000165503 001__ 165503
000165503 005__ 20260112132214.0
000165503 0247_ $$2doi$$a10.1002/aps3.1201
000165503 0248_ $$2sideral$$a145901
000165503 037__ $$aART-2018-145901
000165503 041__ $$aeng
000165503 100__ $$0(orcid)0000-0001-5658-8411$$aViruel, Juan
000165503 245__ $$aAdvances in genotyping microsatellite markers through sequencing and consequences of scoring methods for <i>Ceratonia siliqua</i> (Leguminosae)
000165503 260__ $$c2018
000165503 5060_ $$aAccess copy available to the general public$$fUnrestricted
000165503 5203_ $$aPremise of the Study
Simple sequence repeat (SSR) or microsatellite markers have been used in a broad range of studies mostly scoring alleles on the basis of amplicon size as a proxy for the number of repeat units of an SSR motif. However, additional sources of variation within the SSR or in the flanking regions have largely remained undetected.
Methods
In this study, we implemented a next-generation sequencing–based genotyping approach in a newly characterized set of 18 nuclear SSR markers for the carob tree, Ceratonia siliqua. Our aim was to evaluate the effect of three different methods of scoring molecular variation present within microsatellite markers on the genetic diversity and structure results.
Results
The analysis of the sequences of 77 multilocus genotypes from four populations revealed SSR variation and additional sources of polymorphism in 87% of the loci analyzed (42 single-nucleotide polymorphisms and five insertion/deletion polymorphisms), as well as divergent paralog copies in two loci. Ignoring sequence variation under standard amplicon size genotyping resulted in incorrect identification of 69% of the alleles, with important effects on the genetic diversity and structure estimates.
Discussion
Next-generation sequencing allows the detection and scoring of SSRs, single-nucleotide polymorphisms, and insertion/deletion polymorphisms to increase the resolution of population genetic studies.
000165503 540__ $$9info:eu-repo/semantics/openAccess$$aby-nc-nd$$uhttps://creativecommons.org/licenses/by-nc-nd/4.0/deed.es
000165503 590__ $$a1.232$$b2018
000165503 591__ $$aPLANT SCIENCES$$b137 / 226 = 0.606$$c2018$$dQ3$$eT2
000165503 592__ $$a0.607$$b2018
000165503 593__ $$aPlant Science$$c2018$$dQ2
000165503 593__ $$aEcology, Evolution, Behavior and Systematics$$c2018$$dQ2
000165503 655_4 $$ainfo:eu-repo/semantics/article$$vinfo:eu-repo/semantics/publishedVersion
000165503 700__ $$aHaguenauer, Anne
000165503 700__ $$aJuin, Marianick
000165503 700__ $$aMirleau, Fatma
000165503 700__ $$aBouteiller, Delphine
000165503 700__ $$aBoudagher-Kharrat, Magda
000165503 700__ $$aOuahmane, Lahcen
000165503 700__ $$aLa Malfa, Stefano
000165503 700__ $$aMédail, Frédéric
000165503 700__ $$aSanguin, Hervé
000165503 700__ $$aNieto Feliner, Gonzalo
000165503 700__ $$aBaumel, Alex
000165503 773__ $$g6, 12 (2018), e1201 [10 pp.]$$pAppl. plant sci.$$tApplications in plant sciences$$x2168-0450
000165503 8564_ $$s433849$$uhttps://zaguan.unizar.es/record/165503/files/texto_completo.pdf$$yVersión publicada
000165503 8564_ $$s2622063$$uhttps://zaguan.unizar.es/record/165503/files/texto_completo.jpg?subformat=icon$$xicon$$yVersión publicada
000165503 909CO $$ooai:zaguan.unizar.es:165503$$particulos$$pdriver
000165503 951__ $$a2026-01-12-11:08:43
000165503 980__ $$aARTICLE