Analysis of SSR locus based on the whole genome sequences of Cyclocarya paliurus and the development of polymorphic primers

LIU Li, QU Yinquan, YU Yanhao, WANG Qian, FU Xiangxiang

JOURNAL OF NANJING FORESTRY UNIVERSITY ›› 2024, Vol. 48 ›› Issue (4) : 67-75.

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南京林业大学学报（自然科学版）
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JOURNAL OF NANJING FORESTRY UNIVERSITY ›› 2024, Vol. 48 ›› Issue (4) : 67-75. DOI: 10.12302/j.issn.1000-2006.202206001

Analysis of SSR locus based on the whole genome sequences of Cyclocarya paliurus and the development of polymorphic primers

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Abstract

【Objective】Genomic simple repeat sequence (SSR) loci were analyzed by screening the whole genome of Cyclocarya paliurus. DNA molecular ID cards of 19 excellent medicinal clones of C. paliurus were constructed based on the newly-developed SSR primers. These genomic SSR markers could support further research, such as the evaluation of the germplasm resource, analysis of genetic diversity, and identification of cultivars/clones.【Method】The SSR loci were screened along with the whole genome of C. paliurus and were enriched and analyzed using MISA software. Subsequently, SSR primers were designed using Primer 3.0. Furthermore, a system for identifying clones of C. paliurus was constructed based on selected SSR markers with high reproducibility and stability.【Result】(1) We detected 89 741 SSR loci from the whole genome, with an occurrence frequency of 62.07%. (2) Among all SSR loci, the proportion of SSRs with a mononucleotide motif was the highest (62.67%) and a hexa-nucleotide repeat was the lowest (0.15%). Most of the repeated motifs in the SSR loci were dominated by (A/T)n. (3) The repeat number of mono-nucleotide and di-nucleotide motifs ranged from 6 to 16. With the increase in the repeat number, the frequencies of various SSR repetition types displayed a downward trend. (4) The length of the SSR sequences varied from 10 to 476 bp, and this length variation existed in different repetitive motifs. Additionally, the frequency of SSR occurrence tended to decrease as the repeat number increased. (5) We successfully designed 78 285 pairs of SSR primers using Primer 3.0. A total of 377 primer pairs were randomly synthesized for amplifying polymorphic SSR fragments, among which 75 pairs primers were successful. Moreover, quick response code DNA molecular ID cards for 19 medical-use clones of C. paliurus were constructed by five pairs of polymorphic SSR primers with a mono-nucleotide motif.【Conclusion】The frequency of genomic SSR loci was high, and there was variability in the type of SSR loci. Simple repeat sequences developed from the whole genome of C. paliurus could be effective candidate molecular markers with further applications in germplasm resource evaluation and fingerprint construction for multi-use clones of C. paliurus.

Key words

Cyclocarya paliurus / simple sequence repeat (SSR) / whole genome / DNA molecular ID card

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LIU Li , QU Yinquan , YU Yanhao , et al . Analysis of SSR locus based on the whole genome sequences of Cyclocarya paliurus and the development of polymorphic primers[J]. JOURNAL OF NANJING FORESTRY UNIVERSITY. 2024, 48(4): 67-75 https://doi.org/10.12302/j.issn.1000-2006.202206001

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