Scientific Reports

Table 2 Haplo-pheno analysis of favourable candidate loci for grain quality traits, RS content and predicted glycemic index in rice.

From: Superior haplotypes towards development of low glycemic index rice with preferred grain and cooking quality

Trait	Gene ID (RAP)	Allelic effect	Gene function	Average performance of superior haplotype	Average performance of other haplotype	Lines with superior haplotype	Disrtibution of Superior Haplotype
Trait	Gene ID (RAP)	Allelic effect	Gene function	Average performance of superior haplotype	Average performance of other haplotype	Lines with superior haplotype	Indica	Aus	Admixture
AC	Os06g0232700	0.88	transposon protein, putative, unclassified, expressed	H4- 26.50^a	H1-24.25^b, H2-24.44^b, H3-24.03^b, H5-24.00^b	4	4	0	0
	Os06g18710	0.28	retrotransposon protein, putative, unclassified	H3-25.50^a	H1-24.50^b, H4-24.12^b, H6-23.30^c, H7-24.28^b, H9-22.11^d and H15-24.37^b	2	1	1	0
	Os06g18720	0.28	retrotransposon protein, putative, Ty3-gypsy subclass, expressed	H4-26.58^a	H1-20.00^g, H2-24.45^d, H3-25.00^c, H5-23.80^e, H6-24.64^d, H7-24.9^cd, H8-25.75^b, H10-23.11f., H12-19.5^h, H13-24.75^cd, H14-23.36^ef	3	3	0	0
KB	Os05g0187500	-0.1	IQ calmodulin-binding motif family protein, expressed	H7-2.37^a	H1-2.4^b, H2-2.42^c, H3-2.55^b, H4-2.4^b, H5-2.56f., H6-2.46^de, H9-2.4^b, H11-2.47^e, H12-2.58^g, H13-2.45^d, H14-2.46^de, H15-2.46^e	6	4	2	0
LBR	Os05g0187500	0.18	IQ calmodulin-binding motif family protein, expressed	H9-2.81^a	H1-2.71^b, H2-2.69^c, H3-2.14ⁱ, H4-2.66^de, H5.2.38^j, H6-2.68^cd, H7-2.66^e, H11.2.59^g, H12-2.33^k, H13-2.61f., H14-2.57^h, H15-2.51ⁱ	73	72	0	1
ASV	Os06g0229000	1.96	OsFtsH6 FtsH protease, homologue of AtFtsH6, expressed	H1-3.43^c	H2-3.47^b, H3-3.00^d, H4-3.57^a	9	8	1	0
ASV	Os06g12380	1.96	expressed protein	H11-2.75^c	H5-4.48^h, H6-2.92^d, H8-3.67^g, H9-3.25f., H10-3.00^e, H13-2.58^b, H15-2.60^b	8	8	0	0
KBAC	Os08g01010	-1.16	hypothetical protein	H11-3.17^a	H1-3.40f., H3-3.52^g, H4-3.31^d, H6-3.18^b, H10-3.29^c, H13-3.35^e, H14-3.53^g, H15-3.60^h	8	8	0	0
GC	Os10g0469000	5.01	leucine-rich repeat receptor protein kinase EXS precursor, putative, expressed	H1-56.06^a	H2-47.73^b	6	5	1	0
RS	Os06g11100	1.74	retrotransposon protein, putative, unclassified, expressed	H4-3.28^a	H1-3.06^a, H2-2.42^c, H3-2.85^ab	48	48	0	0
PGI	Os08g12590	-2.91	retrotransposon, putative, centromere-specific	H13-62.52^ab	H1-69.34f., H2-67.64^ef, H5-63.36^b, H6-66.68^de, H9-65.41^c, H11-65.53^c, H14-71.67^g	5	5	0	0

AC—Amylose content, KL—Kernel length, KB—Kernel breadth, LBR—Length/Breadth ratio, ASV—Alkali spreading value, KLAC—Kernel length after cooking, KBAC—Kernel breadth after cooking, LER—Linear elongation ratio, GC—Gel consistency, RS—Resistant starch, PGI—Predicted glycemic index, TPR—Transplanted rice.

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