Table 2 Validation of superior haplotypes on known drought-tolerant and susceptible varieties.

Gene	Chromosome	Total no. of haplotypes	Superior haplotype	Accessions with SH	Superior haplotype sequence	Drought-tolerant varieties							Drought-susceptible varieties
						DRR Dhan 44	DRR Dhan 42	DRR Dhan 46	Sahbhagi Dhan	PSBRc 82	PSBRc 68	Aus 299	Naveen	Swarna	DRR Dhan 48	BPT5204
OsDREB1C	6	4	H3	5	GAAAG	GAAAG (H3)	GAAAG (H3)	GAAAG (H3)	GAAAA (H1)	GAAAG (H3)	GAAAG (H3)	^aGAAAA (H1)	^aGAAAA (H1)	^aGAAAA (H1)	^aGAAAA (H1)	^aGAAAA (H1)
ASR3	2	32	H88	3	T–A--TA------T–A	^bT–A--TA–C------A	^bT–A--TA-C------A	^bT–A--TA–C------A	^bT–A--TA–C------A	^aT-A--TA---G--TT (H99)	^bT–A--TA–CGG–ATT	^aT–A--TA--GG—TT (H112)	^bT–A--TA–C------A	^bT–A--TA–C------A	^bT–A--TA–C------A	^bT–A--TA–C------A
DSM3	3	4	H4	3	GGGAAAGT	^aGATAAAAT (H2)	^aGATAAAAT (H2)	^aGATAAAAT (H2)	^aGATAAAAT (H2)	^bA/GT/GAATACA/G	^aGGGAAACGT (H3)	^aGGGAAACGT (H3)	^aGATAAAAT (H2)	^aGATAAAAT (H2)	^aGATAAAAT (H2)	^aGATAAAAT (H2)
ZFP182	3	16	H4	10	A----A–C CGG--T	^bA----A–C–CGGT–T	^bA----A–C–CGGT–T	^bA----A–C–CGGT–T	^bA----A–C–CGGT–T	^aA-TA-A-C-CGG—T (H8)	^aA-----A-C-C----– (H1)	A----A–C–C–G—T (H2)	^bA----A–C–CGGT–T	^bA----A–C–CGGT–T	^bA----A–C–CGGT–T	^bA----A–C–CGGT–T
OsDIL1	10	14	H22	3	T–ACGAAG–TGC	^bTTACGAAGAT–C	^bTTACGAAGAT–C	^bTTACGAAGAT-C	^bTTACGAAGAT-C	^aT-ACGAAGA-GC (H24)	^aT-ACGAAGA-GC (H24)	^aTT–CAGGG---C (H24)	^bTTACGAAGAT–C	^bTTACGAAGAT–C	^bTTACGAAGAT–C	^bTTACGAAGAT–C

^aThese genotypes possess other alternate haplotypes than the superior haplotype identified for the gene of interest.
^bHaplotype not present in the subset panel.

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