources, phenotypic characterization, and genomic variation.

This review is an investigation of the status of phenotypic and molecular characterization efforts in the National Plant Germplasm System (NPGS) cotton collection, highlighting progress to date to maximize the efficiency and effectiveness of future characterization efforts. We considered recent publications of large-scale characterization activities involving the cotton collection. Reports of qualitative descriptors and quantitative phenotypes were considered as well as reports of molecular genotypes. Approximately 80% of cotton accessions are characterized with standardized descriptors and digital images; in addition, large numbers of accessions have recently been screened for resistance to Fusarium wilt, bacterial blight, and cotton leaf curl virus. Many studies have measured genotypes of accessions using a range of technologies-31% of accessions have been genotyped using simple sequence repeat markers, 5% have been genotyped with single nucleotide polymorphism (SNP) arrays, 7% have been genotyped with SNPs from resequencing, and 0.2% of accessions have been sequenced genomically de novo. These efforts ensure that valuable genetic resources are well-characterized, although only a small fraction of the genetic variability in the cotton collection has been surveyed to date. The integration of NPGS cotton collection resources with phenotypic and genotypic information has illuminated the value of cotton genetic variation and genes associated with important traits such as disease resistance and stress tolerance. The cotton collection is a premier information source and critical foundation of variation essential for cotton research and breeding programs aimed at developing resilient cultivars with superior yield and fiber quality in support of U.S. cotton production.