Rice Science ›› 2016, Vol. 23 ›› Issue (6): 317-325.DOI: 10.1016/j.rsci.2016.05.003
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D. Chowdhury A.1, Haritha G.1, Sunitha T.1, L. Krishnamurthy S.2, Divya B.1, Padmavathi G.1, Ram T.1, Sarla N.1
Received:
2016-03-26
Accepted:
2016-05-24
Online:
2016-12-12
Published:
2016-08-10
D. Chowdhury A., Haritha G., Sunitha T., L. Krishnamurthy S., Divya B., Padmavathi G., Ram T., Sarla N.. Haplotyping of Rice Genotypes Using Simple Sequence Repeat Markers Associated with Salt Tolerance[J]. Rice Science, 2016, 23(6): 317-325.
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Score | Observation | Tolerance |
1 | Normal growth, no leaf symptoms | Highly tolerant |
3 | Nearly normal growth, only the tips of few leaves whitish and rolled | Tolerant |
5 | Growth severely retarded, most leaves rolled, the two youngest leaves were still elongating | Moderately tolerant |
7 | Complete cessation of growth, all lower leaves dried out, the two youngest leaves started to wilt | Susceptible |
9 | The whole plant dried out and dead | Highly susceptible |
Table 1 Scoring criteria for salt tolerance (Gregorio et al, 1997)
Score | Observation | Tolerance |
1 | Normal growth, no leaf symptoms | Highly tolerant |
3 | Nearly normal growth, only the tips of few leaves whitish and rolled | Tolerant |
5 | Growth severely retarded, most leaves rolled, the two youngest leaves were still elongating | Moderately tolerant |
7 | Complete cessation of growth, all lower leaves dried out, the two youngest leaves started to wilt | Susceptible |
9 | The whole plant dried out and dead | Highly susceptible |
Genotype | Designation | Source | Score | Reaction to salinity | Genotype | Designation | Source | Score | Reaction to salinity |
IRSSTN25 (CK) | FL478 (IR66946-3R-178-1-1) | IRRI | 3 | T | KMR3 | KMR3 | India | 9 | HS |
IRSSTN24 (CK) | IR28 | IRRI | 7 | S | IET19543 | DRRH3 | India | 5 | MT |
IET22631 | RP Bio 4919-13-5 (KMR3 × O. rufipogon) | India | 5 | MT | IET23124 | RP Bio 4918-7-1 (Swarna × O. nivara) | India | 9 | HS |
IET22625 | RP Bio 4918-250 (Swarna × O. nivara) | India | 7 | S | IET21542 | RP Bio 4918-248 (Swarna × O. nivara) | India | 9 | HS |
IET21943 | RP Bio 4919-50-13 (KMR3 × O. rufipogon) | India | 3 | T | IET21944 | RP Bio 4919-13-7 (KMR3 × O. rufipogon) | India | 3 | T |
IET22636 | RP Bio 4919-86-18 (KMR3 × O. rufipogon) | India | 5 | MT | IET21940 | RP Bio 4919-463 (KMR3 × O. rufipogon) | India | 3 | T |
IET23183 | RP Bio 4918-230 (Swarna × O. nivara) | India | 9 | HS | IET22628 | RP Bio 4919-50-12 (KMR3 × O. rufipogon) | India | 5 | MT |
IET22627 | RP Bio 4919-50-10 (KMR3 × O. rufipogon) | India | 7 | S | IET22633 | RP Bio 4919-495 (KMR3 × O. rufipogon) | India | 7 | S |
IET22624 | RP Bio 4918-24 (Swarna × O. nivara) | India | 7 | S | IET22626 | RP Bio 4919-50-7 (KMR3 × O. rufipogon) | India | 5 | MT |
IET3116 | Vikas | India | 5 | MT | IRSSTN19 | IRT11173 | IRRI | 5 | MT |
IET19487 | DRR Dhan 39 | India | 5 | MT | IRSSTN5 | IRT11237 | IRRI | 7 | S |
IET9341 | CST7-1 | India | 5 | MT | IRSSTN14 | IRT11160 | IRRI | 5 | MT |
IRSSTN15 | IRT11176 | IRRI | 5 | MT | IRSSTN3 | IRT11239 | IRRI | 5 | MT |
IRSSTN29 | IR45427-2B-2-2B-1-1 | IRRI | 3 | T | IRSSTN21 | Pokkali (ACC108921) | IRRI | 3 | T |
IRSSTN6 | BR11-Saltol | IRRI | 9 | HS | IRSSTN1 | IRT11169 | IRRI | 5 | MT |
IRSSTN11 | IRT11236 | IRRI | 7 | S | IRSSTN9 | IRT11149 | IRRI | 5 | MT |
IRSSTN13 | IRT11260 | IRRI | 5 | MT | IRSSTN22 | Nonabokra | IRRI | 3 | T |
IRSSTN10 | IRT11133 | IRRI | 7 | S | IET18076 | DRRH2 | India | 5 | MT |
IRSSTN17 | IRT11174 | IRRI | 5 | MT | IRSSTN16 | IRT11172 | IRRI | 5 | MT |
IRSSTN30 | A69-1 | India | 5 | MT | IET5656 | Swarna | India | 9 | HS |
IET19046 | Sambha Mahsuri | India | 9 | HS | IET17340 | CSR36 | India | 3 | T |
IRSSTN28 | AT401 | India | 3 | T | IRSSTN8 | IRT11252 | IRRI | 7 | S |
IRSSTN12 | IRT11254 | IRRI | 5 | MT | IRSSTN7 | IRT11170 | IRRI | 7 | S |
IRSSTN27 | IR55179-3B-11-3 | IRRI | 3 | T | IET15420 | Jarava | India | 5 | MT |
IRSSTN2 | IRT11158 | IRRI | 5 | MT | IRSSTN18 | IRT11141 | IRRI | 3 | T |
IRSSTN4 | IRT11247 | IRRI | 5 | MT | IRSSTN20 | IRT11175 | IRRI | 5 | MT |
IRSSTN23 | IR29 | IRRI | 7 | S | IET13765 | CSR27 | India | 3 | T |
T, Tolerant; MT, Moderately tolerant; S, Susceptible; HS, Highly susceptible; IRRI, International Rice Research Institute. |
Table 2 Salinity stress reaction (EC = 10 dSm-1) of 54 rice genotypes at the seedling stage
Genotype | Designation | Source | Score | Reaction to salinity | Genotype | Designation | Source | Score | Reaction to salinity |
IRSSTN25 (CK) | FL478 (IR66946-3R-178-1-1) | IRRI | 3 | T | KMR3 | KMR3 | India | 9 | HS |
IRSSTN24 (CK) | IR28 | IRRI | 7 | S | IET19543 | DRRH3 | India | 5 | MT |
IET22631 | RP Bio 4919-13-5 (KMR3 × O. rufipogon) | India | 5 | MT | IET23124 | RP Bio 4918-7-1 (Swarna × O. nivara) | India | 9 | HS |
IET22625 | RP Bio 4918-250 (Swarna × O. nivara) | India | 7 | S | IET21542 | RP Bio 4918-248 (Swarna × O. nivara) | India | 9 | HS |
IET21943 | RP Bio 4919-50-13 (KMR3 × O. rufipogon) | India | 3 | T | IET21944 | RP Bio 4919-13-7 (KMR3 × O. rufipogon) | India | 3 | T |
IET22636 | RP Bio 4919-86-18 (KMR3 × O. rufipogon) | India | 5 | MT | IET21940 | RP Bio 4919-463 (KMR3 × O. rufipogon) | India | 3 | T |
IET23183 | RP Bio 4918-230 (Swarna × O. nivara) | India | 9 | HS | IET22628 | RP Bio 4919-50-12 (KMR3 × O. rufipogon) | India | 5 | MT |
IET22627 | RP Bio 4919-50-10 (KMR3 × O. rufipogon) | India | 7 | S | IET22633 | RP Bio 4919-495 (KMR3 × O. rufipogon) | India | 7 | S |
IET22624 | RP Bio 4918-24 (Swarna × O. nivara) | India | 7 | S | IET22626 | RP Bio 4919-50-7 (KMR3 × O. rufipogon) | India | 5 | MT |
IET3116 | Vikas | India | 5 | MT | IRSSTN19 | IRT11173 | IRRI | 5 | MT |
IET19487 | DRR Dhan 39 | India | 5 | MT | IRSSTN5 | IRT11237 | IRRI | 7 | S |
IET9341 | CST7-1 | India | 5 | MT | IRSSTN14 | IRT11160 | IRRI | 5 | MT |
IRSSTN15 | IRT11176 | IRRI | 5 | MT | IRSSTN3 | IRT11239 | IRRI | 5 | MT |
IRSSTN29 | IR45427-2B-2-2B-1-1 | IRRI | 3 | T | IRSSTN21 | Pokkali (ACC108921) | IRRI | 3 | T |
IRSSTN6 | BR11-Saltol | IRRI | 9 | HS | IRSSTN1 | IRT11169 | IRRI | 5 | MT |
IRSSTN11 | IRT11236 | IRRI | 7 | S | IRSSTN9 | IRT11149 | IRRI | 5 | MT |
IRSSTN13 | IRT11260 | IRRI | 5 | MT | IRSSTN22 | Nonabokra | IRRI | 3 | T |
IRSSTN10 | IRT11133 | IRRI | 7 | S | IET18076 | DRRH2 | India | 5 | MT |
IRSSTN17 | IRT11174 | IRRI | 5 | MT | IRSSTN16 | IRT11172 | IRRI | 5 | MT |
IRSSTN30 | A69-1 | India | 5 | MT | IET5656 | Swarna | India | 9 | HS |
IET19046 | Sambha Mahsuri | India | 9 | HS | IET17340 | CSR36 | India | 3 | T |
IRSSTN28 | AT401 | India | 3 | T | IRSSTN8 | IRT11252 | IRRI | 7 | S |
IRSSTN12 | IRT11254 | IRRI | 5 | MT | IRSSTN7 | IRT11170 | IRRI | 7 | S |
IRSSTN27 | IR55179-3B-11-3 | IRRI | 3 | T | IET15420 | Jarava | India | 5 | MT |
IRSSTN2 | IRT11158 | IRRI | 5 | MT | IRSSTN18 | IRT11141 | IRRI | 3 | T |
IRSSTN4 | IRT11247 | IRRI | 5 | MT | IRSSTN20 | IRT11175 | IRRI | 5 | MT |
IRSSTN23 | IR29 | IRRI | 7 | S | IET13765 | CSR27 | India | 3 | T |
T, Tolerant; MT, Moderately tolerant; S, Susceptible; HS, Highly susceptible; IRRI, International Rice Research Institute. |
Marker | Chromosome | Frequency of major allele | Number of alleles | PIC value |
RM493 | 1 | 0.46 | 3 | 0.96 |
RM3412 | 1 | 0.53 | 3 | 0.96 |
RM7075 | 1 | 0.26 | 5 | 0.97 |
RM8094 | 1 | 0.24 | 7 | 0.99 |
RM10694 | 1 | 0.57 | 3 | 0.97 |
RM10720 | 1 | 0.43 | 3 | 0.95 |
RM10793 | 1 | 0.32 | 5 | 0.97 |
RM10843 | 1 | 0.39 | 3 | 0.95 |
RM10852 | 1 | 0.35 | 3 | 0.94 |
RM289 | 5 | 0.70 | 2 | 0.55 |
RM413 | 5 | 0.56 | 5 | 0.96 |
RM264 | 8 | 0.70 | 3 | 0.90 |
RM149 | 8 | 0.20 | 4 | 0.77 |
RM222 | 10 | 0.35 | 5 | 0.96 |
Table 3 Frequency of major allele and polymorphic information content (PIC) value of SSR markers for 54 rice genotypes
Marker | Chromosome | Frequency of major allele | Number of alleles | PIC value |
RM493 | 1 | 0.46 | 3 | 0.96 |
RM3412 | 1 | 0.53 | 3 | 0.96 |
RM7075 | 1 | 0.26 | 5 | 0.97 |
RM8094 | 1 | 0.24 | 7 | 0.99 |
RM10694 | 1 | 0.57 | 3 | 0.97 |
RM10720 | 1 | 0.43 | 3 | 0.95 |
RM10793 | 1 | 0.32 | 5 | 0.97 |
RM10843 | 1 | 0.39 | 3 | 0.95 |
RM10852 | 1 | 0.35 | 3 | 0.94 |
RM289 | 5 | 0.70 | 2 | 0.55 |
RM413 | 5 | 0.56 | 5 | 0.96 |
RM264 | 8 | 0.70 | 3 | 0.90 |
RM149 | 8 | 0.20 | 4 | 0.77 |
RM222 | 10 | 0.35 | 5 | 0.96 |
Fig. 2. Dendrogram showing grouping of 54 rice genotypes based on unweighted pair group method with arithmetic averages algorithm clustering and Jaccard coefficient analysis using 14 SSR markers.
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