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

• 专题论坛 • 上一篇    下一篇

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. 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 E-mail:hxg382@126.com
  • 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 Guo1,3, Dalong Guo2,3, Lili Guo1,3, Lin Zhang1,3, Xiaogai Hou1,3*   

  1. 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 E-mail:hxg382@126.com
  • About author:

    ? These authors contributed equally to this paper

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。

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.

表1

牡丹微卫星长度分布"

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

表2

牡丹SSR标记的开发近况"

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

表3

82对牡丹SSR引物信息"

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
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