Premium
High‐throughput SNP discovery in the rabbit ( O ryctolagus cuniculus ) genome by next‐generation semiconductor‐based sequencing
Author(s) -
Bertolini F.,
Schiavo G.,
Scotti E.,
Ribani A.,
Martelli P. L.,
Casadio R.,
Fontanesi L.
Publication year - 2014
Publication title -
animal genetics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.756
H-Index - 81
eISSN - 1365-2052
pISSN - 0268-9146
DOI - 10.1111/age.12121
Subject(s) - biology , genome , snp genotyping , genotyping , sanger sequencing , single nucleotide polymorphism , dna sequencing , genetics , reference genome , genomics , snp , computational biology , gene , genotype
Summary The E uropean rabbit ( O ryctolagus cuniculus ) is a domesticated species with one of the broadest ranges of economic and scientific applications and fields of investigation. Rabbit genome information and assembly are available (oryCun2.0), but so far few studies have investigated its variability, and massive discovery of polymorphisms has not been published yet for this species. Here, we sequenced two reduced representation libraries ( RRL s) to identify single nucleotide polymorphisms ( SNP s) in the rabbit genome. Genomic DNA of 10 rabbits belonging to different breeds was pooled and digested with two restriction enzymes ( H ae III and R sa I ) to create two RRL s which were sequenced using the I on T orrent P ersonal G enome M achine. The two RRL s produced 2 917 879 and 4 046 871 reads, for a total of 280.51 Mb (248.49 Mb with quality >20) and 417.28 Mb (360.89 Mb with quality >20) respectively of sequenced DNA . About 90% and 91% respectively of the obtained reads were mapped on the rabbit genome, covering a total of 15.82% of the oryCun2.0 genome version. The mapping and ad hoc filtering procedures allowed to reliably call 62 491 SNP s. SNP s in a few genomic regions were validated by Sanger sequencing. The Variant E ffect P redictor Web tool was used to map SNP s on the current version of the rabbit genome. The obtained results will be useful for many applied and basic research programs for this species and will contribute to the development of cost‐effective solutions for high‐throughput SNP genotyping in the rabbit.