Development of SSR Markers Based on Transcriptiome of Naematelia aurantialba

doi:10.16420/j.issn.0513-353x.2024-0767

Acta Horticulturae Sinica ›› 2025, Vol. 52 ›› Issue (7): 1780-1788.doi: 10.16420/j.issn.0513-353x.2024-0767

• Genetic & Breeding·Germplasm Resources·Molecular Biology • Previous Articles Next Articles

Development of SSR Markers Based on Transcriptiome of Naematelia aurantialba

LI Xuesong¹^,², HUA Rong¹^,², SUN Dafeng¹^,², YUE Wansong¹, ZHANG Junbo¹, LI Jianying¹, and LIU Shaoxiong¹^,²^,^*()

¹ Kunming Edible Fungi Institute of All China Federation of Supply and Marketing Cooperatives，Kunming 650221，China
² Yunnan Edible Fungi Industry Development Research Institute，Kunming 650221，China

Received:2025-02-02 Revised:2025-05-14 Online:2025-07-23 Published:2025-07-23
Contact: and LIU Shaoxiong

Abstract

Abstract:

Based on experimental validation and bioinformatics，SSR analysis result were exploited from the transcriptiome of Naematelia aurantialba and seven strains. In the meantime，100 SSR were selected for primer design and experimental verification. A total of 4 268 sequences of 6 SSR types were retrieved. The main type of trinucleotide（P3）and hexanucleotide（P6），accounting for 64.20% of the total SSR number. Seven pairs of primers were obtained by verification test and analyzed. UPGMA clustering results showed that the seven N. aurantialba strains were mainly divided into three groups. At the same time，the DNA fingerprint coding of seven pairs of primers was constructed and the 14-digit molecular fingerprint database codes of seven N. aurantialba strains were obtained. In order to provide a theoretical basis for the germplasm resources identification，variety selection and molecular marker-assisted breeding of N. aurantialba.

Key words: Naematelia aurantialba, transcriptiome, SSR, mark development

LI Xuesong, HUA Rong, SUN Dafeng, YUE Wansong, ZHANG Junbo, LI Jianying, and LIU Shaoxiong. Development of SSR Markers Based on Transcriptiome of Naematelia aurantialba[J]. Acta Horticulturae Sinica, 2025, 52(7): 1780-1788.

Figures/Tables 6

References 26

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标记名称 Markers	上游引物（5′-3′） Forward primer	下游引物（5′-3′） Reverse primer	SSR 类型 SSR type	SSR 基元 SSR motif
JESSR003	CATCCCTATGCAATGATTCCACG	TAGAACAAGACTAGAACCGGGAC	P2	（TC）8
JESSR010	GAAGGACGTACAAGGCCGTG	GTGACTAGATTTGATGCTGGCAG	P6	（CCCAGC）4
JESSR032	GCTCTGTTTACGAGGGGATAGG	CCGAATCTGACACCATCATCTCT	P3	（TTG）6
JESSR075	GAGTCTTGAGCGGAGGAGTAC	GACGTACCATGCTGATGCTGAT	P6	（GATGCC）4
JESSR090	TAAAGCACTTCAATTGCGTCTCG	CTAGAGGAGGCCAAGAGGAAGAA	P6	（CATGTG）4
JESSR098	CCTATACCTTAGCCTGAGACAGC	GAGGATCACCATGTCCGTCTC	P3	（CGT）6
JESSR100	CTTGGGGAGGTGGAGAGTATAGG	ACTGTTCTTCGCTTGACCAAATT	P6	（CTGGCA）6

标记名称 Markers	上游引物（5′-3′） Forward primer	下游引物（5′-3′） Reverse primer	SSR 类型 SSR type	SSR 基元 SSR motif
JESSR003	CATCCCTATGCAATGATTCCACG	TAGAACAAGACTAGAACCGGGAC	P2	（TC）8
JESSR010	GAAGGACGTACAAGGCCGTG	GTGACTAGATTTGATGCTGGCAG	P6	（CCCAGC）4
JESSR032	GCTCTGTTTACGAGGGGATAGG	CCGAATCTGACACCATCATCTCT	P3	（TTG）6
JESSR075	GAGTCTTGAGCGGAGGAGTAC	GACGTACCATGCTGATGCTGAT	P6	（GATGCC）4
JESSR090	TAAAGCACTTCAATTGCGTCTCG	CTAGAGGAGGCCAAGAGGAAGAA	P6	（CATGTG）4
JESSR098	CCTATACCTTAGCCTGAGACAGC	GAGGATCACCATGTCCGTCTC	P3	（CGT）6
JESSR100	CTTGGGGAGGTGGAGAGTATAGG	ACTGTTCTTCGCTTGACCAAATT	P6	（CTGGCA）6

标记名称Markers	荧光标记Fluorescence labeling	扩增片段数Fragment number	片段大小/bp Fragment size
JESSR003	FAM	3	172，174，182
JESSR010	FAM	4	166，172，178，184
JESSR032	HEX	3	161，164，167
JESSR075	ROX	3	159．161，179
JESSR090	TAMRA	3	162，168，174
JESSR098	TAMRA	3	129，131，135
JESSR100	TAMRA	3	136，138，142

标记名称Markers	荧光标记Fluorescence labeling	扩增片段数Fragment number	片段大小/bp Fragment size
JESSR003	FAM	3	172，174，182
JESSR010	FAM	4	166，172，178，184
JESSR032	HEX	3	161，164，167
JESSR075	ROX	3	159．161，179
JESSR090	TAMRA	3	162，168，174
JESSR098	TAMRA	3	129，131，135
JESSR100	TAMRA	3	136，138，142

引物Primer	赋值Assignment
引物Primer	0	1	2	3	4
JESSR003	-	173	174	182	-
JESSR010	-	166	172	178	184
JESSR032	-	161	164	167	-
JESSR075	-	159	161	179	-
JESSR090	-	162	168	174	-
JESSR098	-	129	131	135	-
JESSR100	-	136	138	142	-

Development of SSR Markers Based on Transcriptiome of Naematelia aurantialba

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Figures/Tables 6

References 26

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编号 Code	引物 Primer							指纹编号 Fingerprint code
编号 Code	JESSR003	JESSR010	JESSR032	JESSR075	JESSR090	JESSR098	JESSR100	指纹编号 Fingerprint code
ZJJE001	02	24	01	03	02	13	13	02240103021313
ZJJE002	01	01	02	02	03	01	02	01010202030102
ZJJE003	03	01	02	01	03	02	02	03010201030202
J-2	03	03	03	02	03	01	01	03030302030101
J-5	03	01	02	02	03	01	01	03010202030101
J-6	03	13	02	02	03	02	01	03130202030201
J-7	03	01	02	02	13	02	01	03010202130201

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