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Biyoteknolojinin Güncel Uygulamalarının Su Ürünleri Genetik Alanında Kullanılması: Yeni Nesil Dizileme Teknolojileri

Year 2018, Volume: 4 Issue: 3, 192 - 204, 27.12.2018
https://doi.org/10.17216/limnofish.399545

Abstract



Geride bıraktığımız elli yıllık süreçte DNA
dizi bilgisinin belirlenmesine yönelik muazzam çaba gösterilmiştir.
Geliştirilen teknikler sayesinde kısa oligonukleotidlerden milyonlarca
nükleotidlik tüm genom dizilemelerini tek reaksiyonda okuyabilen platformlara
geçilmiştir. Bu ilerlemeler, Yeni Nesil Dizileme (YND) teknolojilerinin
piyasaya sürülmesi ile gerçekleşmiştir. Kullanılan yöntemler, temelde bir
genomun indirgenmiş temsilini oluşturan rastgele kütüphaneler (RADseq,
ddRADseq, 2bRADseq, CROPS ve RRL) ile belli bir bölgeyi hedef alan kütüphaneler
(RNAseq) olmak üzere ikiye ayrılırlar. Örneklerin hazırlanma süreci kısaca, DNA
dizisi çıkarılması hedeflenen türün genomunun restriksiyon ya da sonikasyon
yöntemi ile parçalara ayrılarak bir DNA kütüphanesinin oluşturulması ve
ardından yüksek üretim hacmine sahip dizileme ekipmanları ile yeni sentezlenen
DNA parçalarının yüksek kapasitede (paralel olarak) dizilenmesi, takiben de tüm
bu dizilerin bir araya getirilmesi (assembly making) şeklinde
özetlenebilir. Bu derlemede, literatürde en fazla kullanılan ve restriksiyon
temelli yöntemlerden olan RADseq ve ddRADseq yöntemleri odaklı örneklerin
hazırlanması ve biyoinformatik analizleri ele alınmıştır. Ülkemizde potansiyeli
henüz keşfedilmemiş olan YND teknolojilerinin su ürünleri genetik
literatüründeki kullanım alanları: (i) referans genom haritaları oluşturma
(fiziksel), (ii) genetik bağlantı haritalamaları (QTL haritalama), (iii)
popülasyon genetiği ve filogeni, (iv) TNP chip dizaynında, (v) verifikasyon ve
validasyon çalışmalarında, (vi) ıslah amaçlı genotipleme ile (vii)
sürdürülebilir su ürünleri yetiştiriciliği ve çevresel etkinin en aza
indirilmesi noktasında bilgilendirici genetik izlenebilirlik alt başlıklarında
derlenmiştir.

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Using current applications of biotechnology in aquaculture genetics: Next Generation Sequencing Technologies

Year 2018, Volume: 4 Issue: 3, 192 - 204, 27.12.2018
https://doi.org/10.17216/limnofish.399545

Abstract

There
have been enormous attempts for determining DNA sequences within the last fifty
years. Advances in technology have enabled the shift from the sequencing of
short oligonucleotides to whole genome sequencing of millions of bases within a
single reaction. Such advances have been attained with the launch of Next
Generation Sequencing platforms. Techniques used involve two fundamental
sections as generating a reduced representation of the genome of interest
through random fragmentation based libraries (RADseq, ddRADseq, 2bRADseq, CROPS
ve RRL) and target specific libraries (RNA seq). Briefly, library preparation
involves fragmentation of the genomic DNA to be sequenced by using restriction
digestion or sonication and then sequence massively in parallel via high-throughput
sequencers and make assembly of short fragments. In the present review, RADseq
and ddRADseq, the most commonly used techniques of NGS in the literature, have
been focused on an explanation of library preparation and bioinformatics
analyses. The potential that NGS technologies hold has not been fully
understood in our country yet, the applications in aquaculture genetics are:
(i) reference genome projects (physical), (ii) genetic linkage mapping (i.e.
QTL mapping), (iii) population genetics and phylogeny, (iv) SNP chip design,
(v) verification and validation studies, (vi) genotyping for selective breeding
as well as (vii) genetic traceability studies for sustainable aquaculture and
minimize environmental impacts.

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Details

Primary Language Turkish
Journal Section Review
Authors

Münevver Oral 0000-0001-7318-6641

Publication Date December 27, 2018
Published in Issue Year 2018Volume: 4 Issue: 3

Cite

APA Oral, M. (2018). Biyoteknolojinin Güncel Uygulamalarının Su Ürünleri Genetik Alanında Kullanılması: Yeni Nesil Dizileme Teknolojileri. Journal of Limnology and Freshwater Fisheries Research, 4(3), 192-204. https://doi.org/10.17216/limnofish.399545