*2.1. SSR Marker Analysis*

Among a total of 853 SSR primer pairs used for genotyping 132 accessions, 205 primer pairs were found to be polymorphic with a polymorphism rate of 24%. Accessions with more than 5% missing data were removed and 94 SSRs were dropped; the selected 111 SSR primer pairs can be scored confidently and read clearly on PCR products. Data for monomorphic loci were also excluded from the analysis. Data generated from the selected 111 SSR primer pairs was analyzed. Among 132 accessions, a total of 382 SSR alleles were detected as marker loci with an average of 3.44 alleles per SSR ranging from 2 to 8. All 382 SSR loci were found to be polymorphic. The average polymorphism information content (PIC) value for SSRs was 0.555 with a range of 0.078 to 0.821, and the major allele frequency was 0.738 ranging from 0.541 to 0.959 for the complete panel. Seventy-six (68.468%) SSR markers in total were found to be highly informative with a PIC value ≥0.50, 29 (26.126%) were moderately informative with PICs value ≥0.25 and <0.50, and 6 (5.405%) were least informative with a PIC value <0.25. A summary of marker statistics for *G. hirsutum* accessions is listed in Supplementary Table S2.
