Rapid development of microsatellite markers for Callosobruchus chinensis using Illumina paired-end sequencing

• Published in: PloS one 2014-05, Vol.9 (5), p.e95458-e95458
• Main Authors: Duan, Can-Xing, Li, Dan-Dan, Sun, Su-Li, Wang, Xiao-Ming, Zhu, Zhen-Dong
• Format: Article
• Language: English
• Subjects: Analysis; Animal Distribution; Animals; Assembly; Base Sequence; Biology and Life Sciences; Callosobruchus chinensis; China; Cluster Analysis; Coleoptera - genetics; Crop science; Deoxyribonucleic acid; DNA; DNA Primers - genetics; DNA sequencing; Fabaceae - parasitology; Feasibility studies; Gene mapping; Gene sequencing; Genes; Genetic diversity; Genetic markers; Genetic structure; Genetics, Population; Genomes; Genomics; Genotypes; High-Throughput Nucleotide Sequencing - methods; Informatics; Legumes; Loci; Markers; Microsatellite Repeats - genetics; Microsatellites; Molecular Sequence Data; Next-generation sequencing; Pests; Population genetics; Population studies; Populations; Primers; Resolution; Seeds; Seeds - parasitology; Weevils
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0095458

The adzuki bean weevil, Callosobruchus chinensis L., is one of the most destructive pests of stored legume seeds such as mungbean, cowpea, and adzuki bean, which usually cause considerable loss in the quantity and quality of stored seeds during transportation and storage. However, a lack of genetic information of this pest results in a series of genetic questions remain largely unknown, including population genetic structure, kinship, biotype abundance, and so on. Co-dominant microsatellite markers offer a great resolving power to determine these events. Here, we report rapid microsatellite isolation from C. chinensis via high-throughput sequencing. In this study, 94,560,852 quality-filtered and trimmed reads were obtained for the assembly of genome using Illumina paired-end sequencing technology. In total, the genome with total length of 497,124,785 bp, comprising 403,113 high quality contigs was generated with de novo assembly. More than 6800 SSR loci were detected and a suit of 6303 primer pair sequences were designed and 500 of them were randomly selected for validation. Of these, 196 pair of primers, i.e. 39.2%, produced reproducible amplicons that were polymorphic among 8 C. chinensis genotypes collected from different geographical regions. Twenty out of 196 polymorphic SSR markers were used to analyze the genetic diversity of 18 C. chinensis populations. The results showed the twenty SSR loci were highly polymorphic among these populations. This study presents a first report of genome sequencing and de novo assembly for C. chinensis and demonstrates the feasibility of generating a large scale of sequence information and SSR loci isolation by Illumina paired-end sequencing. Our results provide a valuable resource for C. chinensis research. These novel markers are valuable for future genetic mapping, trait association, genetic structure and kinship among C. chinensis.