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. 2020 Oct 24;10(11):487. doi: 10.1007/s13205-020-02467-z

Table 1.

List of molecular markers (SSRs and InDels) used in the study along with their map positions and genetic diversity parameters

S. no Marker name Chromosome No Map position (bp)b Major allele frequency Allele No Gene diversity (He) Landraces (proportion) showing > 1 alleles PICa Marker typec Availabilityd
1 RM495 1 2,15,956 0.56 8 0.64 0.01 0.6 SSR GDB
2 RM1 1 46,35,793 0.18 17 0.9 0 0.89 SSR GDB
3 RM283 1 48,85,915 0.43 9 0.68 0 0.63 SSR GDB
4 RM259 1 74,45,627 0.22 10 0.84 0 0.82 SSR GDB
5 RM312 1 91,06,659 0.42 5 0.67 0 0.62 SSR GDB
6 RM23 1 91,06,659 0.32 6 0.77 0 0.73 SSR GDB
7 R1M7 1 1,05,18,002 0.98 2 0.05 0.01 0.05 InDel PBS
8 RM229 1 1,84,07,879 0.41 8 0.72 0 0.67 SSR GDB
9 RM5 1 2,39,71,321 0.28 10 0.8 0 0.77 SSR GDB
10 R1M30 1 2,46,60,853 0.7 2 0.42 0.05 0.33 InDel PBS
11 RM237 1 2,83,39,373 0.37 9 0.76 0 0.73 SSR GDB
12 RM212 1 3,30,53,493 0.64 6 0.53 0 0.49 SSR GDB
13 RM1003 1 3,34,75,908 0.52 6 0.61 0 0.54 SSR GDB
14 RM3403 1 3,49,95,620 0.3 22 0.85 0 0.84 SSR GDB
15 R1M47 1 3,68,28,634 0.89 2 0.2 0.01 0.18 InDel PBS
16 RM431 1 3,88,93,890 0.3 8 0.79 0.01 0.76 SSR GDB
17 RM154 2 10,83,820 0.18 13 0.88 0.01 0.87 SSR GDB
18 RM279 2 28,82,052 0.16 15 0.91 0.03 0.9 SSR GDB
19 R2M10 2 71,07,574 0.99 2 0.01 0 0.01 InDel PBS
20 RM53 2 77,06,705 0.28 15 0.84 0 0.82 SSR GDB
21 RM452 2 95,63,257 0.37 7 0.73 0.01 0.69 SSR GDB
22 RM521 2 1,08,04,792 0.49 12 0.72 0 0.7 SSR GDB
23 R2M24 2 1,12,09,429 0.89 2 0.2 0.01 0.18 InDel PBS
24 RM300 2 1,31,91,380 0.37 12 0.75 0.01 0.72 SSR GDB
25 R2M26 2 1,51,04,418 0.84 2 0.27 0.01 0.23 InDel PBS
26 RM29 2 1,74,84,665 0.5 9 0.67 0 0.62 SSR GDB
27 R2M37 2 2,35,63,428 0.51 2 0.5 0.05 0.37 InDel PBS
28 RM263 2 2,58,65,334 0.4 13 0.8 0 0.78 SSR GDB
29 RM221 2 2,76,09,877 0.23 11 0.86 0 0.84 SSR GDB
30 R2M50 2 3,04,06,330 0.88 2 0.21 0.01 0.19 InDel PBS
31 RM60 3 1,05,852 0.37 11 0.73 0 0.69 SSR GDB
32 RM81 3 19,45,837 0.29 9 0.78 0 0.75 SSR GDB
33 RM489 3 43,33,680 0.48 14 0.73 0 0.71 SSR GDB
34 R3M10 3 60,44,614 0.99 2 0.02 0 0.02 InDel PBS
35 RM7 3 1,24,07,382 0.39 8 0.72 0 0.68 SSR GDB
36 RM338 3 1,32,21,482 0.68 7 0.5 0 0.46 SSR GDB
37 R3M23 3 1,56,78,406 0.89 2 0.2 0.01 0.18 InDel PBS
38 R3M30 3 1,98,88,471 0.96 2 0.07 0 0.07 InDel PBS
39 RM6832 3 2,24,00,917 0.66 11 0.53 0 0.5 SSR GDB
40 R3M37 3 2,64,74,984 0.63 3 0.51 0.03 0.44 InDel PBS
41 RM55 3 2,82,31,692 0.39 9 0.75 0 0.72 SSR GDB
42 R3M53 3 3,24,85,490 0.64 2 0.46 0.02 0.36 InDel PBS
43 RM514 3 3,52,81,232 0.27 12 0.84 0 0.83 SSR GDB
44 R4M13 4 81,15,751 0.89 2 0.2 0 0.18 InDel PBS
45 RM307 4 86,10,617 0.25 12 0.84 0 0.82 SSR GDB
46 R4M17 4 1,16,36,507 0.54 2 0.5 0.04 0.37 InDel PBS
47 RM16623 4 1,24,31,839 0.09 30 0.95 0 0.95 SSR GDB
48 R4M30 4 1,81,72,382 0.56 2 0.49 0.01 0.37 InDel PBS
49 RM471 4 1,88,24,746 0.28 10 0.79 0 0.75 SSR GDB
50 R4M43 4 2,45,94,268 0.87 2 0.23 0 0.2 InDel PBS
51 RM1388 4 2,50,35,173 0.09 28 0.95 0 0.95 SSR GDB
52 RM241 4 2,68,57,374 0.16 19 0.92 0.01 0.91 SSR GDB
53 R4M50 4 2,89,89,250 0.74 2 0.39 0.02 0.31 InDel PBS
54 RM17467 4 3,06,74,329 0.39 24 0.8 0.04 0.79 SSR GDB
55 RM124 4 3,47,39,636 0.49 5 0.64 0.01 0.57 SSR GDB
56 RM507 5 1,02,742 0.39 6 0.73 0 0.69 SSR GDB
57 RM413 5 22,12,736 0.28 13 0.86 0 0.84 SSR GDB
58 RM3322 5 42,62,731 0.27 14 0.83 0 0.81 SSR GDB
59 R5M13 5 59,50,163 0.87 2 0.22 0 0.2 InDel PBS
60 R5M30 5 2,14,47,905 0.64 2 0.46 0.01 0.35 InDel PBS
61 RM178 5 2,51,01,829 0.55 6 0.64 0 0.6 SSR GDB
62 RM87 5 2,68,48,154 0.59 7 0.61 0 0.58 SSR GDB
63 RM161 5 2,68,48,154 0.5 8 0.68 0.01 0.64 SSR GDB
64 RM334 5 2,73,42,022 0.15 13 0.89 0 0.88 SSR GDB
65 RM133 6 4,41,616 0.75 4 0.41 0 0.38 SSR GDB
66 RM510 6 28,31,443 0.61 5 0.56 0 0.5 SSR GDB
67 RM585 6 37,22,966 0.43 9 0.76 0.01 0.74 SSR GDB
68 RM217 6 42,12,289 0.14 21 0.92 0.01 0.91 SSR GDB
69 RM253 6 54,25,408 0.23 15 0.88 0 0.87 SSR GDB
70 RM2126 6 59,05,238 0.28 15 0.8 0 0.77 SSR GDB
71 RM7488 6 69,98,987 0.27 19 0.84 0.01 0.82 SSR GDB
72 R6M14 6 74,36,963 0.68 2 0.43 0.01 0.34 InDel PBS
73 RM3330 6 1,10,64,125 0.22 10 0.87 0 0.86 SSR GDB
74 RM7434 6 2,39,34,663 0.37 7 0.71 0 0.66 SSR GDB
75 RM7434 6 2,39,34,663 0.25 8 0.79 0.01 0.76 SSR GDB
76 RM162 6 2,40,35,491 0.41 8 0.71 0.01 0.66 SSR GDB
77 R6M44 6 2,57,35,724 0.89 2 0.2 0.01 0.18 InDel PBS
78 RM454 6 2,85,32,453 0.44 5 0.65 0 0.58 SSR GDB
79 RM481 7 57,35,196 0.26 16 0.88 0.04 0.87 SSR GDB
80 R7M7 7 65,81,196 0.76 2 0.36 0 0.3 InDel PBS
81 RM501 7 67,79,215 0.57 14 0.61 0 0.56 SSR GDB
82 RM125 7 67,79,215 0.46 7 0.68 0 0.64 SSR GDB
83 R7M20 7 1,12,79,013 0.5 2 0.5 0.01 0.38 InDel PBS
84 RM418 7 1,81,32,231 0.37 14 0.79 0 0.77 SSR GDB
85 RM11 7 1,92,56,914 0.38 9 0.75 0 0.71 SSR GDB
86 RM455 7 2,23,50,593 0.65 3 0.48 0 0.39 SSR GDB
87 R7M37 7 2,36,24,859 0.99 2 0.03 0.01 0.03 InDel PBS
88 RM505 7 2,51,01,758 0.42 4 0.65 0 0.58 SSR GDB
89 RM234 7 2,54,72,688 0.52 10 0.66 0 0.62 SSR GDB
90 RM118 7 2,93,39,845 0.36 7 0.73 0 0.69 SSR GDB
91 RM408 8 1,25,275 0.42 6 0.67 0 0.61 SSR GDB
92 RM407 8 5,22,394 0.45 12 0.74 0 0.71 SSR GDB
93 RM152 8 6,82,963 0.36 8 0.78 0 0.75 SSR GDB
94 RM22254 8 6,91,385 0.44 22 0.69 0 0.64 SSR GDB
95 RM44 8 21,14,843 0.45 9 0.67 0 0.62 SSR GDB
96 RM25 8 21,14,843 0.38 9 0.78 0 0.75 SSR GDB
97 RM1148 8 37,39,008 0.39 8 0.74 0 0.7 SSR GDB
98 RM6999 8 39,84,260 0.14 19 0.91 0 0.91 SSR GDB
99 RM3481 8 91,35,139 0.22 12 0.88 0 0.86 SSR GDB
100 RM3395 8 1,02,93,664 0.58 6 0.59 0 0.54 SSR GDB
101 R8M23 8 1,34,82,749 0.95 2 0.2 0 0.01 InDel PBS
102 R8M33 8 2,07,97,429 0.65 2 0.45 0.01 0.35 InDel PBS
103 RM284 8 2,11,42,348 0.62 5 0.57 0 0.53 SSR GDB
104 RM433 8 2,55,90,576 0.29 11 0.8 0 0.77 SSR GDB
105 RM447 8 2,65,46,992 0.41 10 0.66 0 0.6 SSR GDB
106 RM316 9 12,71,123 0.32 11 0.82 0 0.8 SSR GDB
107 R9M10 9 45,15,585 0.74 2 0.38 0 0.31 InDel PBS
108 R9M20 9 93,78,728 0.89 2 0.2 0.01 0.18 InDel PBS
109 RM105 9 1,18,07,446 0.58 5 0.58 0 0.53 SSR GDB
110 RM6839 9 1,45,66,026 0.7 5 0.46 0 0.42 SSR GDB
111 R9M30 9 1,46,47,925 0.84 2 0.27 0 0.23 InDel PBS
112 RM257 9 1,77,19,660 0.21 12 0.85 0.01 0.83 SSR GDB
113 R9M42 9 1,91,15,701 0.99 2 0.02 0 0.02 InDel PBS
114 RM215 9 2,11,89,110 0.35 7 0.75 0 0.71 SSR GDB
115 RM205 9 2,27,20,624 0.39 18 0.77 0.01 0.74 SSR GDB
116 RM474 10 18,18,800 0.42 19 0.78 0 0.77 SSR GDB
117 R10M10 10 52,07,502 0.52 2 0.5 0.06 0.37 InDel PBS
118 RM271 10 53,52,766 0.32 10 0.81 0 0.79 SSR GDB
119 R10M17 10 90,04,292 0.97 2 0.06 0 0.06 InDel PBS
120 RM184 10 1,63,58,895 0.32 7 0.75 0 0.7 SSR GDB
121 R10M30 10 1,71,91,366 0.54 2 0.5 0.04 0.37 InDel PBS
122 RM171 10 1,90,48,795 0.3 12 0.81 0 0.78 SSR GDB
123 R10M40 10 1,96,17,284 0.15 2 0.1 0 0.01 InDel PBS
124 RM484 10 2,10,66,729 0.46 5 0.61 0 0.53 SSR GDB
125 RM228 10 2,22,43,157 0.33 21 0.85 0.01 0.84 SSR GDB
126 RM591 10 2,28,99,617 0.17 27 0.91 0 0.9 SSR GDB
127 RM590 10 2,30,43,156 0.33 7 0.78 0 0.75 SSR GDB
128 RM26063 11 22,56,991 0.18 20 0.9 0.01 0.89 SSR GDB
129 RM552 11 48,43,013 0.12 17 0.91 0 0.91 SSR GDB
130 RM536 11 89,85,132 0.27 9 0.82 0 0.8 SSR GDB
131 RM287 11 1,67,67,319 0.29 9 0.82 0 0.8 SSR GDB
132 RM26771 11 1,73,59,392 0.41 18 0.75 0.01 0.72 SSR GDB
133 RM21 11 1,83,18,826 0.2 16 0.88 0 0.87 SSR GDB
134 R11M23 11 2,01,48,709 0.89 2 0.2 0 0.18 InDel PBS
135 RM26981 11 2,16,89,935 0.09 38 0.96 0 0.96 SSR GDB
136 R11M40 11 2,48,11,386 0.71 2 0.41 0.04 0.33 InDel PBS
137 RM144 11 2,82,81,693 0.31 13 0.84 0 0.83 SSR GDB
138 RiceSSR PODIP 12 6,23,664 0.26 6 0.81 0 0.78 SSR MD
139 RM19 12 31,85,384 0.23 11 0.86 0 0.85 SSR GDB
140 RM27601 12 35,53,566 0.48 16 0.71 0 0.68 SSR GDB
141 R12M10 12 42,89,075 0.99 2 0.02 0.02 0.02 InDel PBS
142 RM277 12 88,26,555 0.67 6 0.5 0 0.45 SSR GDB
143 RM7102 12 1,32,11,325 0.38 8 0.72 0.01 0.68 SSR GDB
144 R12M27 12 1,73,79,856 0.77 2 0.35 0 0.29 InDel PBS
145 RM2972 12 1,91,38,384 0.45 7 0.71 0 0.67 SSR GDB
146 RM519 12 1,99,03,791 0.36 7 0.78 0 0.75 SSR GDB
147 R12M33 12 2,00,06,587 0.55 2 0.5 0 0.37 InDel PBS
148 R12M43 12 2,61,02,497 0.89 2 0.19 0.01 0.17 InDel PBS
Mean 0.49 8.75 0.62 0.01 0.58

aPolymorphic Information Content

bPhysical locations of SSR markers were taken from Gramene: a genomics and genetics resource for rice marker database’ (https://www.gramene.org/markers/microsat/) whereas physical locations of InDel markers were accessed from MSU Rice Genome Annotation Project (https://rice.plantbiology.msu.edu/analyses_search_blast.shtml) based on the BAC accession ID given in the published study of Shen et al. (2004)

cSSR: Simple Sequence Repeats, InDel: Insertion Deletion,

dGDB: adopted from ‘Gramene: a genomics and genetics resource for rice marker database’ (https://www.gramene.org/markers/microsat/), PBS: adopted from the published study of Shen et al. (2004), MD: manually designed for this study