Genetic diversity and selection signatures in synthetic-derived wheats and modern spring wheat

dc.creatorAli, M.
dc.creatorShan, D.
dc.creatorJiankang Wang
dc.creatorSadiq, H.
dc.creatorRasheed, A.
dc.creatorHe Zhonghu
dc.creatorHuihui Li
dc.date2023-01-25T01:10:23Z
dc.date2023-01-25T01:10:23Z
dc.date2022
dc.date.accessioned2023-07-17T20:10:16Z
dc.date.available2023-07-17T20:10:16Z
dc.identifierhttps://hdl.handle.net/10883/22463
dc.identifier10.3389/fpls.2022.877496
dc.identifier.urihttps://repositorioslatinoamericanos.uchile.cl/handle/2250/7514208
dc.descriptionSynthetic hexaploid wheats and their derived advanced lines were subject to empirical selection in developing genetically superior cultivars. To investigate genetic diversity, patterns of nucleotide diversity, population structure, and selection signatures during wheat breeding, we tested 422 wheat accessions, including 145 synthetic-derived wheats, 128 spring wheat cultivars, and 149 advanced breeding lines from Pakistan. A total of 18,589 high-quality GBS-SNPs were identified that were distributed across the A (40%), B (49%), and D (11%) genomes. Values of population diversity parameters were estimated across chromosomes and genomes. Genome-wide average values of genetic diversity and polymorphic information content were estimated to be 0.30 and 0.25, respectively. Neighbor-joining (NJ) tree, principal component analysis (PCA), and kinship analyses revealed that synthetic-derived wheats and advanced breeding lines were genetically diverse. The 422 accessions were not separated into distinct groups by NJ analysis and confirmed using the PCA. This conclusion was validated with both relative kinship and Rogers' genetic distance analyses. EigenGWAS analysis revealed that 32 unique genome regions had undergone selection. We found that 50% of the selected regions were located in the B-genome, 29% in the D-genome, and 21% in the A-genome. Previously known functional genes or QTL were found within the selection regions associated with phenology-related traits such as vernalization, adaptability, disease resistance, and yield-related traits. The selection signatures identified in the present investigation will be useful for understanding the targets of modern wheat breeding in Pakistan.
dc.languageEnglish
dc.publisherFrontiers
dc.relationhttps://datadryad.org/stash/share/ts92LqrXBJVsNhZEd8punew3Uv6irdDkdBuHxC4V4IQ
dc.relationClimate adaptation & mitigation
dc.relationNutrition, health & food security
dc.relationAccelerated Breeding
dc.relationGenetic Innovation
dc.relationHainan Yazhou Bay Seed Laboratory
dc.relationNational Science Foundation of China
dc.relationCGIAR Trust Fund
dc.relationhttps://hdl.handle.net/10568/128240
dc.rightsCIMMYT manages Intellectual Assets as International Public Goods. The user is free to download, print, store and share this work. In case you want to translate or create any other derivative work and share or distribute such translation/derivative work, please contact CIMMYT-Knowledge-Center@cgiar.org indicating the work you want to use and the kind of use you intend; CIMMYT will contact you with the suitable license for that purpose
dc.rightsOpen Access
dc.source13
dc.source1664-462X
dc.sourceFrontiers in Plant Science
dc.source877496
dc.subjectAGRICULTURAL SCIENCES AND BIOTECHNOLOGY
dc.subjectBread Wheat
dc.subjectGenotyping by Sequencing
dc.subjectEigenGWAS
dc.subjectGene Annotation
dc.subjectGenome-Wide Association Study
dc.subjectSOFT WHEAT
dc.subjectGENOTYPING
dc.subjectGENETIC DIVERSITY
dc.subjectSELECTION SIGNATURES
dc.subjectGenetic Resources
dc.titleGenetic diversity and selection signatures in synthetic-derived wheats and modern spring wheat
dc.typeArticle
dc.typePublished Version
dc.coveragePakistan
dc.coverageSwitzerland


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