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Background  Genes, RNAs, and proteins play important roles during germline development. However, the functions of non-coding RNAs (ncRNAs) on germline development remain unclear in avian species. Recent high-throughput techniques have identified several classes of ncRNAs, including micro RNAs (miRNAs), small-interfering RNAs (siRNAs), and PIWI-interacting RNAs (piRNAs). These ncRNAs are functionally important in the genome, however, the identification and annotation of ncRNAs in a genome is challenging. The aim of this study was to identify different types of small ncRNAs particularly piRNAs, and the role of piRNA pathway genes in the protection of chicken primordial germ cells (PGCs).    Results  At first, we performed next-generation sequencing to identify ncRNAs in chicken PGCs, and we performed  ab initio  predictive analysis to identify putative piRNAs in PGCs. Then, we examined the expression of three repetitive sequence-linked piRNAs and 14 genic-transcript-linked piRNAs along with their linked genes using real-time PCR. All piRNAs and their linked genes were highly expressed in PGCs. Subsequently, we knocked down two known piRNA pathway genes of chicken, PIWI-like protein 1 ( CIWI ) and 2 ( CILI ), in PGCs using siRNAs. After knockdown of  CIWI  and  CILI , we examined their effects on the expression of six putative piRNA-linked genes and DNA double-strand breakage in PGCs. The knockdown of  CIWI  and  CILI  upregulated chicken repetitive 1 ( CR1 ) element and  RAP2B , a member of RAS oncogene family, and increased DNA double-strand breakage in PGCs.    Conclusions  Our results increase the understanding of PGC-expressed piRNAs and the role of piRNA pathway genes in the protection of germ cells.    Electronic supplementary material  The online version of this article (doi:10.1186/1471-2164-15-757) contains supplementary material, which is available to authorized users.

Small non-coding RNA profiling and the role of piRNA pathway genes in the protection of chicken primordial germ cells