基于重测序枸橼、柠檬类种质资源的遗传多样性分析和别罗勒烯的全基因组关联分析

doi:10.3864/j.issn.0578-1752.2026.02.012

Abstract

Abstract:

【Objective】 To explore the elite germplasm resources of citron and lemon, this study conducted genetic diversity analysis and comprehensive evaluation based on resequencing and phenotypic data. The research aims to elucidate the population genetic structure of citron and lemon germplasm resources, providing foundational materials for lemon germplasm innovation. 【Method】 In November 2023, 13 fruit traits and 43 volatile functional components in the peel of 158 citron and lemon germplasm resources were measured. In June 2023, the contents of 4 flavonoids in immature fruits were analyzed. Genetic diversity was assessed using the Shannon-Wiener index and coefficient of variation. Combined with correlation analysis, cluster analysis, principal component analysis and other methods, the citron, lemon germplasm resources were comprehensively evaluated. SNP data were used to construct the phylogenetic tree and analyze population genetic structure. Specific accessions were screened based on phenotypic data. Genome-wide association analysis (GWAS) was performed to identify significant variation sites associated with alloocimene. Candidate genes within 10 kb of these sites were annotated and analyzed. 【Result】 The fruit traits of 158 citron, lemon germplasm resources displayed rich genetic diversity and extensive variation, The coefficient of variation of the 13 phenotypic traits (single fruit weight FW, single fruit peel weight PW, fruit transverse diameter FD, fruit longitudinal diameter FL, fruit shape index FSI, peel thickness PT, number of segments SNPF, seed number per fruit SNF, single seed weight SW, soluble solids content TSS, ascorbic acid content AA, titratable acid content TA, solid acid ratio TSS /TA) ranged from 14.81%-143.47%, and the genetic diversity index ranged from 1.21 to 2.01.The genetic diversity index of 4 flavonoids (rutin, naringin, hesperidin and neohesperidin) in fruits ranged from 0.75 to 1.89, and the genetic diversity index of 43 volatile compounds in peel ranged from 0.25 to 1.93. The principal component analysis on 60 quantitative traits of citron, lemon germplasm resources was carried out, the top 5 principal components explained 66.55% of cumulative variance. A comprehensive evaluation was conducted based on the results of principal component analysis, and comprehensive evaluation score ranged from -0.09 to 2.14, specific germplasms such as Volkamer (Citrus volkameriana Pasquale), Fantastico Bergamot (Citrus bergamia Risso), Castagnaro Bergamot (Citrus bergamia Risso), Amber Lemon (Citrus limon (L.) Burm.f.) and Verna Lemon (Citrus limon (L.) Burm.f.) were identified. Germplasm resources were divided into 7 sub-groups, with high consistency between phenotypic clustering and phylogenetic analysis, except Lime (Citrus aurantifolia Swingle) and Citrus limonia sub-groups showed slight divergence. The elite germplasm clustered predominantly in sub-group 3, indicating shared genetic background. The population genetic structure analysis was consistent with the phylogeny analysis results except that the hybrid varieties (e.g., sweet lemon) formed a distinct sub-group. Significant SNP loci associated with alloocimene content were identified. Two cytochrome P450 family genes (C71D7_SOLCH, C71DB_LOTJA) were proposed as potential regulators of alloocimene metabolism. 【Conclusion】 Citron and lemon germplasm exhibit extensive genetic diversity in fruit quality traits. Phenotypic clustering analysis was similar to phylogenetic tree analysis and population genetic structure analysis, it showed that gene introgression from mandarin and pomelo likely drove sub-group differentiation. Citron and lemon germplasm resources with higher scores in the comprehensive evaluation were more concentrated in the same sub-group in phylogenetic tree, indicated similar genetic background were presented in these elite and specific germplasms. The candidate genes of C71D7_SOLCH and C71DB_LOTJA may be involved in the metabolism of alloocimene, a volatile substance in the peel.

Key words: citron, lemon, germplasm resources, phenotypic identification, genetic diversity, resequencing

HE ZhiLin, SUN CuiXia, YUE HongLi, TAN YueXia, ZHANG YaoHai, WANG FuSheng, LIU SiTao, JIANG Dong. Genetic Diversity Analysis and GWAS of Alloocimene Based on Resequencing of Citron, Lemon Germplasm Resources[J].Scientia Agricultura Sinica, 2026, 59(2): 386-401.

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Figures/Tables 11

Table 1

Table 2

Table 3

Statistical values of volatile functional components content in peel of citron, lemon germplasm resources"

种类 Types	最小值 Min	最大值 Max	均值±标准差 Mean±SD	中位数 Med	变异系数 CV (%)	多样性指数 H
反式-2-己烯醛 Trans-2-hexenal (μg·g^-1)	0.00	115.72	14.17±18.86	6.85	133.08	1.53
α-蒎烯α-pinene (μg·g^-1)	46.91	3243.90	451.83±437.87	366.42	96.91	1.53
β-蒎烯β-pinene (μg·g^-1)	0.00	4111.50	789.63±814.04	530.69	103.09	1.63
桧烯Sabenene (μg·g^-1)	0.00	2936.65	256.7±595.63	0.00	232.03	0.85
月桂烯Myrcene (μg·g^-1)	0.00	3700.35	628.33±491.66	544.54	78.25	1.75
α-水芹烯α-phellandrene (μg·g^-1)	0.00	3298.94	70.56±310.22	31.17	439.63	0.49
delta-3-carene (μg·g^-1)	0.00	291.89	36.87±54.32	0	147.32	1.45
α-松油烯α-terpinene (μg·g^-1)	0.00	372.64	47.69±69.76	21.15	146.28	1.51
柠檬烯Limonene (μg·g^-1)	0.00	30464.39	6898.57±3386.06	6450.99	49.08	1.85
顺式-罗勒烯cis-ocimene (μg·g^-1)	0.00	913.36	105.40±174.29	38.25	165.37	1.49
γ-松油烯γ-Terpinene (μg·g^-1)	0.00	5496.34	272.54±619.11	57.28	227.16	0.92
正辛醇1-octanol (μg·g^-1)	0.00	201.46	28.66±31.29	23.12	109.16	1.66
异松油烯Terpinolene (μg·g^-1)	0.00	1029.97	151.13±181.93	84.12	120.38	1.53
芳樟醇Linalool (μg·g^-1)	34.30	4871.18	456.50±829.34	160.16	181.67	0.85
别罗勒烯Alloocimene (μg·g^-1)	0.00	383.26	33.5±61.76	11.63	184.37	1.35
正壬醛Nonanal (μg·g^-1)	0.00	87.67	17.21±24.43	0.00	141.90	1.47
香茅醛Citronellal (μg·g^-1)	0.00	1220.20	70.19±192.28	11.26	273.95	0.75
4-松油烯醇4-terpineol (μg·g^-1)	0.00	356.95	112.70±81.01	106	71.88	1.93
α-松油醇α-terpineol (μg·g^-1)	0.00	2403.68	283.85±356.64	190.04	125.65	1.42
正癸醛Decanal (μg·g^-1)	0.00	359.77	48.70±54.91	35.91	112.75	1.56
香茅醇Citronellol (μg·g^-1)	0.00	780.35	68.08±130.72	0.00	192.01	1.36
香叶醇Geraniol (μg·g^-1)	0.00	954.00	112.81±160.10	34.56	141.92	1.53
反式柠檬醛Trans- geranial (μg·g^-1)	0.00	1968.27	263.11±377.31	91.03	143.40	1.51
二甲基辛二烯3,7-dimethyl-1,6-octadiene (μg·g^-1)	0.00	65.15	11.97±13.62	9.25	113.81	1.62
百里香酚Thymol (μg·g^-1)	0.00	1595.56	20.30±150.09	0.00	739.28	0.25
正十一醛Undecanal (μg·g^-1)	0.00	198.59	14.06±21.17	9.21	150.58	1.54
α-荜澄茄油烯α-cubebene (μg·g^-1)	0.00	113.42	12.22±19.85	1.98	162.45	1.43
乙酸橙花酯Nerylacetate (μg·g^-1)	0.00	866.85	147.59±180.98	66.49	122.62	1.56
古巴烯Copaene (μg·g^-1)	0.00	160.17	17.68±32.46	2.62	183.65	1.43
乙酸香叶酯Geranyl acetate (μg·g^-1)	0.00	754.77	103.86±159.23	49.62	153.30	1.41
榄香烯Elemene (μg·g^-1)	0.00	610.32	29.37±66.27	9.62	225.64	0.85
月桂醛Lauryl aldehyde (μg·g^-1)	0.00	115.80	11.19±17.39	5.29	155.35	1.51
β-石竹烯β-caryophyllene (μg·g^-1)	0.00	666.93	157.12±146.37	117.51	93.16	1.78
毕澄茄烯Cubebene (μg·g^-1)	0.00	65.00	11.01±14.22	3.79	129.18	1.54
金合欢烯Farnesene (μg·g^-1)	0.00	1271.53	86.11±209.31	34.14	243.07	0.57
茂伦烯Muurolene (μg·g^-1)	0.00	109.53	17.41±22.72	7.07	130.48	1.57
大牛儿烯D Germacrone D (μg·g^-1)	0.00	360.37	52.5±75.62	12.82	144.02	1.52
α-香柠檬烯α-bergamotene (μg·g^-1)	0.00	1268.51	272.92±261.71	212.11	95.89	1.89
巴伦西亚橘烯Valencene (μg·g^-1)	0.00	363.39	25.10±52.52	2.98	209.23	0.92
红没药烯Bisabolene (μg·g^-1)	0.00	1791.62	283.99±316.13	217.82	111.32	1.58
杜松烯Cadinene (μg·g^-1)	0.00	335.95	44.83±62.03	13.58	138.36	1.49
橙花醇Nerol (μg·g^-1)	0.00	778.09	89.18±142.53	0.00	159.82	1.39
顺式-柠檬醛cis-neral (μg·g^-1)	0.00	1687.75	161.8±262.28	39.54	162.10	1.49
平均值Mean	-	-	-	-	168.38	1.39

Table 3

Fig. 1

Fig. 2

Fig. 3

Table 4

Table 5

Fig. 4

Fig. 5

Fig. 6

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性状 Traits	最小值 Min	最大值 Max	均值±标准差 Mean±SD	中位数 Med	变异系数 CV (%)	多样性指数 H
单果重FW (g)	22.90	1762	246.70±266.99	163.30	108.22	1.37
果实横径FD (cm)	3.07	14.30	7.12±1.89	6.72	26.51	1.81
果实纵径FL (cm)	2.89	17.30	7.65±2.44	7.33	31.85	1.85
果形指数FSI	0.72	2.29	1.08±0.24	1.05	21.82	1.84
果皮厚度PT (cm)	0.09	2.90	0.39±0.34	0.30	88.36	1.40
单果皮重PW (g)	6.25	861.20	88.00±126.25	52.79	143.47	1.24
囊瓣数SNPF	7.00	17.00	10.27±1.75	10.00	17.05	1.89
单果种子数SNF	0.00	141	26.45±25.05	18.00	94.69	1.76
单粒种子重SW (g)	0.00	0.59	0.19±0.10	0.16	55.26	1.86
可溶性固形物TSS (%)	5.80	13.70	8.34±1.23	8.10	14.81	1.85
可滴定酸TA (g/100 mL)	0.28	9.73	3.67±1.45	3.79	39.59	2.01
固酸比TSS/TA	1.21	27.50	3.16±3.28	2.05	103.90	1.21
抗坏血酸AA (mg/100 mL)	11.40	83.85	32.86±10.74	32.17	32.67	1.92
平均值Mean	—	—	—	—	59.34	1.65

种类 Types	最小值 Min	最大值 Max	均值±标准差 Mean±SD	中位数 Med	变异系数 CV (%)	多样性指数 H
芦丁Rutin (μg·mL^-1)	0.00	27.45	3.94±5.29	2.17	134.18	1.55
柚皮苷Naringin (μg·mL^-1)	0.00	1384.79	154.79±355.34	0.00	229.57	0.75
橙皮苷Hesperidin (μg·mL^-1)	0.00	326.70	64.26±55.96	62.72	87.08	1.89
新橙皮苷Neohesperidin (μg·mL^-1)	0.00	1202.73	99.07±226.69	0.00	228.83	0.76
平均值Mean	—	—	—	—	169.92	1.24

性状 Traits	主成分1 PC1	主成分2 PC2	主成分3 PC3	主成分4 PC4	主成分5 PC5
单果重FW (g)	-0.074	0.277	-0.124	-0.604	0.546
果形指数FSI	0.447	-0.447	-0.423	-0.076	0.312
可溶性固形物TSS (%)	-0.489	0.221	0.362	0.531	0.125
可滴定酸TA (g/100 mL)	0.314	-0.507	-0.087	0.539	0.001
抗坏血酸AA (mg/100 mL)	-0.323	0.093	0.044	0.495	0.600
柚皮苷Naringin (μg·mL^-1)	-0.441	0.520	0.154	0.094	0.009
蒎烯Pinene (μg·g^-1)	0.604	-0.055	0.019	0.430	0.249
桧烯Sabenene (μg·g^-1)	0.050	-0.333	0.514	-0.092	-0.097
月桂烯Myrcene (μg·g^-1)	0.459	0.304	0.570	-0.190	0.353
松油烯Terpinene (μg·g^-1)	0.050	-0.226	0.591	0.038	-0.204
柠檬烯Limonene (μg·g^-1)	0.314	-0.042	0.791	-0.177	0.059
罗勒烯Ocimene (μg·g^-1)	0.644	0.471	-0.137	-0.018	-0.176
芳樟醇Linalool (μg·g^-1)	0.377	0.751	-0.056	0.220	-0.173
乙酸香叶酯Geranyl acetate (μg·g^-1)	0.581	0.630	-0.102	0.149	-0.050
α-香柠檬烯α-bergamotene (μg·g^-1)	0.752	-0.360	0.077	0.011	0.069
特征值Eigenvalue	2.978	2.433	1.961	1.531	1.080
方差贡献率Variance contribution rate (%)	19.855	16.223	13.074	10.204	7.199
累计贡献率Accumulated contribution rate (%)	19.855	36.078	49.152	59.356	66.555

编号 Code	单果重 FW	柚皮苷 Naringin	蒎烯 Pinene	月桂烯 Myrcene	柠檬烯 Limonene	罗勒烯 Ocimene	芳樟醇 Linalool	α-香柠檬烯 α-bergamotene
H4	119.85	0.00	1591.21	2328.93	30464.39	20.67	209.8	779.80
H119	350.12	301.78	2847.78	1646.42	9849.52	707.42	4871.18	345.45
H120	296.52	207.81	3007.67	2038.05	7767.49	1006.22	2861.46	370.65
H97	342.00	125.60	2281.77	797.39	7073.66	736.81	3849.56	204.99
H86	145.80	0.00	1089.39	1235.88	16867.77	45.28	233.77	1055.60
H21	297.35	264.52	2576.17	1873.15	8038.02	367.72	1742.97	342.25
H11	169.63	0.00	5523.10	1288.77	11033.55	137.71	125.81	757.55
MEAN	245.90	128.53	2702.42	1592.71	13013.43	431.64	1985.12	550.86
AVTG	246.70	154.79	789.63	628.33	6898.57	105.40	456.50	272.92

Genetic Diversity Analysis and GWAS of Alloocimene Based on Resequencing of Citron, Lemon Germplasm Resources

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