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

Jiaowen Cheng,Junjie Cui,Cheng Qin,Rafael F Rivera-Bustamante,Kailin Hu,Zicheng Zhao,Diana L Trejo-Saavedra,Shuaicheng Li,Zhiming Wu,Xirong Luo,Bo Li

doi:10.1038/srep18919

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.

Highlights

The sequences of the full set of pepper genomes including nuclear, mitochondrial and chloroplast are available for use
simple sequence repeats (SSR) have been extensively involved in a variety of applications including cultivar identification[6], the determination of ‘hybridity’[7], genetic diversity assessment[8], genetic mapping[9], gene tagging[10], gene flow[11] and molecular evolution[12] in various plant and animal systems
Similar to the nuclear genomes, SSRs in organelle genomes are common[29] and it is generally accepted that polymorphisms due to variations in SSR motif length in the chloroplast or mitochondrial genomes would be of considerable practical value for monitoring gene flow[30], population differentiation[31] and cytoplasmic diversity[32]

Summary

Introduction

The sequences of the full set of pepper genomes including nuclear, mitochondrial and chloroplast are available for use. A comparison of the clustering results with those of a previous study indicated the usability of the newly developed SSR markers 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. A complete analysis of SSR loci in the mitochondrial or chloroplast genomes has been performed only in a relatively limited set of species, such as bryophytes[33], rice[34] and soybean[29] Far, this analysis has rarely been fully conducted in horticultural crops including pepper

Objectives

Methods

Results