Abstract
Single nucleotide polymorphisms (SNPs) are essential for identifying the genetic mechanisms of complex traits. In the present study, we applied genotyping by genome reducing and sequencing (GGRS) method to construct a 252-plex sequencing library for SNP discovery and genotyping in chicken. The library was successfully sequenced on an Illumina HiSeq 2500 sequencer with a paired-end pattern; approximately 400 million raw reads were generated, and an average of approximately 1.4 million good reads per sample were generated. A total of 91,767 SNPs were identified after strict filtering, and all of the 252 samples and all of the chromosomes were well represented. Compared with the Illumina 60K chicken SNP chip data, approximately 34,131 more SNPs were identified using GGRS, and a higher SNP density was found using GGRS, which could be beneficial for downstream analysis. Using the GGRS method, more than 3528 samples can be sequenced simultaneously, and the cost is reduced to $18 per sample. To the best of our knowledge, this study describes the first report of such highly multiplexed sequencing in chicken, indicating potential applications for genome-wide association and genomic selection in chicken.
Highlights
SNP chips have been widely used in genome-wide genetic marker genotyping in chicken [1,2,3,4]
The major limitations are that SNP genotyping data may be subject to an ascertainment bias due to the procedure used to select the SNPs [5,6], and the SNP chips that originated from special breeds that cannot be used to detect novel SNPs [7,8,9], in indigenous chicken genetics research
The electropherogram results showed that the primer dimers and the adapter dimers were either rarely observed or absent in the PCR products of the library constructed using the complementary adapters, and no dimers were found in the sequencing library; the primer dimers and the adapter dimers were clearly observed in the PCR products and the adapter dimers were obviously found in the library constructed using the "forked" adapters (S2 File)
Summary
SNP chips have been widely used in genome-wide genetic marker genotyping in chicken [1,2,3,4]. The major limitations are that SNP genotyping data may be subject to an ascertainment bias due to the procedure used to select the SNPs [5,6], and the SNP chips that originated from special breeds that cannot be used to detect novel SNPs [7,8,9], in indigenous chicken genetics research. Next-generation sequencing (NGS) technologies have been used in genome-wide genetic marker discovery and genotyping [11,12,13,14]. PLOS ONE | DOI:10.1371/journal.pone.0137010 August 27, 2015
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