基于表型性状与SSR标记的冬瓜、节瓜种质资源遗传多样性分析

doi:10.3864/j.issn.0578-1752.2024.17.010

Abstract

Abstract:

【Objective】To analyze the genetic diversity of wax gourd and chieh-qua germplasm resources, this study constructed a comprehensive evaluation system of wax gourd and chieh-qua germplasm and screened out excellent wax gourd and chieh-qua germplasms, so as to provide the valuable theoretical support for the innovation and variety selection of wax gourd and chieh-qua germplasm.【Method】148 wax gourd and chieh-qua germplasms from different sources were used as the test materials, and then the genetic diversity analysis was conducted using 28 phenotypic traits and 19 pairs of SSR markers. A variety of multiple statistical methods, including variation coefficient, Shannon-Wiener genetic diversity index, correlation analysis, principal component analysis, subordinate function value analysis, stepwise regression analysis, and cluster analysis, were used to analyze the genetic diversity and comprehensively evaluate on wax gourd and chieh-qua germplasm resources.【Result】Wax gourd and chieh-qua germplasm resources exhibited high genetic diversity, with the genetic diversity index of the 11 qualitative traits ranging from 0.39 (Generotype) to 1.45 (Fruit shape), the genetic diversity index of the 17 quantitative traits ranging from 1.89 (First male flower node) to 2.09 (Petiole length), and the variation coefficients of the 17 quantitative traits ranging from 9.76% (Seed shape index) to 63.95% (Weight per fruit). The variation coefficients of the first female flower node (42.32%), fruit length (42.95%), fruit shape index (47.05%), first male flower node (47.48%) and weight per fruit (63.95%) were all greater than 40%, which showed great potential for genetic improvement. Principal component analysis showed that the 18 main phenotypic traits were integrated into 6 principal components, with contribution rates ranging from 6.427% to 29.605%, and the additive contributing rate came up to 81.236%. The phenotypic comprehensive evaluation F value calculated by subordinate function values analysis showed that the BR12 (1.47) and BR25 (1.14) had the best characteristics. 15 phenotypic traits were extremely significantly correlated with the F value. The mathematical model of phenotypic evaluation was established by stepwise regression analysis, and 9 phenotypic comprehensive evaluation indicators were screened out. The number of alleles amplified by 19 SSR primers in the population material ranged from 2 to 6, the variation range of polymorphic information was 0.02-0.70, the Shannon’s diversity index distribution range was 0.06-1.48, which showed that 148 wax gourd and chieh-qua germplasm resources had rich genetic diversity. The genetic diversity of chieh-qua population was slightly higher than that of wax gourd population, and the genetic variation within individuals was the main reason for the overall genetic diversity of wax gourd and chieh-qua. Based on the classification of phenotypic traits and molecular markers, 148 wax gourd and chieh-qua germplasm resources were divided into 6 categories and 3 categories, respectively.The clustering results of the two methods did not cluster wax gourd and chieh-qua resources into two categories, and there was no obvious correlation with geographical location.【Conclusion】148 wax gourd and chieh-qua germplasms resources had rich phenotypic genetic variation and high genetic diversity. The leaf length, first female flower node, fruit length, fruit thick, pedicle length, seed width, wax powder, fruit shape and seed type could be used as the key indicators for identifying wax gourd and chieh-qua germplasm resources. The clustering results based on the classification of main agronomic traits and molecular markers were consistent to some extent. There was no obvious correlation between the cluster and the geographical origin.

Key words: wax gourd, chieh-qua, phenotypic traits, SSR markers, genetic diversity, comprehensive evaluation

ZHAI CaiJiao, GE LiJiao, CHENG YuJing, QIU Liang, WANG XiaoQiu, LIU ShuiDong. Genetic Diversity Analysis of Wax Gourd and Chieh-Qua Germplasm Resources Based on Phenotypic Traits and SSR Markers[J].Scientia Agricultura Sinica, 2024, 57(17): 3440-3457.

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Figures/Tables 17

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Table 9

Genetic diversity of 19 SSR markers in 148 wax gourd and chieh-qua germplasm resources"

引物 Primer name	引物序列 Primer sequence (5′-3′)	等位基因数 Number of alleles (Na)	有效等位基因数 Number of effective alleles (Ne)	Shannon’s多样性指数 Shannon’s diversity index (I)	Nei’s多样性指数 Nei’s diversity index (H)	多态性信息含量 Polymorphism information content (PIC)
1c096	F: GACACTACCTTGCGCAGTGA R: TGCTACAACGGCAAATTCCA	3	2.92	1.08	0.66	0.58
1c189	F:GAGAAAAGTTTGACATATCCACTCT R: GAGTGTAGCTCAACTGGCGT	6	3.65	1.48	0.73	0.68
2c053	F: CCCGCCACTCAATCTTCCTT R: AGTGGATGATGAGGTATGCGA	2	1.19	0.30	0.16	0.15
3c190	F: TTTGCTCGACTGACTCCGAC R: ACGAGACACAATGCAGGGAG	4	2.79	1.14	0.64	0.57
4c020	F: ACCTCTGTTCAGGGTAAAGCA R:AGTGACACACTTAAATGGTGAAACC	5	3.95	1.47	0.75	0.70
4c071	F: CGCAACTTGCAACCTACTCG R: ACACTTTTGTTGTCATCCCACCT	2	1.21	0.32	0.18	0.16
5c190	F: TGAACGGTCGTTAACTGCGT R: AGACTCAAACTACTCGGACAAA	2	2.00	0.69	0.50	0.37
8c050	F: GATGCGAGCCTTCTTCAAACA R: AGTACGTATTGTTGCACTTACACT	3	2.20	0.86	0.55	0.44
8c070	F: CTGGAACGCATCTCTCTGCT R: TCCAGTGTCTCTTCATCCGA	2	2.00	0.69	0.50	0.37
8c186	F: CCCGCCAATTCGAACCATTC R: TACCAACCAGGGCAAAACGT	6	1.41	0.53	0.29	0.26
9c051	F: AAAACGAGAAACTGCAGCCG R: TCCTCCTCTTCTCCTCTGCC	2	1.02	0.06	0.02	0.02
9c071	F: ACCCATTTTGTCCTACCATGTGT R: CGTCTTCGTCAAATTGGGACT	3	2.43	0.96	0.59	0.50
9c255	F: CCTTTCTTCCATAAGTCGAGGGT R: AGGTTTGCTCCAACCAAAAAGA	2	1.43	0.48	0.30	0.26
10c006	F: CGATGCGTGCGCCTAAAATT R: ACACGAGAAATTGGCAAACAACT	4	2.63	1.08	0.62	0.54
10c148	F: AAGCGTACCTTCACAGAGCC R: TCCCCAAATGCCCTAACGTC	3	2.34	0.92	0.57	0.48
11c160	F: GCCCACACTCACCTTACACA R: AGCCCCACCGAATTAATGCT	3	2.52	0.99	0.60	0.52
11c204	F: AGAAGCTTGTGGAAAAGTCAACT R: CGAAGTAGCCCAATCAAAGTGT	2	1.28	0.38	0.22	0.19
11c239	F: AGACTCCTAGAACACACACACC R: ACCCCTTCAAATCCAAACTCA	3	1.09	0.20	0.08	0.08
12c147	F: ACAAATCCCCACAAGACGGG R: TGCGTTTTACTTGCCTATGTGA	3	2.57	1.00	0.61	0.53
均值Mean		3.16	2.14	0.77	0.45	0.39

Table 9

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性状 Trait	分级 Classification
性状 Trait	0	1	2	3	4	5	6	7	8
叶片形状 Leaf shape		掌状 Palmate	心脏形Cordate	近圆形 Subround	近三角形Subtriangular
叶片颜色Leaf color		浅绿Light green	绿Green	深绿Dark green
性型 Generotype		纯雌株Gynoecious	强雌株 Predominately gynoecious	雌全株Gynomonoecious	雌雄全株 Dimonoecious	雌雄株Monoecious	完全株Hermaphrodite line	雄全株Androdioecy	纯雄株Androecy
瓜面蜡粉 Wax powder	无 Without	少 Little	中 Medium	多 More
老瓜皮色 Fruit basal color		银灰 Silvery grey	浅绿 Light green	绿 Green	深绿 Dark green	墨绿 Blackish green
棱沟 Furrow depth	无 Without	浅 Shallow	中 Medium	深 Deep
瓜形状 Fruit shape		扁球形 Depressed-globose	球形 Globose	短圆筒 Short cylindrical	椭球形Spheroidicity	梨形 Pyriform	长圆筒 Long cylindrical
瓜瓤类型 Melon flesh type		散瓤 Loose flesh	吊瓤 Lifting flesh
近瓜蒂端瓜面形状 Shape of the fruit surface near the pedicel		凹 Concave	平 Flat	圆 Circle	尖 Sharp
瓜顶形状 Shape of the fruit surface near the top		凹 Concave	平 Flat	圆 Circle	尖 Sharp
种子类型 Seed type		无棱光籽 Light seed without edge	有棱扁籽Corded flat seed

等级 Grade	计算公式 Computational formula	分级标准 Grading standard
1	x-2δ	<x-2δ
2	(x-2δ)+0.5δ	x-2δ—(x-2δ)+0.5δ
3	(x-2δ)+2×0.5δ	(x-2δ)+0.5δ—(x-2δ)+2×0.5δ
4	(x-2δ)+3×0.5δ	(x-2δ)+2×0.5δ—(x-2δ)+3×0.5δ
5	(x-2δ)+4×0.5δ	(x-2δ)+3×0.5δ—(x-2δ)+4×0.5δ
6	(x-2δ)+5×0.5δ	(x-2δ)+4×0.5δ—(x-2δ)+5×0.5δ
7	(x-2δ)+6×0.5δ	(x-2δ)+5×0.5δ—(x-2δ)+6×0.5δ
8	(x-2δ)+7×0.5δ	(x-2δ)+6×0.5δ—(x-2δ)+7×0.5δ
9	(x-2δ)+8×0.5δ	(x-2δ)+7×0.5δ—(x-2δ)+8×0.5δ
10	x+2δ	>x+2δ

性状 Trait	频率Frequency									遗传多样性指数 Genetic diversity index (H′)
性状 Trait	0	1	2	3	4	5	6	7	8	遗传多样性指数 Genetic diversity index (H′)
叶片形状 Leaf shape		0.56	0.34		0.10					0.92
叶片颜色 Leaf color		0.28	0.47	0.25						1.06
性型 Generotype			0.02		0.03	0.92	0.03	0.01		0.39
瓜面蜡粉 Wax powder	0.39	0.15	0.27	0.19						1.32
老瓜皮色 Fruit basal color		0.01	0.51	0.32	0.05	0.10				1.15
棱沟 Furrow depth	0.18	0.61	0.14	0.07						1.08
瓜形状 Fruit shape		0.03	0.05	0.46	0.10	0.11	0.24			1.45
瓜瓤类型 Melon flesh type		0.50	0.50							0.69
近瓜蒂端瓜面形状 Shape of the fruit surface near the pedicel		0.39	0.26	0.32	0.03					1.18
瓜顶形状 Shape of the fruit surface near the top		0.26	0.16	0.36	0.21					1.34
种子类型 Seed type		0.24	0.76							0.55

性状 Trait	最大值 Maximum	最小值 Minimum	平均值 Mean	标准差 Standard deviation	变异系数 Coefficient of variation (CV, %)	遗传多样性指数 Genetic diversity index (H′)
老瓜单瓜重Weight per fruit (kg)	31.52	1.05	8.02	5.13	63.95	1.92
叶片长度 Leaf length (cm)	42.83	21.65	33.35	4.39	13.17	2.06
叶片宽度 Leaf width (cm)	46.07	20.70	33.94	4.56	13.43	2.03
叶柄长度 Petiole length (cm)	25.43	9.87	17.10	3.24	18.94	2.09
首雄花节位 First male flower node	25.33	3.75	10.05	4.77	47.48	1.89
首雌花节位 First female flower node	39.00	5.00	14.42	6.10	42.32	1.96
老瓜纵径 Fruit length (cm)	109.67	14.33	43.37	18.62	42.95	1.93
老瓜横径 Fruit diameter (cm)	34.58	9.60	19.95	6.22	31.19	2.06
老瓜肉厚 Fruit thick (mm)	64.00	18.94	40.41	8.43	20.86	2.02
瓜形指数 Fruit shape index	7.18	0.66	2.34	1.10	47.05	1.94
瓜梗长度 Pedicle length (cm)	12.00	2.73	6.08	1.87	30.80	2.00
可溶性固形物含量 Soluble solid content (%)	4.23	1.73	2.85	0.53	18.46	2.07
种子厚度 Seed thickness (mm)	4.09	1.54	2.59	0.47	17.98	2.05
种子长度 Seed length (mm)	14.46	7.11	11.18	1.76	15.76	1.98
种子宽度 Seed width (mm)	9.74	4.31	6.91	1.31	18.93	1.99
种形指数 Seed shape index	2.14	1.23	1.64	0.16	9.76	2.05
种子千粒重Seed-1000-kernel weight (g)	10.10	1.68	5.33	1.94	36.46	1.95

性状 Trait	主成分 Principal component
性状 Trait	Ⅰ	Ⅱ	Ⅲ	Ⅳ	Ⅴ	Ⅵ
老瓜单瓜重 Weight per fruit	0.847	-0.109	0.179	-0.105	0.224	0.163
叶片长度 Leaf length	0.641	0.447	-0.001	0.404	-0.207	-0.253
叶片宽度 Leaf width	0.656	0.419	0.057	0.382	-0.225	-0.295
叶柄长度 Petiole length	0.503	0.372	-0.144	0.294	-0.535	0.084
首雌花节位 First female flower node	0.344	-0.185	0.389	0.163	0.612	-0.140
老瓜纵径 Fruit length	0.700	0.490	-0.016	-0.235	0.248	0.283
老瓜横径 Fruit diameter	0.694	-0.620	0.182	0.017	-0.018	0.055
老瓜肉厚 Fruit thick	0.655	-0.183	0.468	-0.042	0.135	-0.190
瓜形指数 Fruit shape index	0.142	0.865	-0.103	-0.130	0.226	0.263
瓜梗长度 Pedicle length	0.440	0.290	0.166	0.266	0.313	-0.084
种子长度 Seed length	0.716	-0.393	-0.263	-0.297	-0.186	0.169
种子宽度 Seed width	0.689	-0.401	-0.554	-0.120	0.012	-0.054
种形指数 Seed shape index	-0.179	0.113	0.646	-0.249	-0.318	0.377
种子千粒重 Seed-1000-kernel weight	0.770	-0.369	-0.321	-0.155	-0.127	0.125
瓜面蜡粉 Wax powder	0.000	-0.337	0.090	0.653	0.005	0.507
老瓜皮色 Fruit basal color	0.270	0.400	0.241	-0.514	-0.175	-0.405
瓜形状 Fruit shape	0.194	0.718	-0.212	-0.073	0.131	0.348
种子类型 Seed type	-0.251	0.085	-0.715	0.073	0.329	-0.161
特征值 Eigenvalue	5.329	3.310	2.017	1.469	1.341	1.157
贡献率 Contribution rate (%)	29.605	18.390	11.203	8.159	7.452	6.427
累计贡献率 Accumulated contribution rate (%)	29.605	47.995	59.198	67.357	74.809	81.236

Genetic Diversity Analysis of Wax Gourd and Chieh-Qua Germplasm Resources Based on Phenotypic Traits and SSR Markers

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编号 Material code	主成分因子分值 Principal component value						综合得分 F value	排名 Ranking
编号 Material code	F₁	F₂	F₃	F₄	F₅	F₆	综合得分 F value	排名 Ranking
BR12	3.05	0.48	-0.02	1.36	0.51	0.91	1.47	1
BR25	1.63	0.84	-0.65	1.35	2.21	1.43	1.14	2
BR44	1.34	2.24	1.65	-1.26	0.02	0.51	1.14	2
BR91	0.88	1.82	-0.01	-1.11	2.50	2.56	1.05	3
BR24	1.40	2.02	1.38	-1.16	-0.80	0.06	0.97	4
BR17	1.94	1.62	-0.33	-0.66	0.40	-1.37	0.89	5
BR90	1.49	-0.38	1.37	1.25	1.86	-1.26	0.84	6
BR38	1.07	2.02	0.08	-0.17	1.34	-1.55	0.84	6
BR16	0.93	1.83	1.42	-0.87	0.11	-0.44	0.84	6
BR26	1.47	1.72	0.10	-0.72	0.30	-0.86	0.83	7
BR34	1.38	1.63	-0.44	-0.18	0.92	-0.76	0.82	8
BR19	1.32	1.30	1.61	-1.26	-0.33	-0.30	0.82	8
BR29	1.09	1.65	0.73	-0.12	-0.42	-0.70	0.76	9
BR89	1.53	-0.41	1.41	-0.13	1.96	-1.46	0.71	10

性状 Trait	WPF	LL	LW	PL	FFN	FL	FDM	FT	FSI	PDL	SL	SW	SSI	SKW	WP	FBC	FS	ST
WPF	1
LL	0.38**	1
LW	0.38**	0.93**	1
PL	0.22**	0.59**	0.59**	1
FFN	0.37**	0.13	0.17*	-0.18*	1
FL	0.72**	0.46**	0.44**	0.36**	0.18*	1
FDM	0.76**	0.17*	0.21*	0.10	0.35**	0.20*	1
FT	0.70**	0.33**	0.35**	0.11	0.41**	0.33**	0.64**	1
FSI	0.10	0.33**	0.27**	0.26**	-0.06	0.73**	-0.46**	-0.13	1
PDL	0.30**	0.35**	0.39**	0.25**	0.33**	0.38**	0.08	0.28**	0.26**	1
SL	0.54**	0.17*	0.20*	0.25**	0.12	0.35**	0.64**	0.33**	-0.18*	0.09	1
SW	0.48**	0.20*	0.21**	0.23**	0.13	0.30**	0.59**	0.26**	-0.18*	0.11	0.85**	1
SSI	-0.07	-0.13	-0.11	-0.06	-0.05	-0.03	-0.09	0.02	0.03	-0.06	-0.03	-0.54**	1
SKW	0.57**	0.27**	0.27**	0.30**	0.13	0.38**	0.66**	0.34**	-0.14	0.17*	0.89**	0.86**	-0.22**	1
WP	0.06	-0.04	-0.05	0.05	0.10	-0.18*	0.24**	-0.01	-0.24**	0.06	0	0.01	0	0.04	1
FBC	0.16*	0.23**	0.28**	0.16	-0.03	0.33**	-0.07	0.25**	0.26**	0.19*	0.1	0.01	0.13	0.03	-0.45**	1
FS	0.11	0.30**	0.27**	0.31**	-0.10	0.54**	-0.30**	-0.08	0.70**	0.19*	-0.03	-0.04	0	-0.02	-0.14	0.17*	1
ST	-0.24**	-0.07	-0.14	-0.17*	-0.18*	-0.11	-0.35**	-0.37**	0.09	-0.08	-0.09	0.13	-0.41**	-0.1	-0.1	-0.23**	0.12	1
F值	0.69**	0.70**	0.70**	0.49**	0.42**	0.81**	0.30**	0.53**	0.55**	0.62**	0.21**	0.14	0.05	0.28**	0.09	0.26**	0.49**	-0.31**

性状 Trait	类群Ⅰ Cluster Ⅰ	类群Ⅱ Cluster Ⅱ	类群Ⅲ Cluster Ⅲ	类群Ⅳ Cluster Ⅳ	类群Ⅴ Cluster Ⅴ	类群Ⅵ Cluster Ⅵ
老瓜单瓜重 Weight per fruit (kg)	12.01	8.55	5.95	10.95	10.66	2.68
叶片长度 Leaf length (cm)	35.24	29.15	33.34	36.73	36.45	31.46
叶片宽度 Leaf width (cm)	36.17	29.77	33.68	38.02	36.90	31.72
叶柄长度 Petiole length (cm)	18.38	13.59	17.39	18.40	19.60	16.21
首雌花节位 First female flower node	16.53	20.08	9.04	17.35	14.45	10.86
老瓜纵径 Fruit length (cm)	42.49	35.04	39.28	63.97	63.70	31.61
老瓜横径 Fruit diameter (cm)	27.43	23.17	19.30	19.03	19.90	12.03
老瓜肉厚 Fruit thick (mm)	45.51	42.99	36.22	47.80	42.38	32.79
瓜形指数 Fruit shape index	1.56	1.48	2.17	3.42	3.29	2.72
瓜梗长度 Pedicle length (cm)	6.21	5.76	4.72	7.17	7.81	5.52
种子长度 Seed length (mm)	12.18	11.64	11.97	11.25	12.48	8.63
种子宽度 Seed width (mm)	7.74	7.02	7.52	6.35	8.05	5.18
种形指数 Seed shape index	1.59	1.67	1.59	1.78	1.55	1.67
种子千粒重 Seed-1000-kernel weight (g)	7.01	5.38	5.77	5.27	6.83	2.62

群体 Population	群体大小 Sample size	等位基因数 Number of alleles (Na)	有效等位基因数 Number of effective alleles (Ne)	Shannon’s多样性指数 Shannon’s diversity index (I)	Nei’s多样性指数 Nei’s diversity index (H)	多态性信息含量 Polymorphism information content (PIC)
冬瓜Wax gourd	121	3.16	2.09	0.77	0.44	0.38
节瓜Chieh-qua	27	2.79	2.27	0.78	0.47	0.40

变异来源 Source	自由度 DF	平方和 SS	均方差 MSE	方差分量 Variance component	方差分量百分率 Total variance (%)	基因流 (Nm)
群体间Among population	1	12.887	12.887	0.108	2	—
群体内In population	161	467.244	2.902	0	0	—
个体内In individual	163	896.5	5.5	5.5	98	—
总体Total	325	1376.632		5.608	100	—
平均Mean	—	—	—	—	—	22.014

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