Development of InDel Molecular Markers in Sorghum Using Re-sequencing Technology

doi:10.19586/j.2095-2341.2023.0106

Current Biotechnology ›› 2023, Vol. 13 ›› Issue (5): 730-741.DOI: 10.19586/j.2095-2341.2023.0106

• Articles • Previous Articles Next Articles

Development of InDel Molecular Markers in Sorghum Using Re-sequencing Technology

Weijun PU¹(), Binglan TAN¹, Danchen HE¹^,², Pan ZHANG¹, Yubin LI¹^,³, Li ZHU¹()

^1.Institute of Biotechnology，Chinese Academy of Agricultural Sciences，Beijing 100081，China
^2.School of Food Science and Pharmaceutial Engineering，Nanjing Normal University，Nanjing 210023，China
^3.College of Agronomy，Qingdao Agricultural University，Shandong Qingdao 266109，China

Received:2023-08-11 Accepted:2023-09-01 Online:2023-09-25 Published:2023-10-10
Contact: Li ZHU

利用重测序技术开发高粱InDel分子标记

蒲伟军¹(), 谭冰兰¹, 贺丹晨¹^,², 张盼¹, 李玉斌¹^,³, 朱莉¹()

^1.中国农业科学院生物技术研究所，北京 100081
^2.南京师范大学食品与制药工程学院，南京 210023
^3.青岛农业大学农学院，山东青岛 266109

通讯作者: 朱莉
作者简介:蒲伟军 E-mail: pwj0613@163.com；
基金资助:
国家自然科学基金项目(32272054);国家重点研发计划项目(2018YFD1000702)

Abstract

Abstract:

Sorghum （Sorghum bicolor L. Moench） is one of the most important cereal， and the complete genome of sorghum sequencing variety BTx623 has been published， which provides a research basis for the development of InDel（insertion/deletion） markers in sorghum. InDel markers， as high-throughput molecular markers， have the advantages of high genetic stability， wide distribution， strong polymorphism， and strong universality in plant genomes. At present， it has been widely used in rice， corn， cotton and other major crops. However， there are few studies in sorghum. In this study， the genomic DNA of sweet sorghum variety JIUTIAN1 was selected as the research object， re-sequencing was performed using Illumina platform， and quality control was performed on raw data of sequencing using Trimmomatic software， and low-quality data were eliminated. BWA software was used to compare the obtained high-quality clean data with the reference genome of the sequenced variety BTx623， from which a large number of InDel sites were detected. These InDel sites were used to design 205 evenly distributed markers in the whole genome， and 87 polymorphic markers were selected by PCR verification， with a polymorphism of 42.44%. These 87 InDel markers were characterized with high polymorphism， wide distribution and high stability. The sorghum InDel marker developed in this study was expected to lay a foundation for the construction of sorghum genetic linkage map， genetic diversity analysis， hybrid purity identification， location of genes related to important agronomic traits of sorghum， and marker-assisted selection breeding.

Key words: Sorghum bicolor, InDel, re-sequencing, polymorphic primer, molecular marker

摘要：

高粱是重要的禾谷类作物，其测序品种BTx623的全基因组序列已经公布，为高粱InDel 标记的开发提供了研究基础。插入与缺失（insertion/deletion，InDel）标记作为高通量分子标记，在植物基因组中具有遗传稳定性高、分布广、多态性强、通用性强等优点，目前已在水稻、玉米、棉花等主要作物中得到广泛应用，然而在高粱中的研究尚不多见。以高粱品种JIUTIAN1基因组DNA为研究对象，利用Illumina平台进行重测序，进一步利用Trimmomatic软件对测序原始数据进行质量控制，剔除低质量数据，使用BWA软件将获得的高质量有效数据与测序品种BTx623参考基因组进行序列比对，从中检测出大量InDel位点。利用这些InDel位点在全基因组范围内设计均匀分布的205个标记，通过PCR验证后筛选出87个多态性标记，多态性为42.44%。高粱Indel标记的开发有望为高粱遗传连锁图谱的构建、遗传多样性分析、杂交种纯度鉴定、高粱重要农艺性状相关基因的定位和分子标记辅助选择育种等研究奠定基础。

关键词: 高粱, InDel, 重测序, 多态性引物, 分子标记

CLC Number:

Q343.1+7

Weijun PU, Binglan TAN, Danchen HE, Pan ZHANG, Yubin LI, Li ZHU. Development of InDel Molecular Markers in Sorghum Using Re-sequencing Technology[J]. Current Biotechnology, 2023, 13(5): 730-741.

蒲伟军, 谭冰兰, 贺丹晨, 张盼, 李玉斌, 朱莉. 利用重测序技术开发高粱InDel分子标记[J]. 生物技术进展, 2023, 13(5): 730-741.

Figures/Tables 5

References 28

1	TARI I, LASKAY G, TAKACS Z, et al.. Response of Sorghum to abiotic stresses: a review[J/OL]. J. Agron. Crop Sci., 2013, 199(4): 12017 [2023-05-23]. .
2	MCCORMICK R F, TRUONG S K, SREEDASYAM A, et al.. The Sorghum bicolor reference genome: improved assembly, gene annotations, a transcriptome atlas, and signatures of genome organization[J]. Plant J., 2018, 93(2): 338-354.
3	LUO H, ZHAO W, WANG Y, et al.. SorGSD: a sorghum genome SNP database[J/OL]. Biotechnol. Biofuels, 2016, 9: 6[2023-05-23]. .
4	杨洁, 赫佳, 王丹碧, 等. InDel标记的研究和应用进展[J]. 生物多样性, 2016, 24(2): 237-243..
5	VISSCHER P M, YENGO L, COX N J, et al.. Discovery and implications of polygenicity of common diseases[J]. Science, 2021, 373(6562): 1468-1473.
6	王钰, 马卉, 许学, 等. 水稻功能性插入缺失标记(InDel)的筛选与应用[J]. 作物杂志, 2019(4): 84-93.
7	徐鹏, 蔡继鸿, 杨阳, 等. 陆地棉耐盐相关EST-SSR以及EST-InDel分子标记的开发[J]. 棉花学报, 2016, 28(1): 65-74.
8	毛艇, 李旭, 李振宇, 等. 水稻Wx复等位基因基于PCR的功能标记开发与利用[J]. 作物学报, 2017, 43(11): 1715-1723.
9	YONEMARU J I, ANDO T, MIZUBAYASHI T, et al.. Development of genome-wide simple sequence repeat markers using whole-genome shotgun sequences of Sorghum (Sorghum bicolor (L.) Moench)[J]. DNA Res., 2009, 16(3): 187-193.
10	王平, 王春语, 张丽霞, 等. 利用重测序技术开发高粱多态性SSR分子标记[J]. 生物技术通报, 2019, 35(11): 217-223.
11	BURRELL M, SHARMA A, PATIL N Y, et al.. Sequencing of an anthracnose-resistant Sorghum genotype and mapping of a major QTL reveal strong candidate genes for anthracnose resistance[J]. Crop Sci., 2014, 55(2): 790-799.
12	ASSEFA A, SHIMELIS H, TONGOONA P, et al. Genetic diversity of lowland sorghum landraces assessed by morphological and microsatellite markers[J]. Aust. J. Crop Sci., 2016, 10(3): 291-298.
13	BOUCHET S, OLATOYE M O, MARLA S R, et al.. Increased power to dissect adaptive traits in global Sorghum diversity using a nested association mapping population[J]. Genetics, 2017, 206(2): 573-585.
14	JI G, ZHANG Q, DU R, et al.. Construction of a high-density genetic map using specific-locus amplified fragments in sorghum[J/OL]. BMC Genomics, 2017, 18(1): 51[2023-05-23]. .
15	CHOE M E, KIM J Y, NABI R B S, et al.. Development of InDels markers for the identification of cytoplasmic male sterility in Sorghum by complete chloroplast genome sequences analysis[J/OL]. Front. Plant Sci., 2023, 14: 1188149[2023-05-23]. .
16	BOLGER A M, LOHSE M, USADEL B. Trimmomatic: a flexible trimmer for Illumina sequence data[J]. Bioinformatics, 2014, 30(15): 2114-2120.
17	LI H, DURBIN R. Fast and accurate short read alignment with Burrows-Wheeler transform[J]. Bioinformatics, 2009, 25(14): 1754-1760.
18	LALITHA S. Primer Premier 5[R]. Biotech Software & Internet Report, 2000, 270-272.
19	李荣华, 夏岩石, 刘顺枝, 等. 改进的CTAB提取植物DNA方法[J]. 实验室研究与探索, 2009, 28(9): 14-16.
20	VOORRIPS R E. MapChart: software for the graphical presentation of linkage maps and QTLs[J]. J. Hered., 2002, 93(1): 77-78.
21	赵文杰, 徐薇, 张景龙, 等. 甜高粱生物学性状与SSR分子标记遗传多样性[J]. 浙江农业学报, 2019, 31(12): 1945-1954.
22	HAN Y, LV P, HOU S, et al.. Combining next generation sequencing with bulked segregant analysis to fine map a stem moisture locus in Sorghum (Sorghum bicolor L. moench)[J/OL]. PLoS ONE, 2015, 10(5): e0127065[2023-05-23]. .
23	胡陶铸, 林丽, 胡继军, 等. 利用InDel标记构建番茄新品种指纹图谱[J]. 上海交通大学学报(农业科学版), 2019, 37(2): 24-29.
24	吴迷, 汪念, 沈超, 等. 基于重测序的陆地棉InDel标记开发与评价[J]. 作物学报, 2019, 45(2): 196-203.
25	杨易, 黎庭耀, 李国景, 等. 基于重测序的长豇豆基因组InDel标记开发及应用[J]. 园艺学报, 2022, 49(4): 778-790.
26	TAO Y, LUO H, XU J, et al.. Extensive variation within the pan-genome of cultivated and wild sorghum[J]. Nat. Plants, 2021, 7(6): 766-773.
27	LI J, WANG L, ZHAN Q, et al.. Transcriptome characterization and functional marker development in Sorghum sudanense[J/OL]. PLoS ONE, 2016, 11(5): e0154947[2023-05-23]. .
28	BOATWRIGHT J L, SAPKOTA S, KRESOVICH S. Functional genomic effects of indels using Bayesian genome-phenome wide association studies in sorghum[J/OL]. Front. Genet., 2023, 14: 1143395[2023-05-23]. .

编号	引物名称	引物序列（5'→3'）	编号	引物名称	引物序列（5'→3'）
InDel01	Chr01-NP2-F	5'-TGGTCGAACAAGACTGCAAC-3'	InDel45	Chr05-NP8-F	5'-TTGTGGGATGAAAGGAGCAT-3'
InDel01	Chr01-NP2-R	5'-CACTACGGCGAAATTGGAAG-3'	InDel45	Chr05-NP8-R	5'-GCCTGTACCAGAAACCGAAC-3'
InDel02	Chr01-NP3-F	5'-ATCGGCATCCATCAGATTTT-3'	InDel46	Chr05-NP9-F	5'-AGAATGTTGCACGCATTGAC-3'
InDel02	Chr01-NP3-R	5'-CCTGCCAACTCAGCAATTTT-3'	InDel46	Chr05-NP9-R	5'-GCCGACCATTATTTGTGACC-3'
InDel03	Chr01-NP4-F	5'-TCTTTCCCAGTGGAACAACC-3'	InDel47	Chr05-NP10-F	5'-GCAATTGCAACATCGAACAC-3'
InDel03	Chr01-NP4-R	5'-CAGGGGACTCTTCAAACTGC-3'	InDel47	Chr05-NP10-R	5'-TCCACATCCATCCTCATCAA-3'
InDel04	Chr01-NP6-F	5'-AGATCCGAGCATTTCTGCTG-3'	InDel48	Chr06-MP1-F	5'-CATAGGATTTTGCCACGACA-3'
InDel04	Chr01-NP6-R	5'-AGTTCGCCCAGGTAAGGTCT-3'	InDel48	Chr06-MP1-R	5'-CGTCACAGAGTCCATGCAGA-3'
InDel05	Chr02-NP2-F	5'-TTTCATGGCTTTGAGTGTCA-3'	InDel49	Chr06-MP8-F	5'-TGCGAAAAGAAAAAGGATGG-3'
InDel05	Chr02-NP2-R	5'-ACGCTAACAGAGGGCAGTGT-3'	InDel49	Chr06-MP8-R	5'-CCCAAAATCCACTTTCCTGA-3'
InDel06	Chr02-NP4-F	5'-TGGTCAAGTTTTGGCATGAA-3'	InDel50	Chr06-MP12-F	5'-TACGCTGGTGCTTACGAAAA-3'
InDel06	Chr02-NP4-R	5'-GTCATGTTCTTTCTGATTCCCTCT-3'	InDel50	Chr06-MP12-R	5'-GGGAGAGGAAAGGTGAAACC-3'
InDel07	Chr02-NP7-F	5'-TGCCTCTATTTTTCCCATGC-3'	InDel51	Chr06-NP2-F	5'-ATTGATTTGGGGTCGGGTA-3'
InDel07	Chr02-NP7-R	5'-AATGCCAAGTTTGGTCCATC-3'	InDel51	Chr06-NP2-R	5'-CACCGCAAGCCAAAATAGAG-3'
InDel08	Chr02-NP10-F	5'-TACACACAGTACGCCCATGC-3'	InDel52	Chr06-NP7-F	5'-AGTGGCTGTACGGGTTTGAC-3'
InDel08	Chr02-NP10-R	5'-GGTTTGGTGTCTGGCAACTT-3'	InDel52	Chr06-NP7-R	5'-TTGTGCAGCATCAACGTGTA-3'
InDel09	Chr02-NP11-F	5'-ATATCTGGTTCCCCCAGCTT-3'	InDel53	Chr07-NP1-F	5'-TGGATCCAAGTAAACCCGATA-3'
InDel09	Chr02-NP11-R	5'-GCTCAGCTCGTCTCGTCTCT-3'	InDel53	Chr07-NP1-R	5'-ACTTAAAGGCCCCACTGAAA-3'
InDel10	Chr02-NP12-F	5'-TTTTGCGACACCTACTGCTG-3'	InDel54	Chr07-NP3-F	5'-TAACGGTTTGGGTCTTCGAG-3'
InDel10	Chr02-NP12-R	5'-GGTTTTCTGGGGTGCATAGA-3'	InDel54	Chr07-NP3-R	5'-GCGATGAAAAACACAGCAAA-3'
InDel11	Chr02-NP14-F	5'-TGCAATACCTGTTCCCCACT-3'	InDel55	Chr07-NP6-F	5'-TTCTGGTCTGGTGAATGCAA-3'
InDel11	Chr02-NP14-R	5'-CAACAATGGCTACAGCAACG-3'	InDel55	Chr07-NP6-R	5'-TCCATGACGAACGAGAAATC-3'
InDel12	Chr02-MP1-F	5'-CCTGACCCAGACACACACAC-3'	InDel56	Chr07-MP8-F	5'-GCCAAGTTTGCCAAAATGC-3'
InDel12	Chr02-MP1-R	5'-AGCAATCTTGTCAGGGGATG-3'	InDel56	Chr07-MP8-R	5'-GTTAACGCAACCCAGCAGA-3'
InDel13	Chr02-MP2-F	5'-GCTGATGGCTCTCCAAACTC-3'	InDel57	Chr08-MP1-F	5'-GCCGAGTGTCTCGTTAGACC-3'
InDel13	Chr02-MP2-R	5'-GTTGGTCCCTGAATGCTTGT-3'	InDel57	Chr08-MP1-R	5'-CACGACGGCACCCTACTAAT-3'
InDel14	Chr02-MP4-F	5'-TGACCTAAGGGGTTGTTTGG-3'	InDel58	Chr08-MP12-F	5'-GAACCAAACAGCGTCAGACC-3'
InDel14	Chr02-MP4-R	5'-GCACCTGCCACATCCTATTT-3'	InDel58	Chr08-MP12-R	5'-AGCACCACCCATAACGTGTC-3'
InDel15	Chr02-MP12-F	5'-CAAAGGCCGATGTATTTGCT-3'	InDel59	Chr08-AP2-F	5'-TGACTGTGTCGCTACCTTGC-3'
InDel15	Chr02-MP12-R	5'-TGTGCCAACCCTGTATGTGT-3'	InDel59	Chr08-AP2-R	5'-GATGGCAAGAGTGGGATTTG-3'
InDel16	Chr02-MP13-F	5'-GAAGGCGCTCGTGAATTTTA-3'	InDel60	Chr08-AP4-F	5'-TCCAAACCGGTGGATAATTG-3'
InDel16	Chr02-MP13-R	5'-CAGACACAAAGGCTGTCTCG-3'	InDel60	Chr08-AP4-R	5'-AAGCCTTGTTTGGATGCTGT-3'
InDel17	Chr02-MP14-F	5'-CCGCACAAAGTAGAGCATCA-3'	InDel61	Chr08-AP5-F	5'-CAAAGGACGAGATAAGCA-3'
InDel17	Chr02-MP14-R	5'-CCGTAAGAGAAGCGAGCCTA-3'	InDel61	Chr08-AP5-R	5'-TTCCCTGTCACATCAAAT-3'
InDel18	Chr02-MP16-F	5'-TTTTCAGTCTGGTCGCTTGA-3'	InDel62	Chr08-NP3-F	5'-TCCATGCATATGCCTCAAAA-3'
InDel18	Chr02-MP16-R	5'-CACACCTCACTCGCTTCTCA-3'	InDel62	Chr08-NP3-R	5'-CAAGTTGTGCAGTTGCTGGT-3'
InDel19	Chr03-MP3-F	5'-GGCACATGCATGAAGCACTA-3'	InDel63	Chr09-MP1-F	5'-GACGGAGATACTTAGGGCAGAA-3'
InDel19	Chr03-MP3-R	5'-TGATTCGACAGCTTCCAGAG-3'	InDel63	Chr09-MP1-R	5'-TCTCTCTCCTCCCTTTCCAA-3'
InDel20	Chr03-MP5-F	5'-CGAGAAGACATGACAAAACGAG-3'	InDel64	Chr09-YM1-F	5'-GTCGGCGTAGCTCATCTT-3'
InDel20	Chr03-MP5-R	5'-CTTTGGTCGCATGTATGGAA-3'	InDel64	Chr09-YM1-R	5'-GTAGCACTTTCGTTTGTATTTG-3'
InDel21	Chr03-MP10-F	5'-CCATCTGGATATACACGGGTTAG-3'	InDel65	Chr09-YM2-F	5'-GTCAAGGAGGAACCAAAG-3'
InDel21	Chr03-MP10-R	5'-TGCAAACCGGTTCTCAAAGT-3'	InDel65	Chr09-YM2-R	5'-ATGCCTAAGCCTAAGTAA-3'
InDel22	Chr03-MP12-F	5'-TGCATGCACGTAGTAGACACA-3'	InDel66	Chr09-YM5-F	5'-GTCAAGGAGGAACCAAAG-3'
InDel22	Chr03-MP12-R	5'-CACCACGATAGCAAATCACC-3'	InDel66	Chr09-YM5-R	5'-ATGCCTAAGCCTAAGTAA-3'
InDel23	Chr03-MP14-F	5'-GGTGCAGTGGTGTCTTCCTT-3'	InDel67	Chr09-YM10-F	5'-TCGGCTTGATTTGTTCTT-3'
InDel23	Chr03-MP14-R	5'-ATTTACAGCGCGTGGCTATC-3'	InDel67	Chr09-YM10-R	5'-CTGGCTGCTGAGTAAGTG-3'
InDel24	Chr03-NP3-F	5'-TTAAGGTCTCGTTTAGTTCAGG-3'	InDel68	Chr09-YM11-F	5'-CGAAATGCTTCACGCTGT-3'
InDel24	Chr03-NP3-R	5'-GCCTTGTTCAGTTGGCAAAA-3'	InDel68	Chr09-YM11-R	5'-GAAACCTACCCAATGTCCG-3'
InDel25	Chr03-NP4-F	5'-TCAGATGAGCAGGCTCTACAGT-3'	InDel69	Chr09-MP4-F	5'-TTCCAATAAAGCTGCCGTTC-3'
InDel25	Chr03-NP4-R	5'-GAGCATTTTCGGCATGTGTA-3'	InDel69	Chr09-MP4-R	5'-ATACTAGCGGTGCGGGTTAC-3'
InDel26	Chr03-NP7-F	5'-ACGAAAGAAATGCACCGAAC-3'	InDel70	Chr09-MP5-F	5'-CTGAACAAGGCCTAGGTGGA-3'
InDel26	Chr03-NP7-R	5'-CCCAGCCTAGGAAACATCAA-3'	InDel70	Chr09-MP5-R	5'-GCTCACCACTGCAACTGCTA-3'
InDel27	Chr03-NP9-F	5'-GCGTGACTATTGCAGCTGTT-3'	InDel71	Chr09-MP9-F	5'-ATGTCAGCGAAATGGTTTCC-3'
InDel27	Chr03-NP9-R	5'-CATGCCATCCACTTCCACTA-3'	InDel71	Chr09-MP9-R	5'-CACCAAGTCCTTGCTCATCA-3'
InDel28	Chr04-MP1-F	5'-GCGGTCATAGGCGTTACTGT-3'	InDel72	Chr09-MP11-F	5'-ATGGAATATGAGCCCCAACA-3'
InDel28	Chr04-MP1-R	5'-CGCTGTCACATCGSSTCTTT-3'	InDel72	Chr09-MP11-R	5'-ATCAGGTCGTCCACCAGTTC-3'
InDel29	Chr04-MP2-F	5'-TGGATAGGTTCATGCTGCTG-3'	InDel73	Chr09-NP1-F	5'-ACGAGGATGGCAAGAGGATA-3'
InDel29	Chr04-MP2-R	5'-TTTTTGCCACCTTCCAATTC-3'	InDel73	Chr09-NP1-R	5'-GACGGTGCATGTGCTTTTT-3'
InDel30	Chr04-MP3-F	5'-CTGCCCTATGCATCTGTTCA-3'	InDel74	Chr09-NP2-F	5'-GCGGATGAGGAGGAATCTCT-3'
InDel30	Chr04-MP3-R	5'-CCAACTAGTTCAGGGCAGGA-3'	InDel74	Chr09-NP2-R	5'-TTTACTGCGCCTCGTCTCTT-3'
InDel31	Chr04-MP13-F	5'-TCCGTCCAACTGGAATTGAT-3'	InDel75	Chr09-NP4-F	5'-AGCACTAGCAAATGCCACAA-3'
InDel31	Chr04-MP13-R	5'-AATCCTTCGTGGAAAGCTGA-3'	InDel75	Chr09-NP4-R	5'-ATGACGTTTTTCGGCTTGTC-3'
InDel32	Chr04-NP1-F	5'-ATCTTGCGGCACATACATGA-3'	InDel76	Chr09-NP5-F	5'-GCTGAGCACTTGAGGGTTGT-3'
InDel32	Chr04-NP1-R	5'-CTTCAACACTCAGCCCACCT-3'	InDel76	Chr09-NP5-R	5'-CTGGTCATCGGCTTAGCAAT-3'
InDel33	Chr04-NP2-F	5'-TATAAAGCACCGGTGGAGGT-3'	InDel77	Chr09-NP9-F	5'-GCGGCTTATCACAGCTCCTA-3'
InDel33	Chr04-NP2-R	5'-ACAAATCGTTTCACCGCTTC-3'	InDel77	Chr09-NP9-R	5'-TCACCATGCAAAACGTCCTA-3'
InDel34	Chr04-NP6-F	5'-GGCTGTTGGAGGAATTTTGA-3'	InDel78	Chr10-MP2-F	5'-AGAGATCGAGAGGACGGACA-3'
InDel34	Chr04-NP6-R	5'-CCTTGTACTCTTCTGAGTTTTGGA-3'	InDel78	Chr10-MP2-R	5'-GGAATTCCATGCCCAAATC-3'
InDel35	Chr04-NP7-F	5'-GACCGAGAAAGAAAATCATACACTC-3'	InDel79	Chr10-MP5-F	5'-GCATTTGCATCTGAAAGCTC-3'
InDel35	Chr04-NP7-R	5'-AGGCAAAAAGCCCAACTCTT-3'	InDel79	Chr10-MP5-R	5'-ACCAAACTCTGCAGGAATGC-3'
InDel36	Chr04-NP8-F	5'-ATGCCGTAGATCGTCCTCCT-3'	InDel80	Chr10-MP7-F	5'-AGGCGTTGCCTCTAACACTG-3'
InDel36	Chr04-NP8-R	5'-CAACCGGAGCTGGAAATG-3'	InDel80	Chr10-MP7-R	5'-GTCCGGTGAGTTCGTTTCTC-3'
InDel37	Chr04-NP11-F	5'-AGCTCATCAAAGCGAAAGGA-3'	InDel81	Chr10-MP8-F	5'-CACATGGTTCTTTTCCACGA-3'
InDel37	Chr04-NP11-R	5'-AGTCTAGACGCCTCGACGTT-3'	InDel81	Chr10-MP8-R	5'-GGAGTTGGATGAAAGCCTTG-3'
InDel38	Chr05-MP9-F	5'-ATGGGAAGGCCTACGATTTT-3'	InDel82	Chr10-MP11-F	5'-TGGTAGACGGGTCCTAGTGC-3'
InDel38	Chr05-MP9-R	5'-TGGGTGATGGTAGGAGAATAGA-3'	InDel82	Chr10-MP11-R	5'-TACATCGCTGCTGGAGTGTC-3'
InDel39	Chr05-MP13-F	5'-ATTTAACCTGGCTGCCTGTC-3'	InDel83	Chr10-NP4-F	5'-ACACGGGTCGAAGATCAAAG-3'
InDel39	Chr05-MP13-R	5'-GACCGCGACACTAACAAATG-3'	InDel83	Chr10-NP4-R	5'-GGTGCCAACTTCCTTCATCA-3'
InDel40	Chr05-MP14-F	5'-TTTGCCTAGCCATTTCAGGT-3'	InDel84	Chr10-NP6-F	5'-TTTGCAAGCTGTTTTGGTTC-3'
InDel40	Chr05-MP14-R	5'-CACGGTCAACAATCAGCTCT-3'	InDel84	Chr10-NP6-R	5'-GGGTGAAGGCTACATCGGTA-3'
InDel41	Chr05-NP1-F	5'-AGCATTGGCTGCTAAGCATT-3'	InDel85	Chr10-NP7-F	5'-TACCGTTGTCCGACGCTAAT-3'
InDel41	Chr05-NP1-R	5'-TAGCAGCAACAGCAAACAGG-3'	InDel85	Chr10-NP7-R	5'-TTGTGTAGGCGTCGTGCTTA-3'
InDel42	Chr05-NP2-F	5'-AGAGAGAATCCTCGGCAAGA-3'	InDel86	Chr10-NP9-F	5'-CGACCCTGTCGTATGTATGC-3'
InDel42	Chr05-NP2-R	5'-TTTGTGAGGGGTTCTTGAGC-3'	InDel86	Chr10-NP9-R	5'-TTGTCCTTCTGTGGCTGTTG-3'
InDel43	Chr05-NP5-F	5'-CTTCGTGGACCACATGACAC-3'	InDel87	Chr10-NP11-F	5'-ACGGAATGCAAAAAGCAAAG-3'
InDel43	Chr05-NP5-R	5'-GTACCCTCGCCAGTCAACTC-3'	InDel87	Chr10-NP11-R	5'-GGTGACTTCAACCGGGATTA-3'
InDel44	Chr05-NP6-F	5'-TCTCACGGGTCGAAAGTACC-3'
InDel44	Chr05-NP6-R	5'-CAATCTCGATTGCCTCAACA-3'

编号	引物名称	引物序列（5'→3'）	编号	引物名称	引物序列（5'→3'）
InDel01	Chr01-NP2-F	5'-TGGTCGAACAAGACTGCAAC-3'	InDel45	Chr05-NP8-F	5'-TTGTGGGATGAAAGGAGCAT-3'
InDel01	Chr01-NP2-R	5'-CACTACGGCGAAATTGGAAG-3'	InDel45	Chr05-NP8-R	5'-GCCTGTACCAGAAACCGAAC-3'
InDel02	Chr01-NP3-F	5'-ATCGGCATCCATCAGATTTT-3'	InDel46	Chr05-NP9-F	5'-AGAATGTTGCACGCATTGAC-3'
InDel02	Chr01-NP3-R	5'-CCTGCCAACTCAGCAATTTT-3'	InDel46	Chr05-NP9-R	5'-GCCGACCATTATTTGTGACC-3'
InDel03	Chr01-NP4-F	5'-TCTTTCCCAGTGGAACAACC-3'	InDel47	Chr05-NP10-F	5'-GCAATTGCAACATCGAACAC-3'
InDel03	Chr01-NP4-R	5'-CAGGGGACTCTTCAAACTGC-3'	InDel47	Chr05-NP10-R	5'-TCCACATCCATCCTCATCAA-3'
InDel04	Chr01-NP6-F	5'-AGATCCGAGCATTTCTGCTG-3'	InDel48	Chr06-MP1-F	5'-CATAGGATTTTGCCACGACA-3'
InDel04	Chr01-NP6-R	5'-AGTTCGCCCAGGTAAGGTCT-3'	InDel48	Chr06-MP1-R	5'-CGTCACAGAGTCCATGCAGA-3'
InDel05	Chr02-NP2-F	5'-TTTCATGGCTTTGAGTGTCA-3'	InDel49	Chr06-MP8-F	5'-TGCGAAAAGAAAAAGGATGG-3'
InDel05	Chr02-NP2-R	5'-ACGCTAACAGAGGGCAGTGT-3'	InDel49	Chr06-MP8-R	5'-CCCAAAATCCACTTTCCTGA-3'
InDel06	Chr02-NP4-F	5'-TGGTCAAGTTTTGGCATGAA-3'	InDel50	Chr06-MP12-F	5'-TACGCTGGTGCTTACGAAAA-3'
InDel06	Chr02-NP4-R	5'-GTCATGTTCTTTCTGATTCCCTCT-3'	InDel50	Chr06-MP12-R	5'-GGGAGAGGAAAGGTGAAACC-3'
InDel07	Chr02-NP7-F	5'-TGCCTCTATTTTTCCCATGC-3'	InDel51	Chr06-NP2-F	5'-ATTGATTTGGGGTCGGGTA-3'
InDel07	Chr02-NP7-R	5'-AATGCCAAGTTTGGTCCATC-3'	InDel51	Chr06-NP2-R	5'-CACCGCAAGCCAAAATAGAG-3'
InDel08	Chr02-NP10-F	5'-TACACACAGTACGCCCATGC-3'	InDel52	Chr06-NP7-F	5'-AGTGGCTGTACGGGTTTGAC-3'
InDel08	Chr02-NP10-R	5'-GGTTTGGTGTCTGGCAACTT-3'	InDel52	Chr06-NP7-R	5'-TTGTGCAGCATCAACGTGTA-3'
InDel09	Chr02-NP11-F	5'-ATATCTGGTTCCCCCAGCTT-3'	InDel53	Chr07-NP1-F	5'-TGGATCCAAGTAAACCCGATA-3'
InDel09	Chr02-NP11-R	5'-GCTCAGCTCGTCTCGTCTCT-3'	InDel53	Chr07-NP1-R	5'-ACTTAAAGGCCCCACTGAAA-3'
InDel10	Chr02-NP12-F	5'-TTTTGCGACACCTACTGCTG-3'	InDel54	Chr07-NP3-F	5'-TAACGGTTTGGGTCTTCGAG-3'
InDel10	Chr02-NP12-R	5'-GGTTTTCTGGGGTGCATAGA-3'	InDel54	Chr07-NP3-R	5'-GCGATGAAAAACACAGCAAA-3'
InDel11	Chr02-NP14-F	5'-TGCAATACCTGTTCCCCACT-3'	InDel55	Chr07-NP6-F	5'-TTCTGGTCTGGTGAATGCAA-3'
InDel11	Chr02-NP14-R	5'-CAACAATGGCTACAGCAACG-3'	InDel55	Chr07-NP6-R	5'-TCCATGACGAACGAGAAATC-3'
InDel12	Chr02-MP1-F	5'-CCTGACCCAGACACACACAC-3'	InDel56	Chr07-MP8-F	5'-GCCAAGTTTGCCAAAATGC-3'
InDel12	Chr02-MP1-R	5'-AGCAATCTTGTCAGGGGATG-3'	InDel56	Chr07-MP8-R	5'-GTTAACGCAACCCAGCAGA-3'
InDel13	Chr02-MP2-F	5'-GCTGATGGCTCTCCAAACTC-3'	InDel57	Chr08-MP1-F	5'-GCCGAGTGTCTCGTTAGACC-3'
InDel13	Chr02-MP2-R	5'-GTTGGTCCCTGAATGCTTGT-3'	InDel57	Chr08-MP1-R	5'-CACGACGGCACCCTACTAAT-3'
InDel14	Chr02-MP4-F	5'-TGACCTAAGGGGTTGTTTGG-3'	InDel58	Chr08-MP12-F	5'-GAACCAAACAGCGTCAGACC-3'
InDel14	Chr02-MP4-R	5'-GCACCTGCCACATCCTATTT-3'	InDel58	Chr08-MP12-R	5'-AGCACCACCCATAACGTGTC-3'
InDel15	Chr02-MP12-F	5'-CAAAGGCCGATGTATTTGCT-3'	InDel59	Chr08-AP2-F	5'-TGACTGTGTCGCTACCTTGC-3'
InDel15	Chr02-MP12-R	5'-TGTGCCAACCCTGTATGTGT-3'	InDel59	Chr08-AP2-R	5'-GATGGCAAGAGTGGGATTTG-3'
InDel16	Chr02-MP13-F	5'-GAAGGCGCTCGTGAATTTTA-3'	InDel60	Chr08-AP4-F	5'-TCCAAACCGGTGGATAATTG-3'
InDel16	Chr02-MP13-R	5'-CAGACACAAAGGCTGTCTCG-3'	InDel60	Chr08-AP4-R	5'-AAGCCTTGTTTGGATGCTGT-3'
InDel17	Chr02-MP14-F	5'-CCGCACAAAGTAGAGCATCA-3'	InDel61	Chr08-AP5-F	5'-CAAAGGACGAGATAAGCA-3'
InDel17	Chr02-MP14-R	5'-CCGTAAGAGAAGCGAGCCTA-3'	InDel61	Chr08-AP5-R	5'-TTCCCTGTCACATCAAAT-3'
InDel18	Chr02-MP16-F	5'-TTTTCAGTCTGGTCGCTTGA-3'	InDel62	Chr08-NP3-F	5'-TCCATGCATATGCCTCAAAA-3'
InDel18	Chr02-MP16-R	5'-CACACCTCACTCGCTTCTCA-3'	InDel62	Chr08-NP3-R	5'-CAAGTTGTGCAGTTGCTGGT-3'
InDel19	Chr03-MP3-F	5'-GGCACATGCATGAAGCACTA-3'	InDel63	Chr09-MP1-F	5'-GACGGAGATACTTAGGGCAGAA-3'
InDel19	Chr03-MP3-R	5'-TGATTCGACAGCTTCCAGAG-3'	InDel63	Chr09-MP1-R	5'-TCTCTCTCCTCCCTTTCCAA-3'
InDel20	Chr03-MP5-F	5'-CGAGAAGACATGACAAAACGAG-3'	InDel64	Chr09-YM1-F	5'-GTCGGCGTAGCTCATCTT-3'
InDel20	Chr03-MP5-R	5'-CTTTGGTCGCATGTATGGAA-3'	InDel64	Chr09-YM1-R	5'-GTAGCACTTTCGTTTGTATTTG-3'
InDel21	Chr03-MP10-F	5'-CCATCTGGATATACACGGGTTAG-3'	InDel65	Chr09-YM2-F	5'-GTCAAGGAGGAACCAAAG-3'
InDel21	Chr03-MP10-R	5'-TGCAAACCGGTTCTCAAAGT-3'	InDel65	Chr09-YM2-R	5'-ATGCCTAAGCCTAAGTAA-3'
InDel22	Chr03-MP12-F	5'-TGCATGCACGTAGTAGACACA-3'	InDel66	Chr09-YM5-F	5'-GTCAAGGAGGAACCAAAG-3'
InDel22	Chr03-MP12-R	5'-CACCACGATAGCAAATCACC-3'	InDel66	Chr09-YM5-R	5'-ATGCCTAAGCCTAAGTAA-3'
InDel23	Chr03-MP14-F	5'-GGTGCAGTGGTGTCTTCCTT-3'	InDel67	Chr09-YM10-F	5'-TCGGCTTGATTTGTTCTT-3'
InDel23	Chr03-MP14-R	5'-ATTTACAGCGCGTGGCTATC-3'	InDel67	Chr09-YM10-R	5'-CTGGCTGCTGAGTAAGTG-3'
InDel24	Chr03-NP3-F	5'-TTAAGGTCTCGTTTAGTTCAGG-3'	InDel68	Chr09-YM11-F	5'-CGAAATGCTTCACGCTGT-3'
InDel24	Chr03-NP3-R	5'-GCCTTGTTCAGTTGGCAAAA-3'	InDel68	Chr09-YM11-R	5'-GAAACCTACCCAATGTCCG-3'
InDel25	Chr03-NP4-F	5'-TCAGATGAGCAGGCTCTACAGT-3'	InDel69	Chr09-MP4-F	5'-TTCCAATAAAGCTGCCGTTC-3'
InDel25	Chr03-NP4-R	5'-GAGCATTTTCGGCATGTGTA-3'	InDel69	Chr09-MP4-R	5'-ATACTAGCGGTGCGGGTTAC-3'
InDel26	Chr03-NP7-F	5'-ACGAAAGAAATGCACCGAAC-3'	InDel70	Chr09-MP5-F	5'-CTGAACAAGGCCTAGGTGGA-3'
InDel26	Chr03-NP7-R	5'-CCCAGCCTAGGAAACATCAA-3'	InDel70	Chr09-MP5-R	5'-GCTCACCACTGCAACTGCTA-3'
InDel27	Chr03-NP9-F	5'-GCGTGACTATTGCAGCTGTT-3'	InDel71	Chr09-MP9-F	5'-ATGTCAGCGAAATGGTTTCC-3'
InDel27	Chr03-NP9-R	5'-CATGCCATCCACTTCCACTA-3'	InDel71	Chr09-MP9-R	5'-CACCAAGTCCTTGCTCATCA-3'
InDel28	Chr04-MP1-F	5'-GCGGTCATAGGCGTTACTGT-3'	InDel72	Chr09-MP11-F	5'-ATGGAATATGAGCCCCAACA-3'
InDel28	Chr04-MP1-R	5'-CGCTGTCACATCGSSTCTTT-3'	InDel72	Chr09-MP11-R	5'-ATCAGGTCGTCCACCAGTTC-3'
InDel29	Chr04-MP2-F	5'-TGGATAGGTTCATGCTGCTG-3'	InDel73	Chr09-NP1-F	5'-ACGAGGATGGCAAGAGGATA-3'
InDel29	Chr04-MP2-R	5'-TTTTTGCCACCTTCCAATTC-3'	InDel73	Chr09-NP1-R	5'-GACGGTGCATGTGCTTTTT-3'
InDel30	Chr04-MP3-F	5'-CTGCCCTATGCATCTGTTCA-3'	InDel74	Chr09-NP2-F	5'-GCGGATGAGGAGGAATCTCT-3'
InDel30	Chr04-MP3-R	5'-CCAACTAGTTCAGGGCAGGA-3'	InDel74	Chr09-NP2-R	5'-TTTACTGCGCCTCGTCTCTT-3'
InDel31	Chr04-MP13-F	5'-TCCGTCCAACTGGAATTGAT-3'	InDel75	Chr09-NP4-F	5'-AGCACTAGCAAATGCCACAA-3'
InDel31	Chr04-MP13-R	5'-AATCCTTCGTGGAAAGCTGA-3'	InDel75	Chr09-NP4-R	5'-ATGACGTTTTTCGGCTTGTC-3'
InDel32	Chr04-NP1-F	5'-ATCTTGCGGCACATACATGA-3'	InDel76	Chr09-NP5-F	5'-GCTGAGCACTTGAGGGTTGT-3'
InDel32	Chr04-NP1-R	5'-CTTCAACACTCAGCCCACCT-3'	InDel76	Chr09-NP5-R	5'-CTGGTCATCGGCTTAGCAAT-3'
InDel33	Chr04-NP2-F	5'-TATAAAGCACCGGTGGAGGT-3'	InDel77	Chr09-NP9-F	5'-GCGGCTTATCACAGCTCCTA-3'
InDel33	Chr04-NP2-R	5'-ACAAATCGTTTCACCGCTTC-3'	InDel77	Chr09-NP9-R	5'-TCACCATGCAAAACGTCCTA-3'
InDel34	Chr04-NP6-F	5'-GGCTGTTGGAGGAATTTTGA-3'	InDel78	Chr10-MP2-F	5'-AGAGATCGAGAGGACGGACA-3'
InDel34	Chr04-NP6-R	5'-CCTTGTACTCTTCTGAGTTTTGGA-3'	InDel78	Chr10-MP2-R	5'-GGAATTCCATGCCCAAATC-3'
InDel35	Chr04-NP7-F	5'-GACCGAGAAAGAAAATCATACACTC-3'	InDel79	Chr10-MP5-F	5'-GCATTTGCATCTGAAAGCTC-3'
InDel35	Chr04-NP7-R	5'-AGGCAAAAAGCCCAACTCTT-3'	InDel79	Chr10-MP5-R	5'-ACCAAACTCTGCAGGAATGC-3'
InDel36	Chr04-NP8-F	5'-ATGCCGTAGATCGTCCTCCT-3'	InDel80	Chr10-MP7-F	5'-AGGCGTTGCCTCTAACACTG-3'
InDel36	Chr04-NP8-R	5'-CAACCGGAGCTGGAAATG-3'	InDel80	Chr10-MP7-R	5'-GTCCGGTGAGTTCGTTTCTC-3'
InDel37	Chr04-NP11-F	5'-AGCTCATCAAAGCGAAAGGA-3'	InDel81	Chr10-MP8-F	5'-CACATGGTTCTTTTCCACGA-3'
InDel37	Chr04-NP11-R	5'-AGTCTAGACGCCTCGACGTT-3'	InDel81	Chr10-MP8-R	5'-GGAGTTGGATGAAAGCCTTG-3'
InDel38	Chr05-MP9-F	5'-ATGGGAAGGCCTACGATTTT-3'	InDel82	Chr10-MP11-F	5'-TGGTAGACGGGTCCTAGTGC-3'
InDel38	Chr05-MP9-R	5'-TGGGTGATGGTAGGAGAATAGA-3'	InDel82	Chr10-MP11-R	5'-TACATCGCTGCTGGAGTGTC-3'
InDel39	Chr05-MP13-F	5'-ATTTAACCTGGCTGCCTGTC-3'	InDel83	Chr10-NP4-F	5'-ACACGGGTCGAAGATCAAAG-3'
InDel39	Chr05-MP13-R	5'-GACCGCGACACTAACAAATG-3'	InDel83	Chr10-NP4-R	5'-GGTGCCAACTTCCTTCATCA-3'
InDel40	Chr05-MP14-F	5'-TTTGCCTAGCCATTTCAGGT-3'	InDel84	Chr10-NP6-F	5'-TTTGCAAGCTGTTTTGGTTC-3'
InDel40	Chr05-MP14-R	5'-CACGGTCAACAATCAGCTCT-3'	InDel84	Chr10-NP6-R	5'-GGGTGAAGGCTACATCGGTA-3'
InDel41	Chr05-NP1-F	5'-AGCATTGGCTGCTAAGCATT-3'	InDel85	Chr10-NP7-F	5'-TACCGTTGTCCGACGCTAAT-3'
InDel41	Chr05-NP1-R	5'-TAGCAGCAACAGCAAACAGG-3'	InDel85	Chr10-NP7-R	5'-TTGTGTAGGCGTCGTGCTTA-3'
InDel42	Chr05-NP2-F	5'-AGAGAGAATCCTCGGCAAGA-3'	InDel86	Chr10-NP9-F	5'-CGACCCTGTCGTATGTATGC-3'
InDel42	Chr05-NP2-R	5'-TTTGTGAGGGGTTCTTGAGC-3'	InDel86	Chr10-NP9-R	5'-TTGTCCTTCTGTGGCTGTTG-3'
InDel43	Chr05-NP5-F	5'-CTTCGTGGACCACATGACAC-3'	InDel87	Chr10-NP11-F	5'-ACGGAATGCAAAAAGCAAAG-3'
InDel43	Chr05-NP5-R	5'-GTACCCTCGCCAGTCAACTC-3'	InDel87	Chr10-NP11-R	5'-GGTGACTTCAACCGGGATTA-3'
InDel44	Chr05-NP6-F	5'-TCTCACGGGTCGAAAGTACC-3'
InDel44	Chr05-NP6-R	5'-CAATCTCGATTGCCTCAACA-3'

[1]	Lanlan ZHANG, Caihua LI, Yuzhu FANG, Yan SONG, Wanlin KANG, Zhiyu LI, Xiao ZHANG, Rui ZHANG. Progress on the Application of Mitochondrial SSR Molecular Markers in Plants [J]. Current Biotechnology, 2023, 13(6): 821-826.
[2]	CHEN Feng1§, XU Jiandi1§, JIANG Mingsong1, LIANG Shuimei2, ZHANG Quanfang2, WANG Wenliang3, LI Guangxian1, YANG Lianqun1,2, ZHU Wenyin1, ZHOU Xuebiao1. Molecular Detection of Rice Blast Resistance Genes Pi-ta, Pi-b, Pi54 and Pikm in Japonica Rice of Huang-huai Region [J]. Curr. Biotech., 2018, 8(1): 46-54.
[3]	LIU Wei, JIANG Nonghui, YUAN Peiyuan, QIU Yanping, FAN Chao, YANG Xiaoyan, XIANG Xu*. Application of SSR and SNP Molecular Marker in Litchi Breeding [J]. Curr. Biotech., 2017, 7(1): 7-12.
[4]	ZHANG Zheng1, LIAN Ling-yan2, WANG Gao-hong1, DU Yan-wei1, LI Yan-fang1, ZHAO Jin-feng1*. The Application of Molecular Markers in Maize Breeding [J]. Curr. Biotech., 2015, 5(4): 259-264.
[5]	SONG Zhi-hong, MENG Qing-zhong, ZHANG Tao, ZHANG Sheng-xi, WANG Gui-chun, LI Guo-rong*. Application of ISSR Molecular Marker in Cotton Genetic Breeding [J]. Curr. Biotech., 2014, 4(6): 411-414.
[6]	ZHU Xing-biao1, ZHENG Yu-zhong2, XIE Li-ling1*, ZHANG Zhen-xia2, ZHA Guang-cai2, ZHANG Yong1, LIU Ya-qun1. Research Progress of Alexandrium tamarense, an Algae Species for Harmful Algal Blooms (HAB) [J]. Curr. Biotech., 2014, 4(6): 421-428.
[7]	HE Hu-yi, TAN Guan-ning, HE Xin-min*, HE Hai-wang, LI Li-shu, TANG Zhou-ping, WANG Hui. Application of Several PCR-based Molecular Markers in Sweet Potato Genetic Diversity Researches [J]. Curr. Biotech., 2014, 4(4): 245-250.
[8]	WU Xing-bo1,2, HAO Jun-jie1, ZHANG Xiao-yan1, WAN Shu-wei1, LI Hong-wei1, SHAO Yang1, SUN Ji-lu1. Identification of Powdery Mildew Resistant Genes based on SCAR Markers in Common Bean (Phaseolus vulgaris* L.) [J]. Curr. Biotech., 2013, 3(5): 357-362.
[9]	LI Chang-sheng1, SONG Shu-yu2, ZHANG Wen-gang3, XIA Han1, ZHAO Chuan-zhi1*. Analysis, Evaluation and Application Prospect of Peanut EST Database [J]. journal1, 2011, 1(3): 172-177.
[10]	LUO Li-ming, LIU Li, YU Li-juan, FAN Xing-ming*. Application of Molecular Marker Technology in Seed Purity Identification of Maize [J]. journal1, 2011, 1(1): 7-13.

Development of InDel Molecular Markers in Sorghum Using Re-sequencing Technology

利用重测序技术开发高粱InDel分子标记

RichHTML

PDF

Knowledge

Abstract

Cite this article

share this article

Figures/Tables 5

References 28

Related Articles 10

Recommended Articles

Metrics

Comments