Genetic Mapping and Validation of Quantitative Trait Loci (QTL) for the Grain Appearance and Quality Traits in Rice (Oryza sativa L.) by Using Recombinant Inbred Line (RIL) Population

Table 1

List of polymorphic rice microsatellite (RM) markers used in the QTL mapping.

S. no.	Markers	Chr	Mb	Repeat motif	Tm	Exp. size	Forward primer	Reverse primer
1	RM 8105	1	4	(AG)18	55	100	TCATTCTCGAAGGCTTACGG	TCAAGCCTAAGCAGAGGATG
2	RM 580	1	9.6	(CTT)19	55	221	GATGAACTCGAATTTGCATCC	CACTCCCATGTTTGGCTCC
3	RM 490	1	6.6	(CT)13	55	101	ATCTGCACACTGCAAACACC	AGCAAGCAGTGCTTTCAGAG
4	RM 9	1	23.3	(GA)15GT(GA)2	55	136	GGTGCCATTGTCGTCCTC	ACGGCCCTCATCACCTTC
5	RM 10402	1	6.69	(CT)19	55	286	TGGATTGAAGGGAGCTCTACACC	TTGCTCCACACGATCTACACAGC
6	RM 2318	1	24.1	(AT)25	55	133	CTTTTGCTCATCCATTCG	CCTCTTCATGCGATAAACAT
7	RM 8136	1	42.9	(AT)71	55	225	ATGTAAGCTAGGTAGAGCTG	GCGTACGTACGTAAGTAATA
8	RM 246	1	27.3	(CT)20	55	116	GAGCTCCATCAGCCATTCAG	CTGAGTGCTGCTGCGACT
9	RM 431	1	38.8	(AG)16	55	251	TCCTGCGAACTGAAGAGTTG	AGAGCAAAACCCTGGTTCAC
10	RM 5390	2	10.8	(CA)23	55	107	CTCGACCAAACAGACCAGTAGGG	ATCGCCGCTTAGGAGAATCTGG
11	RM 6	2	29.5	(AG)16	55	163	GTCCCCTCCACCCAATTC	TCGTCTACTGTTGGCTGCAC
12	RM 13380	2	20.2	(TC)10	55	177	GCCTTTCTCTTGATCTCCTCGATCC	CTGGACACTGCGGTTGCTTCC
13	RM 85	3	37.2	(TGG)5(TCT)12	55	107	CCAAAGATGAAACCTGGATTG	GCACAAGGTGAGCAGTCC
14	RM 16109	3	33.9	(TC)16	55	292	CAGAAACTGAGGAGAGAGAAAGATCG	CGATTCAGAGCCATGCTACCG
15	RM 3716	3	6.83	(AG)17	55	127	GTCGTTCGGTTGACTCGTTG	CACACATATATACCCCCCCC
16	RM 148	3	35.8	(TG)12	55	129	ATACAACATTAGGGATGAGGCTGG	TCCTTAAAGGTGGTGCAATGCGAG
17	RM 200	3	13.4	(GA)16	55	122	CGCTAGGGAATTTGGATTGA	CGATGAGCAGGTATCGATGAGAAG
18	RM 15303	3	19.8	(TCT)15	55	199	GAATCGGGTCTACGGTTTAGG	AAAGGAAGAGAAGAGGCAACG
19	RM 5761	3	2.1	(AGA)8	55	104	AGGGGAATGGCAAGATTACC	AGTCGTCCTCTTCACATGGC
20	RM 6314	4	18.4	(CTT)11	50	169	GATTCGTGTCGGTTGTCAAG	GGTTCAGGGACGAATTTCAG
21	RM 7051	4	24.1	(AATC)7	55	176	CTCGATGAGCTTGGCGTC	TTCAGTGTTCATCGCCTCTG
22	RM 16508	4	6.9	(GCC)7	55	188	TTCATTGTCATCGCCTCATTGG	ACAGGTACAGCTGGGTAGAGAGAAGC
23	RM 131	4	34.4	(CT)9	61	215	TCCTCCCTCCCTTCGCCCACTG	CGATGTTCGCCATGGCTGCTCC
24	RM 303	4	28.5	[AC(AT)2-10]9(GT)7(ATGT)6	55	200	GCATGGCCAAATATTAAAGG	GGTTGGAAATAGAAGTTCGGT
25	RM 1024	5	1.2	(AC)13	55	141	GCATATACCATGGGGATTGG	GGGATTGGGATAATGGTGTG
26	RM 1089	5	5.3	(AC)33	55	239	CAGAAGGATTATCTCGATACC	AATAGGGCTTGAAATAAATTG
27	RM 161	5	20.9	(AG)20	61	187	TGCAGATGAGAAGCGGCGCCTC	TGTGTCATCAGACGGCGCTCCG
28	RM 163	5	19.1	(GGAGA)4(GA)11C(GA)20	55	124	ATCCATGTGCGCCTTTATGAGGA	CGCTACCTCCTTCACTTACTAGT
29	RM 274	5	26.8	(GA)15-7-(CGG)5	55	160	CCTCGCTTATGAGAGCTTCG	CTTCTCCATCACTCCCATGG
30	RM 31	5	28.6	(GA)15	55	140	GATCACGATCCACTGGAGCT	AAGTCCATTACTCTCCTCCC
31	RM 190	6	1.7	(CT)11	55	124	CTCTCTCACCATTCCTTCAGTTC	GCAAGACTGGTTTCCACATGG
32	RM 225	6	3.4	(CT)18	55	140	TGCCCATATGGTCTGGATG	GAAAGTGGATCAGGAAGGC
33	RM 3183	6	12.4	(CT)12	50	140	GCTCCACAGAAAAGCAAAGC	TGCAACAGTAGCTGTAGCCG
34	RM 461	6	30.1	(AAAC)6	55	195	GAGACCGGAGAGACAACTGC	TGATGCGGTTTGACTGCTAC
35	RM 217	6	17.9	(CT)20	55	133	ATCGCAGCAATGCCTCGT	GGGTGTGAACAAAGACAC
36	RM 50	6	6.3	(CTAT)4(CT)15	55	201	ACTGTACCGGTCGAAGACG	AAATTCCACGTCAGCCTCC
37	RM 8015	7	8.1	(AT)34	55	130	AAGTTTCTCCAAGCCAAGAG	AATGTGTTTTCCTGGTCAGA
38	RM 1364	7	26.7	(AG)26	55	158	AAGAAATTCAAAACACATGA	AAAACATCTACTTTGATCCA
39	RM 3555	7	27.8	(GA)12	55	154	TGGAAGTTTCCTGGCGATAG	TGGTTGGACTGAAAAGTCCC
40	RM 7338	7	15.3	(CATC)9	55	164	CTTATCTCTCGGCAAGCAGC	CTCACACGCATGGATCAATC
41	RM 214	7	12.7	(CT)14	55	112	CTGATGATAGAAACCTCTTCTC	AAGAACAGCTGACTTCACAA
42	RM 234	7	25.4	(CT)25	55	156	ACAGTATCCAAGGCCCTGG	CACGTGAGACAAAGACGGAG
43	RM 248	7	29.3	(CT)25	55	102	TCCTTGTGAAATCTGGTCCC	GTAGCCTAGCATGGTGCATG
44	RM 20938	7	2.2	(GAG)8	57	454	GGACATCTACTCGCAGCTCTGG	TTACACGCTCTGACAGGTTGTGG
45	RM 2310	8	19.9	(GA)10	55	295	CGAGTAGCGGAACTGGATGAACTCC	GTTCAGGGTACGCGCCAAACG
46	RM 1959	8	0.2	(AT)19	55	160	CTATTGTACCTGCTCTCATC	ACATCGGTACTGATAATGTT
47	RM 1109	8	20.4	(AG)12	55	198	TCAAAATCACGTGTATGTAAGC	TTTACAAAGGACAGAGGGC
48	RM 24432	9	16.4	(TA)29	50	638	GTGTGAGTTTGGTTTGGGAGAGG	GCCCAATACACGGTAGATTCATCC
49	RM 219	9	7.8	(CT)17	55	202	CGTCGGATGATGTAAAGCCT	CATATCGGCATTCGCCTG
50	RM 23904	9	7	(CT)11	55	164	CTCACCGGAGCACCACTAACC	GAGAGCAAGACTGTGAAGTGTGAACC
51	RM24118	9	11.1	(TA)11	55	398	TCTCAATAGTCGCCACCAACACC	GAGCCCGGCAGAAATTTAAAGC
52	RM24262	9	14.1	(ACAT)5	55	255	CTCATCGGCGACATATCACAGC	CTCATCGGCGACATATCACAGC
53	RM8015	9	8.1	(AT)34	55	130	AAGTTTCTCCAAGCCAAGAG	AATGTGTTTTCCTGGTCAGA
54	RM 7545	10	3.8	(TATG)18	61	225	GTATCCGCTCCGTTTTCATC	GAGGGGGGGGTGTAGAATAG
55	RM 6150	10	18.3	(CGC)9	50	180	CTCGACGGAGCTCTCTTCAC	CAAGAAGCAGAGGAAAAGCG
56	RM 147	10	20.9	(TTCC)5(GGT)5	55	97	TACGGCTTCGGCGGCTGATTCC	CCCCCGAATCCCATCGAAACCC
57	RM 271	10	16.2	(GA)15	55	101	TCAGATCTACAATTCCATCC	TCGGTGAGACCTAGAGAGCC
58	RM 441	11	6	(AG)13	55	189	ACACCAGAGAGAGAGAGAGAGAG	TCTGCAACGGCTGATAGATG
59	RM 26675	11	15.7	(ACG)8	55	262	AGCACAGTGTTCACCAGCATTGG	ACGTGGTCGACGAAGGTGACG
60	RM 270	12	10.5	(GA)13	55	108	GGCCGTTGGTTCTAAAATC	TGCGCAGTATCATCGGCGAG
61	RM 19	12	2.4	(ATC)10	55	226	CAAAAACAGAGCAGATGAC	CTCAAGATGGACGCCAAGA
62	RM 27956	12	11.7	(CT)10	55	173	AGCAACCTACCTTGCCAAATTACC	TGTGCATATCCATTGACACAGC
63	RM 3331	12	23.4	(CT)15	50	129	CCTCCTCCATGAGCTAATGC	AGGAGGAGCGGATTTCTCTC
64	RM 27782	12	6.7	(ATT)13	55	414	GAGGAGAGGAGACGGAGAGG	CGAGAGTGGTGATCTCACTTAATAGG
65	RM 28603	12	24.6	(CT)12	55	392	ATCCCGACCTAGGATACGGTTGC	CATGGAGTGTGAGTTCCAAATTGC