Cluster Analysis and Construction of DNA Fingerprinting of 42 Oriental Cultivars of Flowering Cherry Based on SSR Markers

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

Acta Horticulturae Sinica ›› 2023, Vol. 50 ›› Issue (3): 657-668.doi: 10.16420/j.issn.0513-353x.2021-1057

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Cluster Analysis and Construction of DNA Fingerprinting of 42 Oriental Cultivars of Flowering Cherry Based on SSR Markers

SUN Zeshuo¹^,², JIANG Dongyue², LIU Xinhong², SHEN Xin², LI Yingang², QU Yufei³, LI Yonghua¹^,^*()

¹College of Landscape Architecture and Art，Henan Agricultural University，Zhengzhou 450002，China
²Zhejiang Academy of Forestry，Hangzhou 310023，China
³College of Forestry and Biotechnology，Zhejiang A & F University，Hangzhou 310023，China

Received:2022-09-19 Revised:2022-12-01 Online:2023-03-25 Published:2023-04-03
Contact: *（E-mail：liyhhany@henau.edu）

Abstract

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

CLC Number:

S685.99

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.

Figures/Tables 8

References 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

Cluster Analysis and Construction of DNA Fingerprinting of 42 Oriental Cultivars of Flowering Cherry Based on SSR Markers

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引物名称 Primer name	基因型 Genotype	可区分品种数量 Cultivar No. which can be distinguished	区分率/% Identified rate
SSR5	9	5	11.90
SSR11	13	7	16.67
BPPCT008	19	10	23.81
BPPCT040	16	8	19.05
CPSCT021	25	16	38.10
M9a	12	4	9.52
EMPAS11A	16	11	26.19
PceGA25	9	5	11.90
MA016b	9	4	9.52
PS12A02	25	21	50.00
MA007a	8	5	11.90
pchcms1	19	10	23.81
UDP97-403	22	15	35.71
UDP96-005	17	9	21.43
总计（total）	219	—	—
均值（Mean）	15.64	9.29	22.11

品种编号 Number	DNA数字指纹图谱 DNA fingerprinting	品种编号 Number	DNA数字指纹图谱
品种编号 Number	DNA数字指纹图谱 DNA fingerprinting	品种编号 Number	DNA fingerprinting
YH1	A53/53-B129/142-C104/116	YH22	A52/108-B140/146-C104/109
YH2	A51/108-B131/142-C104/104	YH23	A52/120-B140/146-C104/126
YH3	A51/51-B130/142-C104/116	YH24	A101/109-B146/146-C104/127
YH4	A52/52-B130/130-C104/104	YH25	A108/108-B134/164-C131/144
YH5	A52/108-B128/141-C104/116	YH26	A52/108-B142/142-C104/129
YH6	A52/108-B129/135-C104/104	YH27	A52/101-B134/134-C104/104
YH7	A51/96-B130/145-C110/110	YH28	A51/51-B134/134-C104/116
YH8	A51/108-B136/141-C102/102	YH29	A52/109-B133/146-C104/116
YH9	A52/108-B130/151-C127/127	YH30	A51/51-B134/134-C104/115
YH10	A52/52-B128/147-C110/110	YH31	A51/108-B134/134-C104/115
YH11	A52/102-B127/127-C106/106	YH32	A51/108-B134/134-C103/103
YH12	A52/104-B130/139-C125/135	YH33	A108/108-B134/140-C104/104
YH13	A96/116-B132/148-C107/107	YH34	A51/108-B130/146-C104/104
YH14	A108/108-B134/146-C127/144	YH35	A51/120-B134/148-C110/127
YH15	A52/100-B146/146-C104/104	YH36	A51/109-B130/146-C104/104
YH16	A52/102-B130/130-C127/127	YH37	A51/108-B134/164-C104/104
YH17	A100/100-B130/130-C112/129	YH38	A51/108-B140/140-C104/127
YH18	A52/120-B133/146-C104/108	YH39	A52/109-B132/132-C127/127
YH19	A52/108-B134/146-C104/127	YH40	A102/102-B130/130-C103/130
YH20	A102/102-B130/130-C113/113	YH41	A51/51-B140/146-C112/112
YH21	A108/108-B140/146-C104/127	YH42	A102/102-B132/132-C112/112

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