RAD-seq技术研究鹅掌楸属种源遗传多样性和遗传结构

doi:10.11707/j.1001-7488.20220408

摘要/Abstract

摘要：

目的: 揭示鹅掌楸属遗传结构和地理变异特点，为鹅掌楸属遗传资源的保存、利用及改良提供依据。方法: 以9个鹅掌楸种源97份样本和4个北美鹅掌楸种源46份样本为材料，采用RAD-seq测序鉴定各样本SNP标记，计算观测杂合度(H_o)、期望杂合度(H_e)、核苷酸多样性(π)和基因分化系数(G_st)等遗传统计量指标，分析鹅掌楸属种源遗传多样性和遗传结构。结果: 在143份鹅掌楸属样本中共鉴定出4 454个高质量的SNP标记；鹅掌楸种源之间存在较大的遗传分化以及中水平的基因流(G_st=0.241 9、N_m=0.805 1)，北美鹅掌楸种源之间存在很大的的遗传分化以及低水平的基因流(G_st=0.388 6>0.25、N_m=0.397 0)；通过结构分析将13个鹅掌楸属种源分为3个类群，其中9个中国的鹅掌楸种源被分为东部种源群(即类群2)和西部种源群(即类群1)，类群3均为北美鹅掌楸，遗传多样性顺序为：类群3>类群1>类群2。结论: 鹅掌楸属遗传结构的形成与其地理隔离和片段化分布有关，且存在由于小群体效应和片段化影响导致的濒危现象，本研究开发的SNP标记可为鹅掌楸属分子鉴定、种质创新及种质资源收集与保存提供参考。

关键词: 鹅掌楸属, RAD测序, 遗传多样性, 遗传结构

Abstract:

Objective: This study aims to reveal the genetic structure and geographic variation characteristics of Liriodendron populations, in order to provide a basis for the conservation, utilization and improvement of genetic resources of Liriodendron. Method: A total of 97 samples derived from 9 provenances of Liriodendron chinensis and 46 samples derived from 4 provenances of L. tulipifera were collected. The SNP markers of the samples were identified by RAD-Seq sequencing. The observed heterozygosity (H_o), expected heterozygosity (H_e), nucleotide diversity (π), gene differential coefficient (G_st) and other genetic statistics were calculated to analyze the genetic diversity and genetic structure of Liriodendron provenances. Result: A total of 4 454 high quality SNP markers were identified in the 143 samples of Liriodendron. There were Liriodendron maintained moderate genetic differentiation and medium level gene flow among provenances of L. chinensis (G_st=0.241 9, N_m=0.805 1). There were large genetic differentiation and low level gene flow among L. tulipifera provenances (G_st=0.388 6>0.25, N_m=0.397 0). The 13 Liriodendron provenances were divided into 3 subgroups by population structure analysis. Among them, 9 provenances of L. chinensis were divided into eastern provenances (group 2) and western provenances (group 1), and the other provenances belonged to group 3 and they are all L. tulipifera. The order of genetic diversity was: group 3 > group 1 > group 2. Conclusion: The formation of genetic structure of Liriodendron is related to its geographical isolation and fragmented distribution, and there are endangered phenomena caused by small population effect and fragmentation. The SNP markers developed in this study can provide a reference basis for molecular identification, germplasm innovation and collection and preservation of germplasm resources of Liriodendron.

Key words: Liriodendron, RAD-seq, genetic diversity, genetic structure

中图分类号:

潘文婷,孙建军,原勤勤,张利利,邓康桥,厉月桥. RAD-seq技术研究鹅掌楸属种源遗传多样性和遗传结构[J]. 林业科学, 2022, 58(4): 74-81.

Wenting Pan,Jianjun Sun,Qinqin Yuan,Lili Zhang,Kangqiao Deng,Yueqiao Li. Analysis of Genetic Diversity and Structure in Different Provenances of Liriodendron by RAD-seq Technique[J]. Scientia Silvae Sinicae, 2022, 58(4): 74-81.

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种源 Provenance	种源地 Provenance region	北纬 Latitude	东经 Longitude	海拔 Elevation/m	样品数 Number of samples
XY	四川叙永 Sichuang Xuyong	28.20°N	105.5°E	700~900	10
EX	湖北鄂西 Hubei Exi	30.30°N	109.0°E	1 100~1 300	11
MN	贵州陌南 Guizhou Monan	26.80°N	109.5°E	950~1 150	11
LY	湖南浏阳 Hunan Liuyang	28.05°N	113.9°E	1 000~1 200	11
SZ	湖南桑植 Hunan Sangzhi	29.15°N	110.2°E	1 100~1 300	11
LS	江西庐山 Jiangxi Lushan	29.53°N	116.0°E	1 000~1 200	10
WYS	江西武夷山 Jiangxi Wuyishan	27.92°N	117.8°E	900~1 100	10
MSL	密苏里州 Missouri	37.60°N	91.5°W	600~800	11
LYS	路易斯安纳州 Louisiana	31.00°N	93.6°W	0~100	10
BK	北卡罗来纳州 North Carolina	35.13°N	80.1°W	1 000~1 200	12
NK	南卡罗来纳州 South Carolina	34.50°N	81.8°W	100~300	14
YN	云南勐腊 Yunnan Mengla	21.40°N	101.6°E	600~800	11
DBS	大别山舒城 Dabieshan Shucheng	31.13°N	118.2°E	1 350~1 550	11

种源 Provenance	总碱基数 Total nucleotides (Gb)	有效数据 Clean reads (Mb)	RAD标记数 RAD tag	测序深度 Sequencing depth (x)
XY	1.77	5.90	129 420	16.29
EX	2.46	8.19	140 080	20.19
MN	4.20	14.01	155 030	34.20
LY	1.94	6.46	147 270	17.77
SZ	1.41	4.70	157 950	13.70
LS	4.37	14.57	156 650	35.74
WYS	2.71	9.02	128 700	25.34
MSL	3.89	12.97	136 120	39.76
LYS	3.75	12.50	139 340	34.95
BK	1.99	6.62	140 020	19.14
NK	3.14	10.48	128 720	29.78
YN	2.15	7.16	127 330	19.47
DBS	2.16	7.20	149 230	18.97
均值Mean	2.76	9.20	142 130	24.76

种源 Provenance	等位基因数 Allele number	H_o Observed heterozygosity	H_e Expected heterozygosity	π Nucleotide diversity	G_st Gene differential coefficient	N_m Gene flow
XY	4 334	0.035 2	0.059 7	0.064 0	0.211 2	0.933 8
EX	5 573	0.049 6	0.058 1	0.061 7	0.196 8	1.020 3
MN	3 834	0.039 5	0.047 2	0.049 9	0.243 0	0.778 8
LY	2 934	0.036 4	0.049 9	0.053 0	0.237 8	0.801 3
SZ	4 212	0.036 9	0.052 0	0.055 5	0.213 1	0.923 4
LS	855	0.044 8	0.045 9	0.048 9	0.235 4	0.812 2
WYS	758	0.038 9	0.044 8	0.047 3	0.234 9	0.814 4
MSL	1 113	0.038 6	0.038 4	0.040 6	0.439 8	0.318 4
LYS	2 726	0.043 8	0.055 1	0.058 8	0.385 5	0.398 5
BK	2 017	0.044 2	0.058 1	0.061 6	0.367 9	0.429 5
NK	3 309	0.047 1	0.058 8	0.061 6	0.361 5	0.441 6
YN	2 604	0.013 2	0.029 9	0.031 6	0.280 2	0.642 2
DBS	1 245	0.024 4	0.022 2	0.023 6	0.324 8	0.519 8
均值 Mean	2 732	0.037 9	0.047 7	0.050 6	0.287 1	0.679 6

参数 parameters	XY	EX	MN	LY	SZ	LS	WYS	MSL	LYS	BK	NK	YN	DBS
H_o得分H_o score	0.60	1.00	0.72	0.64	0.65	0.87	0.71	0.70	0.84	0.85	0.93	0.00	0.31
H_e得分H_e score	1.00	0.96	0.67	0.74	0.79	0.63	0.60	0.43	0.88	0.96	0.98	0.21	0.00
π得分π score	1.00	0.94	0.65	0.73	0.79	0.63	0.59	0.42	0.87	0.94	0.94	0.20	0.00
综合得分 Comprehensive score	2.60	2.90	2.04	2.10	2.24	2.13	1.90	1.55	2.59	2.75	2.85	0.40	0.31

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