Fast sequence-based microsatellite genotyping development workflow.

Autor:	Lepais O; INRAE, Univ. Bordeaux, BIOGECO, Cestas, France.; INRAE, Université de Pau et Pays de l'Adour, ECOBIOP, Saint-Peé-sur-Nivelle, France., Chancerel E; INRAE, Univ. Bordeaux, BIOGECO, Cestas, France., Boury C; INRAE, Univ. Bordeaux, BIOGECO, Cestas, France., Salin F; INRAE, Univ. Bordeaux, BIOGECO, Cestas, France., Manicki A; INRAE, Université de Pau et Pays de l'Adour, ECOBIOP, Saint-Peé-sur-Nivelle, France., Taillebois L; INRAE, Université de Pau et Pays de l'Adour, ECOBIOP, Saint-Peé-sur-Nivelle, France., Dutech C; INRAE, Univ. Bordeaux, BIOGECO, Cestas, France., Aissi A; LAPAPEZA, University of Batna 1 Hadj Lakhdar, Batna, Algeria., Bacles CFE; INRAE, Université de Pau et Pays de l'Adour, ECOBIOP, Saint-Peé-sur-Nivelle, France., Daverat F; INRAE, EABX, Cestas, France., Launey S; INRAE, Agrocampus Ouest, ESE, Ecology and Ecosystem Health, Rennes, France., Guichoux E; INRAE, Univ. Bordeaux, BIOGECO, Cestas, France.
Jazyk:	angličtina
Zdroj:	PeerJ [PeerJ] 2020 May 04; Vol. 8, pp. e9085. Date of Electronic Publication: 2020 May 04 (Print Publication: 2020).
DOI:	10.7717/peerj.9085
Abstrakt:	Application of high-throughput sequencing technologies to microsatellite genotyping (SSRseq) has been shown to remove many of the limitations of electrophoresis-based methods and to refine inference of population genetic diversity and structure. We present here a streamlined SSRseq development workflow that includes microsatellite development, multiplexed marker amplification and sequencing, and automated bioinformatics data analysis. We illustrate its application to five groups of species across phyla (fungi, plant, insect and fish) with different levels of genomic resource availability. We found that relying on previously developed microsatellite assay is not optimal and leads to a resulting low number of reliable locus being genotyped. In contrast, de novo ad hoc primer designs gives highly multiplexed microsatellite assays that can be sequenced to produce high quality genotypes for 20-40 loci. We highlight critical upfront development factors to consider for effective SSRseq setup in a wide range of situations. Sequence analysis accounting for all linked polymorphisms along the sequence quickly generates a powerful multi-allelic haplotype-based genotypic dataset, calling to new theoretical and analytical frameworks to extract more information from multi-nucleotide polymorphism marker systems. Competing Interests: The authors declare there are no competing interests. (©2020 Lepais et al.)
Databáze:	MEDLINE
Externí odkaz:	Zobrazit plný text záznamu