Genetic diversity analysis of Lagerstroemia germplasm resourcesbased on SNP markers

doi:10.3969/j.issn.1000-2006.202003075

JOURNAL OF NANJING FORESTRY UNIVERSITY ›› 2020, Vol. 44 ›› Issue (4): 18-25.doi: 10.3969/j.issn.1000-2006.202003075

Special Issue: 木本花卉专题

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Genetic diversity analysis of Lagerstroemia germplasm resourcesbased on SNP markers

QIAO Dongya(), WANG Peng, WANG Shu’an, LI Linfang, GAO Lulu, YANG Rutong, WANG Qing(), LI Ya()

Institute of Botany，Jiangsu Province and Chinese Academy of Sciences，Nanjing 210014，China

Received:2020-03-25 Revised:2020-04-02 Online:2020-07-22 Published:2020-08-13
Contact: WANG Qing,LI Ya E-mail:qdylol@outlook.com;1052255718@qq.com;yalicnbg@163. com

Abstract

Abstract: Objective

Lagerstroemia is an economically important ornamental shrub that is distributed from tropical to northern temperate zones. It commonly blooms from summer until fall， and it has a significant value in city landscaping and environmental protection. However， classification of Lagerstroemia plants at the species level is currently challenging. To provide a theoretical support for crape myrtle breeding and identification， 85 Lagerstroemia germplasms were collected and the genetic diversity of Lagerstroemia germplasm resources was studied using single nucleotide polymorphisms （SNP） markers.

Method

85 Lagerstroemia germplasms at home and abroad were used to study genetic diversity. The high-quality SNP markers were selected depending on the mini-sequencing result. The polymorphism information content （PIC）， expected heterozygosity （H_e）， gene diversity， and genetic similarity （GS） were calculated using PowerMarker V3.25 software. The genetic distance between the 85 germplasms was calculated based on Nei’s 1972 method. A dendrogram of 85 Lagerstroemia germplasms was constructed using MEGA 6.0 software according to the genetic similarity based on neighbor-joining method. Additionally， 85 samples were classified based on four different flower colors （46 purple-flowered， 26 red-flowered， 5 white-flowered， and 5 compound-flowered individuals）. Next， the genetic differentiation parameters with the cluster and color groups were computed using GenAIEx 6.5 software， and the genetic diversity and genetic relationship were analyzed among the cluster and color groups.

Result

The 21 high quality SNP markers were selected from MassARRAY sequencing results. The polymorphic information content of Lagerstroemia germplasm resources ranged from 0.04 to 0.37 and the mean was 0.33. The expected heterozygosity ranged from 0.12 to 0.49 and the mean value was 0.33. The genetic similarity ranged from 0.24 to 0.95. The 85 Lagerstroemia germplasms were divided into seven major groups using the unweighted pair group method with the arithmetic mean （UPGMA） method cluster analysis. The cluster group Ⅵ had the highest number of alleles with the 2.00， and the cluster group Ⅶ had the lowest number of alleles with 1.33. In contrast to the expected heterozygosity and observed heterozygosity， cluster group Ⅰ had the highest value and cluster group Ⅱ had the lowest. Meanwhile， the 85 Lagerstroemia germplasms were classified into four major groups based on four different flower colors， including the purple-flowered， red-flowered， white-flowered， and compound-flowered group. The purple-flowered group had the highest number of alleles at 2.00， while the compound-flowered group was the lowest at 1.33.

Conclusion

Lagerstroemia possessed abundant genetic diversity and high levels of gene flow between groups. The purple-flowered and white-flowered groups had the highest genetic diversities. In addition， the SNP markers were useful for analyzing the genetic diversity of Lagerstroemia.

Key words: Lagerstroemia, SNP marker, genetic diversity, genetic relationship, cluster analysis, genetic differentiation

CLC Number:

S722.5

QIAO Dongya, WANG Peng, WANG Shu’an, LI Linfang, GAO Lulu, YANG Rutong, WANG Qing, LI Ya. Genetic diversity analysis of Lagerstroemia germplasm resourcesbased on SNP markers[J]. JOURNAL OF NANJING FORESTRY UNIVERSITY, 2020, 44(4): 18-25.

Figures/Tables 4

Table 1

Germplasm information of Lagerstroemia used in this study"

编号 No.	品种/种 variety/species	花色 flower color	类别 group	来源地 sources	编号 No.	品种/种 variety/species	花色 flower color	类别 group	来源地 sources
1	‘堇绣’	—	堇	中国	44	NL201410	—	红	中国
2	‘金薇’	—	红	中国	45	NL201411	—	堇	中国
3	‘堇薇’	—	堇	中国	46	NL201412	N78C	堇	中国
4	‘粉娇蓉’	—	红	中国	47	NL201413	—	红	中国
5	‘直枝紫’	—	堇	中国	48	NL201414	—	堇	中国
6	‘蓝紫’	—	堇	中国	49	NL201415	—	堇	中国
7	NL20131	61C	堇	中国	50	NL201416	—	红	中国
8	‘小花粉’	61D	堇	中国	51	NL201417	N80B	堇	中国
9	NL20132	58B	红	中国	52	NL201418	—	红	中国
10	NL20133	—	红	中国	53	‘紫玉’	—	复色	中国
11	NL20134	67B	堇	中国	54	NL201419	68A	堇	中国
12	NL20135	72B	堇	中国	55	‘白云映霞’	—	银	中国
13	‘粉蝴蝶’	68A	堇	中国	56	NL201420	N78B	堇	中国
14	NL20136	—	红	中国	57	‘粉绣球’	68A	复色	中国
15	NL20137	58A	红	中国	58	‘平枝紫’	—	堇	中国
16	NL20138	—	红	中国	59	NL201421	—	银	中国
17	‘紫玉’	—	复色	中国	60	NL201422	—	红	中国
18	‘繁花似锦’	—	堇	中国	61	‘小深紫’	—	堇	中国
19	NL20139	—	堇	中国	62	NL201423	75A	堇	中国
20	‘多花粉’	N66D	红	中国	63	NL20151	—	红	中国
21	NL201310	77B	堇	中国	64	NL20152	75A	堇	中国
22	NL201311	N78C	堇	中国	65	NL20153	75A	堇	中国
23	‘直枝紫’	—	堇	中国	66	NL20154	—	堇	中国
24	NL201312	—	红	中国	67	NL20155	N78C	堇	中国
25	NL201313	—	红	中国	68	NL20156	N66C	红	中国
26	NL201314	N81C	堇	中国	69	NL20157	N78C	堇	中国
27	NL201315	76A	堇	中国	70	NL20158	67A	堇	中国
28	NL201316	—	红	中国	71	NL20159	67C	堇	中国
29	NL201317	—	堇	中国	72	NL201510	N78D	复色	中国
30	NL201318	N57D	红	中国	73	NL201511	N78D	堇	中国
31	‘大花紫’	—	堇	中国	74	NL201512	N74D	堇	中国
32	NL201319	—	红	中国	75	NL201513	67B	堇	中国
33	NL20141	—	红	中国	76	NL201514	—	堇	中国
34	‘多瓣紫’	—	堇	中国	77	NL201515	—	红	中国
35	NL20142	—	堇	中国	78	NL201516	—	堇	中国
36	NL20143	67C	堇	中国	79	‘American red’	—	红	美国
37	NL20144	N57C	红	中国	80	福建紫薇^*	—	堇	中国
38	NL20145	67C	堇	中国	81	福氏紫薇^*	—	银	中国
39	‘粉绣球’	—	复色	中国	82	‘Dynamite’	—	红	美国
40	NL20146	67C	堇	中国	83	南紫薇^*	—	银	中国
41	NL20147	—	堇	中国	84	NL20163	—	红	美国
42	NL20148	—	堇	中国	85	桂林紫薇^*	—	银	中国
43	NL20149	—	堇	中国

Table 1

Table 2

Fig.1

Table 3

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SNP_ID	正向引物（5'-3'） forward primer(5'-3')		反向引物（5'-3') reverse primer(5'-3')	退火温度/℃ annealing temperature	GC/%	H	H_e	ρ/%	PIC
Marker41043-2-1	ACGTGGATTTCAAGCACGAC		AAATTGTGGAACCCATCCCC	48.0	60.0	0.49	0.21	90	0.37
Marker144041	GTTCGGATACCTATGCTATG		AGTACCCGAGCTCTTGTTTC	45.4	50.0	0.35	0.06	98	0.28
Marker5926-1	GGTGTTGCTTTGCTATTGCG		CCTGTCTCACAGTACTAAAG	47.5	47.1	0.30	0.12	95	0.25
Marker21345-1	AGGGACTTCTGTTCTTGAGG		TACACGGAGTGGATCTCACC	46.8	53.3	0.13	0.14	100	0.12
Marker59366	TCAGTCCATGTACAAAGCAC		CTCTTGATATTAAGCTGAGCG	49.4	60.0	0.49	0.49	100	0.37
Marker15223	AGAGAATAGAGGGATGCACG		ATGAACTCTCTTGTTTTGGC	45.0	38.9	0.39	0.15	99	0.28
Marker12657	TGAGATTCTTGGGCTACCAG		TGTACCACTGTAAACCTTGC	45.3	43.8	0.05	0.05	99	0.04
Marker31112-2	TTGTCCAAAGTTGACTGTGT		GTAGCAAAGTATCACCAGGC	46.2	60.0	0.42	0.11	94	0.33
Marker46063	GTGTCACGGAAATCATGGAA		GTGTACTACACAACATCACC	47.2	36.8	0.47	0.34	98	0.35
Marker10854-1	ACTGTATAAGGGTACCCCAC		CGGTCCATTGCACTATATCG	48.4	40.0	0.50	0.38	97	0.37
Marker13152-1	GGAACATCAGAAACAGAGAG		TCTTTCTTGCTAGTCTCGCC	50.1	56.3	0.47	0.35	99	0.36
Marker14312-1	ATGCTGCTCCTGAGTATCTC		TTACTAGTTGTGATGCCCCC	46.3	36.8	0.50	0.32	97	0.37
Marker109541	AAAGGCAACGGAAAAAGTGG		ACCGCGTAATAGTACTTATG	47.0	44.4	0.19	0.19	98	0.17
Marker40664	GTATCACCATCTGAGTTGGA		CAAAAGCCCAGTACAAAACG	47.0	31.8	0.43	0.32	93	0.34
Marker53622	CCATCACAGTACTTTGCTTG		ATGTGCTAGGAGATATCGAC	48.5	42.9	0.22	0.13	95	0.20
Marker95228-1	CGTCTTCCCAGCATAGAAAC		CGGTCACGAATTGTTGTACC	45.9	31.6	0.41	0.33	100	0.33
Marker9622-1	GATTTCGGTAGTTCTACCCC		TCGCCCTATATAGATGAATC	49.2	40.0	0.49	0.19	98	0.37
Marker145612	TTCACCCTTACATGGTATCG		CAGTGCATTCTTTTCCTCCG	49.1	39.1	0.50	0.26	98	0.37
Marker151768	CCTCATAATTAATGGCCACC		ATGCTGCGTACTCTCTTTAG	47.1	30.4	0.49	0.39	97	0.36
Marker18072	GGTATCTTCCCAAACTACCC		TACAGCAGCACCTTTCGTTC	46.0	30.4	0.50	0.35	94	0.37
Marker146537	ATTGAACGCAGAATCTCTTG		ATAAGATAAGAAGCCAGGTG	51.8	39.1	0.39	0.25	96	0.30
平均值 average	—	—		—	—	0.38	0.25	96	0.33

群组 groups	居群 popul ation	大小 number	等位基因数 number of alleles	有效等位基因数 number of effective alleles	Shannon's 信息指数Shannon’s information index	期望杂合度 expected heterozygosity	观测杂合度 observed heterozygosity
聚类 cluster	Ⅰ	3	1.91	1.53	0.51	0.33	0.404
	Ⅱ	16	1.70	1.26	0.31	0.19	0.192
	Ⅲ	12	1.62	1.33	0.36	0.23	0.235
	Ⅳ	19	1.62	1.29	0.33	0.20	0.207
	Ⅴ	12	1.71	1.37	0.37	0.23	0.244
	Ⅵ	17	2.00	1.35	0.38	0.24	0.242
	Ⅶ	6	1.33	1.33	0.32	0.21	0.229
花色 clour	堇薇 purple	49	2.00	1.30	0.36	0.23	0.22
	红薇 red	26	1.91	1.34	0.38	0.23	0.24
	银薇 white	5	1.52	1.41	0.39	0.25	0.28
	复色 compound	5	1.33	1.34	0.33	0.21	0.24

Genetic diversity analysis of Lagerstroemia germplasm resourcesbased on SNP markers

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