{"id":81931,"date":"2019-02-22T16:17:29","date_gmt":"2019-02-22T21:17:29","guid":{"rendered":"https:\/\/mrnf.gouv.qc.ca\/nos-publications\/catalog-high-confidence-snps-exome-capture\/"},"modified":"2019-02-22T16:17:29","modified_gmt":"2019-02-22T21:17:29","slug":"catalog-high-confidence-snps-exome-capture","status":"publish","type":"cpt_publication","link":"https:\/\/mrnf.gouv.qc.ca\/en\/our-publications\/catalog-high-confidence-snps-exome-capture\/","title":{"rendered":"A catalog of annotated high-confidence SNPs from exome capture and sequencing reveals highly polymorphic genes in Norway spruce (Picea abies)"},"content":{"rendered":"\n

Published in BMC Genomics 19(1): 942. https:\/\/doi.org\/10.1186\/s12864-018-5247-z<\/a><\/b><\/p>\n

Background<\/b> Norway spruce [Picea abies<\/i> (L.) Karst.] is ecologically and economically one of the most important conifer worldwide. Our main goal was to develop a large catalog of annotated high confidence gene SNPs that should sustain the development of genomic tools for the conservation of natural and domesticated genetic diversity resources, and hasten tree breeding efforts in this species.<\/p>\n

Results<\/b> Targeted sequencing was achieved by capturing P. abies<\/i> exome with probes previously designed from the sequenced transcriptome of white spruce (Picea glauca<\/i> (Moench) Voss). Capture efficiency was high (74.5%) given a high level of exome conservation between the two species. Using stringent criteria, we delimited a set of 61,771 high-confidence SNPs across 13,543 genes. To validate SNPs, a high-throughput genotyping array was developed for a subset of 5571 predicted SNPs representing as many different gene loci, and was used to genotype over 1000 trees. The estimated true positive rate of the resource was 84.2%, which was comparable with the genotyping success rate obtained for P. abies<\/i> control SNPs recycled from previous genotyping efforts. We also analyzed SNP abundance across various gene functional categories. Several GO terms and gene families involved in stress response were found over-represented in highly polymorphic genes.

Conclusion<\/b> The annotated high-confidence SNP catalog developed herein represents a valuable genomic resource, being representative of over 13\u2009K genes distributed across the P. abies<\/i> genome. This resource should serve a variety of population genomics and breeding applications in Norway spruce.<\/p>\n","protected":false},"excerpt":{"rendered":"

Published in BMC Genomics 19(1): 942. https:\/\/doi.org\/10.1186\/s12864-018-5247-z Background Norway spruce [Picea abies (L.) Karst.] is ecologically and economically one of the most important conifer worldwide. Our main goal was to develop a large catalog of annotated high confidence gene SNPs that should sustain the development of genomic tools for the conservation of natural and domesticated […]<\/p>\n","protected":false},"template":"","format":"standard","cptt_secteur":[1179],"cptt_theme":[1180,1181,1208],"cptt_categ_publi":[1149],"cptt_auteurs_ministeriels":[1100],"class_list":["post-81931","cpt_publication","type-cpt_publication","status-publish","format-standard","hentry","cptt_secteur-forests","cptt_theme-forestry-research","cptt_theme-forests","cptt_theme-genetic-improvement-of-trees","cptt_categ_publi-scientific-article","cptt_auteurs_ministeriels-m-h-mottet"],"acf":[],"yoast_head":"\nA catalog of annotated high-confidence SNPs from exome capture and sequencing reveals highly polymorphic genes in Norway spruce (Picea abies) - Minist\u00e8re des Ressources naturelles et des For\u00eats<\/title>\n<meta name=\"description\" content=\"A catalog of annotated high confidence gene SNPs to sustain genomic tools development for genetic diversity resources conservation was developed\" \/>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/mrnf.gouv.qc.ca\/en\/our-publications\/catalog-high-confidence-snps-exome-capture\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"A catalog of annotated high-confidence SNPs from exome capture and sequencing reveals highly polymorphic genes in Norway spruce (Picea abies) - 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