Identification and Development of Polymorphic Genic-SSRs in Tamarix ramosissima in Alxa Region Based on Transcriptome

doi:10.11983/CBB20185

Abstract

Abstract: Simple sequence repeats located in gene transcribed regions (Genic-SSR) can play important roles in plant adaptation to environmental changes. In this study, the transcriptomes of Tamarix ramosissima from five different locations in Alax were sequenced, assembled, and compared. By using CandiSSR software, a total of 1 185 polymorphic Genic-SSRs representing 157 motif types were identified in 1 123 transcripts. Among them, the trinucleotide repeats (596, 50.30%) were the most abundant, followed by dinucleotide repeats (486, 41.01%). Location analysis showed that 411, 239, and 163 Genic-SSRs were located in CDSs, 5′UTRs, and 3′UTRs of the relevant transcripts, respectively; 78.47% of the trinucleotide SSRs were located in CDSs, and 94.07% of the dinucleotide SSRs were located in UTRs. Among SSRs distributed in CDSs, AGC/GCT, AGG/CCT, AAG/CTT, CCG/CGG, and ATC/GAT were relatively abundant, accounting for 64.48% of all the Genic-SSRs; AG/CT and AT/AT were the most abundant repeat types in UTRs, which together account for 55.22% of all the Genic-SSRs in UTRs. Functional annotation showed that polymorphic Genic-SSRs containing genes enriched in a wide range of GO terms and KEGG pathways that highly related to stress response in T. ramosissima. Of the 15 randomly selected Genic-SSRs, 14 were successfully amplified by using polymerase chain reaction technology and 64 alleles were found in these SSR loci. Genetic polymorphism estimation showed that the mean of expected and observed heterozygosity (He, Ho), polymorphism information content (PIC) of these SSRs were 0.553, 0.421, and 0.493, respectively, demonstrating the feasibility of developing SSR markers by RNA-seq.

Key words: Genic-SSR, polymorphism, RNA-seq, Tamarix ramosissima

Yanan Zhang, Lei Huang, Jiabin Li, Lei Zhang, Zhenhua Dang. Identification and Development of Polymorphic Genic-SSRs in Tamarix ramosissima in Alxa Region Based on Transcriptome[J]. Chinese Bulletin of Botany, 2021, 56(4): 433-442.

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URL: https://www.chinbullbotany.com/EN/10.11983/CBB20185

https://www.chinbullbotany.com/EN/Y2021/V56/I4/433

Figures/Tables 6

References 35

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Population	Longitude (E)	Latitude (N)	Altitude (m)	Habitats
TR1	101°00′06″	41°52′16″	939	Wetland
TR2	101°11′44″	41°57′27″	927	Sandy land
TR3	101°03′36″	42°07′02″	915	Wetland
TR4	101°12′26″	41°58′45″	924	Wetland
TR5	101°16′25″	42°01′55″	921	Wetland

Population	Longitude (E)	Latitude (N)	Altitude (m)	Habitats
TR1	101°00′06″	41°52′16″	939	Wetland
TR2	101°11′44″	41°57′27″	927	Sandy land
TR3	101°03′36″	42°07′02″	915	Wetland
TR4	101°12′26″	41°58′45″	924	Wetland
TR5	101°16′25″	42°01′55″	921	Wetland

Sample	CR (No.)	Q30 (%)	GC (%)	Ug (No.)	ML (bp)	N50 (bp)
TR1	47893646	93.12	41.95	37790	1053.09	1953
TR2	43861774	93.06	41.96	35818	1083.87	1983
TR3	46194046	93.04	42.33	39252	995.67	1812
TR4	44817976	93.17	42.87	32175	1099.48	1899
TR5	44190698	92.92	42.49	34364	1082.91	1930
All-unigene				81728	823.46	1364

Sample	CR (No.)	Q30 (%)	GC (%)	Ug (No.)	ML (bp)	N50 (bp)
TR1	47893646	93.12	41.95	37790	1053.09	1953
TR2	43861774	93.06	41.96	35818	1083.87	1983
TR3	46194046	93.04	42.33	39252	995.67	1812
TR4	44817976	93.17	42.87	32175	1099.48	1899
TR5	44190698	92.92	42.49	34364	1082.91	1930
All-unigene				81728	823.46	1364

SSR ID		PS (5′→3′)	RM	Tm (°C)	AS (bp)	Na	PIC	Ho	He
104		F: CAAGGAGGAGCTGTCGTCTG	AG	59.9	123-139	8	0.516	0.286	0.558
	R: GCAGACACGAAGTTTGCGAT		AG	59.9	123-139	8	0.516	0.286
221		F: TGAAGCAGCTGTGTTGGTGA	AT	53.4	158-162	3	0.562	0.321	0.645
	R: TCCTCCTCGATTCCCTACTGA		AT	53.4	158-162	3	0.562	0.321
300		F: GAAGGGTTTGGGTGTTTTCAGA	AT	59.5	155-161	4	0.641	0.643	0.708
	R: AAAACGCACCCTCTCAGCAG		AT	59.5	155-161	4	0.641	0.643
392		F: CGCAACAAGCACAACATCCA	CAG	57.9	100-109	4	0.407	0.608	0.489
	R: GTTAACCGGTCGCACAACTG		CAG	57.9	100-109	4	0.407	0.608
438		F: GGCACCGATACACAAGGACA	CCTT	55.4	192-204	4	0.512	0.500	0.593
	R: CCCACAGGCTTACACCCATT		CCTT	55.4	192-204	4	0.512	0.500
441		F: GCCACCGCCACATTTATCTT	CGAG	50.8	106-122	5	0.520	0.286	0.570
	R: GGAGCTTGACAGGTACAGCA		CGAG	50.8	106-122	5	0.520	0.286
563		F: TCCTGTGCAACGAACTGAGT	GA	51.7	176-186	6	0.593	0.536	0.666
	R: GGGTTTAGCCATGGGTGACA		GA	51.7	176-186	6	0.593	0.536
668		F: ATGGCGATGATGGAGCAACA	GAG	59.9	146-173	7	0.711	0.429	0.758
	R: AGGGATTGGCGGAAGTGAAG		GAG	59.9	146-173	7	0.711	0.429
670		F: GAAGACACAGCACCAAGGGA	GAG	56.7	186-201	5	0.546	0.714	0.627
	R: CGTCTTCCCCAAGTCCGATC		GAG	56.7	186-201	5	0.546	0.714
947		F: TCCCCACACGTAATCCCTTC	TC	50.8	139-149	5	0.445	0.607	0.488
	R: GCGGATGGAAGGAGAAGAGG		TC	50.8	139-149	5	0.445	0.607
1024		F: TGCGCATTTCTTGATTGCCA	TCT	52.1	168-180	5	0.476	0.464	0.516
	R: GGGTTGATGCGGCTTGATTG		TCT	52.1	168-180	5	0.476	0.464
1053		F: GTCGACACTGCAAGCATCAC	TG	56.7	202-204	2	0.293	0.036	0.363
	R: GCACGTACGAGCACATCTCT		TG	56.7	202-204	2	0.293	0.036
1093		F: GAATAGTGGTGGCGGGAGTC	TGC	54.7	117-126	2	0.195	0.250	0.223
	R: GCTTGGCATCGTACCCCTAT		TGC	54.7	117-126	2	0.195	0.250
1114		F: GGTCCTCAGTGTGGCCATAG	TGG	54.1	156-171	4	0.487	0.214	0.543
	R: GTGTTAGAGATGGCGGGCAA		TGG	54.1	156-171	4	0.487	0.214
Mean						4.5	0.493	0.421	0.553