5ec5981d755d3dabae1a70b2f52ff7b4 pmc_10623407.pdf 41adf00552d0a0009079abc6bc9ae89f79b56d37 pmc_10623407.pdf 93aaa055bd8e1f12ef944f46e6a12e0f006ffb7e7196e6fba7c224b730195fc6 pmc_10623407.pdf Title: Almond population genomics and non-additive GWAS reveal new insights into almond dissemination history and candidate genes for nut traits and blooming time Subject: DOI: 10.1093/hr/uhad193, Horticulture Research, 10, 00, 13 10 2023. Abstract: Domestication drastically changed crop genomes, fixing alleles of interest and creating different genetic populations. Genome-wide association studies (GWASs) are a powerful tool to detect these alleles of interest (and so QTLs). In this study, we explored the genetic structure as well as additive and non-additive genotype–phenotype associations in a collection of 243 almond accessions. Our genetic structure analysis strongly supported the subdivision of the accessions into five ancestral groups, all formed by accessions with a common origin. One of these groups was formed exclusively by Spanish accessions, while the rest were mainly formed by accessions from China, Italy, France, and the USA. These results agree with archaeological and historical evidence that separate modern almond dissemination into four phases: Asiatic, Mediterranean, Californian, and southern hemisphere. In total, we found 13 independent QTLs for nut weight, crack-out percentage, double kernels percentage, and blooming time. Of the 13 QTLs found, only one had an additive effect. Through candidate gene analysis, we proposed Prudul26A013473 as a candidate gene responsible for the main QTL found in crack-out percentage, Prudul26A012082 and Prudul26A017782 as candidate genes for the QTLs found in double kernels percentage, and Prudul26A000954 as a candidate gene for the QTL found in blooming time. Our study enhances our knowledge of almond dissemination history and will have a great impact on almond breeding. Keywords: Author: Creator: LaTeX with hyperref package Producer: Acrobat Distiller 23.0 (Windows) CreationDate: Tue Oct 31 06:53:07 2023 CET ModDate: Tue Oct 31 06:53:07 2023 CET Custom Metadata: yes Metadata Stream: yes Tagged: yes UserProperties: no Suspects: no Form: none JavaScript: no Pages: 11 Encrypted: no Page size: 595.26 x 782.337 pts Page rot: 0 File size: 7815835 bytes Optimized: yes PDF version: 1.7 name type encoding emb sub uni object ID ------------------------------------ ----------------- ---------------- --- --- --- --------- NFLEAH+CaeciliaLTStd-Bold Type 1C Custom yes yes yes 1572 0 NFLEBH+CaeciliaLTStd-Roman Type 1C Custom yes yes yes 1573 0 NFLEHG+CaeciliaLTStd-Italic Type 1C Custom yes yes yes 1574 0 NFLEHH+CaeciliaLTStd-Light Type 1C Custom yes yes yes 1575 0 NFLEMG+CaeciliaLTStd-Heavy Type 1C Custom yes yes yes 1576 0 NFLFGE+CaeciliaLTStd-LightItalic Type 1C Custom yes yes yes 1577 0 NFLGKN+ArialMT Type 1C Custom yes yes no 48 0 NFLGLN+Arial-BoldMT Type 1C Custom yes yes no 49 0 NFLIKD+MTSYN Type 1C Custom yes yes yes 50 0 NGBDBI+CaeciliaLTStd-BoldItalic Type 1C Custom yes yes yes 20 0 NGBGAH+MTMI Type 1C Custom yes yes yes 51 0 Jhove (Rel. 1.28.0, 2023-05-18) Date: 2025-03-12 02:09:57 CET RepresentationInformation: pmc_10623407.pdf ReportingModule: PDF-hul, Rel. 1.12.4 (2023-03-16) LastModified: 2025-03-12 02:03:44 CET Size: 7815835 Format: PDF Version: 1.7 Status: Well-Formed and valid SignatureMatches: PDF-hul MIMEtype: application/pdf Profile: Linearized PDF, Tagged PDF PDFMetadata: Objects: 1613 FreeObjects: 1 IncrementalUpdates: 1 DocumentCatalog: ViewerPreferences: HideToolbar: false HideMenubar: false HideWindowUI: false FitWindow: true CenterWindow: false DisplayDocTitle: true NonFullScreenPageMode: UseNone Direction: L2R ViewArea: CropBox ViewClip: CropBox PrintArea: CropBox PageClip: CropBox PageLayout: SinglePage PageMode: UseOutlines Language: en Outlines: Item: Title: Almond population genomics and non-additive GWAS reveal new insights into almond dissemination history and candidate genes for nut traits and blooming time Destination: toc.chapter Children: Item: Title: Introduction Destination: section.17.1.1 Item: Title: Results Destination: section.24.1.2 Item: Title: Discussion Destination: section.37.1.3 Item: Title: Conclusions Destination: section.41.1.4 Item: Title: Materials and methods Destination: section.42.1.5 Item: Title: Acknowledgements Destination: section.57.1.6 Item: Title: Author Contributions Destination: section.58.1.7 Item: Title: Conflict of Interest Destination: section.59.1.8 Item: Title: Data Availability Destination: section.60.1.9 Info: Title: Almond population genomics and non-additive GWAS reveal new insights into almond dissemination history and candidate genes for nut traits and blooming time Author: Subject: DOI: 10.1093/hr/uhad193, Horticulture Research, 10, 00, 13 10 2023. Abstract: Domestication drastically changed crop genomes, fixing alleles of interest and creating different genetic populations. Genome-wide association studies (GWASs) are a powerful tool to detect these alleles of interest (and so QTLs). In this study, we explored the genetic structure as well as additive and non-additive genotype–phenotype associations in a collection of 243 almond accessions. Our genetic structure analysis strongly supported the subdivision of the accessions into five ancestral groups, all formed by accessions with a common origin. One of these groups was formed exclusively by Spanish accessions, while the rest were mainly formed by accessions from China, Italy, France, and the USA. These results agree with archaeological and historical evidence that separate modern almond dissemination into four phases: Asiatic, Mediterranean, Californian, and southern hemisphere. In total, we found 13 independent QTLs for nut weight, crack-out percentage, double kernels percentage, and blooming time. Of the 13 QTLs found, only one had an additive effect. Through candidate gene analysis, we proposed Prudul26A013473 as a candidate gene responsible for the main QTL found in crack-out percentage, Prudul26A012082 and Prudul26A017782 as candidate genes for the QTLs found in double kernels percentage, and Prudul26A000954 as a candidate gene for the QTL found in blooming time. Our study enhances our knowledge of almond dissemination history and will have a great impact on almond breeding. 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Abstract: Domestication drastically changed crop genomes, fixing alleles of interest and creating different genetic populations. Genome-wide association studies (GWASs) are a powerful tool to detect these alleles of interest (and so QTLs). In this study, we explored the genetic structure as well as additive and non-additive genotype–phenotype associations in a collection of 243 almond accessions. Our genetic structure analysis strongly supported the subdivision of the accessions into five ancestral groups, all formed by accessions with a common origin. One of these groups was formed exclusively by Spanish accessions, while the rest were mainly formed by accessions from China, Italy, France, and the USA. These results agree with archaeological and historical evidence that separate modern almond dissemination into four phases: Asiatic, Mediterranean, Californian, and southern hemisphere. In total, we found 13 independent QTLs for nut weight, crack-out percentage, double kernels percentage, and blooming time. Of the 13 QTLs found, only one had an additive effect. Through candidate gene analysis, we proposed Prudul26A013473 as a candidate gene responsible for the main QTL found in crack-out percentage, Prudul26A012082 and Prudul26A017782 as candidate genes for the QTLs found in double kernels percentage, and Prudul26A000954 as a candidate gene for the QTL found in blooming time. Our study enhances our knowledge of almond dissemination history and will have a great impact on almond breeding. © The Author(s) 2023. Published by Oxford University Press on behalf of Nanjing Agricultural University. 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