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Research article
Hongbo Zhu
Guangdong Ocean University
Corresponding Author
ORCiD: https://orcid.org/0000-0001-9921-724X
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The genetic complexity and the lack of genomic resources in sweet potato make genetic improvement extremely challenging. Simple sequence repeats (SSRs) offer an effective molecular marker technology for molecular-based breeding and for locating important loci in crop plants, but only a few have previously been developed in sweet potato. To explore new SSR markers and accelerate its use in sweet potato, we developed a set of 2,431 primer pairs from 133,727 SSRs identified in the sweet potato genome using the Perl script MISA software. The average frequency was one SSR per 6.26 kb with dinucleotides (38.5%) being the most dominant repeat motif. The main motif types in all repeats were AT/AT, AAT/ATT, A/T, AAAT/ATTT, AAAAT/ATTTT and AAAAAT/ATTTTT accounting for 78.29% of the total SSRs. Out of the 100 randomly selected primer pairs, 50% produced clear bands and amplified 251 alleles. On average, the number of alleles was 5.02 per locus for values ranging from 1 to 13 alleles. The UPGMA cluster analysis grouped the 24 sweet potato materials into four clusters at a similarity coefficient of 0.68 showing no relationship between the genotypes and the geographic sources of germplasm. The SSR markers currently developed will provide valuable genetic resources for germplasm identification, and accelerate studies on genetic diversity in sweet potato and related species.
Keywords
genome sequences, SSR markers, sweet potato, genetic diversity, polymorphism
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This is a preprint, a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Research article
Hongbo Zhu
Guangdong Ocean University
Corresponding Author
ORCiD: https://orcid.org/0000-0001-9921-724X
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
History
CURRENT STATUS: Posted
The most recent version of this article is available here.
No community comments so far
Version 1
Posted 16 Apr, 2020
No comments provided
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
Subject Areas
Epigenetics & Genomics
License:
This work is licensed under a CC BY 4.0 License. Read Full License
The most recent version of this article is available here.
The genetic complexity and the lack of genomic resources in sweet potato make genetic improvement extremely challenging. Simple sequence repeats (SSRs) offer an effective molecular marker technology for molecular-based breeding and for locating important loci in crop plants, but only a few have previously been developed in sweet potato. To explore new SSR markers and accelerate its use in sweet potato, we developed a set of 2,431 primer pairs from 133,727 SSRs identified in the sweet potato genome using the Perl script MISA software. The average frequency was one SSR per 6.26 kb with dinucleotides (38.5%) being the most dominant repeat motif. The main motif types in all repeats were AT/AT, AAT/ATT, A/T, AAAT/ATTT, AAAAT/ATTTT and AAAAAT/ATTTTT accounting for 78.29% of the total SSRs. Out of the 100 randomly selected primer pairs, 50% produced clear bands and amplified 251 alleles. On average, the number of alleles was 5.02 per locus for values ranging from 1 to 13 alleles. The UPGMA cluster analysis grouped the 24 sweet potato materials into four clusters at a similarity coefficient of 0.68 showing no relationship between the genotypes and the geographic sources of germplasm. The SSR markers currently developed will provide valuable genetic resources for germplasm identification, and accelerate studies on genetic diversity in sweet potato and related species.
Figure 1
Figure 2
This is a list of supplementary files associated with this preprint. Click to download.
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