Combining QTL Analysis and Genomic Predictions for Four Durum Wheat Populations Under Drought Conditions

cg.contactF.Bassi@cgiar.orgen_US
cg.contributor.centerInternational Center for Agricultural Research in the Dry Areas - ICARDAen_US
cg.contributor.centerMohammed V University - UM5en_US
cg.contributor.centerUniversity of Edinburgh, College of Medicine & Veterinary Medicine, The Roslin Institute - ED - CoM&VM - ROSLINen_US
cg.contributor.crpCGIAR Research Program on Wheat - WHEATen_US
cg.contributor.funderSwedish University of Agricultural Sciences - SLUen_US
cg.contributor.projectGenomic Prediction to Deliver Heat Tolerant Wheat to the Senegal River Basin (Phase II)en_US
cg.contributor.project-lead-instituteInternational Center for Agricultural Research in the Dry Areas - ICARDAen_US
cg.coverage.countrySNen_US
cg.coverage.regionWestern Africaen_US
cg.creator.idKabbaj, Hafssa: 0000-0002-0778-4712en_US
cg.creator.idKehel, Zakaria: 0000-0002-1625-043Xen_US
cg.creator.idBassi, Filippo: 0000-0002-1164-5598en_US
cg.identifier.doihttps://dx.doi.org/10.3389/fgene.2020.00316en_US
cg.isijournalISI Journalen_US
cg.issn1664-8021en_US
cg.journalFrontiers in Geneticsen_US
cg.subject.agrovocdroughten_US
cg.subject.agrovocgenomic selectionen_US
cg.volume11en_US
dc.contributorKabbaj, Hafssaen_US
dc.contributorKehel, Zakariaen_US
dc.contributorGorjanc, Gregoren_US
dc.contributorFilali-Maltouf, Abdelkarimen_US
dc.contributorBelkadi, Bouchraen_US
dc.contributorMiloudi, Nachiten_US
dc.contributorBassi, Filippoen_US
dc.creatorZaim, Meryemen_US
dc.date.accessioned2020-05-21T16:35:11Z
dc.date.available2020-05-21T16:35:11Z
dc.description.abstractDurum wheat is an important crop for the human diet and its consumption is gaining popularity. In order to ensure that durum wheat production maintains the pace with the increase in demand, it is necessary to raise productivity by approximately 1.5% per year. To deliver this level of annual genetic gain the incorporation of molecular strategies has been proposed as a key solution. Here, four RILs populations were used to conduct QTL discovery for grain yield (GY) and 1,000 kernel weight (TKW). A total of 576 individuals were sown at three locations in Morocco and one in Lebanon. These individuals were genotyped by sequencing with 3,202 high-confidence polymorphic markers, to derive a consensus genetic map of 2,705.7 cM, which was used to impute any missing data. Six QTLs were found to be associated with GY and independent from flowering time on chromosomes 2B, 4A, 5B, 7A and 7B, explaining a phenotypic variation (PV) ranging from 4.3 to 13.4%. The same populations were used to train genomic prediction models incorporating the relationship matrix, the genotype by environment interaction, and marker by environment interaction, to reveal significant advantages for models incorporating the marker effect. Using training populations (TP) in full sibs relationships with the validation population (VP) was shown to be the only effective strategy, with accuracies reaching 0.35–0.47 for GY. Reducing the number of markers to 10% of the whole set, and the TP size to 20% resulted in non-significant changes in accuracies. The QTLs identified were also incorporated in the models as fixed effects, showing significant accuracy gain for all four populations. Our results confirm that the prediction accuracy depends considerably on the relatedness between TP and VP, but not on the number of markers and size of TP used. Furthermore, feeding the model with information on markers associated with QTLs increased the overall accuracy.en_US
dc.formatPDFen_US
dc.identifierhttps://mel.cgiar.org/reporting/downloadmelspace/hash/b8258a8281b59ea25431321eb9d7917c/v/fe80a77fb876b87c5f06b51deca06608en_US
dc.identifier.citationMeryem Zaim, Hafssa Kabbaj, Zakaria Kehel, Gregor Gorjanc, Abdelkarim Filali-Maltouf, Bouchra Belkadi, Nachit Miloudi, Filippo Bassi. (6/5/2020). Combining QTL Analysis and Genomic Predictions for Four Durum Wheat Populations Under Drought Conditions. Frontiers in Genetics, 11, pp. 1-15.en_US
dc.identifier.statusOpen accessen_US
dc.identifier.urihttps://hdl.handle.net/20.500.11766/11135
dc.languageenen_US
dc.publisherFrontiers Mediaen_US
dc.rightsCC-BY-4.0en_US
dc.sourceFrontiers in Genetics;11,(2020) Pagination 1-15en_US
dc.subjectqtl analysisen_US
dc.subjectgenotyping by sequencing (gbs)en_US
dc.subjectconsensus mapen_US
dc.subjectimputationen_US
dc.subjectfixed effecten_US
dc.titleCombining QTL Analysis and Genomic Predictions for Four Durum Wheat Populations Under Drought Conditionsen_US
dc.typeJournal Articleen_US
dcterms.available2020-05-06en_US
dcterms.extent1-15en_US
mel.funder.grant#Swedish University of Agricultural Sciences - SLU :SLU-ICARDA Research Collaboration Agreement (Dated: 2018.03.05)en_US
mel.impact-factor3.258en_US
mel.project.openhttps://mel.cgiar.org/projects/uforsk2017en_US

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