The Genetic Dissection of Nitrogen Use-Related Traits in Flax (<i>Linum usitatissimum</i> 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,Vol.24,2023
datacite.alternateIdentifier.doi10.3390/ijms242417624
datacite.creatorSoto Cerda, Braulio J.
datacite.creatorLarama, Giovanni
datacite.creatorCloutier, Sylvie
datacite.creatorFofana, Bourlaye
datacite.creatorInostroza Blancheteau, Claudio
datacite.creatorAravena, Gabriela
datacite.creatorMoustakas, Michael
datacite.date2023
datacite.subject.englishLinum usitatissimum
datacite.subject.englishnitrogen use efficiency
datacite.subject.englishGWAS
datacite.subject.englishRNA-seq
datacite.subject.englishgenomic selection
datacite.titleThe Genetic Dissection of Nitrogen Use-Related Traits in Flax (<i>Linum usitatissimum</i> L.) at the Seedling Stage through the Integration of Multi-Locus GWAS, RNA-seq and Genomic Selection
dc.date.accessioned2024-05-27T18:27:49Z
dc.date.available2024-05-27T18:27:49Z
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.
dc.identifier.urihttps://repositoriodigital.uct.cl/handle/10925/5839
dc.language.isoen
dc.publisherMDPI
dc.sourceINTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
oaire.resourceTypeArticle
uct.indizacionSCI
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