caa a22 4500 445318937 CHVBK 20180317142657.0 cr unu---uuuuu 170323e20110401xx s 000 0 eng 10.1007/s10126-010-9280-4 doi (NATIONALLICENCE)springer-10.1007/s10126-010-9280-4 Development of Type I Genetic Markers from Expressed Sequence Tags in Highly Polymorphic Species [Elektronische Daten] [Woo-Jin Kim, Hyungtaek Jung, Patrick Gaffney] Expressed sequence tag (EST) databases provide a primary source of nuclear DNA sequences for genetic marker development in non-model organisms. To date, the process has been relatively inefficient for several reasons: 1) priming site polymorphism in the template leads to inferior or erratic amplification; 2) introns in the target amplicon are too large and/or numerous to allow effective amplification under standard screening conditions; and 3) at least occasionally, a PCR primer straddles an exon-intron junction and is unable to bind to genomic DNA template. The first is only a minor issue for species or strains with low heterozygosity but becomes a significant problem for species with high genomic variation, such as marine organisms with extremely large effective population sizes. Problems arising from unanticipated introns are unavoidable but are most pronounced in intron-rich species, such as vertebrates and lophotrochozoans. We present an approach to marker development in the Pacific oyster Crassostrea gigas, a highly polymorphic and intron-rich species, which minimizes these problems, and should be applicable to other non-model species for which EST databases are available. Placement of PCR primers in the 3′ end of coding sequence and 3′ UTR improved PCR success rate from 51% to 97%. Almost all (37 of 39) markers developed for the Pacific oyster were polymorphic in a small test panel of wild and domesticated oysters. Springer Science+Business Media, LLC, 2010 EST nationallicence SNP nationallicence Marker nationallicence Indel nationallicence UTR nationallicence Kim Woo-Jin Biotechnology Research Institute, National Fisheries Research and Development Institute, 408-1 Sirang-ri, Gijang-eup, 619-705, Gijang-gun, Busan, South Korea aut Jung Hyungtaek College of Earth, Ocean, and Environment, University of Delaware, 700 Pilottown Road, 19958, Lewes, DE, USA aut Gaffney Patrick College of Earth, Ocean, and Environment, University of Delaware, 700 Pilottown Road, 19958, Lewes, DE, USA aut Marine Biotechnology Springer-Verlag 13/2(2011-04-01), 127-132 1436-2228 13:2<127 2011 13 10126 https://doi.org/10.1007/s10126-010-9280-4 text/html Onlinezugriff via DOI 1 brief-communication jats NATIONALLICENCE 856 40 https://doi.org/10.1007/s10126-010-9280-4 text/html Onlinezugriff via DOI NATIONALLICENCE 700 1- Kim Woo-Jin Biotechnology Research Institute, National Fisheries Research and Development Institute, 408-1 Sirang-ri, Gijang-eup, 619-705, Gijang-gun, Busan, South Korea aut NATIONALLICENCE 700 1- Jung Hyungtaek College of Earth, Ocean, and Environment, University of Delaware, 700 Pilottown Road, 19958, Lewes, DE, USA aut NATIONALLICENCE 700 1- Gaffney Patrick College of Earth, Ocean, and Environment, University of Delaware, 700 Pilottown Road, 19958, Lewes, DE, USA aut NATIONALLICENCE 773 0- Marine Biotechnology Springer-Verlag 13/2(2011-04-01), 127-132 1436-2228 13:2<127 2011 13 10126 Metadata rights reserved Springer special CC-BY-NC licence nationallicence BK010053 XK010053 XK010000 NATIONALLICENCE NATIONALLICENCE NL-springer