Association Analysis of Organ Traits with SSR Markers in Lotus（Nelumbo nucifera）

doi:10.16420/j.issn.0513-353x.2021-0919

Acta Horticulturae Sinica ›› 2023, Vol. 50 ›› Issue (1): 103-115.doi: 10.16420/j.issn.0513-353x.2021-0919

• Research Papers • Previous Articles Next Articles

Association Analysis of Organ Traits with SSR Markers in Lotus（Nelumbo nucifera）

LIU Yiping¹^,², NI Menghui¹, WU Fangfang¹, LIU Hongli¹^,², HE Dan¹^,², KONG Dezheng¹^,²^,^*()

¹College of Landscape Architecture and Art，Henan Agricultural University，Zhengzhou 450002，China
²Henan High-quality Flower and Vegetable Seedling Engineering Technology Center，Zhengzhou 450002，China

Received:2022-09-14 Revised:2022-11-01 Online:2023-01-25 Published:2023-01-18
Contact: *（E-mail：kzxy303@163.com）

Abstract

Abstract:

In order to discover the molecular markers related to the organ traits of lotus flowers，the 18 floral organ traits of 60 lotus germplasm resources were identified and described，16 polymorphic SSR markers were screened to analyze their genetic diversity，and use the generalized linear model（GLM）and mixed linear model（MLM）of TASSEL5.0 software to carry out correlation analysis on 18 traits of floral organs. The results of the study showed that the 16 SSR markers were mainly dinucleotide repeats and trinucleotide repeats，both accounting for 43.75%；105 polymorphic loci were amplified in 60 lotus germplasm materials，with an average number of 6.5625；the primer polymorphism content（PIC）ranged from 0.2898 to 0.7029，with an average value of 0.5242；the average value of Shannon’s information index was 1.1548；and the average value of observed heterozygosity and expected heterozygosity were 0.4308 and 0.5819. The genetic similarity coefficient（GS）of 60 lotus cultivars was from 0.38 to 0.92，with an average value of 0.67. At the GS value of 0.60，60 lotus germplasms were divided into three major populations. GLM model analysis detected 31 SSR loci，with the phenotypic interpretation rate ranged from 15.72% to 76.76%；MLM model analysis detected 13 SSR loci，with a phenotypic interpretation rate ranged from 20.25% to 78.40%；ten of them were detected by both. In addition，nine SSR-labeled loci were detected in 2-5 floral organ traits，showing a significant“one cause and multiple effects”phenomenon.

Key words: lotus, floral organ, trait, SSR molecular marker, association analysis

CLC Number:

S682.32

LIU Yiping, NI Menghui, WU Fangfang, LIU Hongli, HE Dan, KONG Dezheng. Association Analysis of Organ Traits with SSR Markers in Lotus（Nelumbo nucifera）[J]. Acta Horticulturae Sinica, 2023, 50(1): 103-115.

Figures/Tables 11

References 39

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来源 Origin	编号 Code	品种/品系名称 Cultivar/Line name	来源 Origin	编号 Code	品种/品系名称 Cultivar/Line name
中国莲	1	矮牡丹 Aimudan	中国莲	31	雪翠 Xuecui
Nelumbo nucifera	2	粉龙莲 Fenlonglian	N. nucifera Gaertn.	32	瑰丽Guili
Gaertn.	3	红思莲 Hongsilian		33	小红荷Xiaohonghe
	4	中山红台Zhongshan Hongtai		34	淡黄红光Danhuang Hongguang
	5	彩云莲 Caiyunlian		35	翡翠10号 Feicui 10
	6	红重中型Hongchongzhongxing		36	艳阳天Yanyangtian
	7	天地红 Tiandihong		37	鸳鸯出水Yuanyangchushui
	8	高风亮节Gaofengliangjie		38	杏黄Xinghuang
	9	披针粉Pizhenfen		39	太空娇容Taikong Jiaorong
	10	玉翠莲 Yucuilian		40	大紫玉 Daziyu
	11	晚霞 Wanxia		41	娇红 Jiaohong
	12	新披针红Xinpizhenhong		42	山东红牡丹Shandong Hongmudan
	13	粉红重瓣Fenhong Chongban		43	泰泊白玉 Taibo Baiyu
	14	素雅 Suya		44	红云 Hongyun
	15	紫光阁 Ziguang’ge		45	紫重阳 Zichongyang
	16	新深情 Xinshenqing		46	红彩云 Hongcaiyun
	17	乳燕欢 Ruyanhuan		47	桌上珍Zhuoshangzhen
	18	光辉 Guanghui		48	墨红1号 Mohong 1
	19	芙蓉秋色Furong Qiuse		49	南阳黄Nanyanghuang
	20	惊艳 Jingyan	中国莲与美洲黄莲	50	金苹果 Jinpinghuo
	21	红裙 Hongqun	杂交种	51	红莺 Hongying
	22	红飞菊 Hongfeiju	N. nucifera Gaertn. ×	52	莺莺 Yingying
	23	粉团儿 Fentuan’er	N. lutea Pear.	53	黄鹂 Huangli
	24	月华 Yuehua		54	冰娇 Bingjiao
	25	粉霞 Fenxia		55	白兰媚 Bailanmei
	26	露华浓 Luhuanong		56	雪涛 Xuetao
	27	玛瑙红 Ma’naohong		57	友谊牡丹 Youyi Mudan
	28	红牡丹 Hongmudan		58	新云锦 Xinyunjin
	29	红绸 Hongchou		59	雨花情 Yuhuaqing
	30	海南 Hainan		60	黄帅 Huangshuai

来源 Origin	编号 Code	品种/品系名称 Cultivar/Line name	来源 Origin	编号 Code	品种/品系名称 Cultivar/Line name
中国莲	1	矮牡丹 Aimudan	中国莲	31	雪翠 Xuecui
Nelumbo nucifera	2	粉龙莲 Fenlonglian	N. nucifera Gaertn.	32	瑰丽Guili
Gaertn.	3	红思莲 Hongsilian		33	小红荷Xiaohonghe
	4	中山红台Zhongshan Hongtai		34	淡黄红光Danhuang Hongguang
	5	彩云莲 Caiyunlian		35	翡翠10号 Feicui 10
	6	红重中型Hongchongzhongxing		36	艳阳天Yanyangtian
	7	天地红 Tiandihong		37	鸳鸯出水Yuanyangchushui
	8	高风亮节Gaofengliangjie		38	杏黄Xinghuang
	9	披针粉Pizhenfen		39	太空娇容Taikong Jiaorong
	10	玉翠莲 Yucuilian		40	大紫玉 Daziyu
	11	晚霞 Wanxia		41	娇红 Jiaohong
	12	新披针红Xinpizhenhong		42	山东红牡丹Shandong Hongmudan
	13	粉红重瓣Fenhong Chongban		43	泰泊白玉 Taibo Baiyu
	14	素雅 Suya		44	红云 Hongyun
	15	紫光阁 Ziguang’ge		45	紫重阳 Zichongyang
	16	新深情 Xinshenqing		46	红彩云 Hongcaiyun
	17	乳燕欢 Ruyanhuan		47	桌上珍Zhuoshangzhen
	18	光辉 Guanghui		48	墨红1号 Mohong 1
	19	芙蓉秋色Furong Qiuse		49	南阳黄Nanyanghuang
	20	惊艳 Jingyan	中国莲与美洲黄莲	50	金苹果 Jinpinghuo
	21	红裙 Hongqun	杂交种	51	红莺 Hongying
	22	红飞菊 Hongfeiju	N. nucifera Gaertn. ×	52	莺莺 Yingying
	23	粉团儿 Fentuan’er	N. lutea Pear.	53	黄鹂 Huangli
	24	月华 Yuehua		54	冰娇 Bingjiao
	25	粉霞 Fenxia		55	白兰媚 Bailanmei
	26	露华浓 Luhuanong		56	雪涛 Xuetao
	27	玛瑙红 Ma’naohong		57	友谊牡丹 Youyi Mudan
	28	红牡丹 Hongmudan		58	新云锦 Xinyunjin
	29	红绸 Hongchou		59	雨花情 Yuhuaqing
	30	海南 Hainan		60	黄帅 Huangshuai

性状 Trait	遗传多样性指数 H’	性状描述级别 Character description level	资源数 Accessions	分布频率/% Distribution frequency
花色 Flower color	2.19	白色 Black 黄色 Yellow 粉红 Pink 红色 Red 复色 Recolor	12 5 18 17 8	20.00 8.33 30.00 28.33 13.33
花型 Flower type	1.41	单瓣 Single flower 半重瓣 Semidouble flower 重瓣 Double flower 重台 Proliferation Flower	2 7 39 13	3.33 11.67 65.00 21.67
花态 Flower form	1.73	杯状 Cup-shape 碗状 Bowl shape 飞舞状 Flying shape 碟状 Disc shape 叠球状 Stacked sphere shape	9 31 1 16 3	15.00 51.67 1.67 26.67 5.00
花蕾色 Bud color	1.40	绿色 Green 红绿 Red green 红色 Red	15 35 11	25.00 58.33 18.33
花蕾形状 Bud shape	1.04	长卵圆锥形 Long cone shape 卵圆锥形 Cone shape 卵球形 Egg ball shape	5 45 10	8.33 25.00 26.67
雌蕊泡化程度 Degree of pistil vesiculation	1.55	正常 Normal 部分泡化 Partial bubbling 全泡化 Full bubbling 全瓣化 Total petalization	32 15 12 1	53.33 25.00 20.00 1.67
成熟花托形状 Mature receptacle shape	1.76	喇叭形 Trumpet shape 倒圆锥形 Inverted cone shape 伞形 Umbrella shape 扁球形 Oblate shape 碗形 Bowl shape	7 31 1 5 16	11.00 51.67 1.67 8.33 26.67

性状 Trait	遗传多样性指数 H’	性状描述级别 Character description level	资源数 Accessions	分布频率/% Distribution frequency
花色 Flower color	2.19	白色 Black 黄色 Yellow 粉红 Pink 红色 Red 复色 Recolor	12 5 18 17 8	20.00 8.33 30.00 28.33 13.33
花型 Flower type	1.41	单瓣 Single flower 半重瓣 Semidouble flower 重瓣 Double flower 重台 Proliferation Flower	2 7 39 13	3.33 11.67 65.00 21.67
花态 Flower form	1.73	杯状 Cup-shape 碗状 Bowl shape 飞舞状 Flying shape 碟状 Disc shape 叠球状 Stacked sphere shape	9 31 1 16 3	15.00 51.67 1.67 26.67 5.00
花蕾色 Bud color	1.40	绿色 Green 红绿 Red green 红色 Red	15 35 11	25.00 58.33 18.33
花蕾形状 Bud shape	1.04	长卵圆锥形 Long cone shape 卵圆锥形 Cone shape 卵球形 Egg ball shape	5 45 10	8.33 25.00 26.67
雌蕊泡化程度 Degree of pistil vesiculation	1.55	正常 Normal 部分泡化 Partial bubbling 全泡化 Full bubbling 全瓣化 Total petalization	32 15 12 1	53.33 25.00 20.00 1.67
成熟花托形状 Mature receptacle shape	1.76	喇叭形 Trumpet shape 倒圆锥形 Inverted cone shape 伞形 Umbrella shape 扁球形 Oblate shape 碗形 Bowl shape	7 31 1 5 16	11.00 51.67 1.67 8.33 26.67

性状 Trait	最小值 Max	最大值 Min	平均值 Mean	峰度 Kurtosis	偏度 Skewness	变异系数/% CV	遗传多样性指数 H’
花期/d Flowering period	29.00	58.00	49.16 ± 10.32	-1.17	0.22	20.98	5.87
着花密度Flowering density	3.00	12.00	6.86 ± 1.42	-0.86	0.25	35.34	5.82
花高/cm Flower height	39.70	119.40	64.74 ± 17.69	0.94	1.11	27.33	5.85
花冠直径/cm Corolla diameter	5.00	18.50	11.09 ± 3.23	0.32	0.58	29.13	5.85
花被片数量Number of tepals	19.00	264.00	106.42 ± 36.35	0.50	0.67	43.56	5.77
雄蕊数Number of stamens	5.00	140.00	54.56 ± 24.49	-0.21	0.74	63.22	13.44
雌蕊心皮数Number of pistil carpel	5.00	20.00	8.58 ± 3.12	0.79	1.47	36.40	5.83
花丝长/mm Filament length	4.00	14.00	7.66 ± 2.15	0.10	0.40	28.11	5.85
花药长/mm Anthers length	6.00	29.00	10.04 ± 3.41	0.91	1.63	34.03	5.85
花托大小/cm Receptacle size	1.27	3.80	2.28 ± 0.55	0.72	0.73	24.49	5.86
花托直径/cm Torus diameter	1.30	5.30	3.02 ± 1.04	-0.65	0.39	34.52	5.82
均值Average						34.28	6.53

Association Analysis of Organ Traits with SSR Markers in Lotus（Nelumbo nucifera）

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SSR位点 SSR locus	等位基因数 N_a	有效等位基因数 N_e	观测杂合度 H_o	期望杂合度 H_e	香农多样性指数 I	多态性信息含量 PIC
SSR1	5	2.4599	0.5833	0.5985	1.0479	0.5066
SSR2	5	2.2025	0.4667	0.5506	0.9431	0.4417
SSR3	4	2.3990	0.3889	0.5886	1.0397	0.5092
SSR4	5	1.5602	0.1579	0.3639	0.7470	0.3039
SSR5	5	3.2008	0.6552	0.6936	1.3166	0.6203
SSR6	6	1.5632	0.2667	0.3633	0.7234	0.3047
SSR7	10	3.1887	0.2667	0.6922	1.5752	0.6595
SSR8	7	2.6012	0.5833	0.6207	1.2745	0.5896
SSR9	10	4.0268	0.5500	0.7580	1.6393	0.6988
SSR10	5	3.1304	0.2667	0.6863	1.2005	0.6054
SSR11	7	3.2393	0.5088	0.6974	1.4004	0.6100
SSR12	9	1.5094	0.3167	0.3403	0.8078	0.3327
SSR13	10	3.7336	0.5000	0.7385	1.6748	0.7029
SSR14	5	1.4496	0.3000	0.3127	0.5980	0.2898
SSR15	7	2.4271	0.4828	0.5931	1.1267	0.5299
SSR16	5	3.4156	0.6000	0.7132	1.3628	0.6820
平均值Average	6.5625	2.6317	0.4308	0.5819	1.1548	0.5242

性状 Trait	标记 Marker	GLM		MLM
性状 Trait	标记 Marker	P值 P value	表型解释率/% Phenotypic interpretation rate	P值 P value	表型解释率/% Phenotypic interpretation rate
花色 Flower color	S2	0.0980	18.05	—	—
	S7	0.0968	26.77	—	—
	S8	0.0091	34.27	0.0560	32.70
	S15	0.0571	23.66	—	—
花型Flower type	S11	0.0059	42.15	0.0522	44.92
	S13	0.0198	46.39	—	—
	S14	0.0673	15.72	—	—
花态Flower form	S12	0.0306	19.60	0.0725	20.75
花蕾形状Bud shape	S2	0.0163	24.19	—	—
雌蕊泡化程度 Degree of pistil vesiculation	S9	0.0687	37.40	—	—
	S11	0.0865	34.02	—	—
	S13	0.0559	45.17	—	—
花期 Flowering period	S1	0.0132	30.45	0.0726	30.43
花期 Flowering period	S7	0.0242	32.60	0.0822	32.51
着花密度 Flowering density	S1	0.0580	24.67	—	—
	S9	0.0873	37.06	—	—
	S10	—	—	0.0587	25.56
花被片数量 Number of Tepals	S9	0.0961	32.89	—	—
花被片数量 Number of Tepals	S15	0.0851	19.29	—	—
雄蕊数 Number of stamens	S2	—	—	0.0862	20.25
雄蕊数 Number of stamens	S4	0.0803	29.88	—	—
雌蕊心皮数 Number of pistil carpel	S13	0.0680	41.28	—	—
花丝长 Filament length	S4	0.0501	31.33	—	—
	S8	0.0882	25.18	—	—
	S11	0.0208	41.98	—	—
花药长 Anthers length	S5	0.0197	33.54	0.0931	34.20
	S6	0.0006	36.38	0.0147	37.37
	S9	0.0000	70.95	0.0081	74.34
	S11	0.0000	76.76	0.0033	78.40
花托大小 Receptacle size	S1	0.0263	23.21	—	—
	S7	0.0253	27.00	0.0501	31.89
	S8	0.0614	22.13	—	—
花托直径 Torus diameter	S2	—	—	0.0436	22.16
花托直径 Torus diameter	S11	0.0884	32.12	—	—

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