Association Analysis of SCoT Markers and Leaf Phenotypic Traits in Cherry Germplasm

doi:10.16420/j.issn.0513-353x.2020-0262

Acta Horticulturae Sinica ›› 2021, Vol. 48 ›› Issue (2): 325-335.doi: 10.16420/j.issn.0513-353x.2020-0262

• Research Notes • Previous Articles Next Articles

Association Analysis of SCoT Markers and Leaf Phenotypic Traits in Cherry Germplasm

PENG Fangfang¹, LONG Zhijian², WEI Zhaoxin¹, LI Xunlan¹, LUO Youjin¹, HAN Guohui¹^,^*()

¹Fruit Research Institute,Chongqing Agriculture Science Academys,Chongqing 401329,China
²College of Life Science and Engineering,Southwest University of Science and Technology,Mianyang,Sichuan 621010,China

Received:2020-10-15 Revised:2020-12-17 Online:2021-02-25 Published:2021-03-09
Contact: HAN Guohui E-mail:hghui2007@126.com

Abstract

Abstract:

Based on the established SCoT analysis system,the suitable primers were screened,and then SCoT molecular markers,genetic diversity of leaf traits and their correlation were analyzed in 12 cherry varieties. The results showed that 46 marker primers being suitable for cherry genetic analysis were selected from 102 SCoT marker primers,with a screening rate of 45.1%. A total of 77 allele points were obtained from 18 SCoT primers,including 65 polymorphic loci,with a polymorphism rate of 84.4%. The variation coefficient of leaf traits of 12 varieties was 11.49%-36.93%,which was basically consistent with the results of SCoT marker clustering analysis. Pearson’s correlation analysis showed that a total of 54 marker sites were significantly or extremely significantly correlated with 12 leaf traits. Through the multiple linear stepwise regression analysis,eight specific marker sites related to leaf traits were obtained, which explained the change of 47.8%-100.0% of leaf traits. Sequence analysis of eight association marker sites showed that five markers could find homologous sequences in cherry genome;the similarity was more than 75%;and their chromosome positions could be identified. Among them,four markers could find homologous sequences with functional annotation in NCBI,and three markers could not find homologous sequences.

Key words: cherry, SCoT markers, leaf traits, association analysis

CLC Number:

S662.5

PENG Fangfang, LONG Zhijian, WEI Zhaoxin, LI Xunlan, LUO Youjin, HAN Guohui. Association Analysis of SCoT Markers and Leaf Phenotypic Traits in Cherry Germplasm[J]. Acta Horticulturae Sinica, 2021, 48(2): 325-335.

Figures/Tables 10

References 30

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所属种 Genus	品种 Cultivar	来源 Source
欧洲甜樱桃 Prunus avium L.	雷尼 Rainier	宾库 × 先锋 Bing × Van
	艳阳 Sunburst	先锋 × 斯特拉 Van × Stella
	拉宾斯 Lapins	先锋 × 斯特拉 Van × Stella
	早大果 Крупноплодная	乌克兰 Ukraine
	勃兰特 Burlat	法国 France
	龙冠 Longguan	那翁 × 大紫 Royal Ann（Napoleon）× Black Tartarian
	丽特 Lite	美国 USA
	红灯 Hongdeng	那翁 × 黄玉 Royal Ann（Napoleon）× Huangyu
	秦樱1号 Qinying 1	勃兰特自然突变种 Burlat's natural mutant
中国甜樱桃 P. pscudocerasus Lindl.	玛瑙红 Manaohong	中华酸樱桃实生变异 Variety of Chinese acid cherry
	红宝石 Hongbaoshi	重庆 Chongqing
	乌皮樱桃 WupiYingtao	重庆 Chongqing

所属种 Genus	品种 Cultivar	来源 Source
欧洲甜樱桃 Prunus avium L.	雷尼 Rainier	宾库 × 先锋 Bing × Van
	艳阳 Sunburst	先锋 × 斯特拉 Van × Stella
	拉宾斯 Lapins	先锋 × 斯特拉 Van × Stella
	早大果 Крупноплодная	乌克兰 Ukraine
	勃兰特 Burlat	法国 France
	龙冠 Longguan	那翁 × 大紫 Royal Ann（Napoleon）× Black Tartarian
	丽特 Lite	美国 USA
	红灯 Hongdeng	那翁 × 黄玉 Royal Ann（Napoleon）× Huangyu
	秦樱1号 Qinying 1	勃兰特自然突变种 Burlat's natural mutant
中国甜樱桃 P. pscudocerasus Lindl.	玛瑙红 Manaohong	中华酸樱桃实生变异 Variety of Chinese acid cherry
	红宝石 Hongbaoshi	重庆 Chongqing
	乌皮樱桃 WupiYingtao	重庆 Chongqing

引物名称 Primer name	引物序列（5′-3′） Primer sequence	引物名称 Primer name	引物序列（5′-3′） Primer sequence
SCoT02	CAACAATGGCTACCACCC	SCoT52	CAACATGGCTACCACTCG
SCoT03	CAACAATGGCTACCACCG	SCoT53	CAACATGGCTACCACTGC
SCoT04	CAACAATGGCTACCACCT	SCoT54	CAACATGGCTACCACTGA
SCoT05	CAACAATGGCTACCACGA	SCoT55	CAACATGGCTACCACAGC
SCoT14	ACGACATGGCGACCACGC	SCoT56	CCATGGCTACCACTGGCA
SCoT16	ACCATGGCTACCACCGAC	SCoT61	ACAATGGCTACCACCGCG
SCoT17	ACCATGGCTACCACCGAG	SCoT62	ACAATGGCTACCACTCAG
SCoT19	ACCATGGCTACCACCGGC	SCoT65	ACAATGGCTACCACTGGC
SCoT21	ACGACATGGCGACCCACA	SCoT66	CAATGGCTACCACTACAG
SCoT25	ACCATGGCTACCACCGGG	SCoT68	CAATGGCTACCACTAGCG
SCoT26	ACCATGGCTACCACCGTC	SCoT72	CAATGGCTACCACTAACG
SCoT31	CCATGGCTACCACCGCCT	SCoT75	CAATGGCTACCACTGACA
SCoT34	ACCATGGCTACCACCGCA	SCoT76	CAATGGCTACCATTAGCG
SCoT35	CATGGCTACCACCGGCCC	SCoT81	ACAATGGCTACCACTGCC
SCoT36	GCAACAATGGCTACCACC	SCoT83	ACAATGGCTACCACTGCG
SCoT41	ACCATGGCTACCACCGCA	SCoT86	ACAATGGCTACCACTGCA
SCoT42	ACCATGGCTACCACCAGC	SCoT88	ACAATGGCTACCACCAGC
SCoT46	ACCATGGCTACCACGGTC	SCoT89	ACAATGGCTACCACTACC
SCoT47	ACCATGGCTACCACGGCA	SCoT92	ACAATGGCTACCACTAGG
SCoT48	ACCATGGCTACCACGGAC	SCoT94	ACAATGGCTACCACCACA
SCoT49	ACCATGGCTACCAGCGAG	SCoT96	ACCATGGCTACCACGGAG
SCoT50	ACCATGGCTACCAGCGCA	SCoT97	ACCATGGCTACCACGGGC
SCoT51	CAACATGGCTACCACCAC	SCoT101	ACCATGGCTACCAGCGGC

引物名称 Primer name	引物序列（5′-3′） Primer sequence	引物名称 Primer name	引物序列（5′-3′） Primer sequence
SCoT02	CAACAATGGCTACCACCC	SCoT52	CAACATGGCTACCACTCG
SCoT03	CAACAATGGCTACCACCG	SCoT53	CAACATGGCTACCACTGC
SCoT04	CAACAATGGCTACCACCT	SCoT54	CAACATGGCTACCACTGA
SCoT05	CAACAATGGCTACCACGA	SCoT55	CAACATGGCTACCACAGC
SCoT14	ACGACATGGCGACCACGC	SCoT56	CCATGGCTACCACTGGCA
SCoT16	ACCATGGCTACCACCGAC	SCoT61	ACAATGGCTACCACCGCG
SCoT17	ACCATGGCTACCACCGAG	SCoT62	ACAATGGCTACCACTCAG
SCoT19	ACCATGGCTACCACCGGC	SCoT65	ACAATGGCTACCACTGGC
SCoT21	ACGACATGGCGACCCACA	SCoT66	CAATGGCTACCACTACAG
SCoT25	ACCATGGCTACCACCGGG	SCoT68	CAATGGCTACCACTAGCG
SCoT26	ACCATGGCTACCACCGTC	SCoT72	CAATGGCTACCACTAACG
SCoT31	CCATGGCTACCACCGCCT	SCoT75	CAATGGCTACCACTGACA
SCoT34	ACCATGGCTACCACCGCA	SCoT76	CAATGGCTACCATTAGCG
SCoT35	CATGGCTACCACCGGCCC	SCoT81	ACAATGGCTACCACTGCC
SCoT36	GCAACAATGGCTACCACC	SCoT83	ACAATGGCTACCACTGCG
SCoT41	ACCATGGCTACCACCGCA	SCoT86	ACAATGGCTACCACTGCA
SCoT42	ACCATGGCTACCACCAGC	SCoT88	ACAATGGCTACCACCAGC
SCoT46	ACCATGGCTACCACGGTC	SCoT89	ACAATGGCTACCACTACC
SCoT47	ACCATGGCTACCACGGCA	SCoT92	ACAATGGCTACCACTAGG
SCoT48	ACCATGGCTACCACGGAC	SCoT94	ACAATGGCTACCACCACA
SCoT49	ACCATGGCTACCAGCGAG	SCoT96	ACCATGGCTACCACGGAG
SCoT50	ACCATGGCTACCAGCGCA	SCoT97	ACCATGGCTACCACGGGC
SCoT51	CAACATGGCTACCACCAC	SCoT101	ACCATGGCTACCAGCGGC

引物名称 Primer name	等位位点数 Number of alleles	多态性位点数 Number of polymorphic alleles	多态性比率/% Ratio of olymorphic alleles	引物名称 Primer name	等位位点数 Number of alleles	多态性位点数 Number of polymorphic alleles	多态性比率/% Ratio of polymorphic alleles
SCoT2	3	2	66.7	SCoT31	3	2	66.7
SCoT3	4	4	100	SCoT35	4	2	50.0.
SCoT4	4	4	100	SCoT36	4	3	75
SCoT5	4	4	100	SCoT42	5	3	60
SCoT16	4	2	50	SCoT47	4	4	100
SCoT17	9	9	100	SCoT49	6	6	100
SCoT19	2	1	50	SCoT50	8	7	87.5
SCoT21	2	2	100	SCoT54	4	4	100
SCoT25	4	3	75	总计Total	77	65	84.4
SCoT26	3	3	100

Association Analysis of SCoT Markers and Leaf Phenotypic Traits in Cherry Germplasm

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品种 Cultivar	数量性状Quantitative characters							质量性状Qualitative characters
	叶Leaf					叶柄Petiole		叶形 Shape	叶尖 Tip	叶缘 Margin	叶毛 Hair	叶色 Color
	长/mm Length	宽/mm Width	长宽比 Length- width ratio	面积/cm² Area	厚/mm Thickness	长/mm Length	粗/mm Diameter	叶形 Shape	叶尖 Tip	叶缘 Margin	叶毛 Hair	叶色 Color
雷尼 Rainier	119	66	1.8	78	0.19	35	2.3	1	1	1	1	1
艳阳 Sunburst	124	76	1.6	94	0.18	35	2.2	2	2	1	2	1
拉宾斯 Lapins	100	55	1.8	55	0.21	27	2.1	2	2	2	2	1
早大果 Крупноплодная	146	81	1.8	118	0.22	30	2.4	3	1	2	2	1
勃兰特 Burlat	126	57	2.2	72	0.22	34	2.3	2	1	2	2	1
龙冠 Longguan	123	64	1.9	79	0.19	30	2.2	1	1	1	1	1
丽特 Lite	120	70	1.7	84	0.2	38	2.4	2	1	1	2	1
红灯 Hongdeng	113	63	1.8	71	0.19	36	2.1	2	1	2	2	1
秦樱1号 Qinying 1	122	60	2	73	0.19	40	2.3	1	1	1	2	1
玛瑙红 Manaohong	89	44	2	39	0.14	14	1.1	3	1	1	1	2
红宝石 Hongbaoshi	152	73	2.1	111	0.19	16	1.7	3	1	1	1	2
乌皮樱桃 WupiYingtao	109	43	2.5	47	0.17	12	1.3	2	1	1	1	2
标准差 SD	17.31	11.76	0.25	23.52	0.02	9.71	0.43	0.74	0.39	0.49	0.51	0.45
平均值 Mean	120.25	62.67	1.93	76.75	0.19	28.92	2.03	2.00	1.17	1.33	1.58	1.25
变异系数/% Coefficent of variation	14.40	18.76	12.73	30.64	11.49	33.58	21.32	36.93	33.36	36.93	32.52	36.18

性状 Trait	标记 Marker	决定系数/% R²	标准回归系数 Regression coefficient
叶宽 Leaf width	SCoT5-900	53.8	-0.761
长宽比 Length-width ratio	SCoT36-1000	47.8	0.725
叶柄长 Petiole length	SCoT54-1200,SCoT16-1000	92.3	-0.307
叶柄粗 Petiole diameter	SCoT2-1700,SCoT25-1000	93.2	-0.292
叶厚 Leaf thickness	SCoT19-1200	54.1	-0.763
叶尖 Leaf tip	SCoT4-2000	56.0	0.775
叶色 Leaf color	SCoT2-1700	100.0	1

标记 Marker	GDR				NCBI
标记 Marker	数据库 Databases	染色体 Chr	相似性% Similarity	E值 E value	基因登录号 Accession No.	功能注释 Functional annotation	相似性% Similarity	E值 E value
SCoT5-900	Prunus avium Tieton Genome v1.0	—	—	—	—	—	—	—
SCoT36-1000		Chr5	86.03	3.6934e-161	—	—	—	—
SCoT54-1200		Chr4	91.03	0	XP_021807299.1	樱桃U-box结构蛋白质26 U-box domain-containing protein 26-like isoform X2[Prunus avium]	60.25	3e-44
SCoT16-1000		Chr6	77.83	4.71129e-94	XP_021810548.1	樱桃UDP-糖基转移酶87A1 UDP-glycosyltransferase 87A1-like [Prunus avium]	39.82	2e-17
SCoT2-1700		—	—	—	—	—	—	—
SCoT25-1000		—	—	—	—	—	—	—
SCoT4-2000		Chr6	80.77	1.03397e-8	XP_015948098.1	蔓花生N-乙酰转移酶HLS1 probable N-acetyltransferase HLS1-like[Arachis duranensis]	30.00	0.015
SCoT19-1200		Chr1	75.44	9.53086e-59	XP_008220294.1	樱桃天冬氨酸蛋白酶2 aspartic proteinase-like protein 2 [Prunus avium]	51.16	1e-04

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