The narrow genetic base of Upland cotton has slowed growth of its productivity as a crop and perhaps also its use in the world. The need to broaden genetic diversity of Upland cotton is urgent, especially given the contemporary need to improve competitiveness of the fiber attributes, productivity and sustainability. The advent of high-density high-throughput molecular marker genotyping in cotton using the CottonSNP63K array has revolutionized the resolution and accuracy of genetic analysis in cotton. In this study, the CottonSNP63K array is used to analyze two populations, one a set of interspecific chromosome-specific RILs and the other an early-generations interspecific mapping population, both at the 52-chromosome level. A chromosome linkage map was derived from 50 isogenic chromosome-specific recombinant inbred lines, which were derived from a cross between a disomic substitution line CS-B17 homozygous for G. barbadense '3-79' chromosome 17 and its recurrent parent TM-1. Fiber quality and Fusarium wilt race 4 resistance data on the lines were subjected to quantitative trait locus (QTL) analysis. Results indicated that the CS-RIL approach affords high sensitivity, in that it detected seven fiber quality QTLs in chromosome 17, whereas none had been found previously by analysis of conventional TM-1/3-79 populations. However, one lint% QTL was detected previously using a similarly interspecific population. A single locus accounted for multiple FOV4 resistance trait QTLs and corresponded to previous research. In this CS-RIL study, QTLs exhibited exceptionally high R^2 values and consistency across experiments, reflecting avoidance of genetic background noise and GxE interactions. The first high-resolution SNP-based genetic map between G. hirsutum and G. mustelinum was constructed from a 59 individuals of BCv1Fv1 population. The map was highly collinear with the G. hirsutum - G. barbadense map and the G. hirsutum reference genome. In certain chromosomes, some markers exhibited segregation distortion. Co-segregation difference between genetic maps revealed possible chromosomal structure changes among species. Possible errors in the genome assembly were found by alignments of 1,996 low-specificity SNP markers to their homeologs in the reference genome. The genetic map can help guide genome assembly corrections, and facilitate many sorts of future studies, e.g., genetic dissection of complex traits and marker-assisted breeding.
