SSR分子标记在牡丹亲缘关系研究中的应用与研究进展

doi:10.11983/CBB15016

植物学报 ›› 2015, Vol. 50 ›› Issue (5): 652-664.DOI: 10.11983/CBB15016

SSR分子标记在牡丹亲缘关系研究中的应用与研究进展

郭琪^1,³, 郭大龙^2,³, 郭丽丽^1,³, 张琳^1,³, 侯小改^1,^3,^*()

¹河南科技大学农学院, 洛阳 471003
²河南科技大学林学院, 洛阳 471003³河南省油用牡丹工程技术研究中心, 洛阳 471003

收稿日期:2015-02-12 接受日期:2015-06-23 出版日期:2015-09-01 发布日期:2015-10-09
通讯作者: 侯小改
作者简介:? 共同第一作者
基金资助:
国家自然科学基金(No.31370697, No.31372026)、河南省高校科技创新团队支持计划(No.14IRTSTHN014)、河南省高校科技创新人才支持计划(No.13HASTIT004)和河南科技大学创新团队资助(No.2015TTD003)

Application of Simple Sequence Repeat Molecular Markers in the Study of Tree Peony

Qi Guo^1,3, Dalong Guo^2,3, Lili Guo^1,3, Lin Zhang^1,3, Xiaogai Hou^1,3*

¹College of Agriculture, Henan University of Science & Technology, Luoyang 471003, China
²College of Forestry, Henan University of Science & Technology, Luoyang 471003, China
³Henan Engineering Technology Research Center of Paeonia suffruticosa For Oil, Luoyang 471003, China

Received:2015-02-12 Accepted:2015-06-23 Online:2015-09-01 Published:2015-10-09
Contact: Hou Xiaogai
About author:? These authors contributed equally to this paper

摘要/Abstract

摘要： SSR标记具有操作简便、共显性和重复性好等特点。该文总结了通过生物信息学技术、磁珠富集法及二代测序技术开发牡丹(Paeonia suffruticosa) SSR标记引物的方法, 并根据现有研究结果解析了牡丹基因组中SSR位点频率及分布, 详细阐述了SSR标记在牡丹种质资源的遗传多样性、亲缘关系和遗传关系等方面的应用概况, 旨在为今后牡丹SSR标记的研究与应用提供参考。

关键词: 牡丹, SSR, 分子标记, 遗传多样性, 亲缘关系

Abstract: Simple sequence repeat (SSR) markers have the characteristics of simple operation, codominance and reliable reproduciblity in phylogenetic studies. This paper summarizes the techniques for developing peony SSR marker primers: bioinformatics technology, magnetic beads enrichment and next-generation sequencing. Furthermore, we summarize the current findings of the frequency and distribution of SSR loci in peony genome. We hope our summary on the application of SSR markers on tree peony will provide useful references to people who are working on the species.

Key words: Paeonia suffruticosa, simple sequence repeat, molecular marker, genetic diversity, genetic relationship

郭琪, 郭大龙, 郭丽丽, 张琳, 侯小改. SSR分子标记在牡丹亲缘关系研究中的应用与研究进展. 植物学报, 2015, 50(5): 652-664.

Qi Guo, Dalong Guo, Lili Guo, Lin Zhang, Xiaogai Hou. Application of Simple Sequence Repeat Molecular Markers in the Study of Tree Peony. Chinese Bulletin of Botany, 2015, 50(5): 652-664.

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链接本文: https://www.chinbullbotany.com/CN/10.11983/CBB15016

https://www.chinbullbotany.com/CN/Y2015/V50/I5/652

图/表 3

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Base types	Numbers	Percentage (%)
Mononucleotide	4 604	1.90
Dinucleotide	187 934	77.80
Trinucleotide	28 429	11.77
Tetranucleotide	19 087	7.90
Pentanucleotide	164	0.07
Hexanucleotide	1 333	0.55

Base types	Numbers	Percentage (%)
Mononucleotide	4 604	1.90
Dinucleotide	187 934	77.80
Trinucleotide	28 429	11.77
Tetranucleotide	19 087	7.90
Pentanucleotide	164	0.07
Hexanucleotide	1 333	0.55

Author	Total number of sequences examined	Number of SSR- containing sequences	Total number of identified SSRs	Total number of primers designed	Year of publication	Journal of publication
Jing Wu	59 275	4 373	3 787	2 989	2014	Mol Breed
Zhimin Gao	675 221	237 134	164 043	100	2013	BMC Genomics
Haiping Yu	-	-	-	48	2013	Sci Hortic
Barbara Gilmore	48 457 692	11 203	-	1 504	2013	J Am Soc Hortic Sci
Xiaogai Hou	2 204	901	-	29	2011	Am J Bot
Xiaogai Hou	-	362	24	24	2011	Biol Plant
Andreas Homolka	96	56	41	26	2010	Am J Bot
Jingxiu Wang	240	58	-	45	2009	Conserv Genet

Author	Total number of sequences examined	Number of SSR- containing sequences	Total number of identified SSRs	Total number of primers designed	Year of publication	Journal of publication
Jing Wu	59 275	4 373	3 787	2 989	2014	Mol Breed
Zhimin Gao	675 221	237 134	164 043	100	2013	BMC Genomics
Haiping Yu	-	-	-	48	2013	Sci Hortic
Barbara Gilmore	48 457 692	11 203	-	1 504	2013	J Am Soc Hortic Sci
Xiaogai Hou	2 204	901	-	29	2011	Am J Bot
Xiaogai Hou	-	362	24	24	2011	Biol Plant
Andreas Homolka	96	56	41	26	2010	Am J Bot
Jingxiu Wang	240	58	-	45	2009	Conserv Genet

Primer name	Primer sequence (5′-3′)	Expected size (bp)	Repeat motif	Annealing temperature (°C)	GenBank accession number
PS001	F: AAACACCCAAGCAAATCG	475	(CT)₆	54	GBGY01000001
	R: AATGAAACGCCGTCCTCT
PS005	F: GAGACCACCGAGTCACAG	480	(GA)₉	53	GBGY01000005
	R: TCAGAGCATGTCCGAAAC
PS007	F: GACTTCGATAGCCTTGGG	203	(CT)₈	55	GBGY01000007
	R: ATCTCAGCCGTTGTTTGG
PS021	F: AGATGGGAAGTTAAGGTGA	382	(GA)₆	54.5	GBGY01000021
	R: GTATGTTGGTAAATGGGTTT
PS026	F: TTCCCTCCATTCTAACAC	187	(AG)₆	56	GBGY01000026
	R: ACCCTAGCCTCTGACATT
PS041	F: GCACCGATAACTTCCAAAC	488	(TC)₇	57	GBGY01000041
	R: GCAGGCGATGCTACAAAC
PS043	F: TCTCGCATTCATCCTACAT	243	(CT)₇	53	GBGY01000043
	R: TTGCCATAATTCTTCTACCT
PS047	F: AGACGACGAGCAAAGATAT	126	(TC)₈	54	GBGY01000047
	R: AAAGGGCAAGATTGGAAAT
PS052	F: CAAATCTGCTAATTAAAGAC	235	(CT)₇	53	GBGY01000052
	R: GATAGAAGGGAAAGGAAG
PS053	F: ATTGCCAGATTTGTTCAG	407	(AG)₇	55.5	GBGY01000053
	R: CACCACTATTATTCCCTTG
PS054	F: GAAGGATCTGAGAAGCATA	123	(GA)₆	54	GBGY01000054
	R: AGTGAAGGAGACAACCCA
PS057	F: CATCGTCAATTTACTCATC	212	(TC)₆	56	GBGY01000057
	R: TAACATCCAAAGCAACTC
PS068	F: CTTTGGCATTCTCATTCA	174	(TC)₇	55	GBGY01000068
	R: GGTGGTATTGGGCTTCTT
PS074	F: TGCCTTGCTCCTCCTTGT	236	(CT)₇	54	GBGY01000074
	R: CGGTTAGCCATGAATCCC
PS076	F: ATGCCACCTTTTCCTAAT	258	(TC)₈	52	GBGY01000076
	R: TTCTTGTTCCCCTTGTTTC
PS094	F: GCTGCTTGCTTACTCATC	363	(AGC)₆	55	GBGY01000095
	R: TTCTTGTACTCTGCCTCC
PS095	F: TCCCAAGACCTCAAACAAC	394	(CCA)₅	56	GBGY01000096
	R: CCATCAATACGAGCCAAC
PS099	F: GGGTCCAACAACCAAACT	330	(TGG)₅	54	GBGY01000100
	R: GGTCAGCAAGAGCCAAAG
PS105	F: GTCACCGTCGTCTTCATC	196	(CCA)₅	54.5	GBGY01000106
	R: CTGGACCATATTTCGTTGTATG
PS111	F: GCAGATCATGGCGACAAAAC	372	(CAA)₅	52	GBGY01000111
	R: TGCTGAGGCGAAAGAACAG
PS119	F: GCAAAGACAACAGCCTCG	289	(CAG)₆	53	GBGY01000119
	R: CTCACCATCCAATCCCAC
PS121	F: CTGTACCGAACCTGCTTG	365	(TCA)₅	55	GBGY01000123
	R: TGTGGTGAGGCTAAATCC
PS125	F: GCCCTAACCCTATCCCTA	452	(TCA)₇	53	GBGY01000128
	R: AAACCCACCAAGACAAAC
PS134	F: CATCAACTTCGGCTAACA	387	(CAC)₅	54.4	GBGY01000134
	R: CAAACCTACCCAGTCCTAC
PS147	F: TCTGGCAAATACCGTGAA	480	(TTC)₅	56	GBGY01000150
	R: AGCGGAGAAGGATAAATAAG
PS148	F: CTCCACCCGTATCACTCATC	353	(TGG)₅	57.5	GBGY01000151
	R: CGTCTCCTCCATCAACCT
PS153	F: ATGTCCAAACTGGCAATA	260	(CT)₁₀	55	GBGY01000156
	R: CCCTCCCTCAACACTTAC
PS157	F: CTCCCTGAACTCCCTACC	322	(AG)₆	54	GBGY01000160
	R: CTTTCTAAACAGCCAACG
PS160	F: TAGAAGTGGAGGCATCAG	125	(CT)₇	54	GBGY01000162
	R: GAGAAGTTTTGGGTGTCA
PS167	F: TTGTTGGTCGGCATCTCA	317	(AG)₈	57	GBGY01000169
	R: GGGAATGGTCTCGTAGCG
PS173	F: TCTTCCGCCATTACTGAT	120	(GA)₆	54	GBGY01000175
	R: CCTACCTTCGCTAAAACC
PS177	F: GAGAAAGGCAAGCGAGTC	441	(GA)₆	55	GBGY01000179
	R: TCCATTGTTTGTGGGTGT
PS179	F: GTGATGGTCTGATGGAGGA	234	(GA)₆	56	GBGY01000181
	R: AGAAAGCGGAGGAGTGGAG
PS180	F: CCCCGAAATGGAGGAGTC	188	(CT)₆	56	GBGY01000182
	R: AGGGCAGTAGCAGAAGAAAGTC
PS186	F: GAGGTGACGGATGGAGTT	356	(GT)₈	55	GBGY01000188
	R: CCTAAAGAAGGTTGTGGC
PS198	F: TATGCCTTTGGAGTTTGG	277	(TC)₇	54.5	GBGY01000200
	R: TTCGTGGCTTGTTCTGT
PS202	F: GTGGTGGTCCATCTTGAAG	163	(TC)₇	54	GBGY01000204
	R: TTGCTTGAGCGAGTGTTATC
PS203	F: AGTTTTGGGATTCCGTAC	179	(TA)₈	56	GBGY01000205
	R: CAGTGGGATTTTATTTGC
PS219	F: TGACATTGGCATTCCTTG	211	(GAA)₆	54.5	GBGY01000221
	R: CAGACCCTACCCTCTTG
PS227	F: GGGATACTGGGATAGGAC	173	(TTC)₆	53	GBGY01000229
	R: ACTTGGGAATTACTGACG
PS228	F: TGAGGCGTGGTAGAGGTT	121	(TCT)₅	54	GBGY01000230
	R: TCAAGGAGGTGAGGGAGT
PS240	F: AGTAGAATACGAAGAGGCATC	251	(GAA)₆	55	GBGY01000242
	R: CAAGACCGTGAACAAATATC
PS273	F: CCCTCAGATGGGATGGAA	314	(GCCGCT)₄	53	GBGY01000274
	R: CGGTGGTGGTACAACGAAC
PS296	F: CTCTTTCGCTGCCACAAC	419	(GAAGCA)₄	56	GBGY01000296
	R: CTCTGCTCTTCCCGTCTT
PS308	F: ACTACTCTATTGCGAAACC	189	(TC)₇	54.5	GBGY01000308
	R: GTCTTATGGCGGCTATGT
PS309	F: AAGCAAAGCCGTGGAGAT	257	(CT)₆	55	GBGY01000309
	R: GTGCGTGAAAAGGAGACAGAAC
PS318	F: ATCTACTCCCTATCCGTCAC	369	(CCACA)₄	54	GBGY01000318
	R: CCCACAGCTACCTCCTTG
PS321	F: TGCTACCAGCTCCTCCAT	249	(ATCA)₅	53	GBGY01000321
	R: ACCATCTCCACCATTTCG
PS357	F: CACAAGGGTCAGCAGTTT	231	(ATC)₅	53.5	GBGY01000355
	R: CATTGGTAGGCGGTCTTT
PS363	F: TTCAACCACATCTCCCTC	457	(TTG)₇	54	GBGY01000361
	R: CTACCACCATAAGTGTAAGAG
PS364	F: GGAGCAAACCCTAAGCAC	205	(CTT)₅	53.5	GBGY01000362
	R: ATAGCGAGGACCGTGAAT
PS365	F: AACCAAACTAACCCTAAATG	350	(CCA)₇	54	GBGY01000363
	R: GAGTGGATGTGGGAGACG
PS371	F: CATTGAGCCACCCATAGA	219	(CAC)₅	55	GBGY01000369
	R: GCAACAATCCTGGTAGTGA
21A	F: CAACTTTGCCAACTTCGTCCACTTC	295	(TTC)₁₂	55	-
	R: CCCGTCATGAACAAGAAGAAGGAAA
26A	F: TGGGCCCTACAAGTGATGATATTCC	245	(TTG)₇	54	-
	R: ATGGAATCCAGGTTTGTGAATGTGA
42A	F: GTTTGGTTGTCATCAAGGTTGTCGA	345	(TG)₁₈	56	-
	R: ATCAACAAGATTACTCCTACGCCCC
45A	F: TCAAAGCCAAATGGATACGGTCGCG	200	(AC)₁₃	57	-
	R: TTCTTGTTTTCGTTCCTCGCCCCCT
49A	F: TCTGGGTGATAGGTGGAGCTGGTGC	314	(TGC)₅	55	-
	R: GGAAGACGCCCACAATGAAATCACA
51A	F: TATTGGACCCAGTCGATGATGTTTG	259	(CA)₈	54.5	-
	R: GTGTGTGTCGTGCGTTGTGTTAGTG
55A	F: ATCCCAGTCCCGCCTTGCTGCTATC	285	(CT)₈	56	-
	R: TTCACAACACACGCACACACGCACA
56A	F: CAGGTGGCATTTTTGGCTTCTCTCT	388	(AC)₁₅	55	-
	R: TTGGCCCAATCACATGTAATCCCTC
59A	F: TACAACACTTCTCGCCTAACGCACC	270	(AC)₁₈	56	-
	R: AGACATGGTGCAAGTATGGGAGACG
63A	F: CACCGCATATCTCCAACCTCACCTC	277	(TC)₉(AC)₁₇	54	-
	R: TTGGGTAGAGATAGGAGGTTGGGGC
65A	F: CATACCTCCATCATGATGCTGCTGT	355	(TGG)₅	57	-
	R: ATGAAGGCTCAGTAAGAACCTCGGA
73A	F: CCATCTCAGGGTCAGGGTTCTCGTA	375	(CAG)₅	55	-
	R: TAGAGTGTACCTTCACCCCCATCGG
77A	F: AACAGCTCAGGACCATGTGGAAAGT	363	(GA)₁₃	56	-
	R: AATGTATGCGATATCTGACTGCCGA
87A	F: TGTAATCGATCGAGTTTCTTGGGTC	188	(TG)₁₅	54	-
	R: CCTAACACTCCACCACTAAGTCGCT
91A	F: TCAGCCCCTAGCATAGAAGAATCCA	384	(GT)₉ttgta(TG)₁₆	57	-
	R: TCTCACTACCACCTACGCGATGTTC
93A	F: CCTTCTTCTCCTTCGATAGCCACCC	432	(TG)₁₀	55	-
	R: CACGCACTACAACCCAGCCTACACT
99A	F: AAAGGCTGCAAGTCGTATCCTCTCA	406	(TG)₁₄	57	-
	R: AGGCAGTACATCAGGCAGAGGAGGT
Seq4	F: AACTGCTGAGGGCATAGAG	233	(TGG)₆	55	KC121549
	R: CATGATGTTGAGCCACCC
ACG9797	F: GGTCGCTGGGTGTTC	192	(ACG)₈	54	FE529797
	R: GTTGGAGTTGGAGAGGTTG
C-8918	F: AAGAAGGGGAGGAGGAG	201	(AAG)₅(AGG)₄	53	FE528918
	R: GCGAGAAGAAAAGGCAAAAT
PSESP2	F: GACGGAGAGAAAGAGAGCATA	403	(GAA)₅	54	FE528847
	R: GACAAAGACTGACACAGCGAT
PSESP7	F: GGCTAATCTTGTTGCTCAG	174	(A)₂₉	55	FE527983
	R: AACCCCTCTTTCTCCTCA
PAC28	F: CTGCAGGTCGACGATTAC	247	(AC)₁₇	54.5	GQ480169
	R: AGTCCTGAGTAACATTGCCT
PC1	F: CTACCCACGACCCTTTTGAG	243	(AG)₇	56	GQ480171
	R: AGCACTCTCACAACTTTCATAC
Pde106	F: TGGATTCTTATTTGTTTTGAG	86-358	(AG)₁₉	53	-
	R: ACACCGTGTAGCAGATGATGA
Pdel29b	F: CTGCCATTTCTTGCCTTCTTTGT	253-308	(TGG)₆	55	-
	R: TCTACCCTGCCAACAGCACATAC
AT8051F	F: GGTATCAATCCGTGTGC	99-612	(AT)₅	54.5	-
	R: GCGAAAATTTAGATGAGTGT
P05	F: TCGCCCAACCTGTCGTGGAGAT	129-437	(AG)₉	54	-
	R: TTGAATAGAGCGGAATGGAAAA
Pae12	F: AAAGCTTTTGCACAACACACA	97-155	(TA)₆	53	-
	R: ATAGCGCGAAAATTGAGGTG

SSR分子标记在牡丹亲缘关系研究中的应用与研究进展

Application of Simple Sequence Repeat Molecular Markers in the Study of Tree Peony

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