title: A comprehensive characterization of simple sequence repeats in pepper genomes provides valuable resources for marker development in Capsicum.
abstract: 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.
authors.affiliation: College of Horticulture, South China Agricultural University, Guangzhou 510642, China.
authors.forename: Jiaowen
authors.initials: J
authors.lastname: Cheng
authors.affiliation: Department of Computer Science, City University of Hong Kong, Hong Kong 999077, China.
authors.forename: Zicheng
authors.initials: Z
authors.lastname: Zhao
authors.affiliation: College of Horticulture, South China Agricultural University, Guangzhou 510642, China.
authors.forename: Bo
authors.initials: B
authors.lastname: Li
authors.affiliation: Pepper Institute, Zunyi Academy of Agricultural Sciences, Zunyi, Guizhou 563102, China.
authors.forename: Cheng
authors.initials: C
authors.lastname: Qin
authors.affiliation: College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China.
authors.forename: Zhiming
authors.initials: Z
authors.lastname: Wu
authors.affiliation: Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del IPN (Cinvestav)-Unidad Irapuato, Irapuato 36821, México.
authors.forename: Diana L
authors.initials: DL
authors.lastname: Trejo-Saavedra
authors.affiliation: Pepper Institute, Zunyi Academy of Agricultural Sciences, Zunyi, Guizhou 563102, China.
authors.forename: Xirong
authors.initials: X
authors.lastname: Luo
authors.affiliation: College of Horticulture, South China Agricultural University, Guangzhou 510642, China.
authors.forename: Junjie
authors.initials: J
authors.lastname: Cui
authors.affiliation: Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del IPN (Cinvestav)-Unidad Irapuato, Irapuato 36821, México.
authors.forename: Rafael F
authors.initials: RF
authors.lastname: Rivera-Bustamante
authors.affiliation: Department of Computer Science, City University of Hong Kong, Hong Kong 999077, China.
authors.forename: Shuaicheng
authors.initials: S
authors.lastname: Li
authors.affiliation: College of Horticulture, South China Agricultural University, Guangzhou 510642, China.
authors.forename: Kailin
authors.initials: K
authors.lastname: Hu
mesh_terms: D001483:Base Sequence; D002212:Capsicum / Q000235:genetics*; D005787:Gene Frequency; D056426:Genetic Loci; D005819:Genetic Markers; D054628:Genome, Chloroplast; D054629:Genome, Mitochondrial; D018745:Genome, Plant; D018895:Microsatellite Repeats; D058977:Molecular Sequence Annotation; D000069600:Plant Breeding; D011110:Polymorphism, Genetic; D017422:Sequence Analysis, DNA
chemical_list: D005819:Genetic Markers