The frequency of the other haplotypes (Hap_6, Hap_7, Hap_10, and Hap_11) was moderate, between 5.4% and 8.7% (Table 5). The frequencies of GhExp2 haplotypes differed markedly across species ( Table 6). Haplotype diversity ranged from 0.667 in G. arboreum (7 accessions) selleck chemicals llc to 0.767 in G. hirsutum (74 accessions). The difference was particularly evident for the haplotypes (Hap_1, Hap_2, and Hap_3) present only in G. arboreum. The most frequently identified haplotypes were confined to G. hirsutum. Six haplotypes were present in < 10% of accessions sampled, six were unique to one species, and six

were exclusive to accessions from single species, indicating that every allele was unique to one species. Thus, interspecific crossing would create novel alleles. G. hirsutum accessions were largely separated into six haplotypes. In comparison with G. arboreum and G. barbadense, more haplotypes and higher diversity were observed in G. hirsutum ( Table 5). The prerequisite for all subsequent analyses in this study was the characterization of population structure using

the software package Structure 2.3.1 [26]. Based on 132 unlinked SSR markers, providing even coverage of the cotton genome, we ran Structure for K (number of PI3K signaling pathway fixed subpopulations or clusters) ranging from 2 to 10. The model with K = 7 clusters showed higher log likelihood (ln Pr(X|K) = − 9805.2) than for other integer values of K, and the likelihoods for K = 8 and 9 decreased markedly, compared with that for K = 7. Because the likelihood peaked at K = 7 in the range of two to ten subpopulations, the most likely number of putative ancestral populations (K) was identified as seven. very The number of these 92 cotton accessions assigned to each of the seven inferred clusters ranged from 2 to 39. Kullback–Leibler distances of pairwise subpopulations were significant (P < 0.001) and ranged from 0.1251 to 1.4933 (average 0.6856), suggesting a genuine difference among these clusters and supporting the existence of genetic structure ( Fig. 5, Table 7). The G. arboreum

accessions (except for CRZM) and G. barbadense accessions (except for Giza 80) lines were very distinct from all other lines from G. hirsutum because of the genetic isolation that occurred during their development, and were accordingly (6 G. arboreum and 10 G. barbadense accessions) assigned to A (Arboreum) and B (Barbadense) groups, respectively. Giza80 (introduced from Egypt) and CRZM (with fiber length approximating that of tetraploid cotton) were assigned to a seventh M (Mixed) group. Four clusters from G. hirsutum are referred to hereafter as H1 (8 accessions), H2 (19 accessions), H3 (39 accessions) and H4 (8 accessions) subpopulations. These results are consistent with their genomic origins and evolutionary histories.