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Research Article

Evaluation of SSR and SNP Markers for Molecular Breeding in Rice

Zennia Jean Gonzaga1, Kashif Aslam1,2, Endang M. Septiningsih1, Bertrand C.Y. Collard1,*
Plant Breeding and Biotechnology 2015;3(2):139-152.
Published online: June 30, 2015

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*Corresponding author: Bertrand C.Y. Collard, b.collard@irri.org, bcycollard@hotmail.com, Tel: +63-2-580-5600-2478
• Received: May 31, 2015   • Revised: June 17, 2015   • Accepted: June 19, 2015

Copyright © 2015 The Korean Society of Breeding Science

This is an Open-Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Evaluation of SSR and SNP Markers for Molecular Breeding in Rice
Plant Breed. Biotech.. 2015;3(2):139-152.   Published online June 30, 2015
DOI: https://doi.org/10.9787/PBB.2015.3.2.139
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Evaluation of SSR and SNP Markers for Molecular Breeding in Rice
Plant Breed. Biotech.. 2015;3(2):139-152.   Published online June 30, 2015
DOI: https://doi.org/10.9787/PBB.2015.3.2.139
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Evaluation of SSR and SNP Markers for Molecular Breeding in Rice
Image Image Image
Fig. 1 Graphs of PIC values (y axis) plotted for SSR and SNP markers based on chromosome position (x axis).
Fig. 2 Radial tree using unrooted neighbor-joining method of SSR data using Nei’s similarity coefficient.
Fig. 3 Radial tree view of unrooted neighbor-joining tree of SNP data using Nei’s similarity coefficient.

Fig. 1

Fig. 2

Fig. 3

Evaluation of SSR and SNP Markers for Molecular Breeding in Rice

Rice genotypes used for marker evaluation.

Name Alias Parentage Designation GID Information
Swarna-Sub1 Swarna*4/IR49830-7-1-2-3 IR05F102 1847271 New variety with submergence tolerance in India
Samba Mahsuri-Sub1 SAMBHA MAHSURI*3/IR 49830-7-1-2-3 IR07F101 2159598 New variety with submergence tolerance in India
BR11-Sub1 BRRI dhan 52 (Bangladesh) BR 11*3/IR 40931-33-1-3-2 IR07F290 2295328 New variety with submergence tolerance in Bangladesh
CR1009-Sub1 CR 1009*3/IR 49830-7-1-2-3 IR07F291 2403712 New variety with submergence tolerance in India
IR09F434 IRRI 123*2/IRRI 149 IR09F434 2847875 Sub1 near isogenic line (NIL) in popular Philippine variety PSBRc82
Ciherang-Sub1 Inpari 30 (Indonesia) CIHERANG*2/IRRI 149 IR09F436 2847870 New variety with submergence tolerance in Indonesia
PSBRc18-Sub1 PSB RC 18 (IR 51672-62-2-1-1-2-3)*2/IRRI 149 IR09F437 2853229 Sub1 near isogenic line (NIL) in popular Philippine variety awaiting to be released
IR64-Sub1 IRRI 149 or NSICRc194 or “Submarino” (Philippines) IR 40931-33-1-3-2/3*IR 64 IR07F102 2159583 New variety with submergence tolerance in the Philippines
Sabitri IR 1561-228-1/IR 1737//CR 94-13 IRTP 8487 2268099 Popular variety in Nepal
IR6 SIAM 29 (ACC 42)/DEE GEO WOO GEN IRTP 25398 2440173 Popular variety in Pakistan
Super basmati BAS 320/IR 661 IRTP 20918 2274228 Popular basmati variety in Pakistan
IR09F185 BR 11/IR 49830-7-1-2-3//IR04N106 IR 85288-SUB 38-1-1 2707581 Stagnant flooding donor. Parent of RIL population
IR67440-NDR-5-1-1-1-1 CNM 539/IR 53479-B-45-3-2-3 84299 Stagnant flooding donor. Parent of RIL population
FR13A DHALPUTTIA 32293 Donor of Sub1 and highly flood tolerant landrace
IR40931 BKNFR 76106-16-0-1/IR 19661-131-1-2 IR40931-33-1-3-2 71615 Sub1 donor parent.
IR49830 “Popoul” (Myanmar) IR 4568-86-1-3-2/IR 26702-111-1//IR 20992-7-2-2-2-2-3/IR 21567-9-2-2-2-1 IR49830-7-1-2-3 88474 Sub1 and stagnant flooding donor parent/variety
IR42 IR 1561-228-1-2/IR 1737//CR 94-13 IR 2071-586-5-6 13988 IRRI variety released for irrigated and rainfed areas. Susceptible check for submergence tolerance screening.
IRBB66 IRBB 7/IR BB 60 (IR 72920-1-44-4) 1847199 Widely-used bacterial blight gene donor (Xa4, xa5, xa7, xa13 and Xa21) in IR24 background
OR 142-99 Santepheap 3 (Cambodia) PANKAIJ/SIGADIS IRTP 13636 415260 Indian breeding line released as a variety in Cambodia
IRRI 119 PSBRc68 or ‘Sacobia’ (Philippines); Shwe Pyi Tan (Myanmar) IR 43581-57-3-3-6/IR 26940-20-3-3-3-1//KHAO DAWK MALI 105 PSB RC 68 2266161 IRRI variety released with Sub1 for rainfed areas in the Philippines with stagnant flooding tolerance
IRRI 154 NSICRc222 or ‘Tubigan 18’ (Philippines) IR 73012-137-2-2-2/PSB RC 10 (IR 50404-57-2-2-3) IR04A412 1253989 IRRI variety released for irrigated and favourable rainfed areas in the Philippines
FL478 IR 66946-3R-178-1-1 IR 29/POKKALI B IR 66946-3R-178-1-1 1192884 Widely used salinity tolerant donor line
IRRI 148 NSICRc192 or ‘Sahod Ulan 1’ (Philippines) IR 55419-4*2/WAY RAREM IR74371-54-1-1 1161411 Drought released in tolerant the Philippines IRRI variety

Polymorphic SSR markers and PIC values per chromosome.

Chr No. SSRs % monomorphic % polymorphic PIC Min PIC Max PIC Ave
1 107 35.2 64.8 0.087 0.720 0.338
2 64 25.4 74.6 0.087 0.691 0.333
3 60 27.1 72.9 0.087 0.648 0.331
4 61 35.0 65.0 0.087 0.748 0.332
5 56 20.0 80.0 0.087 0.735 0.340
6 53 24.0 76.0 0.087 0.791 0.386
7 38 26.3 73.7 0.087 0.813 0.402
8 52 25.0 75.0 0.087 0.711 0.396
9 102 24.7 75.3 0.087 0.772 0.400
10 33 37.5 62.5 0.087 0.703 0.414
11 42 47.2 52.8 0.087 0.830 0.461
12 54 37.3 62.7 0.087 0.563 0.352

Indica SSR genotyping set based on reliability, polymorphism and marker position.

SSR Name Chr. Physical (Mb) PIC Values
RM495 1 0.2 0.4393
RM1 1 4.6 0.2608
RM243 1 7.9 0.3975
RM582 1 9.1 0.4470
RM449 1 15.1 0.1575
RM24 1 18.9 0.5334
RM237 1 26.8 0.4345
RM84 1 29.7 0.3554
RM486 1 34.9 0.3249
RM14 1 41.3 0.5885
RM154 2 1 0.6913
RM279 2 2.8 0.5468
RM71 2 8.7 0.5623
RM324 2 11.3 0.4394
RM300 2 13.1 0.4925
RM341 2 19.3 0.5192
RM263 2 25.8 0.5109
RM1342 2 28.1 0.5396
RM6 2 29.5 0.3457
RM208 2 35.1 0.5743
RM231 3 2.4 0.5736
RM218 3 8.4 0.6479
RM3297 3 13.2 0.3131
RM15187 3 16.6 0.4551
RM411 3 21.4 0.3604
RM426 3 27.5 0.3850
RM186 3 28.8 0.5736
RM571 3 33.1 0.2970
RM570 3 35.5 0.4647
RM85 3 36.3 0.5038
RM335 4 0.6 0.6550
RM261 4 6.5 0.4065
RM307 4 13.1 0.5623
RM16945 4 20.5 0.2373
RM3839 4 23.9 0.2970
RM252 4 25.1 0.5509
RM3820 4 27.6 0.4898
RM303 4 28.5 0.2922
RM5473 4 31.4 0.7481
RM280 4 34.9 0.4638
RM13 5 2 0.5396
RM592 5 2.7 0.7349
RM17954 5 3.6 0.5425
RM18188 5 9.1 0.6657
RM1115 5 14.7 0.5109
RM5454 5 17.8 0.6221
RM163 5 19.1 0.5509
RM3575 5 21.3 0.4160
RM274 5 26.8 0.0866
RM31 5 28.6 0.4551
RM435 6 0.5 0.3967
RM586 6 1.4 0.6272
RM204 6 3.1 0.7913
RM3408 6 4.5 0.3249
RM276 6 6.2 0.3604
RM549 6 6.9 0.3604
RM136 6 8.7 0.2149
RM3827 6 22.2 0.5179
RM30 6 27.2 0.5921
RM400 6 28.4 0.6172
RM51 7 0.2 0.4368
RM481 7 2.8 0.8129
RM21077 7 4 0.0866
RM214 7 12.7 0.3967
RM500 7 15.9 0.3698
RM2 7 16 0.3457
RM320 7 18.6 0.6175
RM336 7 21.8 0.7137
RM18 7 25.6 0.4252
RM248 7 29.3 0.6398
RM6925 8 0.6 0.6608
RM38 8 2.1 0.4303
RM25 8 4.3 0.4160
RM72 8 6.7 0.6494
RM3395 8 10.2 0.7069
RM22837 8 12.3 0.7109
RM404 8 15.4 0.6024
RM223 8 20.6 0.4368
RM52 8 24.7 0.5109
RM5545 8 28.2 0.5425
RM23679 9 0.8 0.4783
RM23793 9 4.3 0.5603
RM5515 9 7.1 0.4925
RM23958 9 7.9 0.4394
RM3855 9 9.3 0.4160
RM24087 9 10.8 0.5109
RM105 9 12.5 0.5267
RM24260 9 14.1 0.3554
RM410 9 17.6 0.4818
RM242 9 18.8 0.4783
RM108 9 19.3 0.3457
RM205 9 22.7 0.3850
RM24888 10 0.5 0.3554
RM222 10 2.6 0.5015
RM216 10 5.3 0.4842
RM25436 10 14.9 0.5578
RM25459 10 15.2 0.5780
RM258 10 18 0.5880
RM228 10 22.2 0.6801
RM286 11 0.3 0.5877
RM167 11 4 0.2149
RM202 11 9 0.3967
RM26664 11 15.3 0.8295
RM209 11 17.8 0.6982
RM26834 11 18.6 0.5736
RM21 11 19.1 0.6769
RM206 11 22 0.6641
RM224 11 27.2 0.3554
RM27389 11 28.4 0.6690
RM3472 12 3.5 0.5578
RM27809 12 7.4 0.3744
RM27933 12 10.4 0.3975
RM28102 12 16 0.4303
RM1261 12 17.5 0.5629
RM415 12 19.5 0.3026
RM17 12 26.9 0.4813
RM28825 12 27.5 0.2373

SSR markers tightly linked to SUB1.

Genotype Chromosome 9a,b
Marker RM8206 ART5 RM464 RM8300 RM6920 RM5515 RM5526 RM219 SC30 RM23958
Physical position (Mb) 5.92 6.30 6.58 6.60 7.01 7.15 7.31 7.89 8.00 8.00
PIC Value 0.157 0.484 0.425 0.325 0.537 0.493 0.374 0.527 0.568 0.439
Swarna-Sub1 152 200 262 200 300 n/a 172 202 178 98
Samba Mahsuri-Sub1 152 200 262 200 300 124 170 206 178 80
CR1009-Sub1 152 200 262 200 300 124 172 208 184 98
BR11-Sub1 152 200 262 200 250 126 172 204 178 98
PSBRc82-Sub1 152 200 262 200 300 126 172 204 170 80
Ciherang-Sub1 152 200 262 200 300 126 170 206 170 80
PSBRc18-Sub1 154 200 262 200 250 126 170 206 190 98
IR64-Sub1 152 200 262 200 300 126 170 206 178 80
Sabitri 152 210 262 198 300 124 170 206 170 80
IR6 152 210 300 200 250 124 172 208 178 80
Super basmati 158 210 258 200 300 128 172 206 190 82
IR09F185 152 200 262 200 300 126 172 206 178 80
IR67440-NDR-5-1-1-1-1 152 210 262 198 250 124 170 206 170 80
FR13Ab 152 200 262 200 300 126 172 202 178 82
IR40931 152 200 262 200 250 126 172 202 178 82
IR49830 152 200 262 200 300 124 170 206 170 80
IR42 152 210 262 198 290 124 170 206 170 80
IRRBB66 152 210 300 200 290 124 170 206 178 80
OR 142-99 152 210 270 198 250 124 172 208 178 98
IRRI 119 152 n/a n/a 200 290 126 172 206 178 80
IRRI 154 152 210 270 198 290 128 170 206 190 80
FL478 152 210 262 198 300 124 170 206 184 80
IR74371 154 n/a 300 200 300 124 172 204 178 78

aMarker allele sizes (bp).

bSUB1 marker alleles from FR13A are shaded in grey.

Percentage of polymorphic SNP markers and average PIC value per chromosome.

Chr. Total % monomorphic % polymorphic PIC Min PIC Max PIC Ave
1 45 8.9 91.1 0.045 0.531 0.314
2 37 8.1 91.9 0.130 0.574 0.381
3 44 13.6 86.4 0.045 0.574 0.310
4 31 3.2 96.8 0.087 0.588 0.342
5 33 0.0 100.0 0.087 0.490 0.289
6 38 2.6 97.4 0.045 0.501 0.323
7 28 3.6 96.4 0.087 0.527 0.319
8 27 0.0 100.0 0.124 0.580 0.377
9 24 0.0 100.0 0.087 0.530 0.320
10 19 5.3 94.7 0.087 0.517 0.382
11 31 0.0 100.0 0.045 0.537 0.343
12 26 3.9 96.2 0.087 0.501 0.331

Set of genotyping SNPs based on PIC value.

Chr SNP Position (Mb) PIC Values
1 id1003559 4.3 0.5308
1 id1004817 6.1 0.4292
1 ud1000727 16.1 0.5267
1 id1010609 19.1 0.5174
1 id1023158 38.2 0.5290
1 id1028304 44.7 0.5015
2 id2008501 22 0.5578
2 id2008866 23.2 0.4728
2 id2010969 26.1 0.4898
2 id2011561 27.2 0.4842
2 id2014684 34 0.5743
2 id2015767 35.8 0.5743
3 id3000362 0.7 0.5743
3 id3005216 10.1 0.4842
3 id3008333 17.3 0.4336
3 id3011383 27.8 0.5229
3 id3013669 29.9 0.4842
3 id3015399 32.9 0.3750
4 ud4000438 5.8 0.5771
4 id4003973 13.5 0.5629
4 id4007105 21.8 0.5880
4 id4007444 22.8 0.5724
4 id4009293 28.6 0.5880
4 id4010924 32.3 0.5015
5 id5000015 0 0.4898
5 id5001470 2.5 0.4842
5 id5001756 3 0.4336
5 id5006311 15.7 0.4551
5 id5006821 17.1 0.3604
5 id5010661 23.7 0.3658
6 fd17 6.8 0.5015
6 id6004481 7 0.3604
6 id6005350 8.2 0.4460
6 id6011018 21.8 0.4904
6 id6015793 28.5 0.4303
6 id6016490 30.1 0.4292
7 id7000461 2.7 0.4783
7 id7001478 8.2 0.4904
7 id7002051 12.2 0.4160
7 id7002105 13.4 0.5267
7 id7002427 15.9 0.4065
7 id7002859 19.2 0.3604
8 id8000699 2.2 0.4368
8 id8003681 12.5 0.5552
8 ud8001072 16.6 0.5798
8 id8004838 18.4 0.5743
8 id8006727 23.6 0.5290
8 id8007472 27.4 0.4160
9 id9000661 2.3 0.3967
9 id9000881 4.2 0.4160
9 id9003188 12.5 0.4470
9 id9003720 14.4 0.3845
9 id9004168 15.5 0.2970
9 id9006988 20.1 0.5298
10 id10000174 0.9 0.4470
10 id10001250 4 0.5174
10 id10001624 5.2 0.4792
10 wd10001251 6.3 0.4898
10 id10005538 18.9 0.4792
10 id10006726 21.9 0.4292
11 id11003924 10.8 0.5371
11 id11004398 15.1 0.4160
11 id11004812 16.6 0.4898
11 id11005065 17.3 0.4728
11 id11005646 18.4 0.4551
11 id11008862 24.9 0.4908
12 id12000252 0.7 0.5015
12 id12001996 4.4 0.4677
12 id12003019 7.6 0.3026
12 id12004491 12.5 0.4393
12 id12005205 14.6 0.3967
12 id12005501 15.7 0.4842
Table 1 Rice genotypes used for marker evaluation.
Table 2 Polymorphic SSR markers and PIC values per chromosome.
Table 3 Indica SSR genotyping set based on reliability, polymorphism and marker position.
Table 4 SSR markers tightly linked to SUB1.

Marker allele sizes (bp).

SUB1 marker alleles from FR13A are shaded in grey.

Table 5 Percentage of polymorphic SNP markers and average PIC value per chromosome.
Table 6 Set of genotyping SNPs based on PIC value.

Table 1

Table 2

Table 3

Table 4

Table 5

Table 6

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