Over-fishing is one of the most complex and argued issue among the human impacts affecting the marine environment. The development of integrated policies for fish stock conservation and its responsible use are essential. Nowadays, genomics is considered an ultimate tool to define stock boundaries and population structure as it expands the focus on the entire organism’s genetic makeup and its interaction with the environment. An example of effort and capitalization on genomics is shown by the Italian RITMARE Flagship Project, which aims to create a genomic mapping for stocks of two commercially important species, the red mullet (Mullus barbatus L.) and the deep-water rose shrimp (Parapenaeus longirostris Lucas, 1847), through the use of 2b-RAD technology, based on sequencing the uniform fragments produced by type IIB restriction endonucleases. A sampling design covering 8 Geographical Sub-Areas was defined on the basis of nursery areas, abundance and importance in local fishery and it was completed during the MEDITS 2013 survey. After the extraction of high quality genomic DNA from 7 individuals for each species, the 2b-RAD protocol was tested for the first time. Thereafter, a high-throughput sequencing of libraries was accomplished through Illumina® platform and the software STACKS was used to analyze the sequences. Several millions of high quality reads per individual were obtained and approximately from 1.0 to 2.0x10e3 candidate SNP markers were identified. These preliminary results confirm the successful application of 2b-RAD technology on both non model species and, above all, its effective extendibility to larger number of individuals and population samples, necessary to assess stock boundaries and stock units in the Italian Seas.
Stock boundaries of Mullus barbatus (Mullidae) and Parapenaeus longirostris (Penaeidae) populations in the Italian seas: development of genomic 2b-RAD markers
FERRARI, ALICE;CARIANI, ALESSIA
2014
Abstract
Over-fishing is one of the most complex and argued issue among the human impacts affecting the marine environment. The development of integrated policies for fish stock conservation and its responsible use are essential. Nowadays, genomics is considered an ultimate tool to define stock boundaries and population structure as it expands the focus on the entire organism’s genetic makeup and its interaction with the environment. An example of effort and capitalization on genomics is shown by the Italian RITMARE Flagship Project, which aims to create a genomic mapping for stocks of two commercially important species, the red mullet (Mullus barbatus L.) and the deep-water rose shrimp (Parapenaeus longirostris Lucas, 1847), through the use of 2b-RAD technology, based on sequencing the uniform fragments produced by type IIB restriction endonucleases. A sampling design covering 8 Geographical Sub-Areas was defined on the basis of nursery areas, abundance and importance in local fishery and it was completed during the MEDITS 2013 survey. After the extraction of high quality genomic DNA from 7 individuals for each species, the 2b-RAD protocol was tested for the first time. Thereafter, a high-throughput sequencing of libraries was accomplished through Illumina® platform and the software STACKS was used to analyze the sequences. Several millions of high quality reads per individual were obtained and approximately from 1.0 to 2.0x10e3 candidate SNP markers were identified. These preliminary results confirm the successful application of 2b-RAD technology on both non model species and, above all, its effective extendibility to larger number of individuals and population samples, necessary to assess stock boundaries and stock units in the Italian Seas.I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
