Development and identification of SSR markers based on RAD-seq of <i>Lonicera japonica</i>

Li Hui; Liu Dongchao; Xu Ruirui; Hou Lina; Wang Tianqi; Liu Zhonghua; Fu Xiao; Li Shengbo

doi:10.12171/j.1000-1522.20200337

Journal of Beijing Forestry University > 2021 > 43(6): 108-117. > DOI: 10.12171/j.1000-1522.20200337

Li Hui, Liu Dongchao, Xu Ruirui, Hou Lina, Wang Tianqi, Liu Zhonghua, Fu Xiao, Li Shengbo. Development and identification of SSR markers based on RAD-seq of Lonicera japonica[J]. Journal of Beijing Forestry University, 2021, 43(6): 108-117. DOI: 10.12171/j.1000-1522.20200337

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Development and identification of SSR markers based on RAD-seq of Lonicera japonica

Li Hui^{1, 2,},
Liu Dongchao²,
Xu Ruirui²,
Hou Lina^{1, 2},
Wang Tianqi²,
Liu Zhonghua^{1, 2, ,},
Fu Xiao³,
Li Shengbo⁴

1.
National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of State Forestry Administration, Beijing Forestry University, Beijing 100083, China
2.
School of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
3.
Pingyi County Honeysuckle Nectar Development Promotion Center, Pingyi 273300, Shandong, China
4.
Shandong Yate Eco-Tech, Co., Ltd., Junan 266071, Shandong, China

More Information

Received Date: November 08, 2020
Revised Date: December 15, 2020
Available Online: April 21, 2021
Published Date: June 29, 2021

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Abstract

Abstract

Objective Through the development of polymorphic molecular markers to make up for the lack of Lonicera japonica in SSR markers, this paper aims to promote the research in genetic resource management and variety identification, and lay the foundation for future de novo assembling of Lonicera japonica genome.
Method RAD-seq (restriction-site associated DNA sequencing) was used to conduct simplified genome sequencing for two Lonicera japonica samples. The SSR sequences were identified by MISA and the characterizations of SSR sequences and their polymorphisms were analyzed by bioinformatics methods.
Result 27.805 Mbp and 42.560 Mbp clean reads were obtained in ‘Jiufengyihao’ and ‘Yate’ using restriction-site associated DNA (RAD). A total of 46 999 SSR loci were detected among the 45 850 gene sequences assembled, with the highest proportion of mono-nucleotide repeat SSRs (49.15%) and the lowest proportion of hexa-nucleotide repeat SSRs (0.20%). The repeated motifs at SSR loci were dominated by (A/T)n and showed a bias. Apart from mono-nucleotide and di-nucleotide repetition types, the repeat counts of SSR motifs mainly ranged from 5 to 6. The frequency of SSRs repetition types showed a downward trend with the increase of repeat number. The range of SSR length ranged from 10 to 310 bp, and the frequency of SSR sequence tended to decrease as the number of repetitions increasing. 38 507 pairs of SSR primers were successfully designed, with a design success rate of 81.93%. 35 pairs of SSR primers were analyzed for polymorphism, in which the average number of alleles, observed heterozygosity and PIC were 5.057, 0.363 and 0.568, among which there were 26 highly polymorphic loci and 9 moderately polymorphic loci, all of which did not deviate from the Hardy-Weinberg equilibrium.
Conclusion The large-scale development of SSR markers and the screening of polymorphic SSR primers can be realized based on RAD-seq technology, and provide data support for the research of Lonicera japonica in genetic diversity analysis and germplasm identification.
- Lonicera japonica,
- simple sequence repeat (SSR),
- RAD-seq,
- polymorphism

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References (37)

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Development and identification of SSR markers based on RAD-seq of Lonicera japonica