Development and application of specific DNA marker for detecting mutual translocation site SGA of rice large fragment

Abstract

The invention discloses a method for detecting a mutual translocation site SGA of a rice large fragment by using a specific DNA (Deoxyribose Nucleic Acid) amplification primer. In the invention, 55 specific DNA (deoxyribonucleic acid) amplification primers aiming at a normal type and a translocation type are adopted, and the 55 specific DNA amplification primers comprise SGA2-1 to SGA2-14, SGA1-1 to SGA1-18, CHR2-1 to CHR2-7, CHR1-1 to CHR1-12, CHR2, CHR1, LB-CHR2 and RB-CHR1. Through detection, 53 markers except CHR2-3 and CHR1-10 can be used for well detecting the chromosome translocation effect. The specific primers are used for amplifying KN, BMF, non-translocation type and translocation type single plants, and the result shows that the markers can accurately identify whether the rice chromosome translocation exists or not. The DNA amplification marker designed by the invention is high in accuracy, strong in specificity and good in coverage, and has relatively outstanding practicability in molecular breeding identification.

Description

Technical Field

[0001] The invention belongs to the technical field of rice breeding, and relates to the development and application of a specific DNA marker for detecting a large reciprocal translocation site SGA of rice. Background Art

[0002] Rice hybrid sterility mainly revolves around the interaction of genes between species and subspecies that leads to gamete abortion. Three molecular models have been proposed: killer-protection, poison-target and repeated recessive gamete lethality (Ouyang Y, Zhang Q. Understanding reproductive isolation based on the rice model. Annu Rev Plant Biol. 2013; 64: 111-135. https: / / doi.org / 10.1146 / annurev-arplant-050312-120205.). There are relatively few reports on hybrid sterility caused by chromosome translocation. The offspring produced by the hybridization of chromosome translocation plants and normal plants are called translocation heterozygotes (Herickhoff L, Stack S, Sherman J. The relationship between synapsis, recombination nodules and chiasmata in tomato translocation heterozygotes. Heredity. 1993; 71: 373-385. https: / / doi.org / 10.1038 / hdy.). A typical feature of translocation heterozygotes is semi-sterility of male and female gametes and pseudo-linkage of translocation positions. The difficulty in studying chromosome translocation lies in the screening method and the acquisition of breakpoints. Therefore, obtaining new chromosome translocation site information and developing specific DNA amplification primers are of great significance for the efficient, rapid and accurate identification of large-segment chromosome translocation events and the improvement of the utilization of rice hybrid vigor. Summary of the invention

[0003] During the hybridization process between the tropical japonica rice variety Ketan Nangka (KN) and the indica rice variety White Rice Flour (BMF), a reciprocal chromosome translocation with a physical length of 12Mb and 0.8Mb between the tail end of chromosome 1 and the tail end of chromosome 2 respectively occurred. This translocation event was named SGA1 and SGA2, respectively. Specific detection primers were developed for the large-fragment translocation breakpoints at the tail ends of SGA1 and SGA2 to directly distinguish between the translocation type and the non-translocation type. Based on the sequence characteristics at the above two translocation breakpoints, the inventors developed 53 specific DNA amplification primers; the translocation varieties and non-translocation varieties were tested, and it was confirmed that these 53 markers can accurately distinguish between large-fragment chromosome translocation types and non-translocation types.

[0004] The technical problem solved by the present invention is to provide 53 specific DNA amplification markers for detecting rice large fragment reciprocal translocation sites SGA and their detection methods.

[0005] The present invention adopts the following technical solutions:

[0006] The specific DNA amplification primer SGA2-1 for detecting the chromosome 2 translocation type SGA2 is characterized by the following primers: forward primer SGA2-1-F: 5'-GAGAGTAGTGCGCAATGCAA-3';

[0007] Reverse primer SGA2-1-R: 5′-CTGCGAAGTCCCCATGGAAT-3′.

[0008] The specific DNA amplification primer SGA2-2 for detecting the chromosome 2 translocation type SGA2 is characterized in that the primer:

[0009] Forward primer SGA2-2-F: 5′-AGTGCGCAATGCAATCATCT-3′;

[0010] Reverse primer SGA2-2-R: 5′-GTGCAGATAGCCCTGTCGAA-3′.

[0011] The specific DNA amplification primer SGA2-3 for detecting the chromosome 2 translocation type SGA2 is characterized in that the primer:

[0012] Forward primer SGA2-3-F: 5′-AGAGAGTAGTGCGCAATGCAA-3′;

[0013] Reverse primer SGA2-3-R: 5′-TTGACAAGCCAAGACGAGCA-3′.

[0014] The specific DNA amplification primer SGA2-4 for detecting the chromosome 2 translocation type SGA2 is characterized in that the primer:

[0015] Forward primer SGA2-4-F: 5′-GAGTAGTGCGCAATGCAATCA-3′;

[0016] Reverse primer SGA2-4-R: 5′-GAGTGCAGATAGCCCTGTCG-3′.

[0017] The specific DNA amplification primer SGA2-5 for detecting the chromosome 2 translocation type SGA2 is characterized in that the primer:

[0018] Forward primer SGA2-5-F: 5′-AGTAGTGCGCAATGCAATCA-3′;

[0019] Reverse primer SGA2-5-R: 5′-GCAGGACAAAGGCTAACCCA-3′.

[0020] The specific DNA amplification primer SGA2-6 for detecting the chromosome 2 translocation type SGA2 is characterized in that the primer:

[0021] Forward primer SGA2-6-F: 5′-AGAGTAGTGCGCAATGCAATC-3′;

[0022] Reverse primer SGA2-6-R: 5′-GGGGGTCTGAAGAGGTCCTA-3′.

[0023] The specific DNA amplification primer SGA2-7 for detecting chromosome 2 translocation type SGA2 is characterized in that the primer:

[0024] Forward primer SGA2-7-F: 5′-GGGACGGAGAGAGTAGTGCG-3′;

[0025] Reverse primer SGA2-7-R: 5′-TGCGAAGTCCCCATGGAATG-3′.

[0026] The specific DNA amplification primer SGA2-8 for detecting chromosome 2 translocation type SGA2 is characterized in that the primer:

[0027] Forward primer SGA2-8-F: 5′-AGTAGTGCGCAATGCAATCAT-3′;

[0028] Reverse primer SGA2-8-R: 5′-AGCCCTGTCGAAAACAAACG-3′.

[0029] The specific DNA amplification primer SGA2-9 for detecting the chromosome 2 translocation type SGA2 is characterized in that the primer:

[0030] Forward primer SGA2-9-F: 5′-ATGGGACGGAGAGAGTAGTGC-3′;

[0031] Reverse primer SGA2-9-R: 5′-CTGAGTGCAGATAGCCCTGT-3′.

[0032] The specific DNA amplification primer SGA2-10 for detecting the chromosome 2 translocation type SGA2 is characterized in that the primer:

[0033] Forward primer SGA2-10-F: 5′-AGTAGTGCGCAATGCAATCATC-3′;

[0034] Reverse primer SGA2-10-R: 5′-CCGTGGTTGGCATGAATCAA-3′.

[0035] The specific DNA amplification primer SGA2-11 for detecting the chromosome 2 translocation type SGA2 is characterized in that the primer:

[0036] Forward primer SGA2-11-F: 5′-GAGTAGTGCGCAATGCAATCAT-3′;

[0037] Reverse primer SGA2-11-R: 5′-TTTGACAAGCCAAGACGAGC-3′.

[0038] The specific DNA amplification primer SGA2-12 for detecting chromosome 2 translocation type SGA2 is characterized in that the primer:

[0039] Forward primer SGA2-12-F: 5′-AGTGCGCAATGCAATCATCTTT-3′;

[0040] Reverse primer SGA2-12-R: 5′-CGCAGCAGGACAAAGGCTAA-3′.

[0041] The specific DNA amplification primer SGA2-13 for detecting chromosome 2 translocation type SGA2 is characterized in that the primer:

[0042] Forward primer SGA2-13-F: 5′-ATGGGACGGAGAGAGTAGTG-3′;

[0043] Reverse primer SGA2-13-R: 5′-CGAAAGCAAAGGTCATTGCCA-3′.

[0044] The specific DNA amplification primer SGA2-14 for detecting the chromosome 2 translocation type SGA2 is characterized in that the primer:

[0045] Forward primer SGA2-14-F: 5′-TGGTAAGATGTGGAGTAACGGC-3′;

[0046] Reverse primer SGA2-14-R: 5′-AGCCAAGACGAGCATTTGAGA-3′.

[0047] The specific DNA amplification primer SGA1-1 for detecting the chromosome 1 translocation type SGA1 is characterized in that the primer:

[0048] Forward primer SGA1-1-F: 5′-TAGAATGATGGGGGCCATGC-3′;

[0049] Reverse primer SGA1-1-R: 5′-AACGCGATGAATTGGGAGGT-3′.

[0050] The specific DNA amplification primer SGA1-2 for detecting the chromosome 1 translocation type SGA1 is characterized in that the primers:

[0051] Forward primer SGA1-2-F: 5′-ATGGGGGCCATGCCAATAAG-3′;

[0052] Reverse primer SGA1-2-R: 5′-AATGGCGCAAACGGAAGATG-3′.

[0053] The specific DNA amplification primers SGA1-3 for detecting the chromosome 1 translocation type SGA1 are characterized in that the primers:

[0054] Forward primer SGA1-3-F: 5′-CGGTTGTGACACTGCCTGAT-3′;

[0055] Reverse primer SGA1-3-R: 5′-TGTCCGTTGAACCATTTGCG-3′.

[0056] The specific DNA amplification primers SGA1-4 for detecting the chromosome 1 translocation type SGA1 are characterized in that the primers:

[0057] Forward primer SGA1-4-F: 5′-CGTCATCTGGTCCGGTTGTG-3′;

[0058] Reverse primer SGA1-4-R: 5′-GCTCTTCTACCTCCCTCGGT-3′.

[0059] The specific DNA amplification primer SGA1-5 for detecting the chromosome 1 translocation type SGA1 is characterized in that the primers:

[0060] Forward primer SGA1-5-F: 5′-TGGGGGCCATGCCAATAAG-3′;

[0061] Reverse primer SGA1-5-R: 5′-IndexTermGAATGGCGCAAACGGAAGAT-3′.

[0062] The specific DNA amplification primer SGA1-6 for detecting chromosome 1 translocation type SGA1 is characterized in that the primers:

[0063] Forward primer SGA1-6-F: 5′-CATATGCTCTGCACCAAGGGA-3′;

[0064] Reverse primer SGA1-6-R: 5′-IndexTermCAGCGGGCGATTGAAAAGAA-3′.

[0065] The specific DNA amplification primer SGA1-7 for detecting the chromosome 1 translocation type SGA1 is characterized in that the primers:

[0066] Forward primer SGA1-7-F: 5′-CTGCACCAAGGGAGATGCTAT-3′;

[0067] Reverse primer SGA1-7-R: 5′-AGCGGGCGATTGAAAAGAAC-3′.

[0068] The specific DNA amplification primer SGA1-8 for detecting chromosome 1 translocation type SGA1 is characterized in that the primer:

[0069] Forward primer SGA1-8-F: 5′-TCTGCACCAAGGGAGATGCT-3′;

[0070] Reverse primer SGA1-8-R: 5′-TGCAGCTCTTGAGGAATGGC-3′.

[0071] The specific DNA amplification primer SGA1-9 for detecting the chromosome 1 translocation type SGA1 is characterized in that the primers:

[0072] Forward primer SGA1-9-F: 5′-TGCTCTGCACCAAGGGAGAT-3′;

[0073] Reverse primer SGA1-9-R: 5′-GCGGGCGATTGAAAAGAACG-3′.

[0074] The specific DNA amplification primer SGA1-10 for detecting the chromosome 1 translocation type SGA1 is characterized in that the primers:

[0075] Forward primer SGA1-10-F: 5′-TGCACCAAGGGAGATGCTAT-3′;

[0076] Reverse primer SGA1-10-R: 5′-TCCGTTGAACCATTTGCGGT-3′.

[0077] The specific DNA amplification primer SGA1-11 for detecting the chromosome 1 translocation type SGA1 is characterized in that the primer:

[0078] Forward primer SGA1-11-F: 5′-ATATGCTCTGCACCAAGGGA-3′;

[0079] Reverse primer SGA1-11-R: 5′-ACGCGATGAATTGGGAGGTA-3′.

[0080] The specific DNA amplification primer SGA1-12 for detecting the chromosome 1 translocation type SGA1 is characterized in that the primers:

[0081] Forward primer SGA1-12-F: 5′-GGCCCATAAACAACATTGCCA-3′;

[0082] Reverse primer SGA1-12-R: 5′-TCTTGAGGAATGGCGCAAAC-3′.

[0083] The specific DNA amplification primer SGA1-13 for detecting the chromosome 1 translocation type SGA1 is characterized in that the primers:

[0084] Forward primer SGA1-13-F: 5′-CGTCATCTGGTCCGGTTGT-3′;

[0085] Reverse primer SGA1-13-R: 5′-GCGAAAACGCGATGAATTGG-3′.

[0086] The specific DNA amplification primer SGA1-14 for detecting chromosome 1 translocation type SGA1 is characterized in that the primers:

[0087] Forward primer SGA1-14-F: 5′-CATATGCTCTGCACCAAGGG-3′;

[0088] Reverse primer SGA1-14-R: 5′-GACCTCATCAGCTGCGAAAAC-3′.

[0089] The specific DNA amplification primer SGA1-15 for detecting chromosome 1 translocation type SGA1 is characterized in that the primers:

[0090] Forward primer SGA1-15-F: 5′-CGGTTGTGACACTGCCTGATA-3′;

[0091] Reverse primer SGA1-15-R: 5′-CGAAAACGCGATGAATTGGGA-3′.

[0092] The specific DNA amplification primer SGA1-16 for detecting chromosome 1 translocation type SGA1 is characterized in that the primer:

[0093] Forward primer SGA1-16-F: 5′-ACATATGCTCTGCACCAAGGG-3′;

[0094] Reverse primer SGA1-16-R: 5′-GCGGTAAAGAATTGCACTCCC-3′.

[0095] The specific DNA amplification primer SGA1-17 for detecting chromosome 1 translocation type SGA1 is characterized in that the primer:

[0096] Forward primer SGA1-17-F: 5′-ACGTCATCTGGTCCGGTTGT-3′;

[0097] Reverse primer SGA1-17-R: 5′-CTCTTGAGGAATGGCGCAAAC-3′.

[0098] The specific DNA amplification primer SGA1-18 for detecting chromosome 1 translocation type SGA1 is characterized in that the primer:

[0099] Forward primer SGA1-18-F: 5′-TTAGAATGATGGGGGCCATGC-3′;

[0100] Reverse primer SGA1-18-R: 5′-GCGATTGAAAAGAACGGGACC-3′.

[0101] The specific DNA amplification primer CHR2-1 for detecting the normal type of chromosome 2 is characterized in that the primer:

[0102] Forward primer CHR2-1-F: 5′-GGACGGAGAGAGTAGTGCG-3′;

[0103] Reverse primer CHR2-1-R: 5′-AAAAGAACGGGACCTCATCA-3′.

[0104] The specific DNA amplification primer CHR2-2 for detecting the normal type of chromosome 2 is characterized in that the primer:

[0105] Forward primer CHR2-2-F: 5′-ACGGAGAGAGTAGTGCGC-3′;

[0106] Reverse primer CHR2-2-R: 5′-CAGCTCTTGAGGAATGGC-3′.

[0107] The specific DNA amplification primer CHR2-4 for detecting the normal type of chromosome 2 is characterized in that the primer:

[0108] Forward primer CHR2-4-F: 5′-TTCACGCTTATACTGATGGT-3′;

[0109] Reverse primer CHR2-4-R: 5′-TGGTCTCCTGGTGTCTGTAA-3′.

[0110] The specific DNA amplification primer CHR2-5 for detecting the normal type of chromosome 2 is characterized in that the primer:

[0111] Forward primer CHR2-5-F: 5′-CGGCTTATTACTAGCAACTT-3′;

[0112] Reverse primer CHR2-5-R: 5′-GTGGTCTCCTGGTGTCTGTAA-3′.

[0113] The specific DNA amplification primer CHR2-6 for detecting the normal type of chromosome 2 is characterized in that the primer:

[0114] Forward primer CHR2-6-F: 5′-AACGGCTTATTACTAGCAACTT-3′;

[0115] Reverse primer CHR2-6-R: 5′-GGTGGTCTCCTGGTGTCTGT-3′.

[0116] The specific DNA amplification primer CHR2-7 for detecting the normal type of chromosome 2 is characterized in that the primer:

[0117] Forward primer CHR2-7-F: 5′-GGACGGAGAGAGTAGTGCGC-3′;

[0118] Reverse primer CHR2-7-R: 5′-GGGGTGGTCTCCTGGTGTCT-3′.

[0119] The specific DNA amplification primer CHR1-1 for detecting the normal type of chromosome 1 is characterized in that the primer:

[0120] Forward primer CHR1-1-F: 5′-TGTTACATATGCTCTGCACCAA-3′;

[0121] Reverse primer CHR1-1-R: 5′-TGTTTGAATTAATCGCTGGTTC-3′.

[0122] The specific DNA amplification primer CHR1-2 for detecting the normal type of chromosome 1 is characterized in that the primer:

[0123] Forward primer CHR1-2-F: 5′-TTACATATGCTCTGCACCAAGG-3′;

[0124] Reverse primer CHR1-2-R: 5′-AGTGTTTGAATTAATCGCTGGT-3′.

[0125] The specific DNA amplification primers CHR1-3 for detecting the normal type of chromosome 1 are characterized in that the primers:

[0126] Forward primer CHR1-3-F: 5′-CAACCCATGACAATTAGAATG-3′;

[0127] Reverse primer CHR1-3-R: 5′-ACATTTTTGAGGGTGAATCTA-3′.

[0128] The specific DNA amplification primers CHR1-4 for detecting the normal type of chromosome 1 are characterized in that the primers:

[0129] Forward primer CHR1-4-F: 5′-TTACCCTTCTTCAAGCTCCAT-3′;

[0130] Reverse primer CHR1-4-R: 5′-AAAGACTTTGGGGGTCTGAAG-3′.

[0131] The specific DNA amplification primers CHR1-5 for detecting the normal type of chromosome 1 are characterized in that the primers:

[0132] Forward primer CHR1-5-F: 5′-AACTTGAAGGCCAAATATGCC-3′;

[0133] Reverse primer CHR1-5-R: 5′-TGAATCAAGGAAGCAAGTGAT-3′.

[0134] The specific DNA amplification primer CHR1-6 for detecting the normal type of chromosome 1 is characterized in that the primer:

[0135] Forward primer CHR1-6-F: 5′-TCTTTCAGTTGAGTAACCGTATGG-3′;

[0136] Reverse primer CHR1-6-R: 5′-GATTGTGATGCTTTTGCCCTA-3′.

[0137] The specific DNA amplification primer CHR1-7 for detecting the normal type of chromosome 1 is characterized in that the primer:

[0138] Forward primer CHR1-7-F: 5′-CGGTTGTGACACTGCCTGATA-3′;

[0139] Reverse primer CHR1-7-R: 5′-ATGATTGTGATGCTTTTGCCC-3′.

[0140] The specific DNA amplification primer CHR1-8 for detecting the normal type of chromosome 1 is characterized in that the primer:

[0141] Forward primer CHR1-8-F: 5′-GTTGTGACACTGCCTGATAAG-3′;

[0142] Reverse primer CHR1-8-R: 5′-ATGGCACCTCTATGAGTATGA-3′.

[0143] The specific DNA amplification primer CHR1-9 for detecting the normal type of chromosome 1 is characterized in that the primer:

[0144] Forward primer CHR1-9-F: 5′-CTTCTTTCAGTTGAGTAACCG-3′;

[0145] Reverse primer CHR1-9-R: 5′-GTGATGCTTTTGCCCTATACA-3′.

[0146] The specific DNA amplification primer CHR1-11 for detecting the normal type of chromosome 1 is characterized in that the primer:

[0147] Forward primer CHR1-11-F: 5′-GAGATGAGGCCCATAAACAAC-3′;

[0148] Reverse primer CHR1-11-R: 5′-CAATGATTGTGATGCTTTTGC-3′.

[0149] The specific DNA amplification primer CHR1-12 for detecting the normal type of chromosome 1 is characterized in that the primer:

[0150] Forward primer CHR1-12-F: 5′-TCAGTTGAGTAACCGTATGGG-3′;

[0151] Reverse primer CHR1-12-R: 5′-ATCAATGATTGTGATGCTTTT-3′.

[0152] The specific DNA amplification primer LB-Chr2 for detecting the translocation type of chromosome 2 is characterized in that the primer:

[0153] Forward primer LB-Chr2-F: 5′-TGGGACGGAGAGAGTAGTGC-3′;

[0154] Reverse primer LB-Chr2-R: 5′-ACAAGCCAAGACGAGCATTT-3′.

[0155] The specific DNA amplification primer RB-Chr1 for detecting the translocation type of chromosome 1 is characterized in that the primer:

[0156] Forward primer RB-Chr1-F: 5′-ACAAATAAACGGGTCCATCAA-3′;

[0157] Reverse primer RB-Chr1-R: 5′-IndexTermGATTGAAAAGAACGGGACCTC-3′.

[0158] The specific DNA amplification primer Chr2 for detecting the normal type of chromosome 2 is characterized by the following primers: forward primer Chr2-F: 5'-TGGTAAGATGTGGAGTAACGG-3';

[0159] Reverse primer Chr2-R: 5′-CCATTTTGTGTAAACATCTGC-3′.

[0160] The specific DNA amplification primer Chr1 for detecting the normal type of chromosome 1 is characterized in that the primer:

[0161] Forward primer Chr1-F: 5′-GCCAATAAGATTAGACCCCA-3′;

[0162] Reverse primer Chr1-R: 5′-TTTGACAAGCCAAGACGAGC-3′.

[0163] The method for detecting the rice large fragment reciprocal translocation site SGA using the above-mentioned specific DNA marker is as follows:

[0164] (1) Using the genomic DNA of the sample to be tested as a template, PCR amplification was performed using the above 53 markers. Chromosome translocation-specific DNA primers SGA2-1, SGA2-2, SGA2-3, SGA2-4, SGA2-5, SGA2-6, SGA2-7, SGA2-8, SGA2-9, SGA2-10, SGA2-11, SGA2-12, SGA2-13, SGA2-14, SGA1-1, SGA1-2, SGA1-3, SGA1-4, SGA1-5, SGA1-6, SGA1-7, SGA1-8, SGA1-9, SGA1-10, SGA1-11, SGA1-12, SGA1-13, SGA1-14, SGA1-15, SGA1-16, SGA1-17, SGA1-18, CHR2-1, CHR2-2, CHR2 -4, CHR2-5, CHR2-6, CHR2-7, CHR1-1, CHR1-2, CHR1-3, CHR1-4, CHR1-5, CHR1-6, CHR1-7, CHR1-8, CHR1-9, CHR The annealing temperatures of 1-11, CHR1-12, CHR2, CHR1, LB-CHR2 and RB-CHR1 are 54.4°C, 54.4°C, 55.6°C, 55.6°C, 54.4°C, 55.6°C, 55.6°C, 56.7°C, 56.7°C, 54.4°C, 56.7°C, 54.4°C, 54.4°C, 54.4°C, 54.4°C, 53.1°C, 55.6°C, 55.6°C, 54.4°C, 54.4°C, 54.4°C. 4.4°C, 54.4°C, 54.4°C, 55.6°C, 53.1°C, 53.1°C, 55.6°C, 55.6°C, 54.4°C, 55.6°C, 60.0°C, 57.0°C, 58.0°C, 59.0°C, 66.0°C, 54.4°C, 54.4°C, 53.0°C, 55.6°C, 55.6°C, 55.6°C, 55.6°C, 55.6°C, 55.6°C, 55.6°C, 55.6°C, 54.3°C, 55.5°C, 54.4°C, and 55.6°C.

[0165] (2) The PCR products amplified by the primers were separated by 1% agarose gel electrophoresis.

[0166] (3) Determine the chromosome translocation genotypes of the three rice varieties based on the electrophoresis results:

[0167] For the SGA2-1 marker, the 703 bp band that could be detected was the SGA2 chromosome II translocation genotype;

[0168] For the SGA2-2 marker, the 219 bp band that can be detected is the SGA2 chromosome 2 translocation genotype;

[0169] For the SGA2-3 marker, the 538 bp band that could be detected was the SGA2 chromosome II translocation genotype;

[0170] For the SGA2-4 marker, the 225 bp band that can be detected is the SGA2 chromosome 2 translocation genotype;

[0171] For the SGA2-5 marker, the 183 bp band that could be detected was the SGA2 chromosome 2 translocation genotype;

[0172] For the SGA2-6 marker, the 426 bp band that could be detected was the SGA2 chromosome 2 translocation genotype;

[0173] For the SGA2-7 marker, the 710 bp band that could be detected was the SGA2 chromosome II translocation genotype;

[0174] For the SGA2-8 marker, the 214 bp band that could be detected was the SGA2 chromosome II translocation genotype;

[0175] For the SGA2-9 marker, the 239 bp band that can be detected is the SGA2 chromosome 2 translocation genotype;

[0176] For the SGA2-10 marker, the 467 bp band that could be detected was the SGA2 chromosome II translocation genotype;

[0177] For the SGA2-11 marker, the 536 bp band that could be detected was the SGA2 chromosome II translocation genotype;

[0178] For the SGA2-12 marker, the 184 bp band that could be detected was the SGA2 chromosome II translocation genotype;

[0179] For the SGA2-13 marker, the 512bp band can be detected for the SGA2 chromosome II translocation genotype; for the SGA2-14 marker, the 488bp band can be detected for the SGA2 chromosome II translocation genotype; for the SGA1-1 marker, the 655bp band can be detected for the SGA1 chromosome I translocation genotype; for the SGA1-2 marker, the 721bp band can be detected for the SGA1 chromosome I translocation genotype; for the SGA1-3 marker, the 188bp band can be detected for the SGA1 chromosome I translocation genotype; for the SGA1-4 marker, the 188bp band can be detected for the SGA1 chromosome I translocation genotype. Note that the 613bp band that can be detected is the SGA1 chromosome 1 translocation genotype; for the SGA1-5 marker, the 721bp band that can be detected is the SGA1 chromosome 1 translocation genotype; for the SGA1-6 marker, the 830bp band that can be detected is the SGA1 chromosome 1 translocation genotype; for the SGA1-7 marker, the 821bp band that can be detected is the SGA1 chromosome 1 translocation genotype; for the SGA1-8 marker, the 869bp band that can be detected is the SGA1 chromosome 1 translocation genotype; for the SGA1-9 marker, the 824bp band that can be detected is the SGA1 chromosome 1 translocation genotype. The bands were detected for the SGA1 chromosome 1 translocation genotype; for the SGA1-10 marker, the 525bp band was detected for the SGA1 chromosome 1 translocation genotype; for the SGA1-11 marker, the 787bp band was detected for the SGA1 chromosome 1 translocation genotype; for the SGA1-12 marker, the 563bp band was detected for the SGA1 chromosome 1 translocation genotype; for the SGA1-13 marker, the 458bp band was detected for the SGA1 chromosome 1 translocation genotype; for the SGA1-14 marker, the 807bp band was detected for the SGA 1 chromosome translocation genotype; for SGA1-15 markers, the 445bp band can be detected for SGA1 chromosome translocation genotype; for SGA1-16 markers, the 520bp band can be detected for SGA1 chromosome translocation genotype; for SGA1-17 markers, the 536bp band can be detected for SGA1 chromosome translocation genotype; for SGA1-18 markers, the 691bp band can be detected for SGA1 chromosome translocation genotype; for CHR2-1 markers, the 555bp band can be detected for normal chromosome 2 genotype;

[0180] For the CHR2-2 marker, the 610 bp band detected was the normal genotype of chromosome 2;

[0181] For the CHR2-4 marker, the 417 bp band detected was the normal genotype of chromosome 2;

[0182] For the CHR2-5 marker, the 387 bp band that can be detected is the normal genotype of chromosome 2;

[0183] For the CHR2-6 marker, the 387 bp band detected was the normal genotype of chromosome 2;

[0184] For the CHR2-7 marker, the 455 bp band that can be detected is the normal genotype of chromosome 2;

[0185] For the CHR1-1 marker, the 903 bp band that can be detected is the normal genotype of chromosome 1;

[0186] For the CHR1-2 marker, the 903 bp band that can be detected is the normal genotype of chromosome 1;

[0187] For the CHR1-3 marker, the 725 bp band that can be detected is the normal genotype of chromosome 1;

[0188] For the CHR1-4 markers, the 475 bp band that can be detected is the normal genotype of chromosome 1;

[0189] For the CHR1-5 marker, the 533 bp band that can be detected is the normal genotype of chromosome 1;

[0190] For the CHR1-6 marker, the 339 bp band that can be detected is the normal genotype of chromosome 1;

[0191] For the CHR1-7 marker, the 269 bp band that can be detected is the normal genotype of chromosome 1;

[0192] For the CHR1-8 marker, the 293 bp band that can be detected is the normal genotype of chromosome 1;

[0193] For the CHR1-9 marker, the 337 bp band that can be detected is the normal genotype of chromosome 1;

[0194] For the CHR1-11 marker, the 319 bp band that can be detected is the normal genotype of chromosome 1;

[0195] For the CHR1-12 marker, the 341 bp band that can be detected is the normal genotype of chromosome 1;

[0196] For the LB-Chr2 marker, the 543 bp band that could be detected was the SGA2 chromosome II translocation genotype;

[0197] For the RB-Chr1 marker, the 901 bp band that could be detected was the SGA1 chromosome 1 translocation genotype;

[0198] For the Chr2 marker, the 582 bp band detected was the normal genotype of chromosome 2;

[0199] For the Chr1 marker, the 655bp band detected indicates the normal genotype of chromosome 1.

[0200] The specific DNA amplification primers provided by the present invention have good detection effects in detecting the large reciprocal translocation sites SGA1 and SGA2 of rice, and the SGA heterozygous population has a significant phenotype of reduced fruiting rate. The adverse factors caused by the large chromosome translocation of SGA can be effectively eliminated through a fast and convenient screening method, and have universal application value in production practice. Therefore, in the future breeding application process, the specific detection primers of the present invention can be used to detect whether the SGA translocation fragment exists and then adjust the hybridization group of rice varieties to achieve the purpose of fully utilizing the hybrid advantage. BRIEF DESCRIPTION OF THE DRAWINGS

[0201] Figure 1 Detection results of 53 specific DNA markers of the large reciprocal translocation site SGA in rice donor parents and segregating populations. DETAILED DESCRIPTION

[0202] The present invention is further explained below with reference to the accompanying drawings and examples. The experimental methods in the following examples are assumed to be conventional methods unless otherwise specified. The experimental materials, experimental reagents, etc. used in the following examples are all commercially available unless otherwise specified.

[0203] Example 1. Development of specific DNA markers for the large reciprocal translocation site SGA in rice

[0204] We identified a stable segregating family NIL-Y15803 from high-generation recombinant inbred lines of tropical japonica rice variety Ketan Nangka and indica rice variety Baimifen. NIL-Y15803 showed semi-sterility in both male and female gametes, so we named this population Semi-Gametes Abortions (SGA). Subsequently, we genotyped different plants from the SGA segregating population according to fertility and found that the SGA population was controlled by two loci, SGA1 and SGA2, showing a pseudo-linked inheritance pattern without the typical skewed segregation of hybrid sterility. Therefore, we discovered a new mode of rice hybrid sterility. Subsequently, we used the map-based cloning method to narrow down SGA1 to an 800-kb interval and SGA2 to a 160-kb interval. Sequences of different genotypes in the localization interval were sequenced and spliced, and after combining chromosome behavior and inheritance patterns, we found that the cause of hybrid sterility was due to chromosome translocation. Among them, the reference genome of Nipponbare T2T from the RiceSuperPIRdb website (http: / / www.ricesuperpir.com / web / download) was used as the reference genome. According to the missing information in the positioning interval, we used the Tail-PCR method to amplify the unknown flanking sequence and successfully obtained the specific translocation breakpoint information, thereby confirming the existence of chromosome translocation from the sequence level. The translocation breakpoints are located at the ends of chromosomes 1 and 2, respectively. SGA1 and SGA2 are the first reported sites of chromosome translocation regulating hybrid sterility patterns in rice hybrid sterility research. In order to better identify the chromosome translocation breakpoints and eliminate the interference with the fertility of the hybrid combination, we used the sequence near the translocation breakpoint as a template, and used Primer Premier 5 software and NCBI Primerdesign tools to design specific DNA amplification markers for the normal and translocated types of chromosomes 1 and the normal and translocated types of chromosomes 2 500bp above and below. Amplification primer SGA2-1 was designed for chromosome 2 translocation, the forward primer SGA2-1-F sequence was 5'-GAGAGTAGTGCGCAATGCAA-3', and the reverse primer SGA2-1-R sequence was 5'-CTGCGAAGTCCCCATGGAAT-3'. Amplification primer SGA2-2 was designed for chromosome 2 translocation, the forward primer SGA2-2-F sequence was 5'-AGTGCGCAATGCAATCATCT-3', and the reverse primer SGA2-2-R sequence was 5'-GTGCAGATAGCCCTGTCGAA-3'.Amplification primer SGA2-3 was designed for chromosome 2 translocation type, the sequence of forward primer SGA2-3-F was 5'-AGAGAGTAGTGCGCAATGCAA-3', and the sequence of reverse primer SGA2-3-R was 5'-TTGACAAGCCAAGACGAGCA-3'. Amplification primer SGA2-4 was designed for chromosome 2 translocation type, the sequence of forward primer SGA2-4-F was 5'-GAGTAGTGCGCAATGCAATCA-3', and the sequence of reverse primer SGA2-4-R was 5'-GAGTGCAGATAGCCCTGTCG-3'. Amplification primer SGA2-5 was designed for chromosome 2 translocation type, the sequence of forward primer SGA2-5-F was 5'-AGTAGTGCGCAATGCAATCA-3', and the sequence of reverse primer SGA2-5-R was 5'-GCAGGACAAAGGCTAACCCA-3'. Amplification primer SGA2-6 was designed for chromosome 2 translocation, the sequence of forward primer SGA2-6-F was 5'-AGAGTAGTGCGCAATGCAATC-3', and the sequence of reverse primer SGA2-6-R was 5'-GGGGGTCTGAAGAGGTCCTA-3'. Amplification primer SGA2-7 was designed for chromosome 2 translocation, the sequence of forward primer SGA2-7-F was 5'-GGGACGGAGAGAGTAGTGCG-3', and the sequence of reverse primer SGA2-7-R was 5'-TGCGAAGTCCCCATGGAATG-3'. Amplification primer SGA2-8 was designed for chromosome 2 translocation, the sequence of forward primer SGA2-8-F was 5'-AGTAGTGCGCAATGCAATCAT-3', and the sequence of reverse primer SGA2-8-R was 5'-AGCCCTGTCGAAAACAAACG-3'. Amplification primer SGA2-9 was designed for chromosome 2 translocation, the sequence of forward primer SGA2-9-F was 5'-ATGGGACGGAGAGAGTAGTGC-3', and the sequence of reverse primer SGA2-9-R was 5'-CTGAGTGCAGATAGCCCTGT-3'. Amplification primer SGA2-10 was designed for chromosome 2 translocation, the sequence of forward primer SGA2-10-F was 5'-AGTAGTGCGCAATGCAATCATC-3', and the sequence of reverse primer SGA2-10-R was 5'-CCGTGGTTGGCATGAATCAA-3'. Amplification primer SGA2-11 was designed for chromosome 2 translocation, the sequence of forward primer SGA2-11-F was 5'-GAGTAGTGCGCAATGCAATCAT-3', and the sequence of reverse primer SGA2-11-R was 5'-TTTGACAAGCCAAGACGAGC-3'.Amplification primer SGA2-12 was designed for chromosome 2 translocation type, the sequence of forward primer SGA2-12-F was 5'-AGTGCGCAATGCAATCATCTTT-3', and the sequence of reverse primer SGA2-12-R was 5'-CGCAGCAGGACAAAGGCTAA-3'. Amplification primer SGA2-13 was designed for chromosome 2 translocation type, the sequence of forward primer SGA2-13-F was 5'-ATGGGACGGAGAGAGTAGTG-3', and the sequence of reverse primer SGA2-13-R was 5'-CGAAAGCAAAGGTCATTGCCA-3'. Amplification primer SGA2-14 was designed for chromosome 2 translocation type, the sequence of forward primer SGA2-14-F was 5'-TGGTAAGATGTGGAGTAACGGC-3', and the sequence of reverse primer SGA2-14-R was 5'-AGCCAAGACGAGCATTTGAGA-3'. Amplification primer SGA1-1 was designed for chromosome 1 translocation type, the forward primer SGA1-1-F sequence was 5'-TAGAATGATGGGGGCCATGC-3', and the reverse primer SGA1-1-R sequence was 5'-AACGCGATGAATTGGGAGGT-3'. Amplification primer SGA1-2 was designed for chromosome 1 translocation type, the forward primer SGA1-2-F sequence was 5'-ATGGGGGCCATGCCAATAAG-3', and the reverse primer SGA1-2-R sequence was 5'-AATGGCGCAAACGGAAGATG-3'. Amplification primer SGA1-3 was designed for chromosome 1 translocation type, the forward primer SGA1-3-F sequence was 5'-CGGTTGTGACACTGCCTGAT-3', and the reverse primer SGA1-3-R sequence was 5'-TGTCCGTTGAACCATTTGCG-3'. Amplification primers SGA1-4 were designed for chromosome 1 translocation type, the forward primer SGA1-4-F sequence was 5'-CGTCATCTGGTCCGGTTGTG-3', and the reverse primer SGA1-4-R sequence was 5'-GCTCTTCTACCTCCCTCGGT-3'. Amplification primers SGA1-5 were designed for chromosome 1 translocation type, the forward primer SGA1-5-F sequence was 5'-TGGGGGCCATGCCAATAAG-3', and the reverse primer SGA1-5-R sequence was 5'-GAATGGCGCAAACGGAAGAT-3'. Amplification primers SGA1-6 were designed for chromosome 1 translocation type, the forward primer SGA1-6-F sequence was 5'-CATATGCTCTGCACCAAGGGA-3', and the reverse primer SGA1-6-R sequence was 5'-CAGCGGGCGATTGAAAAGAA-3'.Amplification primers SGA1-7 were designed for chromosome 1 translocation type, the sequence of forward primer SGA1-7-F was 5'-CTGCACCAAGGGAGATGCTAT-3', and the sequence of reverse primer SGA1-7-R was 5'-AGCGGGCGATTGAAAAGAAC-3'. Amplification primers SGA1-8 were designed for chromosome 1 translocation type, the sequence of forward primer SGA1-8-F was 5'-TCTGCACCAAGGGAGATGCT-3', and the sequence of reverse primer SGA1-8-R was 5'-TGCAGCTCTTGAGGAATGGC-3'. Amplification primers SGA1-9 were designed for chromosome 1 translocation type, the sequence of forward primer SGA1-9-F was 5'-TGCTCTGCACCAAGGGAGAT-3', and the sequence of reverse primer SGA1-9-R was 5'-GCGGGCGATTGAAAAGAACG-3'. Amplification primer SGA1-10 was designed for chromosome 1 translocation type, the sequence of forward primer SGA1-10-F was 5'-TGCACCAAGGGAGATGCTAT-3', and the sequence of reverse primer SGA1-10-R was 5'-TCCGTTGAACCATTTGCGGT-3'. Amplification primer SGA1-11 was designed for chromosome 1 translocation type, the sequence of forward primer SGA1-11-F was 5'-ATATGCTCTGCACCAAGGGA-3', and the sequence of reverse primer SGA1-11-R was 5'-ACGCGATGAATTGGGAGGTA-3'. Amplification primer SGA1-12 was designed for chromosome 1 translocation type, the sequence of forward primer SGA1-12-F was 5'-GGCCCATAAACAACATTGCCA-3', and the sequence of reverse primer SGA1-12-R was 5'-TCTTGAGGAATGGCGCAAAC-3'. Amplification primers SGA1-13 were designed for chromosome 1 translocation type, the sequence of forward primer SGA1-13-F was 5'-CGTCATCTGGTCCGGTTGT-3', and the sequence of reverse primer SGA1-13-R was 5'-GCGAAAACGCGATGAATTGG-3'. Amplification primers SGA1-14 were designed for chromosome 1 translocation type, the sequence of forward primer SGA1-14-F was 5'-CATATGCTCTGCACCAAGGG-3', and the sequence of reverse primer SGA1-14-R was 5'-GACCTCATCAGCTGCGAAAAC-3'. Amplification primers SGA1-15 were designed for chromosome 1 translocation type, the sequence of forward primer SGA1-15-F was 5'-CGGTTGTGACACTGCCTGATA-3', and the sequence of reverse primer SGA1-15-R was 5'-CGAAAACGCGATGAATTGGGA-3'.Amplification primers SGA1-16 were designed for the translocation type of chromosome 1, the sequence of the forward primer SGA1-16-F was 5'-ACATATGCTCTGCACCAAGGG-3', and the sequence of the reverse primer SGA1-16-R was 5'-GCGGTAAAGAATTGCACTCCC-3'. Amplification primers SGA1-17 were designed for the translocation type of chromosome 1, the sequence of the forward primer SGA1-17-F was 5'-ACGTCATCTGGTCCGGTTGT-3', and the sequence of the reverse primer SGA1-17-R was 5'-CTCTTGAGGAATGGCGCAAAC-3'. Amplification primers SGA1-18 were designed for the translocation type of chromosome 1, the sequence of the forward primer SGA1-18-F was 5'-TTAGAATGATGGGGGCCATGC-3', and the sequence of the reverse primer SGA1-18-R was 5'-GCGATTGAAAAGAACGGGACC-3'. Amplification primers CHR2-1 were designed for the normal type of chromosome 2, the sequence of the forward primer CHR2-1-F was 5'-GGACGGAGAGAGTAGTGCG-3', and the sequence of the reverse primer CHR2-1-R was 5'-AAAAGAACGGGACCTCATCA-3'. Amplification primers CHR2-2 were designed for the normal type of chromosome 2, the sequence of the forward primer CHR2-2-F was 5'-ACGGAGAGAGTAGTGCGC-3', and the sequence of the reverse primer CHR2-2-R was 5'-CAGCTCTTGAGGAATGGC-3'. Amplification primer CHR2-4 was designed for the normal type of chromosome 2, the sequence of the forward primer CHR2-4-F was 5'-TTCACGCTTATACTGATGGT-3', and the sequence of the reverse primer CHR2-4-R was 5'-TGGTCTCCTGGTGTCTGTAA-3'. Amplification primer CHR2-5 was designed for the normal type of chromosome 2, the sequence of the forward primer CHR2-5-F was 5'-CGGCTTATTACTAGCAACTT-3', and the sequence of the reverse primer CHR2-5-R was 5'-GTGGTCTCCTGGTGTCTGTAA-3'. Amplification primer CHR2-6 was designed for the normal type of chromosome 2, the sequence of the forward primer CHR2-6-F was 5'-AACGGCTTATTACTAGCAACTT-3', and the sequence of the reverse primer CHR2-6-R was 5'-GGTGGTCTCCTGGTGTCTGT-3'. Amplification primers CHR2-7 were designed for the normal type of chromosome 2. The sequence of the forward primer CHR2-7-F was 5'-GGACGGAGAGAGTAGTGCGC-3', and the sequence of the reverse primer CHR2-7-R was 5'-GGGGTGGTCTCCTGGTGTCT-3'.Amplification primer CHR1-1 was designed for the normal type of chromosome 1. The sequence of the forward primer CHR1-1-F was 5'-TGTTACATATGCTCTGCACCAA-3', and the sequence of the reverse primer CHR1-1-R was 5'-TGTTTGAATTAATCGCTGGTTC-3'. Amplification primer CHR1-2 was designed for the normal type of chromosome 1. The sequence of the forward primer CHR1-2-F was 5'-TTACATATGCTCTGCACCAAGG-3', and the sequence of the reverse primer CHR1-2-R was 5'-AGTGTTTGAATTAATCGCTGGT-3'. Amplification primer CHR1-3 was designed for the normal type of chromosome 1. The sequence of the forward primer CHR1-3-F was 5'-CAACCCATGACAATTAGAATG-3', and the sequence of the reverse primer CHR1-3-R was 5'-ACATTTTTGAGGGTGAATCTA-3'. Amplification primers CHR1-4 were designed for normal chromosome 1, the sequence of forward primer CHR1-4-F was 5'-TTACCCTTCTTCAAGCTCCAT-3', and the sequence of reverse primer CHR1-4-R was 5'-AAAGACTTTGGGGGTCTGAAG-3'. Amplification primers CHR1-5 were designed for normal chromosome 1, the sequence of forward primer CHR1-5-F was 5'-AACTTGAAGGCCAAATATGCC-3', and the sequence of reverse primer CHR1-5-R was 5'-TGAATCAAGGAAGCAAGTGAT-3'. Amplification primers CHR1-6 were designed for normal chromosome 1, the sequence of forward primer CHR1-6-F was 5'-TCTTTCAGTTGAGTAACCGTATGG-3', and the sequence of reverse primer CHR1-6-R was 5'-GATTGTGATGCTTTTGCCCTA-3'. Amplification primers CHR1-7 were designed for normal chromosome 1, the sequence of forward primer CHR1-7-F was 5'-CGGTTGTGACACTGCCTGATA-3', and the sequence of reverse primer CHR1-7-R was 5'-ATGATTGTGATGCTTTTGCCC-3'. Amplification primers CHR1-8 were designed for normal chromosome 1, the sequence of forward primer CHR1-8-F was 5'-GTTGTGACACTGCCTGATAAG-3', and the sequence of reverse primer CHR1-8-R was 5'-ATGGCACCTCTATGAGTATGA-3'. Amplification primers CHR1-9 were designed for normal chromosome 1, the sequence of forward primer CHR1-9-F was 5'-CTTCTTTCAGTTGAGTAACCG-3', and the sequence of reverse primer CHR1-9-R was 5'-GTGATGCTTTTGCCCTATACA-3'.Amplification primers CHR1-11 were designed for the normal type of chromosome 1. The sequence of the forward primer CHR1-11-F was 5'-GAGATGAGGCCCATAAACAAC-3', and the sequence of the reverse primer CHR1-11-R was 5'-CAATGATTGTGATGCTTTTGC-3'. Amplification primers CHR1-12 were designed for the normal type of chromosome 1. The sequence of the forward primer CHR1-12-F was 5'-TCAGTTGAGTAACCGTATGGG-3', and the sequence of the reverse primer CHR1-12-R was 5'-ATCAATGATTGTGATGCTTTT-3'. Amplification primers LB-Chr2 were designed for the translocation type of chromosome 2. The sequence of the forward primer LB-Chr2-F was 5'-TGGGACGGAGAGAGTAGTGC-3', and the sequence of the reverse primer LB-Chr2-R was 5'-ACAAGCCAAGACGAGCATTT-3'. Amplification primer RB-Chr1 was designed for the translocation type of chromosome 1, the sequence of the forward primer RB-Chr1-F was 5'-ACAAATAAACGGGTCCATCAA-3', and the sequence of the reverse primer RB-Chr1-R was 5'-GATTGAAAAGAACGGGACCTC-3'. Amplification primer Chr2 was designed for the normal type of chromosome 2, the sequence of the forward primer Chr2-F was 5'-TGGTAAGATGTGGAGTAACGG-3', and the sequence of the reverse primer Chr2-R was 5'-CCATTTTGTGTAAACATCTGC-3'. Amplification primer Chr1 was designed for the normal type of chromosome 1, the sequence of the forward primer Chr1-F was 5'-GCCAATAAGATTAGACCCCA-3', and the sequence of the reverse primer Chr1-R was 5'-TTTGACAAGCCAAGACGAGC-3'.

[0205] The CTAB method was used to extract the genomic DNA of samples KN, BMF, Type1, and Type2. The above 53 DNA amplification markers were used for PCR amplification: the annealing temperatures were 54.4°C, 54.4°C, 55.6°C, 55.6°C, 54.4°C, 55.6°C, 54.4°C, 55.6°C, 55.6°C, 56.7°C, 56.7°C, 56.7°C, 54.4°C, 54.4°C, 54.4°C, 54.4°C, 53.1°C, 55.6°C, 55.6°C, 54.4°C, 54.4°C, 54.4°C, 54.4°C, 55.6°C, 53.1°C, 53.1°C, 55.6°C, 55.6°C , 54.4℃, 55.6℃, 60.0℃, 57.0℃, 58.0℃, 59.0℃, 66.0℃, 54.4℃, 54.4℃, 53.0℃, 55.6℃, 55.6℃, 55.6℃, 55.6℃, 55.6℃, 55.6℃, 55.6℃, 55.6℃, 55.6℃, 54.3℃, 55.5℃, 54.4℃, and 55.6℃; except for the annealing temperature, other PCR reaction conditions were the same: pre-denaturation at 94℃ for 2 minutes, denaturation at 94℃ for 30 seconds, annealing for 30 seconds, extension at 72℃ for 1 minute, a total of 33 cycles, final extension at 72℃ for 5 minutes, and storage at 16℃. The results showed that marker SGA2-1 detected a band with a fragment size of about 703 bp, marker SGA2-2 detected a band with a fragment size of about 219 bp, marker SGA2-3 detected a band with a fragment size of about 538 bp, marker SGA2-4 detected a band with a fragment size of about 225 bp, marker SGA2-5 detected a band with a fragment size of about 183 bp, marker SGA2-6 detected a band with a fragment size of about 426 bp, marker SGA2-7 detected a band with a fragment size of about 710 bp, marker SGA2-8 detected a band with a fragment size of about 214 bp, marker SGA2-9 detected a band with a fragment size of about 239 bp, marker SGA2-10 detected a band with a fragment size of about 467 bp, and marker SGA2-11 detected a band with a fragment size of about 547 bp. The fragment size was about 536bp, the marker SGA2-12 detected a band of about 184bp, the marker SGA2-13 detected a band of about 512bp, the marker SGA2-14 detected a band of about 488bp, the marker SGA1-1 detected a band of about 655bp, the marker SGA1-2 detected a band of about 721bp, the marker SGA1-3 detected a band of about 188bp, the marker SGA1-4 detected a band of about 613bp, the marker SGA1-5 detected a band of about 721bp, the marker SGA1-6 detected a band of about 830bp, and the marker SGA1-7 detected a band of about 821bp.The marker SGA1-8 detected a band with a fragment size of about 869 bp, the marker SGA1-9 detected a band with a fragment size of about 824 bp, the marker SGA1-10 detected a band with a fragment size of about 525 bp, the marker SGA1-11 detected a band with a fragment size of about 787 bp, the marker SGA1-12 detected a band with a fragment size of about 563 bp, the marker SGA1-13 detected a band with a fragment size of about 458 bp, the marker SGA1-14 detected a band with a fragment size of about 807 bp, and the marker SGA1-15 detected a band with a fragment size of about 445 bp. , marker SGA1-16 detected a band with a fragment size of about 520 bp, marker SGA1-17 detected a band with a fragment size of about 536 bp, marker SGA1-18 detected a band with a fragment size of about 691 bp, marker CHR2-1 detected a band with a fragment size of about 555 bp, marker CHR2-2 detected a band with a fragment size of about 610 bp, marker CHR2-4 detected a band with a fragment size of about 417 bp, marker CHR2-5 detected a band with a fragment size of about 387 bp, marker CHR2-6 detected a band with a fragment size of about 387 bp, and marker Marker CHR2-7 detected a band of about 455 bp, marker CHR1-1 detected a band of about 903 bp, marker CHR1-2 detected a band of about 903 bp, marker CHR1-3 detected a band of about 725 bp, marker CHR1-4 detected a band of about 475 bp, marker CHR1-5 detected a band of about 533 bp, marker CHR1-6 detected a band of about 339 bp, marker CHR1-7 detected a band of about 269 bp, and marker CHR1 -8 detected a band of about 293 bp, CHR1-9 detected a band of about 337 bp, CHR1-11 detected a band of about 319 bp, CHR1-12 detected a band of about 341 bp, LB-Chr2 detected a band of about 543 bp, RB-Chr1 detected a band of about 901 bp, Chr2 detected a band of about 582 bp, and Chr1 detected a band of about 655 bp. The product sizes were consistent with the theoretical values ​​(, Figure 1 ). These specific primers can be identified under the simplest laboratory conditions, achieving the unique advantages of high efficiency, rapidity and convenience, and providing an important genetic basis for fully realizing the full utilization of hybrid vigor in rice breeding.

Claims

1. A method for detecting a large reciprocal translocation site (SGA) in rice by using specific DNA amplification primers, wherein: Large chromosome translocation SGA The locus is located at the end of rice chromosome 1 SGA1 Translocation breakpoints and the tail end of chromosome 2 SGA2 The translocation breakpoints correspond to the sequence lengths of 12-Mb and 0.8-Mb in the physical map, respectively; characterized in that: (1) Using the genomic DNA of the sample to be tested as a template, using chromosome translocation-specific DNA primers SGA2 -1. SGA2 -2. SGA2 -3. SGA2 -4. SGA2 -5. SGA2 -6. SGA2 -7. SGA2 -8. SGA2 -9. SGA2 -10, SGA2 -11. SGA2 -12, SGA2 -13. SGA2 -14. SGA1 -1. SGA1 -2. SGA1 -3. SGA1 -4. SGA1 -5. SGA1 -6. SGA1 -7. SGA1 -8. SGA1 -9. SGA1 -10, SGA1 -11. SGA1 -12, SGA1 -13. SGA1 -14. SGA1 -15, SGA1 -16, SGA1 -17, SGA1 -18, CHR2-1, CHR2-2, CHR2-4, CHR2-5, CHR2-6, CHR2-7, CHR1-1, CHR1-2, CHR1-3, CHR1-4, CHR1-5, CHR1-6, CHR1-7, CHR1-8, CHR1-9, CHR1-11, CHR1-12, CHR2, CHR1, LB-CHR2 and RB-CHR1 were amplified by PCR; The primers are: SGA2 -1-F:5 '-GAGAGTAGTGCGCAATGCAA-3 '; SGA2 -1-R:5'-CTGCGAAGTCCCCATGGAAT-3'; SGA2 -2-F:5 '-AGTGCGCAATGCAATCATCT-3 '; SGA2 -2-R:5'-GTGCAGATAGCCCTGTCGAA-3'; SGA2 -3-F:5 '-AGAGAGTAGTGCGCAATGCAA-3 '; SGA2 -3-R:5'-TTGACAAGCCAAGACGAGCA-3'; SGA2 -4-F:5 '-GAGTAGTGGCGCAATGCAATCA-3 '; SGA2 -4-R:5'-GAGTGCAGATAGCCCTGTCG-3'; SGA2 -5-F:5′-AGTAGTGCGCAATGCAATCA-3′ SGA2 -5-R:5'-GCAGGACAAAGGCTAACCCA-3'; SGA2 -6-F:5 '-AGAGTAGTGCGCAATGCAATC-3 '; SGA2 -6-R:5'-GGGGGTCTGAAGAGGTCCTA-3'; SGA2 -7-F: 5'-GGGACGGAGAGAGTAGTGCG-3'; SGA2 -7-R:5'-TGCGAAGTCCCCATGGAATG-3'; SGA2 -8-F:5′-AGTAGTGCGCAATGCAATCAT-3′ SGA2 -8-R:5'-AGCCCTGTCGAAAAACAAACG-3'; SGA2 -9-F: 5'-ATGGGACGGAGAGTAGTGC-3'; SGA2 -9-R:5'-CTGAGTGCAGATAGCCCTGT-3'; SGA2 -10-F:5'-AGTAGTGCGCAATGCAATCATC-3'; SGA2 -10-R:5 '-CCGTGGTTGGCATGAATCAA-3 '; SGA2 -11-F:5 '-GAGTAGTGGCGCAATGCAATCAT-3 '; SGA2 -11-R:5'-TTTGACAAGCCAAGACGAGC-3'; SGA2 -12-F:5 '-AGTGCGCAATGCAATCATCTTT-3 '; SGA2 -12-R:5'-CGCAGCAGGACAAAGGCTAA-3'; SGA2 -13-F: 5'-ATGGGACGGAGAGTAGTG-3'; SGA2 -13-R:5 '-CGAAAGCAAAGGTCATTGCCA-3 '; SGA2 -14-F:5 '-TGGTAAGATGTGGAGTAACGGC-3 '; SGA2 -14-R:5 '-AGCCAAGACGAGCATTTGAGA-3 '; SGA1 -1-F:5 '-TAGAATGATGGGGGCCATGC-3 '; SGA1 -1-R:5 '-AACGCGATGAATTGGGAGGT-3 '; SGA1 -2-F:5 '-ATGGGGGCCATGCCAATAAG-3 '; SGA1 -2-R:5'-AATGGCGCAAACGGAAGATG-3'; SGA1 -3-F:5 '-CGGTTGTGACACTGCCTGAT-3 '; SGA1 -3-R:5 '-TGTCCGTTGAACCATTTGCG-3 '; SGA1 -4-F:5 '-CGTCATCTGGTCCGGTTGTG-3 '; SGA1 -4-R:5'-GCTCTTCTACCTCCCTCGGT-3'; SGA1 -5-F:5 '-TGGGGGCCATGCCAATAAG-3 '; SGA1 -5-R:5'-GAATGGCGCAAACGGAAGAT-3'; SGA1 -6-F:5 '-CATATGCTCTGCACCAAGGGA-3 '; SGA1 -6-R:5'-CAGCGGGCGATTGAAAAGAA-3'; SGA1 -7-F:5 '-CTGCACCAAGGGAGATGCTAT-3 '; SGA1 -7-R:5'-AGCGGGCGATTGAAAAGAAC-3'; SGA1 -8-F:5 '-TCTGCACCAAGGGAGATGCT-3 '; SGA1 -8-R:5'-TGCAGCTCTTGAGGAATGGC-3'; SGA1 -9-F:5 '-TGCTCTGCACCAAGGGAGAT-3 '; SGA1 -9-R:5'-GCGGGCGATTGAAAAGAACG-3'; SGA1 -10-F:5 '-TGCACCAAGGGAGATGCTAT-3 '; SGA1 -10-R:5'-TCCGTTGAACCATTTGCGGT-3'; SGA1 -11-F:5 '-ATATGCTCTGCACCAAGGGA-3 '; SGA1 -11-R:5'-ACGCGATGAATTGGGAGGTA-3'; SGA1 -12-F:5 '-GGCCCATAAACAACATTGCCA-3 '; SGA1 -12-R:5'-TCTTGAGGAATGGCGCAAAC-3'; SGA1 -13-F:5 '-CGTCATCTGGTCCGGTTGT-3 '; SGA1 -13-R:5'-GCGAAAACGCGATGAATTGG-3'; SGA1 -14-F:5 '-CATATGCTCTGCACCAAGGG-3 '; SGA1 -14-R:5 '-GACCTCATCAGCTGCGAAAAC-3 '; SGA1 -15-F:5 '-CGGTTGTGACACTGCCTGATA-3 '; SGA1 -15-R:5'-CGAAAACGCGATGAATTGGGA-3'; SGA1 -16-F:5'-ACATATGCTCTGCACCAAGGG-3'; SGA1 -16-R:5 '-GCGGTAAAGAATTGCACTCCC-3 '; SGA1 -17-F:5 '-ACGTCATCTGGTCCGGTTGT-3 '; SGA1 -17-R:5'-CTCTTGAGGAATGGCGCAAAC-3'; SGA1 -18-F:5 '-TTAGAATGATGGGGGCCATGC-3 '; SGA1 -18-R:5'-GCGATTGAAAAAGAACGGGACC-3'; CHR2-1-F: 5'-GGACGGAGAGAGTAGTGCG-3'; CHR2-1-R: 5'-AAAAGAACGGGACCTCATCA-3'; CHR2-2-F: 5'-ACGGAGAGAGTAGTGCGC-3'; CHR2-2-R: 5'-CAGCTCTTGAGGAATGGC-3'; CHR2-4-F: 5'-TTCAGCTTATACTGATGGT-3'; CHR2-4-R: 5'-TGGTCTCCTGGTGTCTGTAA-3'; CHR2-5-F:5'-CGGCTTATTACTAGCAACTT-3'; CHR2-5-R: 5'-GTGGTCTCCTGGTGTCTGTAA-3'; CHR2-6-F: 5'-AACGGCTTATTACTAGCAACTT-3'; CHR2-6-R: 5'-GGTGGTCTCCTGGTGTCTGT-3'; CHR2-7-F: 5'-GGACGGAGAGAGTAGTGCGC-3'; CHR2-7-R: 5'-GGGGTGGTCTCCTGGTGTCT-3'; CHR1-1-F: 5'-TGTTACATATGCTCTGCACCAA-3'; CHR1-1-R:5'-TGTTTGAATTAATCGCTGGTTC-3'; CHR1-2-F:5 '-TTACATATGCTCTGCACCAAGG-3 '; CHR1-2-R:5 '-AGTGTTTGAATTAATCGCTGGT-3 '; CHR1-3-F:5 '-CAACCCATGACAATTAGAATG-3 '; CHR1-3-R:5 '-ACATTTTTGAGGGTGAATCTA-3 '; CHR1-4-F:5 '-TTACCCTTCTTCAAGCTCCAT-3 '; CHR1-4-R:5 '-AAAGACTTTGGGGGTCTGAAG-3 '; CHR1-5-F:5 '-AACTTGAAGGCCAAATATGCC-3 '; CHR1-5-R:5 '-TGAATCAAGGAAGCAAGTGAT-3 '; CHR1-6-F:5 '-TCTTTCAGTTGAGTAACCGTATGG-3 '; CHR1-6-R:5 '-GATTGTGATGCTTTTGCCCTA-3 '; CHR1-7-F:5 '-CGGTTGTGACACTGCCTGATA-3 '; CHR1-7-R:5 '-ATGATTGTGATGCTTTTGCCC-3 '; CHR1-8-F:5 '-GTTGTGACACTGCCTGATAAG-3 '; CHR1-8-R:5 '-ATGGCACCTCTATGAGTATGA-3 '; CHR1-9-F:5 '-CTTCTTTCAGTTGAGTAACCG-3 '; CHR1-9-R:5 '-GTGATGCTTTTGCCCTATACA-3 '; CHR1-10-F:5 '-TGTGACACTGCCTGATAAGCA-3 '; CHR1-10-R:5 '-TTGTGATGCTTTTGCCCTATA-3 '; CHR1-11-F:5 '-GAGATGAGGCCCATAAACAAC-3 '; CHR1-11-R:5 '-CAATGATTGTGATGCTTTTGC-3 '; CHR1-12-F:5 '-TCAGTTGAGTAACCGTATGGG-3 '; CHR1-12-R:5 '-ATCAATGATTGTGATGCTTTT-3 '; CHR2-F:5 '-TGGTAAGATGTGGAGTAACGG-3 '; CHR2-R:5 '-CCATTTTGTGTAAACATCTGC-3 '; CHR1-F:5 '-GCCAATAAGATTAGACCCCA-3 '; CHR1-R:5'-TTTGACAAGCCAAGACGAGC-3'; LB-CHR2-F: 5'-TGGGACGGAGAGAGTAGTGC-3'; LB-CHR2-R:5'-ACAAGCCAAGACGAGCATTT-3'; RB-CHR1-F:5'-ACAAATAAACGGGTCCATCAA-3'; RB-CHR1-R:5'-GATTGAAAAGAACGGGACCTC-3'; (2) The presence of large-segment chromosomal translocations is determined based on the electrophoresis results. Translocations can be divided into those occurring on chromosome 1 and those occurring on chromosome 1. SGA1 Chromosome translocation type CHR1 and chromosome 2 at the breakpoint SGA2 The CHR2 chromosome translocation type at the breakpoint corresponds to the absence of SGA1 and SGA2 The translocation breakpoints are referred to as CHR1 normal genotype and CHR2 normal genotype; On the SGA2-1 primer, the 703 bp band that could be detected was the CHR2 chromosome translocation genotype; exist SGA2 -2 primers, the 219 bp band that can be detected is the CHR2 chromosome translocation genotype; exist SGA2 -3 primers, the 538 bp band that can be detected is the CHR2 chromosome translocation genotype; exist SGA2 -4 primers, the 225 bp band that can be detected is the CHR2 chromosome translocation genotype; exist SGA2 -5 primer, the 183 bp band that can be detected is the CHR2 chromosome translocation genotype; exist SGA2 On the -6 primer, the 426 bp band that can be detected is the CHR2 chromosome translocation genotype; exist SGA2 -7 primers, the 710 bp band that can be detected is the CHR2 chromosome translocation genotype; exist SGA2 -8 primers, the 214 bp band that can be detected is the CHR2 chromosome translocation genotype; exist SGA2 -9 primers, the 239 bp band that can be detected is the CHR2 chromosome translocation genotype; exist SGA2 On the -10 primer, the 467 bp band that can be detected is the CHR2 chromosome translocation genotype; exist SGA2 On the -11 primer, the 536 bp band that can be detected is the CHR2 chromosome translocation genotype; exist SGA2 -12 primers, the 184 bp band that can be detected is the CHR2 chromosome translocation genotype; exist SGA2 On the -13 primer, the 512 bp band that can be detected is the CHR2 chromosome translocation genotype; exist SGA2 On primer -14, the 488 bp band that can be detected is the CHR2 chromosome translocation genotype; exist SGA1 -1 primer, the 655bp band that can be detected is the CHR1 chromosome translocation genotype; exist SGA1 -2 primers, the 721 bp band that can be detected is the CHR1 chromosome translocation genotype; exist SGA1 -3 primers, the 188 bp band that can be detected is the CHR1 chromosome translocation genotype; exist SGA1 On the -4 primer, the 613 bp band that can be detected is the CHR1 chromosome translocation genotype; exist SGA1 -5 primers, the 721 bp band that can be detected is the CHR1 chromosome translocation genotype; exist SGA1 On the -6 primer, the 830 bp band that can be detected is the CHR1 chromosome translocation genotype; exist SGA1 -7 primers, the 821 bp band that can be detected is the CHR1 chromosome translocation genotype; exist SGA1 -8 primers, the 869 bp band that can be detected is the CHR1 chromosome translocation genotype; exist SGA1 -9 primers, the 824 bp band that can be detected is the CHR1 chromosome translocation genotype; exist SGA1 On the -10 primer, the 525 bp band that can be detected is the CHR1 chromosome translocation genotype; exist SGA1 On the -11 primer, the 787 bp band that can be detected is the CHR1 chromosome translocation genotype; exist SGA1 -12 primers, the 563 bp band that can be detected is the CHR1 chromosome translocation genotype; exist SGA1 On the -13 primer, the 458 bp band that can be detected is the CHR1 chromosome translocation genotype; exist SGA1 On primer -14, the 807 bp band that can be detected is the CHR1 chromosome translocation genotype; exist SGA1 On the -15 primer, the 445 bp band that can be detected is the CHR1 chromosome translocation genotype; exist SGA1 On the -16 primer, the 520 bp band that can be detected is the CHR1 chromosome translocation genotype; exist SGA1 On the -17 primer, the 536 bp band that can be detected is the CHR1 chromosome translocation genotype; exist SGA1 On the -18 primer, the 691 bp band that can be detected is the CHR1 chromosome translocation genotype; On the CHR2-1 primer, the 703 bp band that can be detected is the normal genotype of the CHR2 chromosome; On the CHR2-2 primer, the 219 bp band that can be detected is the normal genotype of the CHR2 chromosome; On the CHR2-4 primer, the 225 bp band that can be detected is the normal genotype of the CHR2 chromosome; On the CHR2-5 primer, the 183 bp band that can be detected is the normal genotype of the CHR2 chromosome; On the CHR2-6 primer, the 426 bp band that can be detected is the normal genotype of the CHR2 chromosome; On the CHR2-7 primer, the 710 bp band that can be detected is the normal genotype of the CHR2 chromosome; On the CHR1-1 primer, the 903 bp band that can be detected is the normal genotype of the CHR1 chromosome; On the CHR1-2 primers, the 903 bp band that can be detected is the normal genotype of the CHR1 chromosome; On the CHR1-3 primers, the 725 bp band that can be detected is the normal genotype of the CHR1 chromosome; On the CHR1-4 primers, the 475 bp band that can be detected is the normal genotype of the CHR1 chromosome; On the CHR1-5 primers, the 533 bp band that can be detected is the normal genotype of the CHR1 chromosome; On the CHR1-6 primers, the 339 bp band that can be detected is the normal genotype of the CHR1 chromosome; On the CHR1-7 primers, the 269 bp band that can be detected is the normal genotype of the CHR1 chromosome; On the CHR1-8 primers, the 293 bp band that can be detected is the normal genotype of the CHR1 chromosome; On the CHR1-9 primers, the 337 bp band that can be detected is the normal genotype of the CHR1 chromosome; On the CHR1-11 primer, the 319 bp band that can be detected is the normal genotype of the CHR1 chromosome; On the CHR1-12 primers, the 341 bp band that can be detected is the normal genotype of the CHR1 chromosome; On the CHR2 primer, the 582bp band that can be detected is the normal genotype of the CHR2 chromosome; On the CHR1 primer, the 655 bp band that can be detected is the normal genotype of the CHR2 chromosome; On the LB-CHR2 primer, the 543 bp band that could be detected was the CHR2 chromosome translocation genotype; On the RB-CHR1 primer, the 901bp band that can be detected is the CHR2 chromosome translocation genotype.

2. The method according to claim 1, characterized in that: Chromosomal translocation-specific DNA primers SGA2 -1. SGA2 -2. SGA2 -3. SGA2 -4. SGA2 -5. SGA2 -6. SGA2 -7. SGA2 -8. SGA2 -9. SGA2 -10, SGA2 -11. SGA2 -12, SGA2 -13. SGA2 -14. SGA1 -1. SGA1 -2. SGA1 -3. SGA1 -4. SGA1 -5. SGA1 -6. SGA1 -7. SGA1 -8. SGA1 -9. SGA1 -10, SGA1 -11. SGA1 -12, SGA1 -13. SGA1 -14. SGA1 -15, SGA1 -16, SGA1 -17, SGA1 The annealing temperatures of CHR1-1, CHR2-2, CHR2-4, CHR2-5, CHR2-6, CHR2-7, CHR1-1, CHR1-2, CHR1-3, CHR1-4, CHR1-5, CHR1-6, CHR1-7, CHR1-8, CHR1-9, CHR1-11, CHR1-12, CHR2, CHR1, LB-CHR2 and RB-CHR1 are 54.4°C, 54.4°C, 55.6°C, 55.6°C, 54.4°C, 55.6°C, 55.6°C, 56.7°C, 56.7°C, 54.4°C, respectively. , 56.7°C, 54.4°C, 54.4°C, 54.4°C, 53.1°C, 55.6°C, 55.6°C, 54.4°C, 54.4°C, 54.4°C, 54.4°C, 55.6°C, 53.1°C, 53.1°C, 55.6°C, 55.6°C, 54.4°C, 55.6°C, 60.0°C, 57.0°C, 58.0°C, 59.0°C, 66.0°C, 54.4°C, 54.4°C, 53.0°C, 55.6°C, 55.6°C, 55.6°C, 55.6°C, 55.6°C, 55.6°C, 55.6°C, 55.6°C, 54.3°C, 55.5°C, 54.4°C, and 55.6°C; The remaining PCR reaction conditions were the same: pre-denaturation at 94°C for 2 min, denaturation at 94°C for 30 s, annealing for 15 s, extension at 72°C for 1 min, a total of 34 cycles, final extension at 72°C for 5 min, and storage at 16°C.

3. The method according to claim 1, characterized in that The PCR amplification products are detected by electrophoresis or sequencing to make a judgment.

4. The method according to claim 3, characterized in that The electrophoresis was performed using 1% agarose electrophoresis.

5. Used for testing rice SGA A primer or primer combination for large-segment chromosomal translocation, characterized in that: The primers are any one or more of the following primer pairs: SGA2 -1-F:5 '-GAGAGTAGTGCGCAATGCAA-3 '; SGA2 -1-R:5'-CTGCGAAGTCCCCATGGAAT-3'; SGA2 -2-F:5 '-AGTGCGCAATGCAATCATCT-3 '; SGA2 -2-R:5'-GTGCAGATAGCCCTGTCGAA-3'; SGA2 -3-F:5 '-AGAGAGTAGTGCGCAATGCAA-3 '; SGA2 -3-R:5'-TTGACAAGCCAAGACGAGCA-3'; SGA2 -4-F:5 '-GAGTAGTGGCGCAATGCAATCA-3 '; SGA2 -4-R:5'-GAGTGCAGATAGCCCTGTCG-3'; SGA2 -5-F:5′-AGTAGTGCGCAATGCAATCA-3′ SGA2 -5-R:5'-GCAGGACAAAGGCTAACCCA-3'; SGA2 -6-F:5 '-AGAGTAGTGCGCAATGCAATC-3 '; SGA2 -6-R:5'-GGGGGTCTGAAGAGGTCCTA-3'; SGA2 -7-F: 5'-GGGACGGAGAGAGTAGTGCG-3'; SGA2 -7-R:5'-TGCGAAGTCCCCATGGAATG-3'; SGA2 -8-F:5′-AGTAGTGCGCAATGCAATCAT-3′ SGA2 -8-R:5'-AGCCCTGTCGAAAAACAAACG-3'; SGA2 -9-F: 5'-ATGGGACGGAGAGTAGTGC-3'; SGA2 -9-R:5'-CTGAGTGCAGATAGCCCTGT-3'; SGA2 -10-F:5'-AGTAGTGCGCAATGCAATCATC-3'; SGA2 -10-R:5 '-CCGTGGTTGGCATGAATCAA-3 '; SGA2 -11-F:5 '-GAGTAGTGGCGCAATGCAATCAT-3 '; SGA2 -11-R:5'-TTTGACAAGCCAAGACGAGC-3'; SGA2 -12-F:5 '-AGTGCGCAATGCAATCATCTTT-3 '; SGA2 -12-R:5'-CGCAGCAGGACAAAGGCTAA-3'; SGA2 -13-F: 5'-ATGGGACGGAGAGTAGTG-3'; SGA2 -13-R:5 '-CGAAAGCAAAGGTCATTGCCA-3 '; SGA2 -14-F:5 '-TGGTAAGATGTGGAGTAACGGC-3 '; SGA2 -14-R:5 '-AGCCAAGACGAGCATTTGAGA-3 '; SGA1 -1-F:5 '-TAGAATGATGGGGGCCATGC-3 '; SGA1 -1-R:5 '-AACGCGATGAATTGGGAGGT-3 '; SGA1 -2-F:5 '-ATGGGGGCCATGCCAATAAG-3 '; SGA1 -2-R:5'-AATGGCGCAAACGGAAGATG-3'; SGA1 -3-F:5 '-CGGTTGTGACACTGCCTGAT-3 '; SGA1 -3-R:5 '-TGTCCGTTGAACCATTTGCG-3 '; SGA1 -4-F:5 '-CGTCATCTGGTCCGGTTGTG-3 '; SGA1 -4-R:5'-GCTCTTCTACCTCCCTCGGT-3'; SGA1 -5-F:5 '-TGGGGGCCATGCCAATAAG-3 '; SGA1 -5-R:5'-GAATGGCGCAAACGGAAGAT-3'; SGA1 -6-F:5 '-CATATGCTCTGCACCAAGGGA-3 '; SGA1 -6-R:5'-CAGCGGGCGATTGAAAAGAA-3'; SGA1 -7-F:5 '-CTGCACCAAGGGAGATGCTAT-3 '; SGA1 -7-R:5'-AGCGGGCGATTGAAAAGAAC-3'; SGA1 -8-F:5 '-TCTGCACCAAGGGAGATGCT-3 '; SGA1 -8-R:5'-TGCAGCTCTTGAGGAATGGC-3'; SGA1 -9-F:5 '-TGCTCTGCACCAAGGGAGAT-3 '; SGA1 -9-R:5'-GCGGGCGATTGAAAAGAACG-3'; SGA1 -10-F:5 '-TGCACCAAGGGAGATGCTAT-3 '; SGA1 -10-R:5'-TCCGTTGAACCATTTGCGGT-3'; SGA1 -11-F:5 '-ATATGCTCTGCACCAAGGGA-3 '; SGA1 -11-R:5'-ACGCGATGAATTGGGAGGTA-3'; SGA1 -12-F:5 '-GGCCCATAAACAACATTGCCA-3 '; SGA1 -12-R:5'-TCTTGAGGAATGGCGCAAAC-3'; SGA1 -13-F:5 '-CGTCATCTGGTCCGGTTGT-3 '; SGA1 -13-R:5'-GCGAAAACGCGATGAATTGG-3'; SGA1 -14-F:5 '-CATATGCTCTGCACCAAGGG-3 '; SGA1 -14-R:5 '-GACCTCATCAGCTGCGAAAAC-3 '; SGA1 -15-F:5 '-CGGTTGTGACACTGCCTGATA-3 '; SGA1 -15-R:5'-CGAAAACGCGATGAATTGGGA-3'; SGA1 -16-F:5'-ACATATGCTCTGCACCAAGGG-3'; SGA1 -16-R:5 '-GCGGTAAAGAATTGCACTCCC-3 '; SGA1 -17-F:5 '-ACGTCATCTGGTCCGGTTGT-3 '; SGA1 -17-R:5'-CTCTTGAGGAATGGCGCAAAC-3'; SGA1 -18-F:5 '-TTAGAATGATGGGGGCCATGC-3 '; SGA1 -18-R:5'-GCGATTGAAAAAGAACGGGACC-3'; CHR2-1-F: 5'-GGACGGAGAGAGTAGTGCG-3'; CHR2-1-R: 5'-AAAAGAACGGGACCTCATCA-3'; CHR2-2-F: 5'-ACGGAGAGAGTAGTGCGC-3'; CHR2-2-R: 5'-CAGCTCTTGAGGAATGGC-3'; CHR2-4-F: 5'-TTCAGCTTATACTGATGGT-3'; CHR2-4-R: 5'-TGGTCTCCTGGTGTCTGTAA-3'; CHR2-5-F:5'-CGGCTTATTACTAGCAACTT-3'; CHR2-5-R:5 '-GTGGTCTCCTGGTGTCTGTAA-3 '; CHR2-6-F:5 '-AACGGCTTATTACTAGCAACTT-3 '; CHR2-6-R:5 '-GGTGGTCTCCTGGTGTCTGT-3 '; CHR2-7-F:5 '-GGACGGAGAGAGTAGTGCGC-3 '; CHR2-7-R:5 '-GGGGTGGTCTCCTGGTGTCT-3 '; CHR1-1-F:5 '-TGTTACATATGCTCTGCACCAA-3 '; CHR1-1-R:5 '-TGTTTGAATTAATCGCTGGTTC-3 '; CHR1-2-F:5 '-TTACATATGCTCTGCACCAAGG-3 '; CHR1-2-R:5 '-AGTGTTTGAATTAATCGCTGGT-3 '; CHR1-3-F:5 '-CAACCCATGACAATTAGAATG-3 '; CHR1-3-R:5 '-ACATTTTTGAGGGTGAATCTA-3 '; CHR1-4-F:5 '-TTACCCTTCTTCAAGCTCCAT-3 '; CHR1-4-R:5 '-AAAGACTTTGGGGGTCTGAAG-3 '; CHR1-5-F:5 '-AACTTGAAGGCCAAATATGCC-3 '; CHR1-5-R:5 '-TGAATCAAGGAAGCAAGTGAT-3 '; CHR1-6-F:5 '-TCTTTCAGTTGAGTAACCGTATGG-3 '; CHR1-6-R:5 '-GATTGTGATGCTTTTGCCCTA-3 '; CHR1-7-F:5 '-CGGTTGTGACACTGCCTGATA-3 '; CHR1-7-R:5 '-ATGATTGTGATGCTTTTGCCC-3 '; CHR1-8-F:5 '-GTTGTGACACTGCCTGATAAG-3 '; CHR1-8-R:5 '-ATGGCACCTCTATGAGTATGA-3 '; CHR1-9-F:5 '-CTTCTTTCAGTTGAGTAACCG-3 '; CHR1-9-R:5 '-GTGATGCTTTTGCCCTATACA-3 '; CHR1-10-F:5 '-TGTGACACTGCCTGATAAGCA-3 '; CHR1-10-R:5 '-TTGTGATGCTTTTGCCCTATA-3 '; CHR1-11-F:5′-GAGATGAGGCCCATAAACAAC-3′; CHR1-11-R:5′-CAATGATTGTGATGCTTTTGC-3′ CHR1-12-F:5′-TCAGTTGAGTAACCGTATGGG-3′; CHR1-12-R:5′-ATCAATGATTGTGATGCTTTT-3′ CHR2-F:5′-TGGTAAGATGTGGAGTAACGG-3′; CHR2-R:5′-CCATTTTGTGTAAACATCTGC-3′ CHR1-F:5′-GCCAATAAGATTAGACCCCA-3′; CHR1-R:5′-TTTGACAAGCCAAGACGAGC-3′; LB-CHR2-F:5′-TGGGACGGAGAGAGTAGTGC-3′ LB-CHR2-R:5′-ACAAGCCAAGACGAGCATTT-3′; RB-CHR1-F:5′-ACAAATAAACGGGTCCATCAA-3′; RB-CHR1-R:5′-GATTGAAAAGAACGGGACCTC-3′.

6. The primer or primer combination according to claim 5, characterized in that: The rest of the snowflakes are snowflakes.

7. The method according to any one of claims 1 to 4 for large-segment chromosome translocation SGA Application in sites; specifically, detection of rice SGA1 and SGA2 The translocation genotype and the normal genotype of chromosomes 1 and 2, and the large chromosome translocation SGA locus is composed of the tail end of rice chromosome 1 SGA1 Translocation breakpoints and the tail end of chromosome 2 SGA2 The translocation breakpoints consisted of 12-Mb and 0.8-Mb sequence lengths on the physical map, respectively.

8. Used to detect large chromosome translocation in rice SGA The primer or primer combination of the locus is used to detect rice SGA1 and SGA2 Application in translocation genotype and normal genotype of chromosome 1 and chromosome 2; specifically, detection of rice SGA1 and SGA2 Translocation genotype and normal genotype of chromosomes 1 and 2, and large chromosome translocation SGA The locus is located at the end of rice chromosome 1 SGA1 Translocation breakpoints and the tail end of chromosome 2 SGA2 The translocation breakpoints consisted of 12-Mb and 0.8-Mb sequence lengths on the physical map, respectively.

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