Development and Application of Insertion-Deletion（InDel）Markers in Papaya（Carica papaya）Based on Whole Genome Re-Sequencing Data

doi:10.16420/j.issn.0513-353x.2024-0850

Acta Horticulturae Sinica ›› 2025, Vol. 52 ›› Issue (10): 2597-2612.doi: 10.16420/j.issn.0513-353x.2024-0850

• Genetic & Breeding·Germplasm Resources·Molecular Biology • Previous Articles Next Articles

Development and Application of Insertion-Deletion（InDel）Markers in Papaya（Carica papaya）Based on Whole Genome Re-Sequencing Data

YANG Min, HE Han, ZHOU Chenping, KUANG Ruibin, LIU Chuanhe, WU Xiaming, XU Ze, WEI Yuerong^**()

Guangdong Provincial Key Laboratory of Science and Technology Research on Fruit Tree；Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization，Ministry of Agriculture and Rural Affairs；Institute of Fruit Tree Research，Guangdong Academy of Agricultural Sciences，Guangzhou 510640，China

Received:2025-03-02 Revised:2025-07-28 Online:2025-10-25 Published:2025-10-28
Contact: WEI Yuerong

Abstract

Abstract:

InDel（insertion/deletion）loci were mined using resequencing data of 5 papaya germplasm resources，and efficient and applicable molecular markers were designed based on these loci. After strict screening，3 635 InDel loci that are easy to detect by gel electrophoresis，with a length of more than 30 bp and showing high polymorphism were successfully identified. 360 loci evenly distributed across the genome were selected to design primers. After preliminary screening with 6 papaya materials，it was found that 355 pairs of primers could successfully amplify the target products，among which 271 pairs showed significant polymorphism，accounting for 75.3% of the total number of candidate primers. 72 pairs of highly polymorphic markers were selected for genotyping and genetic diversity analysis of 47 papayagermplasms，and a total of 145 allelic loci were detected. The polymorphism information content （PIC）of the markers ranged from 0.0408 to 0.4523，with an average of 0.3041；the gene diversity index varied from 0.1030 to 0.8735，with an average of 0.5660. Through cluster analysis，the 47 papaya accessions were divided into 4 groups. In addition，based on the amplification results of 20 pairs of highly polymorphic core InDel markers，combined with 4 key agronomic traits（flower color，single fruit weight，fruit shape，and flesh color），molecular identities of different papaya germplasms were constructed. Meanwhile，two InDel markers that can reflect the differences between parents were selected to identify the authenticity of 24 F₁ hybrid progenies of GT1-5 ×‘Huangjinzhong’papaya，and 11 true hybrids were successfully confirmed.

Key words: papaya, InDel marker, genetic diversity, verification of F₁ generation, molecular ID

YANG Min, HE Han, ZHOU Chenping, KUANG Ruibin, LIU Chuanhe, WU Xiaming, XU Ze, WEI Yuerong. Development and Application of Insertion-Deletion（InDel）Markers in Papaya（Carica papaya）Based on Whole Genome Re-Sequencing Data[J]. Acta Horticulturae Sinica, 2025, 52(10): 2597-2612.

Figures/Tables 10

References 41

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染色体编号 Chrosome labels	标记引物数 Number of InDel primers	有效引物数 Number of effective primers	有效扩增率/% Effective amplification ratios	多态引物数 Number of polymorphic primers	引物多态率/% Polymorphic primer ratios
Chr1	40	36	90.0	31	77.5
Chr2	40	40	100.0	34	85.0
Chr3	40	39	97.5	31	77.5
Chr4	40	40	100.0	32	80.0
Chr5	40	40	100.0	28	70.0
Chr6	40	40	100.0	27	67.5
Chr7	40	40	100.0	28	70.0
Chr8	40	40	100.0	29	72.5
Chr9	40	40	100.0	31	77.5
合计Total	360	355	98.6	271	75.3

染色体编号 Chrosome labels	标记引物数 Number of InDel primers	有效引物数 Number of effective primers	有效扩增率/% Effective amplification ratios	多态引物数 Number of polymorphic primers	引物多态率/% Polymorphic primer ratios
Chr1	40	36	90.0	31	77.5
Chr2	40	40	100.0	34	85.0
Chr3	40	39	97.5	31	77.5
Chr4	40	40	100.0	32	80.0
Chr5	40	40	100.0	28	70.0
Chr6	40	40	100.0	27	67.5
Chr7	40	40	100.0	28	70.0
Chr8	40	40	100.0	29	72.5
Chr9	40	40	100.0	31	77.5
合计Total	360	355	98.6	271	75.3

标记号 InDel labels	标记类型 Type	差异长度/bp Length	上游扩增引物（5′-3′） Forward primer	下游扩增引物（5′-3′） Reverse primer	标记引物扩增位置 Amplification location
Chr1-09	插入 Insertion	35	ACCTTGACATACATGCATGCA	TGCCTTGAGTCACACGGA	Chr1:2749817-2750039
Chr1-10	插入 Insertion	36	GAACCTCCTCCCCCGCTA	TGAACCACCTGCTCGCAT	Chr1:2857128-2857366
Chr1-15	插入 Insertion	49	TGTTCCATGTGTTATGGACGT	ACAAGCTTGGTGCATATGCT	Chr1:3213152-3213384
Chr1-26	缺失 Deletion	-46	CGCCCTCTCCCGTAAAGC	ACCACAGGTACTTGGCCG	Chr1:7259239-7259506
Chr1-29	缺失 Deletion	-30	CGTGAGGTGCTCGCTGAT	GGGACATCTCGTGCACGT	Chr1:7846667-7846868
Chr1-30	插入 Insertion	42	GAACGCAAAAGACTGACTCCT	AGGTTCTGAAGACATGCACTT	Chr1:8015769-8016044
Chr1-39	插入 Insertion	39	GTCCTCAGGACGACCCTAGA	ATCTGGTGGCAGTGGCAG	Chr1:10631445-10631724
Chr2-01	插入 Insertion	37	GCTCCAACGAGAGAGATGACT	CGGTGCTGGTGACGAAGA	Chr2:307044-307320
Chr2-02	插入 Insertion	31	CAGGATTTTGCTAGGGTCAGT	AGACTTGCCTGCTGGAGC	Chr2:612393-612613
Chr2-13	缺失 Deletion	-34	ACCAACCGTCGATCCTCA	TGGCAAAACGTCGTGATGT	Chr2:5215597-5215796
Chr2-15	插入 Insertion	44	TGCTGGGAATGCTTTGTGC	TGGTCCATGATGCCAGCTG	Chr2:5922591-5922860
Chr2-18	插入 Insertion	44	GGTTAGACTGTCAAGTGGGCT	CGCCCTGAAAACATGGTGC	Chr2:10719434-10719712
Chr2-20	缺失 Deletion	-31	ACAACCTGAGAGCTCTTCCC	AGCTGCTTCTACCTGCTTGA	Chr2:12083278-12083527
Chr2-29	插入 Insertion	48	TGGAATCAAGATTTGCACCGA	TTCCAGTTTCCGAACAACCA	Chr2:23526410-23526648
Chr2-31	缺失 Deletion	-33	GGCAGCACTTCATTGCCG	GGGTCTTACACTGGTTGCCA	Chr2:28941802-28942025
Chr2-38	插入 Insertion	38	ACGAGTCTTCAAGCTTGCCA	TGCCAGTCTGTAAATTGCGG	Chr2:34031300-34031578
Chr3-03	插入 Insertion	48	GCCAACACAAGAACGGAAACT	TGCAGTTCAAGTGGCGCT	Chr3:627145-627348
Chr3-17	缺失 Deletion	-44	CTCCTGCACAGTCGCCAT	GCTTGCTTTGCTCTCCGC	Chr3:6901713-6901929
Chr3-21	缺失 Deletion	-46	CCCTTCCCCCTCCCAAGA	TTCTGCCGTCGGTTGAGC	Chr3:10826323-10826544
Chr3-22	插入 Insertion	39	TCCCGGACATCTGACCCC	AGCCTTTGATTCCCACTGCA	Chr3:10886342-10886562
Chr3-23	插入 Insertion	31	GGAGCACAAGCCATGGGT	AGCCACCAGTCAGACCTCT	Chr3:11351904-11352128
Chr3-30	插入 Insertion	34	ACGGTGACAGCATGAGGC	CACATGCAAGATGCCGGC	Chr3:16193105-16193338
Chr3-31	插入 Insertion	42	AGCCAACCCACCACAAGT	CTCAGCCTATTTGTTGGTCCA	Chr3:16707449-16707694
Chr3-33	插入 Insertion	33	TGCTGGAAAACACCCGCA	GCCTCCCCAAGTCAGCTG	Chr3:21024394-21024593
Chr4-03	缺失 Deletion	-33	CCAGCATCAGAACTCGAGGT	TTGGTTGCGGGGAATGCA	Chr4:1324489-1324712
Chr4-08	插入 Insertion	42	CGAGCCTGTGTACCTGGT	TCACTTTCGTCAGTTGCCTGA	Chr4:4076944-4077153
Chr4-14	插入 Insertion	41	GCGGTGAGCCTGAGATGA	AGACTCGTGGAGAACAAAGCA	Chr4:9192243-9192474
Chr4-24	缺失 Deletion	-40	ACGGGGCGTACATGTGTG	ACGAGGCCACCCCTAAGA	Chr4:21621919-21622128
Chr4-25	插入 Insertion	45	TGGTTTCGCAAGTTCGCA	GTGCTAGTTGTTTTGCATGCT	Chr4:22997264-22997514
Chr4-26	缺失 Deletion	-46	AGAGGGGTTAGGCAGGGG	TCCCCACATTGATGTTGACCA	Chr4:23149465-23149734
Chr4-34	缺失 Deletion	-32	TCACGAGTTGAGGGAGGTCT	ACTTGTTGAGGGTTGAAAGCC	Chr4:28955964-28956194
Chr4-40	插入 Insertion	46	GACGTGGTGCTTATCCCGT	GGCAGTCCAGTTCTATAGGGG	Chr4:34041449-34041703
Chr5-02	缺失 Deletion	-49	TGCGCACAACATTCAGGTC	GGCTATGTTGTGCCTGGGA	Chr5:59655-59828
Chr5-07	插入 Insertion	38	TGAGTGGAAAGAAGATGCGGA	TCATCCCTCCATCCACAAACT	Chr5:272642-272800
Chr5-08	缺失 Deletion	-34	GACAAAGCAAAACTGCATCGT	TGATTTGGCAGCCCCTGG	Chr5:699745-699920
Chr5-11	缺失 Deletion	-35	GCGGCAATCAGAGGAGCA	GCACCACACAGACAAAAATCA	Chr5:1024290-1024446
Chr5-15	缺失 Deletion	-33	TGGGAGGTAGCTGACGGA	CAGCATGCCTAACCGTGC	Chr5:1509285-1509412
Chr5-18	缺失 Deletion	-33	GACTCCGATGATGTCCTCTGT	CGTGAAGGAAATCGGTGTGC	Chr5:1615976-1616100
Chr5-24	插入 Insertion	31	GGGCTTGAGTTTGGGCCT	CCCAGTCCCATACCCCGA	Chr5:44035468-44035705
Chr5-29	缺失 Deletion	-42	GGAGGAAATTTTGGCTTGGGG	ACCAAAAACATGGAACCACCT	Chr5:44418169-44418332
Chr5-30	插入 Insertion	34	GCAACTGTCTGATCCTTTGGG	ACTTCGCATTTCAGGGGAGA	Chr5:45207382-45207589
Chr6-09	缺失 Deletion	-38	CTAGACGCCCACGAAGCC	TCTTCCCTCTGCCGACCA	Chr6:9710183-9710427
Chr6-10	插入 Insertion	46	ACATGCATGCCTAGTCACGA	GGGTTGTTGGAAGGGTCCT	Chr6:10024162-10024384
Chr6-27	插入 Insertion	45	ATGTTGGGTCGCAGTGGC	AGGGCGGAGGGGATTTCT	Chr6:26274037-26274275
Chr6-28	缺失 Deletion	-32	TGAAAACAACTGCGAAACACT	ACTTCAGATGGGTACTTCTGC	Chr6:26872028-26872241
Chr6-29	缺失 Deletion	-44	CGGCAAGAGGAGAAGGGC	GGGGTTTCCAAGGAAGGGG	Chr6:28571296-28571513
Chr6-32	缺失 Deletion	-43	ACGCTAATGTTGCCGCCA	CGTCGAGCTTTACCCGCA	Chr6:33681522-33681724
Chr7-01	插入 Insertion	37	TGCTCGGACGACCACAAC	AGTGGCCAACGAGCAGAG	Chr7:12591-12775
Chr7-02	缺失 Deletion	-47	GCAGCGGCCAATGCTAAG	GGGTGGTTGATGCTTCGC	Chr7:30560-30830
Chr7-06	插入 Insertion	31	GGGGTTTAGCGTGGGTCC	AATGGCTGGTCTCACGCG	Chr7:449549-449763
Chr7-12	缺失 Deletion	-46	TGCATAAGGTCTGGAGACTGT	ACCCGAGCTACACCACAA	Chr7:2509875-2510036
Chr7-19	缺失 Deletion	-41	GCCTAGAGCCTCCAAACCA	GGAGATCCCTGTGCTGCC	Chr7:5959628-5959858
Chr7-21	缺失 Deletion	-45	ACTGAGTGAGCGATGGCAC	TGGGATGGCAGTAAAGCGG	Chr7:6662961-6663207
Chr7-24	缺失 Deletion	-49	ACCCTGGCTAAACGCGTC	ATGGGGGCGGGTCAACTA	Chr7:8693948-8694111
Chr7-28	插入 Insertion	33	ACTCGTGTTCCCCAAAACA	ACCTATCAATTCTCCCGTCGA	Chr7:11076056-11076250
Chr7-35	缺失 Deletion	-38	AGAACCCCATCAACGGAAACT	ACCTTCCCACCTCACTCGT	Chr7:15440638-15440766
Chr8-09	缺失 Deletion	-42	ATCAGGCAAATGCATGGTTGA	AACCATCCTGGACCCGGA	Chr8:1320235-1320497
Chr8-16	缺失 Deletion	-47	TGGCTCCACAATCTGGCA	TGCCAACTGGTTTCCTCTTTC	Chr8:3251541-3251789
Chr8-18	缺失 Deletion	-44	CCCGCCTTTTCCACGTGA	AGTCATTCTGGTTCGGGTTGA	Chr8:3574827-3575078
Chr8-19	缺失 Deletion	-42	GCTTGCGGCAATTGGTTTC	ACGAGGATTGACAGGCAGC	Chr8:3680573-3680739
Chr8-26	缺失 Deletion	-46	AGTGGCAAGCAGTGTAGGA	CTTTCACTGCCGGGGAGT	Chr8:6135649-6135902
Chr8-29	插入 Insertion	44	ACATCAGCTGCTCATTCCAT	TTGTACAGTCCCAAGTTGTGT	Chr8:7246002-7246208
Chr8-30	缺失 Deletion	-33	TGAAGGCCCCAGTTTTCCA	TGCATGTATTCGACCTTGTGG	Chr8:7761356-7761536
Chr8-32	插入 Insertion	36	ACACTGCACTGCACTAGCT	GGCCAGTTTAGCCCGTCT	Chr8:8396708-8396836
Chr9-09	缺失 Deletion	-32	TCCGTTAACGCTCCGCAG	TGTGGTGGTTCTCTCCTTGTG	Chr9:5206000-5206184
Chr9-15	插入 Insertion	45	CGACATGCAAGGAACTGGG	GACTTGGGTGCCGAAGCT	Chr9:6742034-6742244
Chr9-17	缺失 Deletion	-34	GGCGTTGTATGGCTCACG	GAGATTGCTCAGGTGTGGGA	Chr9:8310123-8310248
Chr9-22	插入 Insertion	30	CCAACACCCCATTCCCCA	TGCACTAGACTCCTCCATCCA	Chr9:9397358-9397476
Chr9-25	缺失 Deletion	-31	CTTGTCCACGCGTGAGGT	GCTCGTCCCCTTTGCACA	Chr9:12450328-12450471
Chr9-26	缺失 Deletion	-39	CCGGTATCACTGAGGGCC	CAGTCGTGTGGAGTTGGGA	Chr9:14289457-14289653
Chr9-27	缺失 Deletion	-31	CTAGCACCAGGCCGTCAG	CCGCTGCACCTGGAGAAA	Chr9:14871648-14871817
Chr9-31	缺失 Deletion	-45	AGTTAGCCCATGCGCGTT	AGGGCCTCCTCCACTGAC	Chr9:27896823-27896950

标记号 InDel labels	标记类型 Type	差异长度/bp Length	上游扩增引物（5′-3′） Forward primer	下游扩增引物（5′-3′） Reverse primer	标记引物扩增位置 Amplification location
Chr1-09	插入 Insertion	35	ACCTTGACATACATGCATGCA	TGCCTTGAGTCACACGGA	Chr1:2749817-2750039
Chr1-10	插入 Insertion	36	GAACCTCCTCCCCCGCTA	TGAACCACCTGCTCGCAT	Chr1:2857128-2857366
Chr1-15	插入 Insertion	49	TGTTCCATGTGTTATGGACGT	ACAAGCTTGGTGCATATGCT	Chr1:3213152-3213384
Chr1-26	缺失 Deletion	-46	CGCCCTCTCCCGTAAAGC	ACCACAGGTACTTGGCCG	Chr1:7259239-7259506
Chr1-29	缺失 Deletion	-30	CGTGAGGTGCTCGCTGAT	GGGACATCTCGTGCACGT	Chr1:7846667-7846868
Chr1-30	插入 Insertion	42	GAACGCAAAAGACTGACTCCT	AGGTTCTGAAGACATGCACTT	Chr1:8015769-8016044
Chr1-39	插入 Insertion	39	GTCCTCAGGACGACCCTAGA	ATCTGGTGGCAGTGGCAG	Chr1:10631445-10631724
Chr2-01	插入 Insertion	37	GCTCCAACGAGAGAGATGACT	CGGTGCTGGTGACGAAGA	Chr2:307044-307320
Chr2-02	插入 Insertion	31	CAGGATTTTGCTAGGGTCAGT	AGACTTGCCTGCTGGAGC	Chr2:612393-612613
Chr2-13	缺失 Deletion	-34	ACCAACCGTCGATCCTCA	TGGCAAAACGTCGTGATGT	Chr2:5215597-5215796
Chr2-15	插入 Insertion	44	TGCTGGGAATGCTTTGTGC	TGGTCCATGATGCCAGCTG	Chr2:5922591-5922860
Chr2-18	插入 Insertion	44	GGTTAGACTGTCAAGTGGGCT	CGCCCTGAAAACATGGTGC	Chr2:10719434-10719712
Chr2-20	缺失 Deletion	-31	ACAACCTGAGAGCTCTTCCC	AGCTGCTTCTACCTGCTTGA	Chr2:12083278-12083527
Chr2-29	插入 Insertion	48	TGGAATCAAGATTTGCACCGA	TTCCAGTTTCCGAACAACCA	Chr2:23526410-23526648
Chr2-31	缺失 Deletion	-33	GGCAGCACTTCATTGCCG	GGGTCTTACACTGGTTGCCA	Chr2:28941802-28942025
Chr2-38	插入 Insertion	38	ACGAGTCTTCAAGCTTGCCA	TGCCAGTCTGTAAATTGCGG	Chr2:34031300-34031578
Chr3-03	插入 Insertion	48	GCCAACACAAGAACGGAAACT	TGCAGTTCAAGTGGCGCT	Chr3:627145-627348
Chr3-17	缺失 Deletion	-44	CTCCTGCACAGTCGCCAT	GCTTGCTTTGCTCTCCGC	Chr3:6901713-6901929
Chr3-21	缺失 Deletion	-46	CCCTTCCCCCTCCCAAGA	TTCTGCCGTCGGTTGAGC	Chr3:10826323-10826544
Chr3-22	插入 Insertion	39	TCCCGGACATCTGACCCC	AGCCTTTGATTCCCACTGCA	Chr3:10886342-10886562
Chr3-23	插入 Insertion	31	GGAGCACAAGCCATGGGT	AGCCACCAGTCAGACCTCT	Chr3:11351904-11352128
Chr3-30	插入 Insertion	34	ACGGTGACAGCATGAGGC	CACATGCAAGATGCCGGC	Chr3:16193105-16193338
Chr3-31	插入 Insertion	42	AGCCAACCCACCACAAGT	CTCAGCCTATTTGTTGGTCCA	Chr3:16707449-16707694
Chr3-33	插入 Insertion	33	TGCTGGAAAACACCCGCA	GCCTCCCCAAGTCAGCTG	Chr3:21024394-21024593
Chr4-03	缺失 Deletion	-33	CCAGCATCAGAACTCGAGGT	TTGGTTGCGGGGAATGCA	Chr4:1324489-1324712
Chr4-08	插入 Insertion	42	CGAGCCTGTGTACCTGGT	TCACTTTCGTCAGTTGCCTGA	Chr4:4076944-4077153
Chr4-14	插入 Insertion	41	GCGGTGAGCCTGAGATGA	AGACTCGTGGAGAACAAAGCA	Chr4:9192243-9192474
Chr4-24	缺失 Deletion	-40	ACGGGGCGTACATGTGTG	ACGAGGCCACCCCTAAGA	Chr4:21621919-21622128
Chr4-25	插入 Insertion	45	TGGTTTCGCAAGTTCGCA	GTGCTAGTTGTTTTGCATGCT	Chr4:22997264-22997514
Chr4-26	缺失 Deletion	-46	AGAGGGGTTAGGCAGGGG	TCCCCACATTGATGTTGACCA	Chr4:23149465-23149734
Chr4-34	缺失 Deletion	-32	TCACGAGTTGAGGGAGGTCT	ACTTGTTGAGGGTTGAAAGCC	Chr4:28955964-28956194
Chr4-40	插入 Insertion	46	GACGTGGTGCTTATCCCGT	GGCAGTCCAGTTCTATAGGGG	Chr4:34041449-34041703
Chr5-02	缺失 Deletion	-49	TGCGCACAACATTCAGGTC	GGCTATGTTGTGCCTGGGA	Chr5:59655-59828
Chr5-07	插入 Insertion	38	TGAGTGGAAAGAAGATGCGGA	TCATCCCTCCATCCACAAACT	Chr5:272642-272800
Chr5-08	缺失 Deletion	-34	GACAAAGCAAAACTGCATCGT	TGATTTGGCAGCCCCTGG	Chr5:699745-699920
Chr5-11	缺失 Deletion	-35	GCGGCAATCAGAGGAGCA	GCACCACACAGACAAAAATCA	Chr5:1024290-1024446
Chr5-15	缺失 Deletion	-33	TGGGAGGTAGCTGACGGA	CAGCATGCCTAACCGTGC	Chr5:1509285-1509412
Chr5-18	缺失 Deletion	-33	GACTCCGATGATGTCCTCTGT	CGTGAAGGAAATCGGTGTGC	Chr5:1615976-1616100
Chr5-24	插入 Insertion	31	GGGCTTGAGTTTGGGCCT	CCCAGTCCCATACCCCGA	Chr5:44035468-44035705
Chr5-29	缺失 Deletion	-42	GGAGGAAATTTTGGCTTGGGG	ACCAAAAACATGGAACCACCT	Chr5:44418169-44418332
Chr5-30	插入 Insertion	34	GCAACTGTCTGATCCTTTGGG	ACTTCGCATTTCAGGGGAGA	Chr5:45207382-45207589
Chr6-09	缺失 Deletion	-38	CTAGACGCCCACGAAGCC	TCTTCCCTCTGCCGACCA	Chr6:9710183-9710427
Chr6-10	插入 Insertion	46	ACATGCATGCCTAGTCACGA	GGGTTGTTGGAAGGGTCCT	Chr6:10024162-10024384
Chr6-27	插入 Insertion	45	ATGTTGGGTCGCAGTGGC	AGGGCGGAGGGGATTTCT	Chr6:26274037-26274275
Chr6-28	缺失 Deletion	-32	TGAAAACAACTGCGAAACACT	ACTTCAGATGGGTACTTCTGC	Chr6:26872028-26872241
Chr6-29	缺失 Deletion	-44	CGGCAAGAGGAGAAGGGC	GGGGTTTCCAAGGAAGGGG	Chr6:28571296-28571513
Chr6-32	缺失 Deletion	-43	ACGCTAATGTTGCCGCCA	CGTCGAGCTTTACCCGCA	Chr6:33681522-33681724
Chr7-01	插入 Insertion	37	TGCTCGGACGACCACAAC	AGTGGCCAACGAGCAGAG	Chr7:12591-12775
Chr7-02	缺失 Deletion	-47	GCAGCGGCCAATGCTAAG	GGGTGGTTGATGCTTCGC	Chr7:30560-30830
Chr7-06	插入 Insertion	31	GGGGTTTAGCGTGGGTCC	AATGGCTGGTCTCACGCG	Chr7:449549-449763
Chr7-12	缺失 Deletion	-46	TGCATAAGGTCTGGAGACTGT	ACCCGAGCTACACCACAA	Chr7:2509875-2510036
Chr7-19	缺失 Deletion	-41	GCCTAGAGCCTCCAAACCA	GGAGATCCCTGTGCTGCC	Chr7:5959628-5959858
Chr7-21	缺失 Deletion	-45	ACTGAGTGAGCGATGGCAC	TGGGATGGCAGTAAAGCGG	Chr7:6662961-6663207
Chr7-24	缺失 Deletion	-49	ACCCTGGCTAAACGCGTC	ATGGGGGCGGGTCAACTA	Chr7:8693948-8694111
Chr7-28	插入 Insertion	33	ACTCGTGTTCCCCAAAACA	ACCTATCAATTCTCCCGTCGA	Chr7:11076056-11076250
Chr7-35	缺失 Deletion	-38	AGAACCCCATCAACGGAAACT	ACCTTCCCACCTCACTCGT	Chr7:15440638-15440766
Chr8-09	缺失 Deletion	-42	ATCAGGCAAATGCATGGTTGA	AACCATCCTGGACCCGGA	Chr8:1320235-1320497
Chr8-16	缺失 Deletion	-47	TGGCTCCACAATCTGGCA	TGCCAACTGGTTTCCTCTTTC	Chr8:3251541-3251789
Chr8-18	缺失 Deletion	-44	CCCGCCTTTTCCACGTGA	AGTCATTCTGGTTCGGGTTGA	Chr8:3574827-3575078
Chr8-19	缺失 Deletion	-42	GCTTGCGGCAATTGGTTTC	ACGAGGATTGACAGGCAGC	Chr8:3680573-3680739
Chr8-26	缺失 Deletion	-46	AGTGGCAAGCAGTGTAGGA	CTTTCACTGCCGGGGAGT	Chr8:6135649-6135902
Chr8-29	插入 Insertion	44	ACATCAGCTGCTCATTCCAT	TTGTACAGTCCCAAGTTGTGT	Chr8:7246002-7246208
Chr8-30	缺失 Deletion	-33	TGAAGGCCCCAGTTTTCCA	TGCATGTATTCGACCTTGTGG	Chr8:7761356-7761536
Chr8-32	插入 Insertion	36	ACACTGCACTGCACTAGCT	GGCCAGTTTAGCCCGTCT	Chr8:8396708-8396836
Chr9-09	缺失 Deletion	-32	TCCGTTAACGCTCCGCAG	TGTGGTGGTTCTCTCCTTGTG	Chr9:5206000-5206184
Chr9-15	插入 Insertion	45	CGACATGCAAGGAACTGGG	GACTTGGGTGCCGAAGCT	Chr9:6742034-6742244
Chr9-17	缺失 Deletion	-34	GGCGTTGTATGGCTCACG	GAGATTGCTCAGGTGTGGGA	Chr9:8310123-8310248
Chr9-22	插入 Insertion	30	CCAACACCCCATTCCCCA	TGCACTAGACTCCTCCATCCA	Chr9:9397358-9397476
Chr9-25	缺失 Deletion	-31	CTTGTCCACGCGTGAGGT	GCTCGTCCCCTTTGCACA	Chr9:12450328-12450471
Chr9-26	缺失 Deletion	-39	CCGGTATCACTGAGGGCC	CAGTCGTGTGGAGTTGGGA	Chr9:14289457-14289653
Chr9-27	缺失 Deletion	-31	CTAGCACCAGGCCGTCAG	CCGCTGCACCTGGAGAAA	Chr9:14871648-14871817
Chr9-31	缺失 Deletion	-45	AGTTAGCCCATGCGCGTT	AGGGCCTCCTCCACTGAC	Chr9:27896823-27896950

标记号 InDel labels	等位基因数（N_a） Number of alleles	有效等位基因数（N_e） Effective number of alleles	基因多样性指数（H） Gene diversity index	多态性信息含量（PIC） Polymorphic information content	遗传距离（Nei’s） Nei’s genetic distance	标记号 InDel labels	等位基因数（N_a） Number of alleles	有效等位基因数（N_e） Effective number of alleles	基因多样性指数（H） Gene diversity index	多态性信息含量（PIC） Polymorphic information content	遗传距离（Nei’s） Nei’s genetic distance
Chr1-09	2.00	1.8579	0.6544	0.3551	0.4617	Chr5-29	2.00	1.2605	0.3609	0.1853	0.2067
Chr1-10	2.00	1.9991	0.6929	0.3749	0.4998	Chr5-30	2.00	1.2865	0.3819	0.1979	0.2227
Chr1-15	2.00	1.3665	0.4390	0.3657	0.4817	Chr6-09	2.00	1.9919	0.6911	0.3740	0.4980
Chr1-26	2.00	1.9293	0.6747	0.2322	0.2682	Chr6-10	2.00	1.5589	0.5441	0.2943	0.3585
Chr1-29	2.00	1.1357	0.2374	0.1124	0.1195	Chr6-27	2.00	1.3937	0.4562	0.2426	0.2825
Chr1-30	2.00	1.8776	0.6602	0.3582	0.4674	Chr6-28	2.00	1.3937	0.4562	0.2426	0.2825
Chr1-39	2.00	1.9293	0.6747	0.3657	0.4817	Chr6-29	2.00	1.4761	0.5033	0.2705	0.3225
Chr2-01	2.00	1.9293	0.6747	0.0957	0.1007	Chr5-30	2.00	1.2865	0.3819	0.1979	0.2227
Chr2-02	2.00	2.0000	0.6931	0.3677	0.4855	Chr6-09	2.00	1.9919	0.6911	0.3740	0.4980
Chr2-13	2.00	1.9437	0.6786	0.3013	0.3696	Chr6-10	2.00	1.5589	0.5441	0.2943	0.3585
Chr2-15	2.00	1.6934	0.5997	0.3657	0.4817	Chr6-27	2.00	1.3937	0.4562	0.2426	0.2825
Chr2-18	2.00	1.9856	0.6895	0.3609	0.4726	Chr6-32	2.00	1.8579	0.6544	0.3551	0.4617
Chr2-20	2.00	1.5864	0.5564	0.3256	0.4095	Chr7-01	2.00	1.7686	0.6262	0.2322	0.2682
Chr2-29	2.00	1.1120	0.2078	0.3732	0.4964	Chr7-02	2.00	1.8776	0.6602	0.3013	0.3696
Chr2-31	2.00	2.0000	0.6931	0.3750	0.5000	Chr7-06	2.00	1.6136	0.5681	0.3694	0.4889
Chr2-38	2.00	1.8961	0.6655	0.3750	0.5000	Chr7-12	2.00	1.9566	0.6820	0.3657	0.4817
Chr3-03	2.00	1.1636	0.2691	0.3709	0.4919	Chr7-19	2.00	1.7442	0.6179	0.3402	0.4346
Chr3-17	2.00	1.9293	0.6747	0.2322	0.2682	Chr7-21	2.00	1.5864	0.5564	0.2740	0.3277
Chr3-21	2.00	1.7686	0.6262	0.3657	0.4817	Chr7-24	2.00	1.3665	0.4390	0.3356	0.4267
Chr3-22	2.00	1.9679	0.6850	0.3677	0.4855	Chr7-28	2.00	1.9293	0.6747	0.3582	0.4674
Chr3-23	2.00	1.9437	0.6786	0.3402	0.4346	Chr7-35	2.00	1.4875	0.5093	0.3080	0.3803
Chr3-30	2.00	1.6672	0.5897	0.3443	0.4421	Chr8-09	2.00	1.4210	0.4727	0.0408	0.0416
Chr3-31	2.00	1.7923	0.6340	0.3201	0.4002	Chr8-16	2.00	1.0435	0.1030	0.1853	0.2067
Chr3-33	2.00	1.3665	0.4390	0.1307	0.1406	Chr8-18	2.00	1.3665	0.4390	0.2524	0.2963
Chr4-03	2.00	1.5589	0.5441	0.3582	0.4674	Chr8-19	2.00	1.9293	0.6747	0.3013	0.3696
Chr4-08	2.00	1.5589	0.5441	0.3551	0.4617	Chr8-26	2.00	1.5864	0.5564	0.3740	0.4980
Chr4-14	2.00	1.8579	0.6544	0.2426	0.2825	Chr8-29	2.00	1.9293	0.6747	0.3657	0.4817
Chr4-24	2.00	1.3937	0.4562	0.1979	0.2227	Chr8-30	2.00	1.2605	0.3609	0.2322	0.2682
Chr4-25	2.00	1.8776	0.6602	0.2943	0.3585	Chr8-32	2.00	1.9919	0.6911	0.3657	0.4817
Chr4-26	2.00	1.8078	0.6390	0.2943	0.3585	Chr9-09	3.00	2.0664	0.8735	0.4523	0.5161
Chr4-34	2.00	1.6672	0.5897	0.3470	0.4468	Chr9-15	2.00	1.6405	0.5792	0.3732	0.4964
Chr4-40	2.00	1.2865	0.3819	0.3201	0.4002	Chr9-17	2.00	1.5158	0.5236	0.3634	0.4774
Chr5-02	2.00	1.4210	0.4727	0.2524	0.2963	Chr9-22	2.00	1.5589	0.5441	0.3142	0.3904
Chr5-07	2.00	1.8961	0.6655	0.3609	0.4726	Chr9-25	2.00	1.9856	0.6895	0.2943	0.3585
Chr5-08	2.00	1.6136	0.5681	0.3080	0.3803	Chr9-26	2.00	1.9134	0.6703	0.2868	0.3470
Chr5-11	2.00	1.3129	0.4019	0.2099	0.2383	Chr9-27	2.00	1.5314	0.5312	0.2824	0.3403
Chr5-15	2.00	1.6934	0.5997	0.3256	0.4095	Chr9-31	2.00	1.9097	0.6693	0.3629	0.4764
Chr5-18	2.00	1.2865	0.3819	0.1979	0.2227	平均值	2.01	1.6692	0.5660	0.3041	0.3828
Chr5-24	2.00	1.9134	0.6703	0.3634	0.4774	Average

Development and Application of Insertion-Deletion（InDel）Markers in Papaya（Carica papaya）Based on Whole Genome Re-Sequencing Data

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编号 No.	种质 Germplasm	花色 Flower color	单果质量 Fruit weight	果实形状 Fruit shape	果肉颜色 Pulp color	分子身份证编码 Molecular ID
1	PX412	黄Yellow	中Moderate	椭圆Ellipse	橙红Orange-red	11221101011001101010111001011010100110100111
2	紫晖-1 Zihui-1	黄Yellow	中Moderate	长椭圆Long ellipse	橙红Orange-red	11320111010101101111111010101111111101011011
3	YN	白White	轻Light	椭圆Ellipse	黄Yellow	00200101111101110110111111100111100111111001
4	M26	白White	中Moderate	椭圆Ellipse	橙红Orange-red	01221110101110110111111111011111011011111111
5	GT1V	黄Yellow	重Heavy	长椭圆Long ellipse	橙红Orange-red	12320110110101111010101110100111100101111010
6	PL1	白White	轻Light	椭圆Ellipse	橙红Orange-red	00221110111110100101111111011001110110100101
7	PT1	白White	中Moderate	长椭圆Long ellipse	橙红Orange-red	01321110011011100110101001011111010110100101
8	P1	白White	中Moderate	长椭圆Long ellipse	橙红Orange-red	01320111010101010101101011011010110110111001
9	P50	白White	轻Light	长椭圆Long ellipse	橙红Orange-red	00321110111011110110100111010111101101110110
10	P51	白White	中Moderate	长椭圆Long ellipse	橙黄Orange-yellow	01311001011011111010100111011111100101100101
11	GY6	白White	中Moderate	长椭圆Long ellipse	橙黄Orange-yellow	01310110101110100111111011011001011001101010
12	GY11	白White	重Heavy	长椭圆Long ellipse	橙红Orange-red	02321111111111011101101110101110110111111110
13	金锤Jinchui	黄Yellow	轻Light	梨形Pear shaped	橙红Orange-red	10021010110101111101101010111110011111111010
14	贮丰-1 Zhufeng-1	白White	中Moderate	椭圆Ellipse	橙红Orange-red	01221111011010111101100111010111011011011110
15	FJ	白White	轻Light	长椭圆Long ellipse	黄Yellow	00301111110101011001111010100111010101111010
16	Y61	白White	中Moderate	长椭圆Long ellipse	橙红Orange-red	01320110111110010101101010101011100111111010
17	Y8	白White	中Moderate	长椭圆Long ellipse	橙黄Orange-yellow	01310110110101011010101010100111100101101010
18	GX-1	白White	轻Light	椭圆Ellipse	橙红Orange-red	00221110110110010111101001011111011001100101
19	GX-2	白White	轻Light	椭圆Ellipse	红Red	00230110111001101110100101011111100111100101
20	GX-13	白White	中Moderate	长椭圆Long ellipse	橙黄Orange-yellow	01311110110110010111011001011011010111111010
21	穗黄Suihuang	白White	中Moderate	长椭圆Long ellipse	橙黄Orange-yellow	01311101111111111011011110010110110111100110
22	BG	白White	轻Light	梨形Pear shaped	橙红Orange-red	00020110101010100110100101010110010101100101
23	K1	白White	中Moderate	圆形Round	橙黄Orange-yellow	01111011110101010110111011011010100110101001
24	K2	黄Yellow	轻Light	长椭圆Long ellipse	黄Yellow	10301011011111011011101011011110100111110111
25	K3	白White	中Moderate	长椭圆Long ellipse	橙红Orange-red	01321111111111110111110110011101111011111110
26	P440785049	白White	中Moderate	椭圆Ellipse	橙黄Orange-yellow	01211010100111110101010110011011111010111110
27	2017443059	白White	中Moderate	长椭圆Long ellipse	橙黄Orange-yellow	01311011101101100111010111101011110111101110
28	P440205014	白White	中Moderate	长椭圆Long ellipse	橙红Orange-red	01321010111101101101011011101010101010100110
29	GZ8	白White	中Moderate	长椭圆Long ellipse	橙黄Orange-yellow	01311111111010101110101101011110110110100101
30	2017441341	白White	中Moderate	圆形Round	橙红Orange-red	01120111111111010111101011011110100110111101
31	2017442041	白White	中Moderate	椭圆Ellipse	橙红Orange-red	01221010110101110111011011011011101011111111
32	黄花佑 Huanghuayou	黄Yellow	中Moderate	梨形 Pear shaped	橙红Orange-red	11020111111111011011101010100110101011111111
33	G3	白White	中Moderate	长椭圆Long ellipse	橙红Orange-red	01321010011010100110100111100110111101011010
34	T3-1	白White	中Moderate	长椭圆Long ellipse	黄Yellow	01301001010110101010011010101010101001011010
35	T4	白White	重Heavy	长椭圆Long ellipse	橙黄Orange-yellow	02310111111111110111110110111101111011111110
36	T5	白White	重Heavy	长条形Long strip	橙黄Orange-yellow	02411010100110011010100110101011101010011010
37	T6	白White	中Moderate	长条形Long strip	橙黄Orange-yellow	01411001011001011010011001011011101010101010
38	夏选Xiaxuan	白White	中Moderate	椭圆Ellipse	橙红Orange-red	01220101011111111110011111011111111011100111
39	42031	黄Yellow	中Moderate	长椭圆Long ellipse	橙红Orange-red	11321001011010011010101010010111100110100101
40	一尺瓜 Yichigua	白White	中Moderate	椭圆Ellipse	橙红Orange-red	01221001011010100110101001011111010101100101
41	紫晖-2 Zihui-2	黄Yellow	中Moderate	长椭圆Long ellipse	橙红Orange-red	11320111010101101111111010101111111101011011
42	GT1-5	黄Yellow	中Moderate	长椭圆Long ellipse	橙红Orange-red	11320111010101101111111010101111111101011011
43	大白Dabai	黄Yellow	轻Light	椭圆Ellipse	橙红Orange-red	10221111011011111010101111011110100111100101
44	黄金钟 Huangjin- zhong	黄Yellow	中Moderate	圆形Round	橙红Orange-red	11121111110101011001111010110110010101111010
45	红妃Hongfei	黄Yellow	重Heavy	长椭圆Long ellipse	橙红Orange-red	12321010100110010101011110101001010110011010
46	T3-2	白White	中Moderate	长椭圆Long ellipse	黄Yellow	01301001100110101010011010101010101001011010
47	贮丰-2 Zhufeng-2	白White	中Moderate	椭圆Ellipse	橙红Orange-red	01221111011010111101100111010110011011011110

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