A comprehensive characterization of simple sequence repeats in pepper genomes provides valuable resources for marker development in Capsicum

The sequences of the full set of pepper genomes including nuclear, mitochondrial and chloroplast are now available for use. However, the overall of simple sequence repeats (SSR) distribution in these genomes and their practical implications for molecular marker development in Capsicum have not yet b...

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Bibliographic Details
Published in:Scientific reports 2016-01, Vol.6 (1), p.18919-18919, Article 18919
Main Authors: Cheng, Jiaowen, Zhao, Zicheng, Li, Bo, Qin, Cheng, Wu, Zhiming, Trejo-Saavedra, Diana L., Luo, Xirong, Cui, Junjie, Rivera-Bustamante, Rafael F., Li, Shuaicheng, Hu, Kailin
Format: Article
Language:English
Subjects:
631/449/711
631/61/212/748
Base Sequence
Bioinformatics
Capsicum - genetics
Gene Frequency
Genetic Loci
Genetic Markers
Genome, Chloroplast
Genome, Mitochondrial
Genome, Plant
Genomes
Genotypes
Humanities and Social Sciences
Microsatellite Repeats
Mitochondria
Molecular Sequence Annotation
multidisciplinary
Plant Breeding
Polymorphism, Genetic
Science
Sequence Analysis, DNA
Simple sequence repeats
Vegetables
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Summary:The sequences of the full set of pepper genomes including nuclear, mitochondrial and chloroplast are now available for use. However, the overall of simple sequence repeats (SSR) distribution in these genomes and their practical implications for molecular marker development in Capsicum have not yet been described. Here, an average of 868,047.50, 45.50 and 30.00 SSR loci were identified in the nuclear, mitochondrial and chloroplast genomes of pepper, respectively. Subsequently, systematic comparisons of various species, genome types, motif lengths, repeat numbers and classified types were executed and discussed. In addition, a local database composed of 113,500 in silico unique SSR primer pairs was built using a homemade bioinformatics workflow. As a pilot study, 65 polymorphic markers were validated among a wide collection of 21 Capsicum genotypes with allele number and polymorphic information content value per marker raging from 2 to 6 and 0.05 to 0.64, respectively. Finally, a comparison of the clustering results with those of a previous study indicated the usability of the newly developed SSR markers. In summary, this first report on the comprehensive characterization of SSR motifs in pepper genomes and the very large set of SSR primer pairs will benefit various genetic studies in Capsicum .
ISSN:2045-2322
2045-2322
DOI:10.1038/srep18919