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

摘要/Abstract

摘要：

【目的】 基于重测序数据和表型数据的遗传多样性分析和综合评价，阐明枸橼、柠檬类种质资源的群体遗传结构，为实现柠檬种质创新提供基础材料。【方法】 2023年11月测定158份枸橼、柠檬类种质资源成熟期果实的13个果实表型性状和43个果皮挥发性功能成分，2023年6月测定幼果期果实的4种类黄酮含量，利用Shannon-Wiener指数和变异系数对158份枸橼、柠檬类种质资源进行遗传多样性分析，结合相关性分析、聚类分析、主成分分析等方法进行综合评价。利用SNP数据构建系统进化树和群体遗传结构分析图，并基于表型数据筛选特异种质。利用表型数据和基因型数据开展全基因组关联分析，筛选出与别罗勒烯相关联的显著变异位点，结合以往报道和基因功能注释，在显著变异位点10 kb附近挖掘出相关的候选基因。【结果】 参试的158份枸橼、柠檬类种质资源的果实品质性状具有丰富的遗传多样性和广泛的变异，13个果实表型性状（单果重FW、单果皮重PW、果实横径FD、果实纵径FL、果形指数FSI、果皮厚度PT、囊瓣数SNPF、单果种子数SNF、单粒种子重SW、可溶性固形物含量TSS、抗坏血酸含量AA、可滴定酸含量TA、固酸比TSS/TA）的变异系数为14.81%—143.47%，遗传多样性指数为1.21—2.01。芦丁、柚皮苷、橙皮苷和新橙皮苷4种类黄酮成分含量的遗传多样性指数为0.75—1.89，43个果皮挥发性功能成分含量的遗传多样性指数为0.25—1.93。将参试枸橼、柠檬类种质资源的60个数量性状进行主成分分析，选出的前5个主成分累计贡献率达66.55%。结合主成分分析结果进行综合评价，得出枸橼、柠檬类种质资源综合得分范围为-0.09—2.14，筛选出沃尔卡默、方达斯蒂柯巴柑檬、卡斯塔奈罗巴柑檬、琥珀、维尔纳柠檬等特异种质。表型聚类分析和基于基因型的系统进化树分析将参试枸橼、柠檬类种质资源分为7个亚群，除在梾檬、㰀檬的分群上有较大差异外，其他种质的分群结果都比较相似，综合评价中得分较高的优异种质资源大多集中于系统进化树的第Ⅲ亚群。群体遗传结构分析结果显示，除将甜柠檬等杂交品种重新划分为一个亚群外，其他品种与系统进化树分析得出的分群结果基本一致。基于别罗勒烯含量的全基因组关联分析筛选出候选基因C71D7_SOLCH和C71DB_LOTJA，均属于细胞色素P450家族。【结论】 参试枸橼、柠檬类种质资源的果实品质性状存在广泛的变异和丰富的遗传多样性。枸橼与宽皮柑橘、柚等不同资源类型的杂交是推动亚群遗传分化的重要因子。综合评价中得分较高的枸橼、柠檬类种质资源在系统进化树中比较集中，表明这些优异和特异种质具有相似的遗传背景。C71D7_SOLCH和C71DB_LOTJA可能参与果皮挥发性物质别罗勒烯的代谢。

关键词: 枸橼, 柠檬, 种质资源, 表型鉴定, 遗传多样性, 重测序

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

何治霖, 孙翠霞, 岳红丽, 谈月霞, 张耀海, 王福生, 刘思涛, 江东. 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[J]. 中国农业科学, 2026, 59(2): 386-401.

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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https://www.chinaagrisci.com/CN/Y2026/V59/I2/386

图/表 11

表1

表2

表3

枸橼、柠檬类种质资源果皮挥发性功能成分含量的统计值"

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

表3

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图2

图3

表4

表5

图4

图5

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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