Rapid, economical single-nucleotide polymorphism and microsatellite discovery based on de novo assembly of a reduced representation genome in a non-model organism: a case study of Atlantic cod Gadus morhua

被引：14

作者：

Carlsson, J. ^{[1
,2
]}

Gauthier, D. T. ^{[3
]}

Carlsson, J. E. L. ^{[1
]}

Coughlan, J. P. ^{[1
]}

Dillane, E. ^{[1
]}

Fitzgerald, R. D. ^{[4
]}

Keating, U. ^{[1
]}

McGinnity, P. ^{[1
]}

Mirimin, L. ^{[4
]}

Cross, T. F. ^{[1
]}

机构：

[1] Natl Univ Ireland Univ Coll Cork, Aquauculture & Fisheries Dev Ctr, Sch Biol Earth & Environm Sci, Beaufort Genet Res Programme, Cork, Ireland

[2] Univ Coll Dublin, UCD Sci Educ & Res Ctr West, Sch Biol & Environm Sci, Dublin 4, Ireland

[3] Old Dominion Univ, Dept Biol Sci, Norfolk, VA 23529 USA

[4] Natl Univ Ireland, Ryan Inst, Carna Res Stn, Connemara, Co Galway, Ireland

来源：

JOURNAL OF FISH BIOLOGY | 2013年 / 82卷 / 03期

关键词：

454; Celtic Sea; next-generation sequencing; pyrosequencing; teleost; SNP DISCOVERY; MUTATION MODEL; IDENTIFICATION; LOCI; EVOLUTION; THOUSANDS; SEQUENCE; RAINBOW;

D O I：

10.1111/jfb.12034

中图分类号：

S9 [水产、渔业];

学科分类号：

0908 ;

摘要：

By combining next-generation sequencing technology (454) and reduced representation library (RRL) construction, the rapid and economical isolation of over 25 000 potential single-nucleotide polymorphisms (SNP) and>6000 putative microsatellite loci from c. 2% of the genome of the non-model teleost, Atlantic cod Gadus morhua from the Celtic Sea, south of Ireland, was demonstrated. A small-scale validation of markers indicated that 80% (11 of 14) of SNP loci and 40% (6 of 15) of the microsatellite loci could be amplified and showed variability. The results clearly show that small-scale next-generation sequencing of RRL genomes is an economical and rapid approach for simultaneous SNP and microsatellite discovery that is applicable to any species. The low cost and relatively small investment in time allows for positive exploitation of ascertainment bias to design markers applicable to specific populations and study questions.

引用

页码：944 / 958

页数：15

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