ALK6 web Termined to be 3, which are represented as POP1, POP2, and POP3 (Figure 4b). POP1 was the largest sub-population and constituted of 52 genotypes, of which 38 were pure forms and 14 were admixture forms. POP2 consisted of ten genotypes such as 8 pure sorts and 2 admixture kinds, even though POP3 comprised of 34 genotype which includes 23 pure kinds and 11 had been admixed. The fixation index (Fst) was 0.75, 0.96, and 0.83 for the sub-populations POP1, POP2, and POP3, respectively, plus the typical distance among folks inside a sub-population was 0.12, 0.03, and 0.09, respectively. The allelic frequency divergence of POP1 from POP2 was 0.49, and from POP3 was 0.25, although involving POP2 and POP3 it was 0.45.Plants 2021, 10,six ofFigure 4. STRUCTURE evaluation. (a) The K value was highest for the model parameter K = 3 than for other values of K. (b) The bar plot showing each and every rice selection belonging to 3 subpopulations.two.four. Genome-Wide Association Study for Traits Linked with Salinity Tolerance A total of 23 MTAs have been identified for CYP1 Storage & Stability twelve traits inside the current study. Out of 23 MTAs, 21 MTAs had been positioned either in or close to the previously reported QTLs/MTAs linked with seedling stage salinity tolerance and two MTAs had been novel. These MTAs are located on rice chromosomes 1, two, five, six, 7, 9, and 12 and explained the trait phenotypic variance ranging from 13.98 to 29.88 (Table 1). Manhattan plots and quantile uantile (Q-Q) plots generated by means of the model are presented in Figure 5. The Q-Q plots indicate that the model was well fitted for the information as the observed p-values showed much less deviation from the anticipated p-values.Plants 2021, 10,7 ofTable 1. Specifics on the marker-trait associations (MTAs) identified for salt tolerance connected traits at seedling stage. S.No 1 2 3 SFW Traits SL RL MTAs qSL2 qRL2 qSFW2 qSFW7 qSFW9 four 5 SEW RFW qRFW2 qSEW2 qSEW7 qSEW9 six SDW 7 8 9 SNC ten 11 12 SKC RNK SNK RDW RNC qSDW2.1 qSDW2.2 qSDW12.1 qRDW6 qRDW7 qRNC2.1 qRNC2.2 qSNC1 qSNC2 qSNC5 qSKC1 qSKC6 qRNK1 qSNK1 SNP AX-95920196 AX-95920196 AX-95921620 AX-95937657 AX-95931839 AX-95921620 AX-95921620 AX-95937657 AX-95931839 AX-95920663 AX-95934798 AX-95939149 AX-95956901 AX-95929366 AX-95921298 AX-95920628 AX-95940587 AX-95920537 AX-95927105 AX-95940587 AX-95937335 AX-95918556 AX-95940642 Chr. two two 2 7 9 two two 7 9 2 two 12 six 7 two two 1 2 5 1 six 1 1 Position 23947447 23947447 23533590 20788892 16483542 23533590 23533590 20788892 16483542 5664763 10213902 17404747 29729562 20782724 23260124 22172032 13758487 22171212 19697164 13758487 3429601 11022718 13322813 p Value 6.74 10-5 7.54 10-5 five.18 10-4 6.79 four.61 10-4 10-4 R2 15.11 19.26 14.64 13.98 14.92 14.64 15.43 15.31 14.77 25.51 22.52 20.24 22.05 22.62 18.17 15.15 16.26 16.64 18.08 16.26 14.33 25.11 29.88 Previous Report qPH2 [24]; qGP-2 [41] qPH2 [24]; qGP-2 [41] qPH2, qRKC2, qCHL2 [24]; qGP-2 [41] qRSW7 [42] qSNK9, qRNK9, qSES9 [24]; qGP-9 [41] qPH2, qRKC2, qCHL2 [24]; qGP-2 [41] qPH2, qRKC2, qCHL2 [24]; qGP-2 [41] qRSW7 [42] qSNK9, qRNK9 [24]; qGP-9 [41] OsVTE1 [43]; OsGMST1 [44] qSES12, qSUR12, qCHL12 [24] OsCMO [45] qSES7.1, KR7.1 [46] qRKC2 [24]; qGP-2 [41] qRKC2 [24]; qGP-2 [41] qSKC, qSNK, qRNK [24] qRKC2 [24]; qGP-2 [41] qSKC, qSNK, qRNK [24] qRFWn6.1, qRDWn6.1 [47] qRNK1, qSNC, qSKC, qRKC [24] qSKC, qSNK, qRNK [24]5.18 10-4 three.87 10-4 four.07 five.06 10-4 10-1.42 10-5 four.05 10-5 9.22 10-5 5.79 10-5 four.74 10-5 six.30 10-5 9.45 10-5 8.16 10-5 eight.35 10-5 9.39 10-5 7.86 10-5 8.21 10-5 6.26 10-6 2.93 10-For SL and RL, 1 widespread MTA (SNP-AX.