Genetic diversity analysis of Lagerstroemia indica based on fluorescent SSR markers

doi:10.12302/j.issn.1000-2006.202203038

JOURNAL OF NANJING FORESTRY UNIVERSITY ›› 2023, Vol. 47 ›› Issue (2): 61-69.doi: 10.12302/j.issn.1000-2006.202203038

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Genetic diversity analysis of Lagerstroemia indica based on fluorescent SSR markers

WANG Zhiyi¹^,²(), LI Zhenfang², PENG Chan², CHEN Ying¹^,^*(), ZHANG Xinye²^,^*()

1. College of Forestry, Nanjing Forestry University, Nanjing 210037, China
2. Huibei Academy of Forestry, Wuhan 430075, China

Received:2022-03-20 Revised:2022-05-06 Online:2023-03-30 Published:2023-03-28

Abstract

Abstract:

【Objective】 In this study, 239 germplasms of Lagerstroemia and one germplasm of Heimia were used to analyze the interspecific characteristics and genetic diversity of germplasm resources within L. indica, providing a scientific basis for collection, conservation and rational utilization of germplasm resources.【Method】 Genotypes of samples were identified based on 16 pairs of fluorescent primers; genotypes were read by the GeneMarker software. The characteristic loci of 239 germplasms of L. indica and one germplasm of H. myrtifolia were analyzed. The POPGENE, Cervus, NTSYS and GenAlEx software were used to estimate genetic diversity parameters, the cluster analysis and principal corrdinate analysis of 227 L. indica germplasms. 【Result】 Characteristic loci information of L. indica was the most abundant. Among the characteristic loci information reflected by 15 primers, L. indica all had unique loci that were different from the other six species, and some specific characteristic loci were not found in L. limii, L. excelsa and L. caudata. A total of 143 alleles were detected by 16 pairs of SSR(simple sequence repeat) fluorescent primers; there was an average of 8.938 alleles per locus and the average number of alleles per locus (N_e) was 3.600; Shannon’s Information Index (I) was 1.459, the average observed heterozygosity (H_o) was 0.577, the average expected heterozygosity (H_e) was 0.687, the average value of Nei’s genetic diversity index (H) was 0.685, and the average polymorphism information (PIC) in primers was 0.648. From the genetic diversity of 227 L. indica. based on the genetic distance between samples, a genetic cluster map was drawn and the samples were divided into 10 groups. The L. indica germplasm introduced from United States and wild L. indica germplasm from Hubei were relatively independent and clustered into different groups. The cluster analysis showed that L. indica germplasms were divided into 10 groups, among which the imported L. indica germplasm from the United States and the wild L. indica germplasm from Hubei were clustered into different groups. The principal corrdinate analysis showed that the 10 groups could be roughly divided into three regions, among which the wild L. indica germplasm from Hubei Province and the germplasm introduced from the United States were relatively clustered together.【Conclusion】 SSR markers can effectively reflect genetic diversity among L. indica germplasm resources, and can further optimize the collection and preservation of L. indica germplasm resources, build the core germplasm, create new varieties and provide a scientific basis for the rational development and utilization.

Key words: Lagerstroemia indica, genetic diversity, simple sequence repeat (SSR), clustering analysis

CLC Number:

S722

WANG Zhiyi, LI Zhenfang, PENG Chan, CHEN Ying, ZHANG Xinye. Genetic diversity analysis of Lagerstroemia indica based on fluorescent SSR markers[J]. JOURNAL OF NANJING FORESTRY UNIVERSITY, 2023, 47(2): 61-69.

Figures/Tables 9

Table 1

Fig.1

Table 2

Information of different characteristic bands at 16 loci"

样本 sample	特征谱带/bp characteristic band
样本 sample	P10	P11	P13	P19	P1	P27	P32	P39	P3	P42	P43	P45	P49	P50	P51	P6
黄薇 Heimia myrtifolia			169			114、136、 139		344	125、140				168	212		159、181
大花紫薇 L. speciosa	168、179		165、173	249	205、219	120、142	278、287	344、349	125	308、314	281	196	148、166、 168	212	262	187
屋久岛紫薇 L. fauriei	154、168、	326	169、177	263	219、226	114、139	278	344、349	140、172	314	281、297	194、196	166、168	212	250、264	153、159
福建紫薇 L. limii	166、176^**		173	239^**	211、213	111、120	287	348^**	127、159	290	295	181^**	184、188	220	248	153
川黔紫薇 L. excelsa	158、168		169、177	233^**	201^**	136	281	328^**	133、140	290、296	295	194、198	176、178	210、212		155、157^**
尾叶紫薇 L. caudata	158、162、 164、168、 170、172^**	300^**、312	165、169、 177	229^、 230^、 237^**	203^、 206^、 217^、 218^、 223^**、 226	108^、 114、117^、 130^**	269^**、 275、278、 284	333^、 335、336、 337^、 340^、 345^	115、119^、 121^、 123^、 129^、 131^**、 140、147、 153	292、302、 308	295、297、 299	194、196、 198	174、178、 180^**	212	250、251、 253、259^**	149^、 155、 157^、 161^**
紫薇 L. indica	154、158、 160^、162、 164、166、 168、170、 177^、179	304^、312、 314^、316^、 322^、326、 328^*	161^、165、 169、 173、 177、 185^	243^、245^、246^、248^、249、254^、256^、257^、261^、263、265^、271^、273^*	202^、205、207^、211、 213、 215^*、 219、 226	111、 114、 120、 123^、 133^、 136、 139、 142、 149^、 158^	275、 278、 281、 284、 287	322^、330^、331^、332^、335、 336、339^、344、346^、349、350^、352^	115、125、 127、133、 137^、140、142^、145^、147、 153、157^、159、161^、167^、172、174^*	290、294^、296、 302、304^、308、310^、314、317^、394^*	281、 283^、 295、 297、 299、 303、 304^	184^*、194、196、 198	140^、 148、 166、 168、 170^、 174、 176、 178、 182^*、 184、 188	208^、210、 212、214^、220、 232^*	248^、250、 251、 253、256^、262、263^、264、265^、266^*	151、153、 155、159、 175^、181、 185^、187

Table 2

Table 3

Fig.2

Table 4

Table 5

Table 6

Fig.3

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引物名称 primer	上游引物序列 forward primer	下游引物序列 reverse primer	产物大小/bp length	重复基元 repeat motif	退火温度/℃ annealing temperature
P1	AGAGAAAGAGAGGAGCGGGAGT	ACCTTCTTCCCCAATTCAATCC	213	(GT)6GC(GT)6	55.0
P3	GGTGGAGATGCTAACAAGCAAG	GGATTTTTGCTGTAGGGTGATT	161	(TG)16	55.0
P6	ACATGGCTCCCATCACACAG	CAGGGGATTCTTGTTTTGCTTT	160	(AC)6	55.0
P10	ACGGTAGATAAGGTGAGC	GGTTTCGTATCGTCGTAG	166	(CT)9T(CTGT)GT(CTGT)4	52.0
P11	TACTGGGTATCCGTTTCT	ACAGGTGCATTTACTTCC	317	(CT)6CC(CT)12	50.0
P13	GGGAATTTGGGATATGGA	TAAAGAAACGACCGAGCC	179	(AAAG)5	52.0
P19	TAGTCCATTCATGTCAAG	GGATTCACCAAACTACTT	246	(AG)14	52.0
P27	GTCTCACTCTCTCAACTCAAGGGC	TGAGAAAGAATTTTTCCTGAACCG	137	(TCT)6	55.0
P32	CCCAAGTTCAACAAATCTCC	ATCGTTTCCTGGCGTCT	279	(GAA)6GAG(GAA)3	56.0
P39	GATGGGTTTGGCTCTGC	GTCCTCCTCACTTGTTTCC	348	(AG)17	54.0
P42	GGACTGTGAAGGGCTGTG	ACGGAAGTAGGGACCAAA	297	(GGA)5	53.5
P43	AAGTCAAGTAGTTAGCAAGT	AACATAAACAGCCAGAGT	282	(TC)6	46.2
P45	CTTCGGTTCTTTCTTAGTG	GTGATTTGCTTGCCTTGA	200	(AG)6	48.5
P49	ATGCCCGACTTCCACCAA	CAACGGATGTCCTTCACC	169	(CT)7	50.8
P50	AAGGAGTTGGTGAGGGAA	AGAAGGAAGCAAGGCAGA	208	(TC)9	50.1
P51	CGGGACTCGCTCAGAGGACA	CTTCGCCGCTGCGTTTCA	248	(TCT)5	57.3

位点 locus	N_a	N_e	I	H_o	H_e	H	多态信息指数PIC
P10	10	4.698	1.760	0.753	0.789	0.787	0.758
P11	7	3.387	1.371	0.375	0.706	0.705	0.656
P13	6	3.241	1.357	0.634	0.693	0.692	0.643
P19	13	4.449	1.746	0.630	0.777	0.775	0.744
P1	8	4.002	1.536	0.643	0.752	0.750	0.709
P27	10	4.002	1.641	0.674	0.752	0.750	0.719
P32	5	1.578	0.724	0.374	0.367	0.366	0.339
P39	12	4.629	1.744	0.727	0.786	0.784	0.753
P3	16	3.719	1.884	0.789	0.733	0.731	0.715
P42	10	4.978	1.760	0.687	0.801	0.799	0.772
P43	7	2.361	1.121	0.520	0.578	0.576	0.537
P45	4	2.470	1.002	0.326	0.596	0.595	0.524
P49	11	2.041	1.155	0.327	0.511	0.510	0.481
P50	6	2.817	1.214	0.496	0.647	0.645	0.586
P51	10	2.933	1.376	0.537	0.661	0.659	0.621
P6	8	6.297	1.959	0.744	0.843	0.841	0.823
均值 mean	8.938	3.600	1.459	0.577	0.687	0.685	0.648

来源 source	自由度 df	平方和 SS	均方 MS	估计方差 estimated variance	总变异百分比/% percentage of total variation
组群间 between groups	9	468.986	52.110	1.237	21
个体间 between individuals	217	976.219	4.499	0.000	0
个体内 within the individual	227	1 047.500	4.615	4.615	79
总体 total	453	2 492.705		5.851	100

组群 group	A	B	C	D	E	F	G	H	I	J
A	—	0.706	0.802	0.619	0.779	0.509	0.611	0.599	0.753	0.300
B	0.348	—	0.497	0.472	0.491	0.383	0.325	0.393	0.640	0.261
C	0.221	0.699	—	0.722	0.794	0.633	0.685	0.713	0.623	0.402
D	0.480	0.752	0.326	—	0.668	0.451	0.459	0.456	0.457	0.488
E	0.249	0.712	0.231	0.403	—	0.460	0.510	0.653	0.577	0.346
F	0.675	0.961	0.457	0.795	0.776	—	0.453	0.406	0.476	0.338
G	0.493	1.124	0.378	0.778	0.673	0.793	—	0.435	0.484	0.385
H	0.512	0.935	0.338	0.785	0.426	0.901	0.833	—	0.457	0.281
I	0.284	0.447	0.474	0.783	0.550	0.743	0.726	0.782	—	0.294
J	1.205	1.343	0.911	0.717	1.062	1.085	0.954	1.270	1.223	—

Genetic diversity analysis of Lagerstroemia indica based on fluorescent SSR markers

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组群 group	种质数量 germplasm quantity	全同胞种质 (美国) full sib germplasm (USA)	半同胞种质 (美国) half sib germplasm (USA)	品种 (美国) variety (USA)	野生紫薇 (中国湖北) wild crape myrtle (Hubei, China)	杂交种质 (中国国内) hybrid germplasm (China)	品种 (中国国内) variety (China)
A	90	17	38	16	4	2	13
B	38	1	28	7	1	1
C	38		1	3	32		2
D	32				32
E	7				1		6
F	2				2
G	5		1		2		2
H	2				1		1
I	10	1		4		3	2
J	3				3

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组群 group	种质数量 germplasm quantity	全同胞种质 (美国) full sib germplasm (USA)	半同胞种质 (美国) half sib germplasm (USA)	品种 (美国) variety (USA)	野生紫薇 (中国湖北) wild crape myrtle (Hubei, China)	杂交种质 (中国国内) hybrid germplasm (China)	品种 (中国国内) variety (China)
A	90	17	38	16	4	2	13
B	38	1	28	7	1	1
C	38		1	3	32		2
D	32				32
E	7				1		6
F	2				2
G	5		1		2		2
H	2				1		1
I	10	1		4		3	2
J	3				3

组群 group	种质数量 germplasm quantity	全同胞种质 (美国) full sib germplasm (USA)	半同胞种质 (美国) half sib germplasm (USA)	品种 (美国) variety (USA)	野生紫薇 (中国湖北) wild crape myrtle (Hubei, China)	杂交种质 (中国国内) hybrid germplasm (China)	品种 (中国国内) variety (China)
A	90	17	38	16	4	2	13
B	38	1	28	7	1	1
C	38		1	3	32		2
D	32				32
E	7				1		6
F	2				2
G	5		1		2		2
H	2				1		1
I	10	1		4		3	2
J	3				3