The genomics of linkage drag in inbred lines of sunflower.

Autor:	Huang K; Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.; Biodiversity Research Centre, University of British Columbia, Vancouver, BC V6T 1Z4, Canada., Jahani M; Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.; Biodiversity Research Centre, University of British Columbia, Vancouver, BC V6T 1Z4, Canada., Gouzy J; Laboratoire des Interactions Plantes-Microbes-Environnement, Centre national de la recherche scientifique (CNRS), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Université de Toulouse, Castanet-Tolosan, F-31326 France., Legendre A; Laboratoire des Interactions Plantes-Microbes-Environnement, Centre national de la recherche scientifique (CNRS), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Université de Toulouse, Castanet-Tolosan, F-31326 France., Carrere S; Laboratoire des Interactions Plantes-Microbes-Environnement, Centre national de la recherche scientifique (CNRS), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Université de Toulouse, Castanet-Tolosan, F-31326 France., Lázaro-Guevara JM; Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.; Biodiversity Research Centre, University of British Columbia, Vancouver, BC V6T 1Z4, Canada., González Segovia EG; Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.; Biodiversity Research Centre, University of British Columbia, Vancouver, BC V6T 1Z4, Canada., Todesco M; Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.; Biodiversity Research Centre, University of British Columbia, Vancouver, BC V6T 1Z4, Canada., Mayjonade B; Laboratoire des Interactions Plantes-Microbes-Environnement, Centre national de la recherche scientifique (CNRS), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Université de Toulouse, Castanet-Tolosan, F-31326 France., Rodde N; Centre National de Ressources Génomiques Végétales (CNRGV), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Castanet-Tolosan, F-31326 France., Cauet S; Centre National de Ressources Génomiques Végétales (CNRGV), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Castanet-Tolosan, F-31326 France., Dufau I; Centre National de Ressources Génomiques Végétales (CNRGV), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Castanet-Tolosan, F-31326 France., Staton SE; Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.; Biodiversity Research Centre, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.; Research and Development Department, NRGene Canada Inc., Saskatoon, SK S7N 3R3, Canada., Pouilly N; Laboratoire des Interactions Plantes-Microbes-Environnement, Centre national de la recherche scientifique (CNRS), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Université de Toulouse, Castanet-Tolosan, F-31326 France., Boniface MC; Laboratoire des Interactions Plantes-Microbes-Environnement, Centre national de la recherche scientifique (CNRS), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Université de Toulouse, Castanet-Tolosan, F-31326 France., Tapy C; Laboratoire des Interactions Plantes-Microbes-Environnement, Centre national de la recherche scientifique (CNRS), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Université de Toulouse, Castanet-Tolosan, F-31326 France., Mangin B; Laboratoire des Interactions Plantes-Microbes-Environnement, Centre national de la recherche scientifique (CNRS), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Université de Toulouse, Castanet-Tolosan, F-31326 France., Duhnen A; Laboratoire des Interactions Plantes-Microbes-Environnement, Centre national de la recherche scientifique (CNRS), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Université de Toulouse, Castanet-Tolosan, F-31326 France., Gautier V; Gentyane Genomic Platform, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Clermont Ferrand, 63000 France., Poncet C; Gentyane Genomic Platform, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Clermont Ferrand, 63000 France., Donnadieu C; Plateforme Génome et Transcriptome (GeT-PlaGe), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Castanet-Tolosan, F-31326 France., Mandel T; MIGAL Galilee Research Institute, Tel-Hai Academic College, Upper Galilee, 11016 Israel., Hübner S; MIGAL Galilee Research Institute, Tel-Hai Academic College, Upper Galilee, 11016 Israel., Burke JM; Department of Plant Biology, University of Georgia, Athens, GA 30602., Vautrin S; Centre National de Ressources Génomiques Végétales (CNRGV), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Castanet-Tolosan, F-31326 France., Bellec A; Centre National de Ressources Génomiques Végétales (CNRGV), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Castanet-Tolosan, F-31326 France., Owens GL; Department of Biology, University of Victoria, Victoria, BC V8W 2Y2, Canada., Langlade N; Laboratoire des Interactions Plantes-Microbes-Environnement, Centre national de la recherche scientifique (CNRS), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Université de Toulouse, Castanet-Tolosan, F-31326 France., Muños S; Laboratoire des Interactions Plantes-Microbes-Environnement, Centre national de la recherche scientifique (CNRS), Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE), Université de Toulouse, Castanet-Tolosan, F-31326 France., Rieseberg LH; Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.; Biodiversity Research Centre, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
Jazyk:	angličtina
Zdroj:	Proceedings of the National Academy of Sciences of the United States of America [Proc Natl Acad Sci U S A] 2023 Apr 04; Vol. 120 (14), pp. e2205783119. Date of Electronic Publication: 2023 Mar 27.
DOI:	10.1073/pnas.2205783119
Abstrakt:	Crop wild relatives represent valuable sources of alleles for crop improvement, including adaptation to climate change and emerging diseases. However, introgressions from wild relatives might have deleterious effects on desirable traits, including yield, due to linkage drag. Here, we analyzed the genomic and phenotypic impacts of wild introgressions in inbred lines of cultivated sunflower to estimate the impacts of linkage drag. First, we generated reference sequences for seven cultivated and one wild sunflower genotype, as well as improved assemblies for two additional cultivars. Next, relying on previously generated sequences from wild donor species, we identified introgressions in the cultivated reference sequences, as well as the sequence and structural variants they contain. We then used a ridge-regression best linear unbiased prediction (BLUP) model to test the effects of the introgressions on phenotypic traits in the cultivated sunflower association mapping population. We found that introgression has introduced substantial sequence and structural variation into the cultivated sunflower gene pool, including >3,000 new genes. While introgressions reduced genetic load at protein-coding sequences, they mostly had negative impacts on yield and quality traits. Introgressions found at high frequency in the cultivated gene pool had larger effects than low-frequency introgressions, suggesting that the former likely were targeted by artificial selection. Also, introgressions from more distantly related species were more likely to be maladaptive than those from the wild progenitor of cultivated sunflower. Thus, breeding efforts should focus, as far as possible, on closely related and fully compatible wild relatives.
Databáze:	MEDLINE
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