基于SSR标记的42份樱花品种的聚类分析及DNA指纹图谱构建

doi:10.16420/j.issn.0513-353x.2021-1057

摘要/Abstract

摘要：

通过14对SSR引物基于UPGMA法对42份樱花品种进行聚类分析，并采用引物和基因型组合法构建DNA指纹图谱。结果表明：14对SSR引物共检测出187个等位基因，每对引物平均13.36个，有效等位基因平均6.10个，观察杂合度平均0.31，期望杂合度平均0.80，Shannon’s信息指数平均2.01，多态信息含量平均0.77；共检测出219个基因型，平均15.64个，平均区分率为22.11%。在Dice遗传相似系数约为0.18处时可分为3组，A组主要是山樱系、豆樱系和江户彼岸樱系的品种，B组是钟花樱系的品种，C组中只有尾叶樱；当Dice遗传相似系数约为0.37时，除八重红枝垂樱外，A组又可以分为6个小组。采用引物和基因型组合法构建了42份樱花品种的DNA指纹图谱，为今后樱花品种资源的分子鉴定提供依据。

关键词: 樱花, SSR, 品种, 聚类分析, DNA指纹图谱

Abstract:

In this study，14 pairs of SSR primers were used to cluster 42 oriental cultivars of flowering cherry based on UPGMA method，and to construct DNA fingerprints by combining primers and genotypes. The results showed that a total of 187 alleles were detected from 14 pairs of SSR primers，with an average of 13.36 alleles per pair of primers and an average of 6.10 effective alleles. The average observed heterozygosity was 0.31，the average expected heterozygosity was 0.80，the average Shannon’s information index was 2.01，and the average polymorphism information content was 0.77. In total，there were 219 genotypes detected，with an average of 15.64 genotypes and an average identified rate of 22.11%. When the Dice genetic similarity coefficient was about 0.18，they could be divided into three groups. Group A mainly consisted of cultivars of Prunus serrulata series，P. incisa series and P. spachiana series，group B consisted of cultivars of P. campanulata series，and group C only had P. dielsiana. When the Dice genetic similarity coefficient was about 0.37，group A could be divided into six groups in addition to P. spachiana‘Plena Rosea’. Meanwhile，the DNA fingerprints of 42 oriental cultivars of flowering cherry were constructed by primers and genotypes. This study can provide a reliable basis for molecular identification of oriental cultivars of flowering cherry in the future.

Key words: flowering cherry, SSR, cultivar, cluster analysis, DNA fingerprint

中图分类号:

S685.99

孙泽硕, 蒋冬月, 柳新红, 沈鑫, 李因刚, 屈雨飞, 李永华. 基于SSR标记的42份樱花品种的聚类分析及DNA指纹图谱构建[J]. 园艺学报, 2023, 50(3): 657-668.

SUN Zeshuo, JIANG Dongyue, LIU Xinhong, SHEN Xin, LI Yingang, QU Yufei, LI Yonghua. Cluster Analysis and Construction of DNA Fingerprinting of 42 Oriental Cultivars of Flowering Cherry Based on SSR Markers[J]. Acta Horticulturae Sinica, 2023, 50(3): 657-668.

图/表 8

参考文献 34

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遗传背景 Genetic background	编号 Number	品种 Cultivar	花色 Flower color	花型 Flower type
江户彼岸樱系 Prunus spachiana	YH1	染井吉野樱 Prunus × yedoensis ‘Somei- yoshino’	淡红白色 Light white red	单瓣 Single
series	YH3	美国樱 Prunus × yedoensis‘America’	淡粉红色 Rose pink	单瓣 Single
	YH5	江户彼岸樱 Prunus × subhirtella	淡红色 Light red	单瓣 Single
	YH7	八重红彼岸樱 Prunus × subhirtella‘Yaebeni- higan’	淡红色 Light red	半重瓣 Semidouble
	YH10	越彼岸樱 Prunus × subhirtella‘Koshiensis’	深粉红色 Rediance	单瓣 Single
	YH13	八重红枝垂樱 Prunus spachiana‘Plena Rosea’	淡红色 Light red	半重瓣 Semidouble
	YH18	小松乙女樱 Prunus spachiana‘Komatsu- otome’	淡粉色 Light pink	单瓣 Single
	YH35	御帝吉野樱 Prunus × yedoensis ‘Mikado- yoshino’	白色 White	单瓣 Single
	YH37	思川樱 Prunus × subhirtella‘Omoigawa’	淡紫红色 Light purple red	单瓣 Single
山樱系 Prunus	YH2	白妙樱 Prunus serrulata‘Sirotae’	白色 White	半重瓣 Semidouble
serrulata series	YH4	苔清水樱 Prunus serrulata‘Kokeshimidsu’	淡粉红色 Rose pink	单瓣 Single
	YH6	蝴蝶樱 Prunus serrulata‘Kocho’	淡粉色 Light pink	单瓣 Single
	YH8	郁金樱 Prunus serrulata‘Grandiflora’	淡黄绿色 Light yellowish green	半重瓣 Semidouble
	YH9	红华樱 Prunus serrulata‘Kouka’	淡红色 Light red	重瓣 Double
	YH14	麒麟樱 Prunus serrulata‘Kirin’	淡紫红色 Light purple red	重瓣 Double
	YH15	松前早咲樱 Prunus serrulata‘Matsumae- hayazaki’	淡紫红色 Light purple red	半重瓣 Semidouble
	YH19	银河山樱 Prunus serrulata‘Erecta’	淡红色 Light red	半重瓣 Semidouble
	YH21	御衣黄樱 Prunus serrulata‘Gioiko’	黄绿色 Yellowish green	半重瓣 Semidouble
	YH23	花笠樱 Prunus serrulata‘Hanagasa’	淡红色 Light red	重瓣 Double
	YH24	福禄寿樱 Prunus serrulate‘Contorta’	淡紫红色 Light purple red	半重瓣 Semidouble
	YH25	红时雨樱 Prunus serrulata‘Beni-shigure’	淡紫红色 Light purple red	重瓣 Double
	YH26	仙台屋樱 Prunus jamasakura‘Sendaiya’	淡紫红色 Light purple red	单瓣 Single
	YH29	霞樱 Prunus verecunda	白色 White	单瓣 Single
	YH31	八重红大岛樱 Prunus serrulata ‘Yaebeni- ohshima’	淡红色 Light red	重瓣 Double
	YH32	御车返樱 Prunus serrulata‘Mikurumakaishi’	淡紫红色 Light purple red	单瓣 Single
	YH33	一叶樱 Prunus serrulata‘Hisakura’	淡红色 Light red	重瓣 Double
	YH38	太白樱 Prunus serrulata‘Taihaku’	白色 White	单瓣 Single
	YH41	山樱花 Prunus serrulata	白色 White	单瓣 Single
豆樱系 Prunus	YH27	豆樱 Prunus incisa	白色 White	单瓣 Single
incisa series	YH28	绿樱 Prunus incisa‘Yamadei’	白色 White	单瓣 Single
	YH30	御殿场樱 Prunus × incisa‘Gotenba-zakura’	淡紫红色 Light purple red	单瓣 Single
钟花樱系 Prunus	YH11	钟花樱1 Prunus campanulata	玫红色 Rose red	单瓣 Single
campanulata series	YH12	紫荆樱 Prunus cerasoides	紫红色 Purplish red	单瓣 Single
	YH16	中国红樱 Prunus campanulata‘Zhongguohong’	深红色 Deep red	单瓣 Single
	YH17	红粉佳人樱 Prunus sp.	玫红色 Rose red	单瓣 Single
	YH20	椿寒樱 Prunus pseudocerasus‘Introrsa’	粉红色 Pink	单瓣 Single
	YH22	寒樱 Prunus × kanzakura‘Praecox’	淡红色 Light red	单瓣 Single
	YH34	大渔樱 Prunus × kanzakura‘Tairyo-zakura’	淡紫红色 Light purple red	单瓣 Single
	YH36	大寒樱 Prunus × kanzakura‘Oh-kanzakuru’	淡红色 Light red	单瓣 Single
	YH39	雅樱 Prunus‘Miyabi’	紫红色 Purplish red	单瓣 Single
	YH40	钟花樱2 Prunus campanulata	玫红色 Rose red	单瓣 Single
尾叶樱系 Prunus dielsiana series	YH42	尾叶樱 Prunus dielsiana	粉白色 Pink white	单瓣 Single

遗传背景 Genetic background	编号 Number	品种 Cultivar	花色 Flower color	花型 Flower type
江户彼岸樱系 Prunus spachiana	YH1	染井吉野樱 Prunus × yedoensis ‘Somei- yoshino’	淡红白色 Light white red	单瓣 Single
series	YH3	美国樱 Prunus × yedoensis‘America’	淡粉红色 Rose pink	单瓣 Single
	YH5	江户彼岸樱 Prunus × subhirtella	淡红色 Light red	单瓣 Single
	YH7	八重红彼岸樱 Prunus × subhirtella‘Yaebeni- higan’	淡红色 Light red	半重瓣 Semidouble
	YH10	越彼岸樱 Prunus × subhirtella‘Koshiensis’	深粉红色 Rediance	单瓣 Single
	YH13	八重红枝垂樱 Prunus spachiana‘Plena Rosea’	淡红色 Light red	半重瓣 Semidouble
	YH18	小松乙女樱 Prunus spachiana‘Komatsu- otome’	淡粉色 Light pink	单瓣 Single
	YH35	御帝吉野樱 Prunus × yedoensis ‘Mikado- yoshino’	白色 White	单瓣 Single
	YH37	思川樱 Prunus × subhirtella‘Omoigawa’	淡紫红色 Light purple red	单瓣 Single
山樱系 Prunus	YH2	白妙樱 Prunus serrulata‘Sirotae’	白色 White	半重瓣 Semidouble
serrulata series	YH4	苔清水樱 Prunus serrulata‘Kokeshimidsu’	淡粉红色 Rose pink	单瓣 Single
	YH6	蝴蝶樱 Prunus serrulata‘Kocho’	淡粉色 Light pink	单瓣 Single
	YH8	郁金樱 Prunus serrulata‘Grandiflora’	淡黄绿色 Light yellowish green	半重瓣 Semidouble
	YH9	红华樱 Prunus serrulata‘Kouka’	淡红色 Light red	重瓣 Double
	YH14	麒麟樱 Prunus serrulata‘Kirin’	淡紫红色 Light purple red	重瓣 Double
	YH15	松前早咲樱 Prunus serrulata‘Matsumae- hayazaki’	淡紫红色 Light purple red	半重瓣 Semidouble
	YH19	银河山樱 Prunus serrulata‘Erecta’	淡红色 Light red	半重瓣 Semidouble
	YH21	御衣黄樱 Prunus serrulata‘Gioiko’	黄绿色 Yellowish green	半重瓣 Semidouble
	YH23	花笠樱 Prunus serrulata‘Hanagasa’	淡红色 Light red	重瓣 Double
	YH24	福禄寿樱 Prunus serrulate‘Contorta’	淡紫红色 Light purple red	半重瓣 Semidouble
	YH25	红时雨樱 Prunus serrulata‘Beni-shigure’	淡紫红色 Light purple red	重瓣 Double
	YH26	仙台屋樱 Prunus jamasakura‘Sendaiya’	淡紫红色 Light purple red	单瓣 Single
	YH29	霞樱 Prunus verecunda	白色 White	单瓣 Single
	YH31	八重红大岛樱 Prunus serrulata ‘Yaebeni- ohshima’	淡红色 Light red	重瓣 Double
	YH32	御车返樱 Prunus serrulata‘Mikurumakaishi’	淡紫红色 Light purple red	单瓣 Single
	YH33	一叶樱 Prunus serrulata‘Hisakura’	淡红色 Light red	重瓣 Double
	YH38	太白樱 Prunus serrulata‘Taihaku’	白色 White	单瓣 Single
	YH41	山樱花 Prunus serrulata	白色 White	单瓣 Single
豆樱系 Prunus	YH27	豆樱 Prunus incisa	白色 White	单瓣 Single
incisa series	YH28	绿樱 Prunus incisa‘Yamadei’	白色 White	单瓣 Single
	YH30	御殿场樱 Prunus × incisa‘Gotenba-zakura’	淡紫红色 Light purple red	单瓣 Single
钟花樱系 Prunus	YH11	钟花樱1 Prunus campanulata	玫红色 Rose red	单瓣 Single
campanulata series	YH12	紫荆樱 Prunus cerasoides	紫红色 Purplish red	单瓣 Single
	YH16	中国红樱 Prunus campanulata‘Zhongguohong’	深红色 Deep red	单瓣 Single
	YH17	红粉佳人樱 Prunus sp.	玫红色 Rose red	单瓣 Single
	YH20	椿寒樱 Prunus pseudocerasus‘Introrsa’	粉红色 Pink	单瓣 Single
	YH22	寒樱 Prunus × kanzakura‘Praecox’	淡红色 Light red	单瓣 Single
	YH34	大渔樱 Prunus × kanzakura‘Tairyo-zakura’	淡紫红色 Light purple red	单瓣 Single
	YH36	大寒樱 Prunus × kanzakura‘Oh-kanzakuru’	淡红色 Light red	单瓣 Single
	YH39	雅樱 Prunus‘Miyabi’	紫红色 Purplish red	单瓣 Single
	YH40	钟花樱2 Prunus campanulata	玫红色 Rose red	单瓣 Single
尾叶樱系 Prunus dielsiana series	YH42	尾叶樱 Prunus dielsiana	粉白色 Pink white	单瓣 Single

引物名称 Primer name	引物序列（5′-3′） Primer sequence	退火温度/℃ T_m	来源 Source
SSR5	F：GATGTAGAGGGAGGTTCTGTATTTG	56	基因组测序开发
	R：CGGATCTAGTGAGGGATGGGTATG		Genome sequencing development
SSR11	F：TAGTCTCAGCAGAACCACCAAATAC	56
	R：ATGATACTGATTACGAGAGGCTTAG
BPPCT008	F：ATGGTGTGTATGGACATGATGA	55	Dirlewanger et al.，2002
	R：CCTCAACCTAAGACACCTTCACT
BPPCT040	F：ATGAGGACGTGTCTGAATGG	55
	R：AGCCAAACCCCTCTTATACG
CPSCT021	F：GCCACTTCGGCTAAAAGAGA	55	Mnejja et al.，2004
	R：TCCATATCTCCTCCTGCTTGA
M9a	F：GCCGAAACCCTAGGTGAGCG	58	Yamamoto et al.，2002
	R：CAGGATGCTTGCGGTGCTTG
MA016b	F：TGGCTGGTGGAGACGGAGGA	56
	R：ATGATACCCAGCCTCCCGGG
MA007a	F：GTGCATCGTTAGGAACTGCC	56
	R：GCCCCTGAGATACAACTGCA
EMPaS11A	F：ACCACTTTGAGGAACTTGGG	55	Vaughan & Russell，2004
	R：CTGCCTGGAAGAGCAATAAC
PceGA25	F：GCAATTCGAGCTGTATTTCAGATG	58	Cantini et al.，2001
	R：CAGTTGGCGGCTATCATGTCTTAC
PS12A02	F：GCCACCAATGGTTCTTCC	56	Downey & Lezzoni，2000
	R：AGCACCAGATGCACCTGA
pchcms1	F：GTTACACCTCTGTCACA	56	Sosinski et al.，2000
	R：CTTGGCTGGCATTCCTA
UDP97-403	F：CTGGCTTACAACTCGCAAGC	56	Cipriani et al.，1999
	R：CGTCGACCAACTGAGACTCA
UDP96-005	F：GTAACGCTCGCTACCACAAA	56
	R：CCTGCATATCACCACCCAG

引物名称 Primer name	引物序列（5′-3′） Primer sequence	退火温度/℃ T_m	来源 Source
SSR5	F：GATGTAGAGGGAGGTTCTGTATTTG	56	基因组测序开发
	R：CGGATCTAGTGAGGGATGGGTATG		Genome sequencing development
SSR11	F：TAGTCTCAGCAGAACCACCAAATAC	56
	R：ATGATACTGATTACGAGAGGCTTAG
BPPCT008	F：ATGGTGTGTATGGACATGATGA	55	Dirlewanger et al.，2002
	R：CCTCAACCTAAGACACCTTCACT
BPPCT040	F：ATGAGGACGTGTCTGAATGG	55
	R：AGCCAAACCCCTCTTATACG
CPSCT021	F：GCCACTTCGGCTAAAAGAGA	55	Mnejja et al.，2004
	R：TCCATATCTCCTCCTGCTTGA
M9a	F：GCCGAAACCCTAGGTGAGCG	58	Yamamoto et al.，2002
	R：CAGGATGCTTGCGGTGCTTG
MA016b	F：TGGCTGGTGGAGACGGAGGA	56
	R：ATGATACCCAGCCTCCCGGG
MA007a	F：GTGCATCGTTAGGAACTGCC	56
	R：GCCCCTGAGATACAACTGCA
EMPaS11A	F：ACCACTTTGAGGAACTTGGG	55	Vaughan & Russell，2004
	R：CTGCCTGGAAGAGCAATAAC
PceGA25	F：GCAATTCGAGCTGTATTTCAGATG	58	Cantini et al.，2001
	R：CAGTTGGCGGCTATCATGTCTTAC
PS12A02	F：GCCACCAATGGTTCTTCC	56	Downey & Lezzoni，2000
	R：AGCACCAGATGCACCTGA
pchcms1	F：GTTACACCTCTGTCACA	56	Sosinski et al.，2000
	R：CTTGGCTGGCATTCCTA
UDP97-403	F：CTGGCTTACAACTCGCAAGC	56	Cipriani et al.，1999
	R：CGTCGACCAACTGAGACTCA
UDP96-005	F：GTAACGCTCGCTACCACAAA	56
	R：CCTGCATATCACCACCCAG

引物名称 Primer name	产物大小/bp Production size	等位基因 N_a	有效等位基因 N_e	观察杂合度 H_o	期望杂合度 H_e	Shannon’s指数 I	多态信息含量 PIC
SSR5	209 ~ 331	9	3.13	0.03	0.69	1.53	0.65
SSR11	57 ~ 266	12	5.56	0.29	0.83	2.02	0.80
BPPCT008	51 ~ 120	12	5.70	0.64	0.83	1.99	0.80
BPPCT040	115 ~ 154	15	9.07	0.07	0.90	2.41	0.88
CPSCT021	127 ~ 164	20	8.38	0.60	0.89	2.47	0.87
M9a	141 ~ 167	10	4.95	0.23	0.81	1.85	0.77
EMPAS11A	63 ~ 129	13	5.75	0.20	0.84	2.06	0.81
PceGA25	60 ~ 175	7	2.25	0.50	0.56	1.16	0.52
MA016b	101 ~ 114	8	3.97	0.04	0.76	1.71	0.72
PS12A02	145 ~ 187	23	12.90	0.35	0.94	2.84	0.92
MA007a	48 ~ 123	8	2.68	0.08	0.63	1.23	0.56
pchcms1	142 ~ 175	14	6.16	0.81	0.85	2.18	0.82
UDP97-403	102 ~ 144	20	5.22	0.50	0.82	2.26	0.80
UDP96-005	100 ~ 193	16	9.69	0.02	0.91	2.49	0.89
平均Mean		13.36	6.10	0.31	0.80	2.01	0.77