Rice Science ›› 2019, Vol. 26 ›› Issue (3): 147-156.DOI: 10.1016/j.rsci.2018.08.006
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Khlaimongkhon Sudthana1, Chakhonkaen Sriprapai2, Pitngam Keasinee2, Ditthab Khanittha2, Sangarwut Numphet2, Panyawut Natjaree2, Wasinanon Thiwawan2, Mongkolsiriwatana Chareerat3, Chunwongse Julapark1, Muangprom Amorntip1,2()
Received:
2018-07-09
Accepted:
2018-08-24
Online:
2019-05-28
Published:
2019-01-25
Khlaimongkhon Sudthana, Chakhonkaen Sriprapai, Pitngam Keasinee, Ditthab Khanittha, Sangarwut Numphet, Panyawut Natjaree, Wasinanon Thiwawan, Mongkolsiriwatana Chareerat, Chunwongse Julapark, Muangprom Amorntip. Molecular Markers and Candidate Genes for Thermo-Sensitive Genic Male Sterile in Rice[J]. Rice Science, 2019, 26(3): 147-156.
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Fig. 1. Pollen staining of thermo-sensitive genic male sterility (TGMS) mutant and wild type. A, Abortive anther of the TGMS mutant grown under high temperature (32 ± 2) ºC. B, Normal anther of the TGMS mutant grown under low temperature (24 ± 2) ºC. C, Normal anther of wild type grown under high temperature (32 ± 2) ºC. D, Normal anther of wild type grown under low temperature (24 ± 2) ºC.
F2 population | Total No. of lines | No. of fertile individuals | No. of sterile individuals | Segregation rate | χ2 |
---|---|---|---|---|---|
B2 × B30 | 917 | 700 | 217 | 3.22 | 0.91 |
B2 × B11 | 981 | 722 | 259 | 2.79 | 0.98 |
B2 × KM9 | 1 784 | 1 334 | 450 | 2.96 | 0.042 |
Table 1 Segregation patterns of F2 populations for fertility and sterility.
F2 population | Total No. of lines | No. of fertile individuals | No. of sterile individuals | Segregation rate | χ2 |
---|---|---|---|---|---|
B2 × B30 | 917 | 700 | 217 | 3.22 | 0.91 |
B2 × B11 | 981 | 722 | 259 | 2.79 | 0.98 |
B2 × KM9 | 1 784 | 1 334 | 450 | 2.96 | 0.042 |
Marker | Forward primers (5´-3´) | Reverse primers (5´-3´) | Position (Mb) |
---|---|---|---|
RM12557 | AGCACCACCTCCTCGAACTCC | CAACCCTACCTTGCTTCTTCTTGC | 4.19 |
RM4355 | GGGATGAGAGTAGAAGGCACAAGG | GCTTAATGCCTTTGATCGTTGC | 4.26 |
RM12593 | ACAATACGCTGTGCCAATCTGC | TATTGGCCGTGATGATGAAGTGC | 4.57 |
RM12601 | GCGAACTCGACGACTACTCAACC | CACAACGTCGTCTCCAAGTGC | 4.69 |
RM7638 | GGCTGTCCGTCTTGTAGTGAGAAGC | TCCTTGCAACTTCCGGAGACC | 4.86 |
RM12632 | GGCTTTATTTGTTCTGGCCTTGTGG | CCAAATCAAATGGGTCCTTTGTGC | 5.08 |
RM12649 | TTGAGGTAGGGCACGAGGTCTGG | AATCCGAATGGGACCGAATCACC | 5.25 |
RM12655 | AGGACCAATCCAAAGCGTTTAGC | CCTGCAGTAGATTGCATTGAACC | 5.34 |
RM5664 | GTTCGGCTCCACCTAAACCAAGC | GGCATTCGTCTCGTCTTTGAGG | 5.37 |
RM6378 | CTGATCATCTCATGCCTCCTACG | TCCATCTCCCAATATGACCAACC | 5.47 |
2gAP004869 | AGCTTAAACATATTGGCTGCACG | TAGCCAAGCACGTATACACTCCC | 5.67 |
RM12674 | TAAATGCCAACCAACTCCAAGC | AACTGCGTTTGGGAATATCTCG | 5.68 |
RM12676 | ACTGACGATTGGGCACATTATTCC | CTGCAAATTGGTGGGTGATTGC | 5.74 |
2gAP004045 | CCGAAACCATATATCCAACACGA | TCAAATGTTATTTGGGCGTAACTTT | 5.76 |
2gAP0050058 | CAAACAACCACTTTTGTTCAGCA | ATATATGCTGTGGGCAGGATCAA | 5.81 |
2gAP003974 | CAATTCGGAGATTACATTCGGTC | ACTATAGACGCAGCTTGTGTGCC | 6 .0 |
vf0206114052 | CGAGACCAATCGATCCTCCA | TAACCTGCATCTGTGGTGGA | 6.11 |
2gAP004085 | TGGCAACTAATAGGCATCGTCG | TCTTGTAGCTGCAACATCCCCC | 6.26 |
2gAP004086 | TCAAGCAATCACAACCCCTTCC | GGCTACCCAAACCATGCATCA | 6.28 |
Os02g12300 | TCCCATTTAATTTGGTTCATCG | GCTAACGTGCGTGGATTGAG | 6.4 |
Os02g12350 | TCCATCTGCAAATCCATAGCA | TCTGGTGCATAGCTGCTGGT | 6.42 |
Os02g12370 | ACTTATGCGGTGGTCAAGCA | TTGTTCCTCCACGGCTGATA | 6.44 |
2gAP005394 | TGCAAACAGTTGGATTAGCTTGA | TGACAGTGCGCTTATCTTCCATA | 7.17 |
2gAP005756 | AATTCATTGGACGCACACACAT | TGCATTGGGAAATTGAAAAGATT | 7.26 |
2gAP004070 | ATGGTGCCGGATAACGTATTACA | GGCTTGCGGTAAGAATATAGGAGA | 7.44 |
Supplemental Table 1 Markers on chromosome 2 linked to the tms gene using F2 male sterile plants from B2 × B30, B2 × B11 and B2 × KM9.
Marker | Forward primers (5´-3´) | Reverse primers (5´-3´) | Position (Mb) |
---|---|---|---|
RM12557 | AGCACCACCTCCTCGAACTCC | CAACCCTACCTTGCTTCTTCTTGC | 4.19 |
RM4355 | GGGATGAGAGTAGAAGGCACAAGG | GCTTAATGCCTTTGATCGTTGC | 4.26 |
RM12593 | ACAATACGCTGTGCCAATCTGC | TATTGGCCGTGATGATGAAGTGC | 4.57 |
RM12601 | GCGAACTCGACGACTACTCAACC | CACAACGTCGTCTCCAAGTGC | 4.69 |
RM7638 | GGCTGTCCGTCTTGTAGTGAGAAGC | TCCTTGCAACTTCCGGAGACC | 4.86 |
RM12632 | GGCTTTATTTGTTCTGGCCTTGTGG | CCAAATCAAATGGGTCCTTTGTGC | 5.08 |
RM12649 | TTGAGGTAGGGCACGAGGTCTGG | AATCCGAATGGGACCGAATCACC | 5.25 |
RM12655 | AGGACCAATCCAAAGCGTTTAGC | CCTGCAGTAGATTGCATTGAACC | 5.34 |
RM5664 | GTTCGGCTCCACCTAAACCAAGC | GGCATTCGTCTCGTCTTTGAGG | 5.37 |
RM6378 | CTGATCATCTCATGCCTCCTACG | TCCATCTCCCAATATGACCAACC | 5.47 |
2gAP004869 | AGCTTAAACATATTGGCTGCACG | TAGCCAAGCACGTATACACTCCC | 5.67 |
RM12674 | TAAATGCCAACCAACTCCAAGC | AACTGCGTTTGGGAATATCTCG | 5.68 |
RM12676 | ACTGACGATTGGGCACATTATTCC | CTGCAAATTGGTGGGTGATTGC | 5.74 |
2gAP004045 | CCGAAACCATATATCCAACACGA | TCAAATGTTATTTGGGCGTAACTTT | 5.76 |
2gAP0050058 | CAAACAACCACTTTTGTTCAGCA | ATATATGCTGTGGGCAGGATCAA | 5.81 |
2gAP003974 | CAATTCGGAGATTACATTCGGTC | ACTATAGACGCAGCTTGTGTGCC | 6 .0 |
vf0206114052 | CGAGACCAATCGATCCTCCA | TAACCTGCATCTGTGGTGGA | 6.11 |
2gAP004085 | TGGCAACTAATAGGCATCGTCG | TCTTGTAGCTGCAACATCCCCC | 6.26 |
2gAP004086 | TCAAGCAATCACAACCCCTTCC | GGCTACCCAAACCATGCATCA | 6.28 |
Os02g12300 | TCCCATTTAATTTGGTTCATCG | GCTAACGTGCGTGGATTGAG | 6.4 |
Os02g12350 | TCCATCTGCAAATCCATAGCA | TCTGGTGCATAGCTGCTGGT | 6.42 |
Os02g12370 | ACTTATGCGGTGGTCAAGCA | TTGTTCCTCCACGGCTGATA | 6.44 |
2gAP005394 | TGCAAACAGTTGGATTAGCTTGA | TGACAGTGCGCTTATCTTCCATA | 7.17 |
2gAP005756 | AATTCATTGGACGCACACACAT | TGCATTGGGAAATTGAAAAGATT | 7.26 |
2gAP004070 | ATGGTGCCGGATAACGTATTACA | GGCTTGCGGTAAGAATATAGGAGA | 7.44 |
Fig. 2. Samples of genotyping F2 male sterile plants. P1, Female parent (IR68301S, B2); P2, Male parent (IR14632, B30); 1-10, F2 male sterile individuals of B2 × B30 (indica × japonica) using Os02g12370 marker; P3, Male parent (Supanburi 91062, B11); 11-20, F2 male sterile individuals of B2 × B11 (indica × indica) using vf0206114052 marker.
Fig. 3. Genetic linkage map of thermo-sensitive genic male sterility gene on chromosome 2.The linkage maps were analyzed based on male sterile F2 populations of IR68301S × IR14632 (A), IR68301S × Supanburi 91062 (B) and IR68301S × IR67966-188-2-2-1 (C). Distances of each marker in centiMorgans (cM) from tms gene were given on the left side of the genetic map.
Gene | Description |
---|---|
Os02g0202500 | Conserved hypothetical protein |
Os02g0202600 | Tetratricopeptide-like helical domain containing protein |
Os02g0202800 | Zinc ion binding protein |
Os02g0202900 | OsFBK3-F-box domain and kelch repeat containing protein |
Os02g0202950 | Concanavalin A-like lectin/glucanases superfamily and Legume lectin domain |
Os02g0203000 | Carbohydrate binding, sequence-specific DNA binding, sequence-specific DNA binding transcription factor activity |
Os02g0203300 | UDP-glucuronosyl/UDP-glucosyltransferase |
Os02g0203401 | hypothetical gene, protein coding |
Os02g0203500 | Putative uncharacterized protein OJ1135_F06.25; Putative uncharacterized protein P0544H11.7 |
Os02g0203700 | Zinc finger protein; Zinc finger transcription factor ZFP30 |
Table 2 Genes located between the two flanking markers RM12676 and 2gAP0050058.
Gene | Description |
---|---|
Os02g0202500 | Conserved hypothetical protein |
Os02g0202600 | Tetratricopeptide-like helical domain containing protein |
Os02g0202800 | Zinc ion binding protein |
Os02g0202900 | OsFBK3-F-box domain and kelch repeat containing protein |
Os02g0202950 | Concanavalin A-like lectin/glucanases superfamily and Legume lectin domain |
Os02g0203000 | Carbohydrate binding, sequence-specific DNA binding, sequence-specific DNA binding transcription factor activity |
Os02g0203300 | UDP-glucuronosyl/UDP-glucosyltransferase |
Os02g0203401 | hypothetical gene, protein coding |
Os02g0203500 | Putative uncharacterized protein OJ1135_F06.25; Putative uncharacterized protein P0544H11.7 |
Os02g0203700 | Zinc finger protein; Zinc finger transcription factor ZFP30 |
Fig. 4. Relative expression levels of genes in panicles by quantitative real-time PCR. HT, High temperature condition (32 ºC); LT, Low temperature condition (24 ºC); TGMS, Thermo-sensitive genic male sterility.Data represent Mean ± SE, and the same lowercase letter(s) indicate no significant difference at P < 0.05 by Duncan’s new multiple range test.
Marker | Forward primers (5´-3´) | Reverse primers (5´-3´) | Position (Mb) |
---|---|---|---|
vf0205500813 | CGGGTCGACTTGCCTGAATA | AGAAATGGCGTTGGAAGCAG | 5.5 |
vf0205520833 | GTCACGCCGATATCGTCAAC | ACGTCATCATCCACTAACAAGT | 5.52 |
vf0205535398 | ACCATAATGATTCCGGCCAT | TTCGACGCACCGGTAGATTA | 5.53 |
vf0205536817 | ATACACGACGTACGACTGCT | GGGAGGTGTTCGACAGTGTA | 5.53 |
vf0205547503 | ACAGGATTGAAATACCCTAACACA | TCCCTAAATGTTTGATGCCGT | 5.54 |
vf0205558302 | AGACCATTAGAGCCCCCATA | GGGGCTAAACCAAAATGACCA | 5.55 |
vf0205705182 | GTGCAGGTTACCCCCGATTA | TTCTCTATGGACTAGTTGCACAA | 5.7 |
vf0205722820 | TTAGGCTTAGGCTCATTGGC | TGCATTGCTCAGCTCATGTT | 5.72 |
vf0205735923 | ATAAACCATCTGCGCACACG | TTGGCGGTGTTCATGGAAAG | 5.73 |
vf0205742366 | CCTGGATGCGGTTCTTCTTG | ATGGGGAAAAACCGAAAGCC | 5.74 |
vf0205765597 | ATAGTATGAGGCGGATGCGG | GAAAATTCGCTCCCATGGGG | 5.76 |
vf0205774130 | GCCTTTGAGCCTCCAAGATG | AGCGAGCCAATGAAAATCCG | 5.77 |
vf0205774202 | GCCTTTGAGCCTCCAAGATG | AGCGAGCCAATGAAAATCCG | 5.77 |
vf0205797421 | ATATGCAACCACCGTCTTGC | GGAGATCAACCACCGTCTCA | 5.79 |
vf0205822727 | ACCATGTTACCCTCTGCCTC | TGGCCATCCATTTTTACGATCA | 5.82 |
vf0205851262 | GAGTCCTCTTTAGCGGTGGT | ATCCCGACATGTTGGTCACT | 5.85 |
vf0205858260 | GGAGTCAAATGCTGCTTGCT | GAGGTGTCCAACTTGTGCTG | 5.85 |
vf0205863221 | CCAAGGCACAGTCTAGGACA | CTGATGCTCCTATACCCGCA | 5.86 |
vf0205902152 | CAAAGCCATTTCAACGCCAC | TCACTGCAACCACTAGACTACA | 5.9 |
vf0205943497 | GGACCACAGGAAAAATACAGGA | CCTTTTTAGGCCCCCTTTGA | 5.94 |
vf0205962045 | TGGTGTTTTTCTGCTGGTCG | CCAACTGCCACAATGTGACA | 5.96 |
vf0206109126 | CACCAATCGAAAGCTAGCAAA | CGGTGATGATGTTGCATGCT | 6.1 |
vf0206114052 | CGAGACCAATCGATCCTCCA | TAACCTGCATCTGTGGTGGA | 6.11 |
vf0206119327 | TCAACCTCAACGAGAAGGGA | ATGTGAAGGCCGTTTTCCTC | 6.11 |
vf0206201082 | GAGGCTATGAGCTGTCGTCA | TGGCTGCATAAAAATATCCCACA | 6.2 |
vf0206219603 | GTGTCAATTGCTCTGCCGAT | TCCACGAACATGGTAGCACA | 6.21 |
vf0206255541 | GGAAGAAAGGTTGCCCAGTG | AGCTCATCCCTTCAAGTGCT | 6.25 |
vf0206256377 | TTGCAGAAGTCCAGGGATGT | TGCGGGCATGTCTGTACTTA | 6.25 |
vf0206257411 | ACACATCAATTTCCAGTGACCT | AAGCGTGCCTTGCAGATATG | 6.25 |
vf0206280178 | TGGTATACCTGACCACATGCT | GGTGACAGACCTCCACCTTT | 6.28 |
Supplemental Table 2 InDel markers on chromosome 2 covering flanking region from 5.50 to 6.28 Mb.
Marker | Forward primers (5´-3´) | Reverse primers (5´-3´) | Position (Mb) |
---|---|---|---|
vf0205500813 | CGGGTCGACTTGCCTGAATA | AGAAATGGCGTTGGAAGCAG | 5.5 |
vf0205520833 | GTCACGCCGATATCGTCAAC | ACGTCATCATCCACTAACAAGT | 5.52 |
vf0205535398 | ACCATAATGATTCCGGCCAT | TTCGACGCACCGGTAGATTA | 5.53 |
vf0205536817 | ATACACGACGTACGACTGCT | GGGAGGTGTTCGACAGTGTA | 5.53 |
vf0205547503 | ACAGGATTGAAATACCCTAACACA | TCCCTAAATGTTTGATGCCGT | 5.54 |
vf0205558302 | AGACCATTAGAGCCCCCATA | GGGGCTAAACCAAAATGACCA | 5.55 |
vf0205705182 | GTGCAGGTTACCCCCGATTA | TTCTCTATGGACTAGTTGCACAA | 5.7 |
vf0205722820 | TTAGGCTTAGGCTCATTGGC | TGCATTGCTCAGCTCATGTT | 5.72 |
vf0205735923 | ATAAACCATCTGCGCACACG | TTGGCGGTGTTCATGGAAAG | 5.73 |
vf0205742366 | CCTGGATGCGGTTCTTCTTG | ATGGGGAAAAACCGAAAGCC | 5.74 |
vf0205765597 | ATAGTATGAGGCGGATGCGG | GAAAATTCGCTCCCATGGGG | 5.76 |
vf0205774130 | GCCTTTGAGCCTCCAAGATG | AGCGAGCCAATGAAAATCCG | 5.77 |
vf0205774202 | GCCTTTGAGCCTCCAAGATG | AGCGAGCCAATGAAAATCCG | 5.77 |
vf0205797421 | ATATGCAACCACCGTCTTGC | GGAGATCAACCACCGTCTCA | 5.79 |
vf0205822727 | ACCATGTTACCCTCTGCCTC | TGGCCATCCATTTTTACGATCA | 5.82 |
vf0205851262 | GAGTCCTCTTTAGCGGTGGT | ATCCCGACATGTTGGTCACT | 5.85 |
vf0205858260 | GGAGTCAAATGCTGCTTGCT | GAGGTGTCCAACTTGTGCTG | 5.85 |
vf0205863221 | CCAAGGCACAGTCTAGGACA | CTGATGCTCCTATACCCGCA | 5.86 |
vf0205902152 | CAAAGCCATTTCAACGCCAC | TCACTGCAACCACTAGACTACA | 5.9 |
vf0205943497 | GGACCACAGGAAAAATACAGGA | CCTTTTTAGGCCCCCTTTGA | 5.94 |
vf0205962045 | TGGTGTTTTTCTGCTGGTCG | CCAACTGCCACAATGTGACA | 5.96 |
vf0206109126 | CACCAATCGAAAGCTAGCAAA | CGGTGATGATGTTGCATGCT | 6.1 |
vf0206114052 | CGAGACCAATCGATCCTCCA | TAACCTGCATCTGTGGTGGA | 6.11 |
vf0206119327 | TCAACCTCAACGAGAAGGGA | ATGTGAAGGCCGTTTTCCTC | 6.11 |
vf0206201082 | GAGGCTATGAGCTGTCGTCA | TGGCTGCATAAAAATATCCCACA | 6.2 |
vf0206219603 | GTGTCAATTGCTCTGCCGAT | TCCACGAACATGGTAGCACA | 6.21 |
vf0206255541 | GGAAGAAAGGTTGCCCAGTG | AGCTCATCCCTTCAAGTGCT | 6.25 |
vf0206256377 | TTGCAGAAGTCCAGGGATGT | TGCGGGCATGTCTGTACTTA | 6.25 |
vf0206257411 | ACACATCAATTTCCAGTGACCT | AAGCGTGCCTTGCAGATATG | 6.25 |
vf0206280178 | TGGTATACCTGACCACATGCT | GGTGACAGACCTCCACCTTT | 6.28 |
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