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Background  Heterosis has been extensively utilized in different crops and made a significant contribution to global food security. Genetic distance (GD) is one of the valuable criteria for selecting parents in hybrid breeding. The objectives of this study were to estimate the GD between parents using both simple sequence repeat (SSR) markers and single nucleotide polymorphism (SNP) markers and to investigate the efficiency of the prediction of hybrid performance based on GD. The experiment comprised of four male parents, 282 female parents and 1128 F 1 , derived from NCII mating scheme. The hybrids, their parents and two check cultivars were evaluated for two years. Performance of F 1 , mid-parent heterosis (MPH), and best parent heterosis (BPH) were evaluated for ten agronomic and fiber quality traits, including plant height, boll weight, boll number, lint percentage, fiber length, fiber strength, fiber uniformity, fiber elongation ratio, micronaire, and spinning consistent index.    Results  Heterosis was observed in all hybrids and, the traits like plant height, boll number, boll weight and lint percentage exhibited higher heterosis than the fiber quality traits. Correlations were significant between parental and F 1  performances. The F 1  performances between three hybrid sets (Elite×Elite, Exotic×Elite, and Historic×Elite) showed significant differences in eight traits, including boll number, lint percentage, fiber length, fiber strength, fiber uniformity, fiber elongation ratio, micronaire, and spinning consistent index. The correlation of the GD assessed by both SSR and SNP markers was significantly positive. The cluster analysis based on GD results estimated using SNP showed that all the female parents divided into five groups and the F 1  performance between these five groups showed significant differences in four traits, including lint percentage, micronaire, fiber strength, and fiber elongation ratio. The correlation between GD and F 1  performance, MPH and BPH were significant for lint percentage and micronaire.    Conclusions  Our results suggested that GD between parents could be helpful in heterosis prediction for certain traits. This study reveals that molecular marker analysis can serve as a basis for assigning germplasm into heterotic groups and to provide guidelines for parental selection in hybrid cotton breeding.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12864-021-07431-6.

Assessment of heterosis based on parental genetic distance estimated with SSR and SNP markers in upland cotton (Gossypium hirsutum L.)