Chromosome Substitution Line Analysis Using SNP Kasp Assays

Chromosome substitution (CS) is a powerful means of interspecific wild germplasm introgression.  Such introgression is one of the most powerful means of diversifying the genetic base of Upland cotton and other domesticated forms of G. hirsutum (L.). The primary means of developing CS lines has been by modified backcrossing, where the recurrent parent is a chromosomally deficient type, usually a monosomic or monotelodisomic individual lacking a whole chromosome, or nearly all of a chromosome "arm".  Most of these stocks were developed on the basis of cytogenetic analyses and phenotyping, but without the benefit of molecular marker analyses.  We will report on recent SNP-based analysis of CS lines to better characterize their content. Our main aims are to either verify their desired constitution, or, if incorrect, to more accurately define their genetic content.  Whether whole-chromosome or chromosome-segment substitutions, the product lines are valuable components of an isogenic platform for quantitative genetic analysis, as has been demonstrated so ably by our USDA-ARS collaborators at Starkville, MS.  The power of this quantitative platform can be greatly amplified by combined use of high-throughput SNP genotyping to localize then identify important QTLs and gene-gene epistatic interactions.