Genetic Evaluation and Crossing Strategy of Upland Cotton Germplasm Based on a Liquid-Phase Chip

Upland cotton (Gossypium hirsutum L.) dominates Xinjiang’s cotton production, but the narrow genetic base of modern cultivars limits further yield gains. Here, 356 Xinjiang upland cotton accessions (184 northern, 172 southern) were genotyped at 280 elite trait locus–trait combinations (270 unique markers) using a liquid-phase chip. Pairwise kinship was inferred with the KING-robust estimator and cross-validated by IBS similarity, population structure was examined by PCA, and a marker-weighted comprehensive elite genotype index (S) was constructed. The overall missing rate was 0.43%, and five identical and 101 near-identical accession pairs were detected. PC1 and PC2 explained only 9.81% and 7.29% of the variation, with substantial regional overlap. Index S ranged from 0.39 to 0.57, led by Tkuo, Y80, Ba 44435, Ziyu R040068 and Youzhi 5; salt tolerance (0.07), lint yield (0.14), seed index (0.19) and fiber strength (0.22) showed the lowest carriage of the marker-defined elite alleles scored here. After excluding close relatives, 62,252 crosses (98.52%) satisfied the constraint, and 30 crosses (19 inter-regional) were recommended, the best being Ziyu TY112 × Tkuo (joint coverage U = 0.65). These parents and crosses provide candidates for parental selection, pending field validation.