ABFT SNP · Isolation and characterization of single nucleotide polymorpisms (SNPs) in Atlantic bluefin tuna (Thunnus thynnus)
7РП — „Хора“ (Действия „Мария Кюри“)
- Период
- 2011-07-01 → 2013-07-31
- Финансиране от ЕС
- 157 720 €
- Участници
- 1
- Схема
- MC-IEF
Линиите свързват координатора с партньорите.
Накратко на български
Генетичните разлики (SNP) при атлантическия син риба-тунец се анализират чрез секвениране на неговия транскриптом. Това помага за разбирането на вариациите в популациите на този важен за риболова вид.
Кратко обяснение, генерирано от езиков модел по текста на CORDIS. Оригиналът е по-долу.
Резултати накратко
Isolation and characterization of single nucleotide polymorpisms (SNPs) in Atlantic bluefin tuna (Thunnus thynnus)
Executive Summary: The majority of recent studies suggest population structuring of bluefin tuna in the Mediterranean, but evidence is still not conclusive. Genetic characterization of this important fishery species was until recently very limited. We sequenced the bluefin tuna transcriptome with the aims of isolating polymorphic SNPs and providing a genomic resource for this species. Results The sequencing and characterization of the bluefin tuna transcriptome has uncovered a high level of polymorphism. Combining functional annotation and information on synonymous and non-synonymous substitutions allows to select polymorphic markers based on their putative biological significance. Based on the results we selected 128 SNP loci for designing a custom OpenArray® genotyping chip: 14 experimentally validated SNP loci with annotations 19 annotated loci with synonymous SNPs 20 annotated loci with non-synonymous SNP mutations from or to stop codons 29 loci annotated as enzymes with non-synonymous SNP mutations from or to polar and non polar amino acids 23 annotated loci with non-synonymous SNP mutations from the 17 least likely amino acid changes in a PAM2 matrix 23 annotated loci with other non-synonymous SNP mutations Despite initial difficulties due to sample unavailability, except for the delaying of genotyping, the objectives of the project have been achieved or exceeded: a number of SNPs much larger than anticipated has been discovered and characterized in detail. This has allowed to select polymorphic markers for genotyping based on expected biological function inferred from the annotation; furthermore, the genomic resource obtained allows the selection of marker panels covering specific genes from a pool of more then 12,000, enabling the study of population variability for traits relevant to fitness and survival. A draft transcriptome has been produced; and a reference genome based assembly has just been completed. Other classes of polymorphism such as SSRs and SINEs have been discovered and their characterization is still in progress. Finally, the availability of a large pool of well characterized polymorphic markers constitutes an important resource for this species, enabling to address a broad range of questions.
Текст от CORDIS, на английски · Данни: CORDIS, © Европейски съюз
Цел на проекта
The Atlantic bluefin tuna Thunnus thynnus (Linnaeus 1758) is a highly migratory pelagic species found in the North Atlantic and Mediterranean Sea. The high market value of bluefin tuna has led to substantial overfishing, possibly lead to stock depletion unless sustainable catch quotas are enforced. Rational fish stock management requires knowledge of population structure; currently two separate Eastern and Western Atlantic stocks are recognized, spawning in the Mediterranean and the Gulf of Mexico respectively. Analysis of DNA markers such as microsatellite DNA and hypervariable mtDNA sequences mostly support the hypothesis of the Eastern and Western stocks, but suggest a more complex population structuring and the presence of other spawning sites in the Mediterranean. Single nucleotide polymorphisms (SNPs) are the most abundant polymorphisms in genomes; as sequencing is required for their characterisation, large numbers of SNPs were previously available only for model organisms. The advent of massively parallel sequencing platforms allows isolation of large numbers of SNPs in non-model species; current high-throughput genotyping platforms allow simultaneous analysis of SNPs of the same order of magnitude. Due to these technological advances, the use of SNPs in population studies is increasing and is anticipated to complement and eventually replace current DNA-based makers. The availability of a large number of SNP markers in the bluefin tuna would allow to analyse population structure in greater detail than with the currently used markers while facilitating data standardization across labs; addditionally, the genomic resources obtained from the project would significantly increase the level of genetic characterisation of ABFT and can provide the basis for future studies such as microarray development, marker validation and genetic linkage analysis.""
Оригинален текст от CORDIS (на английски).
Участници
- HELLENIC CENTRE FOR MARINE RESEARCH · Attikia AnavissosКоординаторГърция
Връзки
Данни: CORDIS, © Европейски съюз