半糯粳稻品种核心标记的筛选及DNA指纹图谱的构建

doi:10.3864/j.issn.0578-1752.2022.23.001

Abstract

Abstract:

【Objective】 A set of variety DNA fingerprint identification system based on the core markers of genes regulating rice important traits was constructed, which will establish a foundation for strengthening the germplasm management and protection of the mainly promoted semi-waxy japonica rice varieties with high eating quality.【Method】 34 semi-waxy japonica rice varieties mainly cultivated in Jiangsu, Zhejiang and Shanghai were used as the test materials. The key differential sequence sites in genes regulating rice important traits were screened and core SNP or InDel markers were developed through multiple methods such as polymorphism testing of existing markers, gene sequence alignment from public databases and genome resequencing. SNP markers were developed into simple PCR markers based on electrophoretic bands by As-PCR technology. Genotype information was obtained by electrophoretic band characterization and type analysis, and the DNA fingerprint database of the semi-waxy japonica rice varieties was constructed..【Result】 54 core markers derived from 40 key genes regulating rice important traits were obtained, including 18 SNP and 36 InDel markers; 155 characteristic and effective bands were identified by 54 markers in the tested rice varieties, which were transformed into 155 0/1 data sites. The DNA fingerprint database of each variety was established and could distinguish it from all tested varieties. Genetic diversity analysis showed that the variation range of genetic similarity among varieties was 0.47-0.90, among which the lowest similarity coefficient was detected between Nanjing 7718 and Suxiangjing 100, while the highest similarity coefficient was detected between Nanjing 9308 and Nanjing 9036, among which there were 8 differential data sites. Genetic relationship analysis indicated that 34 varieties were divided into 6 branches, of which Nanjing 7718 was an independent branch, suggesting it has a distant relationship from other varieties. Further verification of the identification effect of core markers showed that the set of markers could effectively distinguish 14 new semi-waxy japonica rice varieties. The cluster diagram showed that they were distributed in three groups of Ⅱ, Ⅲ and Ⅳ, confirming the differences of genotype information among varieties; using this set of markers, the authenticity of an unknown semi-waxy rice variety was also identified. According to genotype and cluster analysis, it was determined as Nanjing 9108.【Conclusion】 After optimization and screening, 54 core markers that could accurately distinguish all the tested semi-waxy japonica varieties were obtained, and developed into simple PCR markers detected by electrophoresis. Using this set of marker combinations, the DNA fingerprints of 34 semi-waxy japonica varieties in Jiangsu, Zhejiang and Shanghai were constructed.

Key words: rice (Oryza sativa L.), semi-waxy japonica rice, DNA fingerprints, molecular markers

ZHAO ChunFang,ZHAO QingYong,LÜ YuanDa,CHEN Tao,YAO Shu,ZHAO Ling,ZHOU LiHui,LIANG WenHua,ZHU Zhen,WANG CaiLin,ZHANG YaDong. Screening of Core Markers and Construction of DNA Fingerprints of Semi-Waxy Japonica Rice Varieties[J].Scientia Agricultura Sinica, 2022, 55(23): 4567-4582.

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URL: https://www.chinaagrisci.com/EN/10.3864/j.issn.0578-1752.2022.23.001

https://www.chinaagrisci.com/EN/Y2022/V55/I23/4567

Figures/Tables 9

Table 1

Primer sequence and detailed information of 54 markers"

引物 Primer	正向引物 Forward primer (5′-3′)	反向引物 Reverse primer (5′-3′)	物理位置 Physical position (bp)	染色体 Chromosome	扩增片段长度Amplified fragment (bp)	基因注释 Gene annotation	出处 Reference
SNP-1	IF: GGCATTCGGTCTAACCGA AAATTGCA	IR: CGGTCTTCACTTTTCAA AGACCGAACCC	19368231	2	108/127	淀粉去分支酶基因Ⅲ Starch debranching enzyme Ⅲ	重测序 Resequencing
SNP-1	OF: ACTTGACACCGAATCCG TTTATCCTCCC	OR: TGTTGAATTTCAGTCAA GACCGAGACCGA	19368231	2	108/127	淀粉去分支酶基因Ⅲ Starch debranching enzyme Ⅲ	重测序 Resequencing
SNP-2	IF: CACGGCTCGAACCGCGA CGGCATCAGTAG	IR: ATCACGGCGGGCGCCGA CGGCT	31234046	2	143/214	淀粉合成酶基因Ⅱc Starch synthase Ⅱc	重测序 Resequencing
SNP-2	OF: GCCCGAGCGCGTCGATC ATCCGGTTC	OR: CGGACCTGGAGGAGAT GCTGCGGCGGTT	31234046	2	143/214	淀粉合成酶基因Ⅱc Starch synthase Ⅱc	重测序 Resequencing
SNP-3	IF: CTCGCGCGCCCGCTCCCG CGCTGA	IR: GCGCTGGAGGAGAA GA CCGCGGCGGGCG	7237582	3	104/128	松散株型基因LPA1 Loose plant architecture 1	重测序 Resequencing
SNP-3	OF: GCCTTCTCGAGCTCCCC GCGCGCCCGGT	OR: CGCCGCGGCGGCAGGA GGGGAGGAGGAG	7237582	3	104/128	松散株型基因LPA1 Loose plant architecture 1	重测序 Resequencing
SNP-4	IF: AGAATGTTGATCTCTGAC AATATCAAGAAGGTA	IR: CTTTGTGGAGGTCCAAA CATTGAGA	31512460	3	184/203	抽穗期基因Hd6 Heading date 6	重测序 Resequencing
SNP-4	OF: ATGAAGGCTCAATGAAG ACCTTGAGTAG	OR: TCATCAAGATACTCAA GCCTGTGAAGAA	31512460	3	184/203	抽穗期基因Hd6 Heading date 6	重测序 Resequencing
SNP-5	IF: TTTGGCAATACCAGACA ACTGTCTTCTT	IR: GCCGTCTGGTTCAACAA GATTATCG	6942503	4	149/183	水稻抗胁迫基因OsLecRK1 Rice stress resistance gene OsLecRK1	重测序 Resequencing
SNP-5	OF: GACCAGACCGGTCTTTC AGTGAGAG	OR: AACTCAGAAGAACATC ACATTGGGCTC	6942503	4	149/183	水稻抗胁迫基因OsLecRK1 Rice stress resistance gene OsLecRK1	重测序 Resequencing
SNP-6	IF: GGTAGGGGTATTGAGATT CTTTACAGTTGACTG	IR: TCCACATGTAAGTGACA AAGGCATTAGGT	20430813	4	169/216	籽粒体型控制基因GIF1 Grain incomplete filling 1	重测序 Resequencing
SNP-6	OF: CTCCTAGGCCTGGTTCC ACTCGT	OR: GAGTAGGAGGTGAGTG AATGCTTCAACC	20430813	4	169/216	籽粒体型控制基因GIF1 Grain incomplete filling 1	重测序 Resequencing
SNP-7	IF: CCGCGGGAGGCGGCGGC GGAGA	IR: CGGAAGAGGGGTCGAG CTCGACGCCGCAGC	1159544	5	134/172	水稻淀粉调节因子RSR1 Rice starch regulator 1	重测序 Resequencing
SNP-7	OF: AGCTGCTGGTGTTGGTG GTGCGGCGGCG	OR: GAGACGGCGGCGAGGA GCGACTCCGGCA	1159544	5	134/172	水稻淀粉调节因子RSR1 Rice starch regulator 1	重测序 Resequencing
SNP-8	IF: GGGAAAAGCTCAACGGC GGCGA	IR: CATTAGGAGCCACGTCA GCTGGCTGC	15615574	5	130/165	G蛋白基因RGA1 G protein gene RGA1	重测序 Resequencing
SNP-8	OF: CACGTGGAACCCACAAG CCAACTAGCAA	OR: GGGTGGGGAGAAGGCG AGCAGTTGTAGT	15615574	5	130/165	G蛋白基因RGA1 G protein gene RGA1	重测序 Resequencing
SNP-9	IF: CGTGGCGTGCGACGTGC AGGGGT	IR: GCCGGGAGCGGGTTCGC GGATTG	9336850	6	130/183	抽穗期基因Hd1 Heading date 1	重测序 Resequencing
SNP-9	OF: GTACCTGTGCGCGTCGT GCGACGCG	OR: TCCACCTCCTCGTCCTT GTCGCCGAGGA	9336850	6	130/183	抽穗期基因Hd1 Heading date 1	重测序 Resequencing
SNP-10	IF: TTATTAATCTACGTTTAA TATTTTGAATGTGTTTC	IR: AGTTTTGGTGTGTAACA TCAGATATAGGA	25097788	6	151/191	千粒重基因TGW6 Thousand-grain weight gene TGW6	重测序 Resequencing
SNP-10	OF: AATCTTTTAAGCCTAATT GCTCCATAAT	OR: AATTGTTCGTTTTACAT CTTTATACGGA	25097788	6	151/191	千粒重基因TGW6 Thousand-grain weight gene TGW6	重测序 Resequencing
SNP-11	IF: CCGCCGCGCGCTCCAAGT CTCC	IR: CGAGGTGTTCCCCGGCT GCCGGAAAT	6259232	7	109/126	胚乳蛋白基因RAG2 Endosperm protein gene RAG2	重测序 Resequencing
SNP-11	OF: CCAGTAGCAGACACCAC CTGTCCCATTGGGGA	OR: CAGGTGCTCGGCGCTC AACCACATGGTT	6259232	7	109/126	胚乳蛋白基因RAG2 Endosperm protein gene RAG2	重测序 Resequencing

Table 1

Continued Table 1

引物 Primer	正向引物 Forward primer (5′-3′)	反向引物 Reverse primer (5′-3′)	物理位置 Physical position (bp)	染色体 Chromosome	扩增片段长度Amplified fragment (bp)	基因注释 Gene annotation	出处 Reference
SNP-12	IF: TTTGACGAATCTAGATAA GGAGCCTGTATG	IR: CCTATAATATAAGGGAT TTTTTAGGGAGGGCT	9158633	7	159/218	穗粒数、株高和抽穗期基因Ghd7 Grain number, plant height and heading date 7	重测序 Resequencing
SNP-12	OF: CGCTATAAAGGTTACGT AAACATATCGCAG	OR: TTCTTTTTGGAACGGAG GGAGTAAGTAT	9158633	7	159/218		重测序 Resequencing
SNP-13	IF: ATGGCGGACCAATCTCCG GTGTGCACCC	IR: CGCTCCCAGCAGACCTG CGGTGCCC	29617569	7	130/154	抽穗期基因DTH7 Days to heading 7	重测序 Resequencing
SNP-13	OF: CCGCTCATCACAACCAA ACCGCCGGCTC	OR: GCAGGGCACTGACCAC CTGCCTGGTGGA	29617569	7	130/154	抽穗期基因DTH7 Days to heading 7	重测序 Resequencing
SNP-14	IF: AAAAAAATAATTGGAGT TACAATCTAACATTAC	IR: AAGTTCTGCAATTTACA GTGTAAATACGT	4328377	8	128/162	产量和抽穗期基因Ghd8 Gran yield and heading date gene 8	重测序 Resequencing
SNP-14	OF: TACAAAATATCTGGTAT TTGTTGAATGG	OR: CAGCATAAAATGACTG TAAAACGTAAAC	4328377	8	128/162	产量和抽穗期基因Ghd8 Gran yield and heading date gene 8	重测序 Resequencing
SNP-15	IF: AGTGCCAGCGGTGGTGG CCGCA	IR: TCATGAACTTCTTGAAA CTGAATCATACCTGAGC	5352201	8	130/180	淀粉合成酶基因Ⅲa Starch synthase Ⅲa	重测序 Resequencing
SNP-15	OF: AGGAGGCACCGCTAGGT GGTGTGTTCAG	OR: AATCTTGCATGCCCCTT CAGAAGGACGA	5352201	8	130/180	淀粉合成酶基因Ⅲa Starch synthase Ⅲa	重测序 Resequencing
SNP-16	IF: ATGTTGTGTTCTTGTGTT CTTTGCAGGC	IR: GTAGATCTTCTCACCGG TCTTTCCCCAA	1564914	6	125/154	颗粒型淀粉合酶基因GBSSI Granule-bound starch synthase I	重测序 Resequencing
SNP-16	OF: GGGTGAGGTTTTTCCAT TGCTACAATCG	OR: GTCGATGAACACACGG TCGACTCAAT	1564914	6	125/154	颗粒型淀粉合酶基因GBSSI Granule-bound starch synthase I	重测序 Resequencing
SNP-17	IF: TTCCCTGTTCAATTGCAG AATAATCAACT	IR: AGGACCCTGCAAGGGTT GTCTCT	1797083	9	128/157	抽穗期基因OsFCA Heading date gene OsFCA	重测序 Resequencing
SNP-17	OF: ACCTTTTACTTTGTAGG GCATGAACCCT	OR: GACCAGATAACCTATT CTGGCCAAAAGA	1797083	9	128/157	抽穗期基因OsFCA Heading date gene OsFCA	重测序 Resequencing
SNP-18	IF: CGCAGCAGGCGGCGGTG GTTGC	IR: CCTGCCAGGGTTGCAAC TTCGCCGACA	14739998	10	154/224	早穗期基因Ehd2 Early heading date 2	重测序 Resequencing
SNP-18	OF: TGACACATGCGATCGAT GTGGCATTGGCA	OR: GGCGCCGGCTCACTAG GGACTTCCTCGG	14739998	10	154/224	早穗期基因Ehd2 Early heading date 2	重测序 Resequencing
InDel-1	F: CGCGGGGTGGCGACGAC AAC	R: ACCGCCTATAGACCAAC GAC	24106264	2	176—192	低直链淀粉含量基因du3 Low amylose content gene du3	重测序 Resequencing
InDel-2	F: GGAAGGGATCCGTAATA CAAA	R: CCCATATCTACATGACGG TT	30480729	2	125—151	穗粒数、株高和抽穗期基因Ghd2 Grain number, plant height and heading date 2	重测序 Resequencing
InDel-3	F: GGAAATGGGAGTCGCC	R: CGAAGAAACCACGCTCA	31242178	6	164—266	淀粉分支酶基因I Starch branching enzyme I	[22]
InDel-4	F: CAATATGCCTGAAGTCC AC	R: TGTGCTCAATTGCTAGC TT	25197305	3	136—145	落粒性基因OsYABBY2 Shattering gene OsYABBY2	NCBI序列比对 NCBI Sequence Alignment
InDel-5	F: CCAAAACGACTTACTTTA GAGC	R: TTCCTCCGTACTCATAAG AGC	32998659	3	151—187	酪蛋白激酶基因CKI Casein kinase I	NCBI序列比对 NCBI Sequence Alignment
InDel-6	F: CTCGATCCCCTAGCTCTC	R: TCACCTCGTTCTCGATCC	19168790	12	151—163	MADS转录因子 MADS transcription factor	NCBI序列比对 NCBI Sequence Alignment

Continued Table 1

Continued Table 1

引物 Primer	正向引物 Forward primer (5′-3′)	反向引物 Reverse primer (5′-3′)	物理位置 Physical position (bp)	染色体 Chromosome	扩增片段长度Amplified fragment (bp)	基因注释 Gene annotation	出处 Reference
InDel-7	F: CCAGTGTCGCCTTCTCCG GCTT	R: GGGGAAACGAGACGGCG GTCCA	6946008	4	159—175	水稻抗胁迫基因OsLecRK1 Rice stress resistance gene OsLecRK1	NCBI序列比对 NCBI Sequence Alignment
InDel-8	F: TATGTGCAGCGTTCATTG ACCT	R: AGGGTCAGTCATAACCT CAGT	33631382	4	150—161	谷氨酰胺合成酶基因OsGS2 Glutamine synthase 2	NCBI序列比对 NCBI Sequence Alignment
InDel-9	F: AGCAGCAAACATCCAAA GGCA	R: GGGTGTCAAGTCGAATC CAGC	9336223	6	116—125	抽穗期基因Hd1 Heading date 1	重测序 Resequencing
InDel-10	F: GATAACCATCGGTAATTG CT	R: GGCAATCATGAAGATTC GAAG	5360339	5	155—167	粒重基因GW5 Grain weight gene GW5	重测序 Resequencing
InDel-11	F: GGAACAATTGGTTAAATA CTTCA	R: AGAAAAAATTGGATCTT TGTCA	25379188	7	135—144	直立型密穗基因DEP2 Dense and erect panicle 2	NCBI序列比对 NCBI Sequence Alignment
InDel-12	F: TCCGAATATATTTCTGGA TTGTG	R: GGAAAAATAATAATGGC TTC	29615978	7	152—167	抽穗期控制基因DTH7 Days to heading 7	重测序 Resequencing
InDel-13	F: AGCAGGTTATAAGCTAGG CC	R: CTACCAACAAGTTCATC AAA	9811234	12	877/1052	稻瘟病抗性基因Pita Rice blast resistance-ta	[25]
InDel-14	F: GTGCGTGACCCTTTGCTG TT	R: ATCTTCCAGGTTCCAATT CTTC	271526	8	138—145	早穗基因Ehd3 Early heading date 3	重测序 Resequencing
InDel-15	F: CGGGGCATAAACTTCAC CT	R: ATTACTCCCAAATGTTTG TCGAT	8049753	9	116—121	组蛋白甲基转移酶基因SDG724 Histone Methyltransferase gene SDG724	NCBI序列比对 NCBI Sequence Alignment
InDel-16	F: TAACTGACTCCTTTGGCTA	R: TATATGCATGAAGAACA TGTC	17081627	10	120—131	早穗基因Ehd1 Early heading date 1	重测序 Resequencing
InDel-17	F: GAACAATGCCCAAACTTG AGA	R: GGGTCCACATGTCAGTG AGC	37285710	2	452—550	稻瘟病抗性基因Pib Rice blast resistance-b	[26]
InDel-18	F: CGTCTTGCAACCAACGCC GA	R: GAGCGTGTGTAGGGAAG GAGCT	5360550	5	759/1970	粒重基因GW5 Grain weight gene GW5	[27]
InDel-19	F: AAGCAATGTAAGTTCAAG TAGC	R: GATTAGGGATGATGGTT TTC	5358972	8	177—197	淀粉合成酶基因Ⅲa Starch synthase Ⅲa	NCBI序列比对 NCBI Sequence Alignment
InDel-20	F: GGGAGGCGCTGAAGAG GA	R: GGGTAGTCACCACCCTA CCTTG	20380278	8	100—107	香味基因OsBADH2 Fragrance gene OsBADH2	[28]
InDel-21	F: ATACCCCATCAATCGAA AT	R: GAAAAGGACAACATTGA GAA	20382842	8	195—204	香味基因OsBADH2 Fragrance gene OsBADH2	[28]
InDel-22	F: CTTCTATCCATTCCTTAAT CCCA	R: ATGCTATTGATGTTAAGA GGGC	3080720	6	69—76	淀粉合成酶基因Ⅰ Starch synthaseⅠ	[23]
InDel-23	F: TGCTACATAACACGCATA CAAAGT	R: AGACAAAAGCGAAAGG TAATGAG	30906227	6	280—290	淀粉分支酶基因Ⅰ Starch branching enzymeⅠ	NCBI序列比对 NCBI Sequence Alignment

Continued Table 1

Continued Table 1

引物 Primer	正向引物 Forward primer (5'-3′)	反向引物 Reverse primer (5′-3′)	物理位置 Physical position (bp)	染色体 Chromosome	扩增片段长度Amplified fragment (bp)	基因注释 Gene annotation	出处 Reference
InDel-24	F: GTGGGGAAAACAAGTAA GTCTG	R: AGTTCCATCAGAAGAAT CAGGG	30904211	6	279—294	淀粉分支酶基因Ⅰ Starch branching enzymeⅠ	NCBI序列比对 NCBI Sequence Alignment
InDel-25	F: GTCGCCGCCGTCGTCAGC AC	R: AGCTCTGCCTCCGTCCCT T	31242110	2	127—140	淀粉合成酶基因Ⅱc Starch synthaseⅡc	NCBI序列比对 NCBI Sequence Alignment
InDel-26	F: CCATCACCTCAAATACAT CACTC	R: AGACTGGAATGCCCCTT AGG	20066875	4	93—106	淀粉分支酶基因Ⅳ Starch branching enzyme Ⅳ	NCBI序列比对 NCBI Sequence Alignment
InDel-27	F: CCAATACCGTAAACTAGC GACTATG	R: TACAGGTAGAATGGCAG TGGTG	6747791	6	81—90	淀粉合成酶基因Ⅱa Starch synthaseⅡa	[22]
InDel-28	F: GCACTCCTGCCTGTTTATC TGAAG	R: GTCGTACAGCTTGAAGT GATCCAG	6750552	6	160—171	淀粉合成酶基因Ⅱa Starch synthaseⅡa	NCBI序列比对 NCBI Sequence Alignment
InDel-29	F: GGTTCTCGGTGAAGATG GC	R: GTGGTCCCAGCTGAGGT CC	6751745	6	310—326	淀粉合成酶基因Ⅱa Starch synthaseⅡa	NCBI序列比对 NCBI Sequence Alignment
InDel-30	F: CTTTGATAGTTCGAATGG TT	R: CAATGTTTCTCCGTGATG AT	6742084	6	242—344	淀粉合成酶基因Ⅱa Starch synthaseⅡa	NCBI序列比对 NCBI Sequence Alignment
InDel-31	F: GAACTTGTGCCTTAAGCT GACTG	R: GGAATAGTAAGCCGAAG GACTT	5619311	8	177—197	淀粉合成酶基因Ⅲa Starch synthaseⅢa	[22]
InDel-32	F: AAGTCCTTCGGCTTACTA TTCC	R: GGAGAAGGAACATAAC AGGGAC	5619486	8	700—902	淀粉合成酶基因Ⅲa Starch synthase Ⅲa	[23]
InDel-33	F: GACCAACCGATTACCTTC TT	R: TTGCTCTTTTCTCAACCT GT	5619157	8	366—386	淀粉合成酶基因Ⅲa Starch synthase Ⅲa	NCBI序列比对 NCBI Sequence Alignment
InDel-34	F: TACGCTATGCTCTTGAA AC	R: TATCTTCCCAGTAACCAT CA	7247406	9	184—215	ADP葡萄糖焦磷酸化酶小亚基基因 ADP-glucose pyrophosphorylase small subunit 1	[23]
InDel-35	F: AAGGTTAGCATTGGTTGG TGAG	R: TCTCCTTGAACAGCGAC AGC	19354696	2	210—238	淀粉分支酶基因Ⅲ Starch branching enzyme Ⅲ	NCBI序列比对 NCBI Sequence Alignment
InDel-36	F: CACCAATTATATTAGCGT GCTCC	R: CGTGGCTCTTGGCTCTC TTG	20066321	4	233—255	淀粉分支酶基因Ⅳ Starch branching enzyme Ⅳ	[23]

Continued Table 1

Fig. 1

Fig. 2

Table 2

DNA fingerprint database of 20 semi-waxy japonica varieties"

品种 Variety	指纹信息 Fingerprint information
南粳46 Nanjing 46 (D1)	01100-11001-01000-10010-01010-00000-10001-00010-00100-01000-01001-00101-01010-10101-10010-10110-01100-10110-01010-10110-01100-11010-10100-10101-00101-10101-01010-01011-01001-10101-00110
南粳5055 Nanjing 5055 (D2)	01100-11001-00100-01001-00110-00000-10010-00010-01001-00000-10000-11001-01011-00101-01010-10110-01011-01010-01011-01010-01100-11010-10100-10101-01001-10101-00110-01100-10110-10011-01010
南粳9108 Nanjing 9108 (D3)	10100-11001-00100-10010-01010-00000-10001-00010-01000-10001-00001-00101-10010-10101-10100-10101-01100-11010-01010-10110-01100-11010-10100-10101-00101-10101-01010-10100-10101-01100-11010
南粳505 Nanjing 505 (D4)	01100-11000-10100-10001-01010-00000-10010-00011-00001-00000-01001-00101-01011-00110-10100-10110-10101-01010-00010-11010-01100-11010-01001-10011-00101-10101-00101-10100-10110-10101-00110
南粳2728 Nanjing 2728 (D5)	01100-11001-01000-01001-01000-01000-10001-00011-00000-01000-00100-10101-10100-10110-10100-10101-01010-10110-11010-10110-10100-11010-01001-10011-00101-01101-01001-10100-11001-10011-00110
南粳5718 Nanjing 5718 (D6)	10010-11001-00100-01001-00100-10001-00000-10100-10000-00100-10001-01001-01011-00110-01010-10110-10100-10110-00010-11010-01011-01010-10100-10101-00101-10101-00110-01100-11001-01100-11010
南粳56 Nanjing 56 (D7)	01100-10011-01000-10000-11001-00000-10000-11000-01010-00001-00000-10101-01100-11010-10100-10101-01100-11010-00010-10110-01100-11010-10100-01101-00101-10101-01010-01100-10110-01100-11010
南粳9308 Nanjing 9308 (D8)	10100-10101-01000-10000-11010-00000-10000-10010-10000-10000-10001-00101-10010-10101-10100-10101-01100-10110-01010-10110-10100-11010-10100-10101-00101-10101-01010-01011-00110-01011-00110
南粳9036 Nanjing 9036 (D9)	01100-11001-00010-01001-01001-00000-10010-00011-00001-00000-01000-10110-01101-00110-10101-01010-10101-00110-11010-11010-01100-11010-01010-10010-11010-10101-00110-10100-11001-10100-11001
南粳7718 Nanjing 7718 (D10)	10100-10101-00100-10010-01000-00010-10001-00011-00000-10000-10000-10101-10010-10101-10010-10101-01100-10110-01010-10110-10100-11010-10100-10101-00101-10101-01010-01010-10110-01011-00110
嘉58 Jia 58 (D11)	01100-11001-01000-10001-01001-00001-00001-00011-00001-00000-10001-01001-01011-00110-01100-11001-10010-10110-01011-00110-01100-11010-10010-10100-11010-10101-00101-01011-01001-10101-00110
沪早香软1号 Huzaoxiangruan 1 (D12)	01100-10101-01000-01001-00101-00000-10001-00010-01001-00000-01001-01001-01010-10101-01011-01010-01100-11010-00010-10101-01100-11010-10100-10101-00101-10100-11001-01010-10110-10101-00110
武香粳113 Wuxiangjing 113 (D13)	01100-11001-01000-01001-01000-10000-10000-10011-00000-00010-01001-00101-01101-00101-10011-01010-10100-11001-11100-10110-01100-11010-10100-10101-00110-10101-00110-01011-00101-10100-11010
金香玉1号 Jinxiangyu 1 (D14)	10100-11001-00100-10010-01010-00000-10001-00010-01000-10001-00000-11001-10010-10101-10100-10101-01100-11010-01100-10110-01100-11010-10100-10100-10110-10101-01010-01010-11010-10010-10101
苏香粳100 Suxiangjing 100 (D15)	01010-11001-00100-10010-00100-10001-00001-00100-10000-10000-00100-11001-01010-10101-01010-10101-10100-11010-11010-10110-10100-11010-10100-10101-00101-10100-11010-01010-10110-10011-01010
宁粳8号 Ningjing 8 (D16)	10100-11001-01000-01001-01000-01001-00001-00011-00000-00010-10000-11001-01100-10110-01100-10110-10101-01010-10010-11010-10011-00110-10100-10101-00101-10101-00110-01101-00110-10011-00110
徐稻9号 Xudao 9 (D17)	01101-01001-01000-00101-00101-00000-10000-10010-00101-00000-10001-00101-01101-00110-10010-10110-10100-10110-00010-10110-01100-11010-10100-10101-00110-10100-10110-01100-11010-01101-00110
沪软1212 Huruan 1212 (D18)	10101-01000-11000-10001-00110-00000-10000-10100-10000-10000-10001-01001-01011-00101-01100-10101-01100-10110-00100-11010-01100-11010-10100-10101-00101-10100-10110-01011-01001-10101-01010
苏香粳3号 Suxiangjing 3 (D19)	10101-01001-00101-00001-00100-00101-00001-00010-00100-01000-00011-01001-01010-10101-10010-10110-01100-10110-10100-10110-10100-11010-10100-10101-01001-10101-01001-01011-00101-01100-10110
早香粳1号 Zaoxiangjing 1 (D20)	10100-11001-01000-01001-01000-10001-00100-00010-10001-00000-00101-01001-01011-00101-10010-10110-01100-10110-01010-10110-10010-11010-10100-10101-01010-10010-10110-01101-00101-01101-01010

Table 2

Fig. 3

Table 3

DNA fingerprint database of 14 other semi-waxy japonica varieties"

品种 Variety	指纹信息 Fingerprint information
南粳晶谷 Nanjing jinggu (D21)	01100-11001-01000-10001-01010-00000-10001-00010-00101-00000-10001-00110-01011-00101-01100-11010-10101-01010-01010-11010-01100-11010-10100-10101-00101-10101-00110-01100-11010-10101-00110
南粳518 Nanjing 518 (D22)	01100-11001-00010-01001-01000-10000-01000-10010-00100-01001-00000-11001-01100-11001-10100-10110-01100-10110-11010-10110-10100-11010-10100-10101-00101-10101-00110-01100-10101-10011 -01010
南粳3908 Nanjing 3908 (D23)	01100-11001-00100-01001-01000-00100-10000-10011-00010-00000-10001-01001-01011-00101-01100-10110-10101-01010-01010-11010-01100-11010-10100-10101-00101-10101-00110-01100-11010-10101-00110
南粳5713 Nanjing 5713 (D24)	01100-11001-01000-01001-01010-00000-10000-10010-01001-00001-00001-00110-01010-10101-01011-01010-01100-10110-11010-10110-10100-11010-10100-10101-00101-10101-01010-01011-01001-10101-00110
南粳66 Nanjing 66 (D25)	10100-10101-01000-10010-01000-00100-10000-11000-01000-01000-01000-10101-10010-10101-10100-10110-01100-10110-01010-10110-01100-11010-10100-10101-00101-10101-01010-01100-10110-10011-00110
南粳5818 Nanjing 5818 (D26)	10100-11001-00100-10010-01000-00010-10001-00011-00000-01000-10000-10101-10010-10101-10100-10101-01100-11010-01010-10110-01100-11010-10100-10100-10110-10101-01010-10100-11001-01100-11001
松早香1号 Songzaoxiang 1 (D27)	10101-01001-01000-01001-01010-00000-10000-10011-00001-00000-10000-11010-01011-00101-10010-11010-01010-10110-11101-01010-10100-11001-10100-10100-11010-10101-01001-01011-00110-01100-10110
嘉农早香 Jianongzaoxiang (D28)	10101-01001-00100-10010-01000-10001-00001-00011-00010-00001-00001-01001-01010-10110-10010-10110-01100-10110-10010-10110-10100-11010-10100-01100-11010-10101-01001-01101-01001-01011-00101
松香粳1018 Songxiangjing 1018 (D29)	01100-10101-01000-01010-01000-01001-00001-01001-00001-00001-00000-10110-01100-10101-01101-01010-10100-10110-11010-10110-10100-11010-10100-10101-00101-10100-10110-01100-10101-10101-01001
嘉农粳6号 Jianongjing 6 (D30)	10100-11000-11001-00001-01001-00000-10100-00010-10001-00001-00001-00101-01011-00101-10101-01010-01100-10110-00010-10110-01100-11010-10100-10101-00101-01100-11010-01011-01001-01100-10110
宁香粳9号 Ningxiangjing 9 (D31)	01100-11001-01000-00101-00100-01000-10000-10101-00000-00010-00010-10101-10100-10110-10100-10110-10100-10110-10010-10110-10010-11010-10100-10101-00101-10010-10110-01100-10110-01011-00110
扬农香粳28 Yangnongxiangjing 28 (D32)	10010-11001-01000-10010-01000-00101-00001-00010-01000-01000-10000-11001-10100-10101-01100-10110-01100-11010-11100-10110-01100-11010-10100-10101-01001-10100-11010-10011-01001-10100-11001
丰粳1606 Fengjing 1606 (D33)	10100-10011-01000-00101-01001-00000-10010-00011-00000-10000-10001-01001-10101-00101-01100-11010-10101-01010-01010-11010-10100-11010-10100-10101-01001-10010-10110-01101-00110-01011-01010
常香粳1813 Changxiangjing 1813 (D34)	01010-10101-00100-10010-01000-10000-10001-00100-10001-00000-00100-10101-10010-10110-01100-10101-10100-10110-01010-10110-10100-11010-10100-10101-00101-10100-10110-01100-11001-10101-00110

Table 3

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Screening of Core Markers and Construction of DNA Fingerprints of Semi-Waxy Japonica Rice Varieties

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