The Genetic Dissection of Nitrogen Use-Related Traits in Flax (Linum usitatissimum L.) at the Seedling Stage through the Integration of Multi-Locus GWAS, RNA-seq and Genomic Selection

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datacite.alternateIdentifier.citationInternational Journal of Molecular Sciences, 24 (24), 2023
datacite.alternateIdentifier.doi10.3390/ijms242417624
datacite.alternateIdentifier.issn1422-0067
datacite.creatorSoto-Cerda, Braulio Jorge
datacite.creatorLarama, Giovanni A.
datacite.creatorCloutier, Sylvie J.
datacite.creatorFofana, Bourlaye
datacite.creatorInostroza-Blancheteau, Claudio
datacite.creatorAravena, Gabriela A.
datacite.date2023
datacite.rightsAcceso abierto
datacite.subjectGenomic Selection
datacite.subjectGwas
datacite.subjectLinum Usitatissimum
datacite.subjectNitrogen Use Efficiency
datacite.subjectRna-seq
datacite.subjectNitrogen
datacite.subjectNitrogen
datacite.subjectNitrogen
datacite.subjectAccuracy
datacite.subjectAmino Acid Transport
datacite.subjectArticle
datacite.subjectBiomass
datacite.subjectCatabolism
datacite.subjectControlled Study
datacite.subjectDifferential Gene Expression
datacite.subjectFlax
datacite.subjectGene Linkage Disequilibrium
datacite.subjectGene Locus
datacite.subjectGene Structure
datacite.subjectGenetic Selection
datacite.subjectGenetic Trait
datacite.subjectGenome-wide Association Study
datacite.subjectNitrogen Metabolism
datacite.subjectNonhuman
datacite.subjectPhenotypic Variation
datacite.subjectPlant Root
datacite.subjectPlant Stress
datacite.subjectQuantitative Trait Locus
datacite.subjectRna Sequencing
datacite.subjectRoot Development
datacite.subjectSeedling
datacite.subjectSingle Nucleotide Polymorphism
datacite.subjectTranscriptomics
datacite.subjectGenetics
datacite.subjectGenomics
datacite.subjectMetabolism
datacite.subjectPlant Breeding
datacite.subjectSexually Transmitted Disease
datacite.subjectFlax
datacite.subjectGenome-wide Association Study
datacite.subjectGenomics
datacite.subjectNitrogen
datacite.subjectPlant Breeding
datacite.subjectRna-seq
datacite.subjectSeedlings
datacite.subjectSexually Transmitted Diseases
datacite.titleThe Genetic Dissection of Nitrogen Use-Related Traits in Flax (Linum usitatissimum L.) at the Seedling Stage through the Integration of Multi-Locus GWAS, RNA-seq and Genomic Selection
dc.contributor.authorSOTO CERDA, BRAULIO JORGE
dc.contributor.authorSOTO CERDA, BRAULIO JORGE
dc.contributor.authorINOSTROZA BLANCHETEAU, CLAUDIO ANDRES
dc.description.abstractNitrogen (N), the most important macro-nutrient for plant growth and development, is a key factor that determines crop yield. Yet its excessive applications pollute the environment and are expensive. Hence, studying nitrogen use efficiency (NUE) in crops is fundamental for sustainable agriculture. Here, an association panel consisting of 123 flax accessions was evaluated for 21 NUE-related traits at the seedling stage under optimum N (N+) and N deficiency (N?) treatments to dissect the genetic architecture of NUE-related traits using a multi-omics approach integrating genome-wide association studies (GWAS), transcriptome analysis and genomic selection (GS). Root traits exhibited significant and positive correlations with NUE under N? conditions (r = 0.33 to 0.43, p < 0.05). A total of 359 QTLs were identified, accounting for 0.11% to 23.1% of the phenotypic variation in NUE-related traits. Transcriptomic analysis identified 1034 differentially expressed genes (DEGs) under contrasting N conditions. DEGs involved in N metabolism, root development, amino acid transport and catabolism and others, were found near the QTLs. GS models to predict NUE stress tolerance index (NUE_STI) trait were tested using a random genome-wide SNP dataset and a GWAS-derived QTLs dataset. The latter produced superior prediction accuracy (r = 0.62 to 0.79) compared to the genome-wide SNP marker dataset (r = 0.11) for NUE_STI. Our results provide insights into the QTL architecture of NUE-related traits, identify candidate genes for further studies, and propose genomic breeding tools to achieve superior NUE in flax under low N input. © 2024 Elsevier B.V., All rights reserved.
dc.description.ia_keywordtraits, related, under, nitrogen, flax, genome, wide
dc.formatPDF
dc.identifier.issn1661-6596
dc.identifier.urihttps://repositoriodigital.uct.cl/handle/10925/5839
dc.language.isoen
dc.publisherMultidisciplinary Digital Publishing Institute (MDPI)
dc.relationinstname: ANID
dc.relationreponame: Repositorio Digital RI2.0
dc.rights.driverinfo:eu-repo/semantics/openAccess
dc.sourceInternational Journal of Molecular Sciences
dc.subject.ia_odsODS 2: Hambre cero
dc.subject.ia_oecd1nCiencias Naturales
dc.subject.ia_oecd2nCiencias Biológicas
dc.subject.ia_oecd3nBiología General
dc.type.driverinfo:eu-repo/semantics/article
dc.type.driverhttp://purl.org/coar/resource_type/c_2df8fbb1
dc.type.openaireinfo:eu-repo/semantics/publishedVersion
dspace.entity.typePublication
oaire.citationEdition2023
oaire.citationIssue24
oaire.citationTitleInternational Journal of Molecular Sciences
oaire.citationVolume24
oaire.fundingReferenceANID FONDECYT 1200241 (Regular)
oaire.fundingReferenceUniversidad Católica de Temuco
oaire.fundingReferenceAgriculture and Agri-Food Canada (AAFC)
oaire.fundingReferenceGenome Canada TUFGEN
oaire.licenseConditionObra bajo licencia Creative Commons Atribución 4.0 Internacional
oaire.licenseCondition.urihttps://creativecommons.org/licenses/by/4.0/
oaire.resourceTypeArtículo
oaire.resourceType.enArticle
relation.isAuthorOfPublication8e8b0607-b16f-4744-887c-bb6b4544a8a8
relation.isAuthorOfPublication8e8b0607-b16f-4744-887c-bb6b4544a8a8
relation.isAuthorOfPublication25287ee1-cae8-401d-b42c-ee3f8fc05d2a
relation.isAuthorOfPublication.latestForDiscovery8e8b0607-b16f-4744-887c-bb6b4544a8a8
uct.catalogadorjvu
uct.comunidadRecursos Naturalesen_US
uct.departamentoDepartamento de Ciencias Agropecuarias y Acuícolas
uct.facultadFacultad de Recursos Naturales
uct.indizacionScience Citation Index Expanded - SCIE
uct.indizacionScopus
uct.indizacionPubMed Central (PMC)
uct.indizacionChemical Abstracts Service (CAS)
uct.indizacionMEDLINE
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