Figure 1: Amplification patterns of different cotton hybrids and their parents with TMB0409 marker M: ladder (100–1000 bp), T1: G. Cot 16, T2: GSHV 185, S1: L 1384, S2: TCH 1777, T1T2: G. Cot 16×GSHV 185, T2T1: GSHV 185×G. Cot 16, T2S1: GSHV 185×L 1384, S1T2: L 1384×GSHV 185, S1S2 : L 1384×TCH 1777, S2S1: TCH 1777× L 1384, T2S2: GSHV 185×TCH 1777, S2T2: TCH 1777×GSHV 185, S2T1: TCH 1777× G. Cot 16, T1S2: G. Cot 16×TCH 1777, T1S1: G. Cot 16×L 1384, S1T1: L 1384×G. Cot 16

Figure 2: Amplification patterns of different cotton hybrids and their parents with DPL0094 marker M: ladder (100–1000 bp), T1: G. Cot 16, T2: GSHV 185, S1: L 1384, S2: TCH 1777, T1T2: G. Cot 16×GSHV 185, T2T1: GSHV 185×G. Cot 16, T2S1: GSHV 185×L 1384, S1T2: L 1384×GSHV 185, S1S2 : L 1384×TCH 1777, S2S1: TCH 1777× L 1384, T2S2: GSHV 185×TCH 1777, S2T2: TCH 1777×GSHV 185, S2T1: TCH 1777× G. Cot 16, T1S2: G. Cot 16×TCH 1777, T1S1: G. Cot 16×L 1384, S1T1: L 1384×G. Cot 16

Table 1: Amplification and analysis details of SSR primers

Figure 3: Amplification patterns of different cotton hybrids and their parents with BNL686 marker M: ladder (100–1000 bp), T1: G. Cot 16, T2: GSHV 185, S1: L 1384, S2: TCH 1777, T1T2: G. Cot 16×GSHV 185, T2T1: GSHV 185×G. Cot 16, T2S1: GSHV 185×L 1384, S1T2: L 1384×GSHV 185, S1S2: L 1384×TCH 1777, S2S1: TCH 1777×L 1384, T2S2: GSHV 185×TCH 1777, S2T2: TCH 1777×GSHV 185, S2T1: TCH 1777×G. Cot 16, T1S2: G. Cot 16×TCH 1777, T1S1: G. Cot 16×L 1384, S1T1: L 1384×G. Cot 16

Figure 4: Amplification patterns of different cotton hybrids and their parents with JESPR153 marker M: ladder (100–1000 bp), T1: G. Cot 16, T2: GSHV 185, S1: L 1384, S2: TCH 1777, T1T2: G. Cot 16×GSHV 185, T2T1: GSHV 185×G. Cot 16, T2S1: GSHV 185×L 1384, S1T2: L 1384×GSHV 185, S1S2: L 1384×TCH 1777, S2S1: TCH 1777× L 1384, T2S2: GSHV 185×TCH 1777, S2T2: TCH 1777×GSHV 185, S2T1: TCH 1777× G. Cot 16, T1S2: G. Cot 16×TCH 1777, T1S1: G. Cot 16×L 1384, S1T1: L 1384×G. Cot 16

Figure 5: Amplification patterns of different cotton hybrids and their parents with CM45 marker M: ladder (100–1000 bp), T1: G. Cot 16, T2: GSHV 185, S1: L 1384, S2: TCH 1777, T1T2: G. Cot 16×GSHV 185, T2T1: GSHV 185×G. Cot 16, T2S1: GSHV 185×L 1384, S1T2: L 1384×GSHV 185, S1S2: L 1384×TCH 1777, S2S1: TCH 1777× L 1384, T2S2: GSHV 185×TCH 1777, S2T2: TCH 1777×GSHV 185, S2T1: TCH 1777× G. Cot 16, T1S2: G. Cot 16×TCH 1777, T1S1: G. Cot 16×L 1384, S1T1: L 1384×G. Cot 16

Figure 6: Amplification patterns of different cotton hybrids and their parents with MGHES06 marker M: ladder (100–1000 bp), T1: G. Cot 16, T2: GSHV 185, S1: L 1384, S2: TCH 1777, T1T2: G. Cot 16×GSHV 185, T2T1: GSHV 185×G. Cot 16, T2S1: GSHV 185×L 1384, S1T2: L 1384×GSHV 185, S1S2: L 1384×TCH 1777, S2S1: TCH 1777× L 1384, T2S2: GSHV 185×TCH 1777, S2T2: TCH 1777×GSHV 185, S2T1: TCH 1777× G. Cot 16, T1S2: G. Cot 16×TCH 1777, T1S1: G. Cot 16×L 1384, S1T1: L 1384×G. Cot 16

Table 2: Jaccard’s similarity coefficient among different cotton parents and their hybrids based on molecular analysis

Figure 7: Dendrogram depicting the genetic relationship among the different cotton hybrids and their parents based on molecular analysis

Figure 8: Principle component analysis based on the molecular marker (Unit variance scaling is applied to rows; SVD with imputation is used to calculate principal components. X and Y axis show principal component 1 and principal component 2 that explains 34.9% and 26.3% of the total variance, respectively. N = 12 data points.)

Figure 9: Heatmap analysis of molecular marker and genotypes (Heatmap shows unit variance scaling is applied to rows. Both rows and columns are clustered using correlation distance and average linkage)

Figure 1: Amplification patterns of different cotton hybrids and their parents with TMB0409 marker M: ladder (100–1000 bp), T1: G. Cot 16, T2: GSHV 185, S1: L 1384, S2: TCH 1777, T1T2: G. Cot 16×GSHV 185, T2T1: GSHV 185×G. Cot 16, T2S1: GSHV 185×L 1384, S1T2: L 1384×GSHV 185, S1S2 : L 1384×TCH 1777, S2S1: TCH 1777× L 1384, T2S2: GSHV 185×TCH 1777, S2T2: TCH 1777×GSHV 185, S2T1: TCH 1777× G. Cot 16, T1S2: G. Cot 16×TCH 1777, T1S1: G. Cot 16×L 1384, S1T1: L 1384×G. Cot 16

Figure 2: Amplification patterns of different cotton hybrids and their parents with DPL0094 marker M: ladder (100–1000 bp), T1: G. Cot 16, T2: GSHV 185, S1: L 1384, S2: TCH 1777, T1T2: G. Cot 16×GSHV 185, T2T1: GSHV 185×G. Cot 16, T2S1: GSHV 185×L 1384, S1T2: L 1384×GSHV 185, S1S2 : L 1384×TCH 1777, S2S1: TCH 1777× L 1384, T2S2: GSHV 185×TCH 1777, S2T2: TCH 1777×GSHV 185, S2T1: TCH 1777× G. Cot 16, T1S2: G. Cot 16×TCH 1777, T1S1: G. Cot 16×L 1384, S1T1: L 1384×G. Cot 16

Table 1: Amplification and analysis details of SSR primers

Figure 3: Amplification patterns of different cotton hybrids and their parents with BNL686 marker M: ladder (100–1000 bp), T1: G. Cot 16, T2: GSHV 185, S1: L 1384, S2: TCH 1777, T1T2: G. Cot 16×GSHV 185, T2T1: GSHV 185×G. Cot 16, T2S1: GSHV 185×L 1384, S1T2: L 1384×GSHV 185, S1S2: L 1384×TCH 1777, S2S1: TCH 1777×L 1384, T2S2: GSHV 185×TCH 1777, S2T2: TCH 1777×GSHV 185, S2T1: TCH 1777×G. Cot 16, T1S2: G. Cot 16×TCH 1777, T1S1: G. Cot 16×L 1384, S1T1: L 1384×G. Cot 16

Figure 4: Amplification patterns of different cotton hybrids and their parents with JESPR153 marker M: ladder (100–1000 bp), T1: G. Cot 16, T2: GSHV 185, S1: L 1384, S2: TCH 1777, T1T2: G. Cot 16×GSHV 185, T2T1: GSHV 185×G. Cot 16, T2S1: GSHV 185×L 1384, S1T2: L 1384×GSHV 185, S1S2: L 1384×TCH 1777, S2S1: TCH 1777× L 1384, T2S2: GSHV 185×TCH 1777, S2T2: TCH 1777×GSHV 185, S2T1: TCH 1777× G. Cot 16, T1S2: G. Cot 16×TCH 1777, T1S1: G. Cot 16×L 1384, S1T1: L 1384×G. Cot 16

Figure 5: Amplification patterns of different cotton hybrids and their parents with CM45 marker M: ladder (100–1000 bp), T1: G. Cot 16, T2: GSHV 185, S1: L 1384, S2: TCH 1777, T1T2: G. Cot 16×GSHV 185, T2T1: GSHV 185×G. Cot 16, T2S1: GSHV 185×L 1384, S1T2: L 1384×GSHV 185, S1S2: L 1384×TCH 1777, S2S1: TCH 1777× L 1384, T2S2: GSHV 185×TCH 1777, S2T2: TCH 1777×GSHV 185, S2T1: TCH 1777× G. Cot 16, T1S2: G. Cot 16×TCH 1777, T1S1: G. Cot 16×L 1384, S1T1: L 1384×G. Cot 16

Figure 6: Amplification patterns of different cotton hybrids and their parents with MGHES06 marker M: ladder (100–1000 bp), T1: G. Cot 16, T2: GSHV 185, S1: L 1384, S2: TCH 1777, T1T2: G. Cot 16×GSHV 185, T2T1: GSHV 185×G. Cot 16, T2S1: GSHV 185×L 1384, S1T2: L 1384×GSHV 185, S1S2: L 1384×TCH 1777, S2S1: TCH 1777× L 1384, T2S2: GSHV 185×TCH 1777, S2T2: TCH 1777×GSHV 185, S2T1: TCH 1777× G. Cot 16, T1S2: G. Cot 16×TCH 1777, T1S1: G. Cot 16×L 1384, S1T1: L 1384×G. Cot 16

Table 2: Jaccard’s similarity coefficient among different cotton parents and their hybrids based on molecular analysis

Figure 7: Dendrogram depicting the genetic relationship among the different cotton hybrids and their parents based on molecular analysis

Figure 8: Principle component analysis based on the molecular marker (Unit variance scaling is applied to rows; SVD with imputation is used to calculate principal components. X and Y axis show principal component 1 and principal component 2 that explains 34.9% and 26.3% of the total variance, respectively. N = 12 data points.)

Figure 9: Heatmap analysis of molecular marker and genotypes (Heatmap shows unit variance scaling is applied to rows. Both rows and columns are clustered using correlation distance and average linkage)

Figure 1: Amplification patterns of different cotton hybrids and their parents with TMB0409 marker M: ladder (100–1000 bp), T1: G. Cot 16, T2: GSHV 185, S1: L 1384, S2: TCH 1777, T1T2: G. Cot 16×GSHV 185, T2T1: GSHV 185×G. Cot 16, T2S1: GSHV 185×L 1384, S1T2: L 1384×GSHV 185, S1S2 : L 1384×TCH 1777, S2S1: TCH 1777× L 1384, T2S2: GSHV 185×TCH 1777, S2T2: TCH 1777×GSHV 185, S2T1: TCH 1777× G. Cot 16, T1S2: G. Cot 16×TCH 1777, T1S1: G. Cot 16×L 1384, S1T1: L 1384×G. Cot 16

Figure 2: Amplification patterns of different cotton hybrids and their parents with DPL0094 marker M: ladder (100–1000 bp), T1: G. Cot 16, T2: GSHV 185, S1: L 1384, S2: TCH 1777, T1T2: G. Cot 16×GSHV 185, T2T1: GSHV 185×G. Cot 16, T2S1: GSHV 185×L 1384, S1T2: L 1384×GSHV 185, S1S2 : L 1384×TCH 1777, S2S1: TCH 1777× L 1384, T2S2: GSHV 185×TCH 1777, S2T2: TCH 1777×GSHV 185, S2T1: TCH 1777× G. Cot 16, T1S2: G. Cot 16×TCH 1777, T1S1: G. Cot 16×L 1384, S1T1: L 1384×G. Cot 16

Table 1: Amplification and analysis details of SSR primers

Figure 3: Amplification patterns of different cotton hybrids and their parents with BNL686 marker M: ladder (100–1000 bp), T1: G. Cot 16, T2: GSHV 185, S1: L 1384, S2: TCH 1777, T1T2: G. Cot 16×GSHV 185, T2T1: GSHV 185×G. Cot 16, T2S1: GSHV 185×L 1384, S1T2: L 1384×GSHV 185, S1S2: L 1384×TCH 1777, S2S1: TCH 1777×L 1384, T2S2: GSHV 185×TCH 1777, S2T2: TCH 1777×GSHV 185, S2T1: TCH 1777×G. Cot 16, T1S2: G. Cot 16×TCH 1777, T1S1: G. Cot 16×L 1384, S1T1: L 1384×G. Cot 16

Figure 4: Amplification patterns of different cotton hybrids and their parents with JESPR153 marker M: ladder (100–1000 bp), T1: G. Cot 16, T2: GSHV 185, S1: L 1384, S2: TCH 1777, T1T2: G. Cot 16×GSHV 185, T2T1: GSHV 185×G. Cot 16, T2S1: GSHV 185×L 1384, S1T2: L 1384×GSHV 185, S1S2: L 1384×TCH 1777, S2S1: TCH 1777× L 1384, T2S2: GSHV 185×TCH 1777, S2T2: TCH 1777×GSHV 185, S2T1: TCH 1777× G. Cot 16, T1S2: G. Cot 16×TCH 1777, T1S1: G. Cot 16×L 1384, S1T1: L 1384×G. Cot 16

Figure 5: Amplification patterns of different cotton hybrids and their parents with CM45 marker M: ladder (100–1000 bp), T1: G. Cot 16, T2: GSHV 185, S1: L 1384, S2: TCH 1777, T1T2: G. Cot 16×GSHV 185, T2T1: GSHV 185×G. Cot 16, T2S1: GSHV 185×L 1384, S1T2: L 1384×GSHV 185, S1S2: L 1384×TCH 1777, S2S1: TCH 1777× L 1384, T2S2: GSHV 185×TCH 1777, S2T2: TCH 1777×GSHV 185, S2T1: TCH 1777× G. Cot 16, T1S2: G. Cot 16×TCH 1777, T1S1: G. Cot 16×L 1384, S1T1: L 1384×G. Cot 16

Figure 6: Amplification patterns of different cotton hybrids and their parents with MGHES06 marker M: ladder (100–1000 bp), T1: G. Cot 16, T2: GSHV 185, S1: L 1384, S2: TCH 1777, T1T2: G. Cot 16×GSHV 185, T2T1: GSHV 185×G. Cot 16, T2S1: GSHV 185×L 1384, S1T2: L 1384×GSHV 185, S1S2: L 1384×TCH 1777, S2S1: TCH 1777× L 1384, T2S2: GSHV 185×TCH 1777, S2T2: TCH 1777×GSHV 185, S2T1: TCH 1777× G. Cot 16, T1S2: G. Cot 16×TCH 1777, T1S1: G. Cot 16×L 1384, S1T1: L 1384×G. Cot 16

Table 2: Jaccard’s similarity coefficient among different cotton parents and their hybrids based on molecular analysis

Figure 7: Dendrogram depicting the genetic relationship among the different cotton hybrids and their parents based on molecular analysis

Figure 8: Principle component analysis based on the molecular marker (Unit variance scaling is applied to rows; SVD with imputation is used to calculate principal components. X and Y axis show principal component 1 and principal component 2 that explains 34.9% and 26.3% of the total variance, respectively. N = 12 data points.)

Figure 9: Heatmap analysis of molecular marker and genotypes (Heatmap shows unit variance scaling is applied to rows. Both rows and columns are clustered using correlation distance and average linkage)

Table 1: Amplification and analysis details of SSR primers

Table 1: Amplification and analysis details of SSR primers

Table 1: Amplification and analysis details of SSR primers

Table 1: Amplification and analysis details of SSR primers

Table 1: Amplification and analysis details of SSR primers

Table 1: Amplification and analysis details of SSR primers

Table 1: Amplification and analysis details of SSR primers

Table 1: Amplification and analysis details of SSR primers

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