Flax domesticationprocesses as inferred from genome-wide SNP data
Flax (Linum usitatissimum L.) is one of the founder crops domesticated for oil and fiber uses in the Near-Eastern Fertile Crescent, but its domestication history remains largely elusive. Genetic inferences so far have expanded our knowledge in several aspects of flax domestication such as the wild p...
Gespeichert in:
| Veröffentlicht in: | Scientific reports Jg. 15; H. 1; S. 8731 |
|---|---|
| 1. Verfasser: | |
| Format: | Journal Article |
| Sprache: | Englisch |
| Veröffentlicht: |
England
13.03.2025
|
| Schlagworte: | |
| ISSN: | 2045-2322, 2045-2322 |
| Online-Zugang: | Volltext |
| Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
| Abstract | Flax (Linum usitatissimum L.) is one of the founder crops domesticated for oil and fiber uses in the Near-Eastern Fertile Crescent, but its domestication history remains largely elusive. Genetic inferences so far have expanded our knowledge in several aspects of flax domestication such as the wild progenitor, the first use of domesticated flax, and domestication events. However, little is known about flax domestication processes involving multiple domestication events. This study applied genotyping-by-sequencing to infer flax domestication processes. Ninety-three Linum samples representing four flax domestication groups (oilseed, fiber, winter and capsular dehiscence) and its wild progenitor (or pale flax; L. bienne Mill.) were sequenced. SNP calling identified 16,998 SNPs that were widely distributed across 15 flax chromosomes. Diversity analysis found that pale flax had the largest nucleotide diversity, followed by indehiscent, winter, oilseed and fiber cultivated flax. Pale flax seemed to be under population contraction, while the other four domestication groups were under population expansion after bottleneck. Demographic inferences showed that five Linum groups carried clear genetic signals of multiple mixture events that were associated largely with oilseed flax. Phylogenetic analysis revealed that oilseed, fiber and winter flax formed two separate phylogenetic subclades. One subclade had abundant winter flax, along with some oilseed and fiber flax, mainly originating in the Near East and nearby regions. The other subclade mainly had oilseed and fiber flax originating from Europe and other parts of the world. Dating genetic divergences with an assumption of 10,000 years before present (BP) of flax domestication revealed that oilseed and fiber flax spread to Europe 5800 years BP and domestication for winter hardiness occurred in the Near East 5100 years BP. These findings provide new significant insights into flax domestication processes. |
|---|---|
| AbstractList | Flax (Linum usitatissimum L.) is one of the founder crops domesticated for oil and fiber uses in the Near-Eastern Fertile Crescent, but its domestication history remains largely elusive. Genetic inferences so far have expanded our knowledge in several aspects of flax domestication such as the wild progenitor, the first use of domesticated flax, and domestication events. However, little is known about flax domestication processes involving multiple domestication events. This study applied genotyping-by-sequencing to infer flax domestication processes. Ninety-three Linum samples representing four flax domestication groups (oilseed, fiber, winter and capsular dehiscence) and its wild progenitor (or pale flax; L. bienne Mill.) were sequenced. SNP calling identified 16,998 SNPs that were widely distributed across 15 flax chromosomes. Diversity analysis found that pale flax had the largest nucleotide diversity, followed by indehiscent, winter, oilseed and fiber cultivated flax. Pale flax seemed to be under population contraction, while the other four domestication groups were under population expansion after bottleneck. Demographic inferences showed that five Linum groups carried clear genetic signals of multiple mixture events that were associated largely with oilseed flax. Phylogenetic analysis revealed that oilseed, fiber and winter flax formed two separate phylogenetic subclades. One subclade had abundant winter flax, along with some oilseed and fiber flax, mainly originating in the Near East and nearby regions. The other subclade mainly had oilseed and fiber flax originating from Europe and other parts of the world. Dating genetic divergences with an assumption of 10,000 years before present (BP) of flax domestication revealed that oilseed and fiber flax spread to Europe 5800 years BP and domestication for winter hardiness occurred in the Near East 5100 years BP. These findings provide new significant insights into flax domestication processes. Flax (Linum usitatissimum L.) is one of the founder crops domesticated for oil and fiber uses in the Near-Eastern Fertile Crescent, but its domestication history remains largely elusive. Genetic inferences so far have expanded our knowledge in several aspects of flax domestication such as the wild progenitor, the first use of domesticated flax, and domestication events. However, little is known about flax domestication processes involving multiple domestication events. This study applied genotyping-by-sequencing to infer flax domestication processes. Ninety-three Linum samples representing four flax domestication groups (oilseed, fiber, winter and capsular dehiscence) and its wild progenitor (or pale flax; L. bienne Mill.) were sequenced. SNP calling identified 16,998 SNPs that were widely distributed across 15 flax chromosomes. Diversity analysis found that pale flax had the largest nucleotide diversity, followed by indehiscent, winter, oilseed and fiber cultivated flax. Pale flax seemed to be under population contraction, while the other four domestication groups were under population expansion after bottleneck. Demographic inferences showed that five Linum groups carried clear genetic signals of multiple mixture events that were associated largely with oilseed flax. Phylogenetic analysis revealed that oilseed, fiber and winter flax formed two separate phylogenetic subclades. One subclade had abundant winter flax, along with some oilseed and fiber flax, mainly originating in the Near East and nearby regions. The other subclade mainly had oilseed and fiber flax originating from Europe and other parts of the world. Dating genetic divergences with an assumption of 10,000 years before present (BP) of flax domestication revealed that oilseed and fiber flax spread to Europe 5800 years BP and domestication for winter hardiness occurred in the Near East 5100 years BP. These findings provide new significant insights into flax domestication processes.Flax (Linum usitatissimum L.) is one of the founder crops domesticated for oil and fiber uses in the Near-Eastern Fertile Crescent, but its domestication history remains largely elusive. Genetic inferences so far have expanded our knowledge in several aspects of flax domestication such as the wild progenitor, the first use of domesticated flax, and domestication events. However, little is known about flax domestication processes involving multiple domestication events. This study applied genotyping-by-sequencing to infer flax domestication processes. Ninety-three Linum samples representing four flax domestication groups (oilseed, fiber, winter and capsular dehiscence) and its wild progenitor (or pale flax; L. bienne Mill.) were sequenced. SNP calling identified 16,998 SNPs that were widely distributed across 15 flax chromosomes. Diversity analysis found that pale flax had the largest nucleotide diversity, followed by indehiscent, winter, oilseed and fiber cultivated flax. Pale flax seemed to be under population contraction, while the other four domestication groups were under population expansion after bottleneck. Demographic inferences showed that five Linum groups carried clear genetic signals of multiple mixture events that were associated largely with oilseed flax. Phylogenetic analysis revealed that oilseed, fiber and winter flax formed two separate phylogenetic subclades. One subclade had abundant winter flax, along with some oilseed and fiber flax, mainly originating in the Near East and nearby regions. The other subclade mainly had oilseed and fiber flax originating from Europe and other parts of the world. Dating genetic divergences with an assumption of 10,000 years before present (BP) of flax domestication revealed that oilseed and fiber flax spread to Europe 5800 years BP and domestication for winter hardiness occurred in the Near East 5100 years BP. These findings provide new significant insights into flax domestication processes. |
| Author | Fu, Yong-Bi |
| Author_xml | – sequence: 1 givenname: Yong-Bi surname: Fu fullname: Fu, Yong-Bi email: yong-bi.fu@agr.gc.ca organization: Plant Gene Resources of Canada, Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, Saskatoon, SK, Canada. yong-bi.fu@agr.gc.ca |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/40082459$$D View this record in MEDLINE/PubMed |
| BookMark | eNpNj0tLAzEUhYNUbK39Ay4kSzfRPG5mkmUpVoWigroeMskdGZlHncyg_nsDVvBs7uHwcTnnlMy6vkNCzgW_ElyZ6whCW8O41MxYSM4ekYXkoJlUUs7--TlZxfjOk7S0IOwJmQPnRoK2C7LeNu6Lhr7FONbejXXf7YfeY4wYqYu07iocBgy0GvqWvmGXSPZZB6TPD080uNGdkePKNRFXh7skr9ubl80d2z3e3m_WO7aXQo1McOGVcZnVJfjcBAiWe13lxoZS2wwqgzxTjnvgNugUAVQhC8IFJVBAUEty-fs39fuYUt2iraPHpnEd9lMslMhzoSXPs4ReHNCpbDEU-6Fu3fBd_M1WP0R3W8k |
| ContentType | Journal Article |
| Copyright | 2025. Crown. |
| Copyright_xml | – notice: 2025. Crown. |
| DBID | CGR CUY CVF ECM EIF NPM 7X8 |
| DOI | 10.1038/s41598-025-89498-9 |
| DatabaseName | Medline MEDLINE MEDLINE (Ovid) MEDLINE MEDLINE PubMed MEDLINE - Academic |
| DatabaseTitle | MEDLINE Medline Complete MEDLINE with Full Text PubMed MEDLINE (Ovid) MEDLINE - Academic |
| DatabaseTitleList | MEDLINE MEDLINE - Academic |
| Database_xml | – sequence: 1 dbid: NPM name: PubMed url: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed sourceTypes: Index Database – sequence: 2 dbid: 7X8 name: MEDLINE - Academic url: https://search.proquest.com/medline sourceTypes: Aggregation Database |
| DeliveryMethod | fulltext_linktorsrc |
| Discipline | Biology |
| EISSN | 2045-2322 |
| ExternalDocumentID | 40082459 |
| Genre | Journal Article |
| GrantInformation_xml | – fundername: Agriculture and Agri-Food Canada grantid: J-003159 |
| GroupedDBID | 0R~ 4.4 53G 5VS 7X7 88E 88I 8FE 8FH 8FI 8FJ AAFWJ AAJSJ AAKDD AASML ABDBF ABUWG ACGFS ACUHS ADBBV ADRAZ AENEX AEUYN AFKRA AFPKN ALIPV ALMA_UNASSIGNED_HOLDINGS AOIJS AZQEC BAWUL BBNVY BCNDV BENPR BHPHI BPHCQ BVXVI C6C CCPQU CGR CUY CVF DIK DWQXO EBD EBLON EBS ECM EIF ESX FYUFA GNUQQ GROUPED_DOAJ GX1 HCIFZ HH5 HMCUK HYE KQ8 LK8 M1P M2P M7P M~E NAO NPM OK1 PHGZM PHGZT PIMPY PQQKQ PROAC PSQYO RNT RNTTT RPM SNYQT UKHRP 7X8 PJZUB PPXIY PQGLB PUEGO |
| ID | FETCH-LOGICAL-p213t-101c38a695b4c78d4d90c5f789db5964f8e063a0c409d5b5944fd6d1ad31e14d3 |
| ISICitedReferencesCount | 4 |
| ISICitedReferencesURI | http://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=Summon&SrcAuth=ProQuest&DestLinkType=CitingArticles&DestApp=WOS_CPL&KeyUT=001444877000015&url=https%3A%2F%2Fcvtisr.summon.serialssolutions.com%2F%23%21%2Fsearch%3Fho%3Df%26include.ft.matches%3Dt%26l%3Dnull%26q%3D |
| ISSN | 2045-2322 |
| IngestDate | Fri Sep 05 11:37:53 EDT 2025 Thu May 15 23:18:06 EDT 2025 |
| IsDoiOpenAccess | false |
| IsOpenAccess | true |
| IsPeerReviewed | true |
| IsScholarly | true |
| Issue | 1 |
| Keywords | Winter flax Pale flax Indehiscent flax Genotyping-by-sequencing Cultivated flax |
| Language | English |
| License | 2025. Crown. |
| LinkModel | OpenURL |
| MergedId | FETCHMERGED-LOGICAL-p213t-101c38a695b4c78d4d90c5f789db5964f8e063a0c409d5b5944fd6d1ad31e14d3 |
| Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 |
| PMID | 40082459 |
| PQID | 3177152076 |
| PQPubID | 23479 |
| ParticipantIDs | proquest_miscellaneous_3177152076 pubmed_primary_40082459 |
| PublicationCentury | 2000 |
| PublicationDate | 2025-03-13 |
| PublicationDateYYYYMMDD | 2025-03-13 |
| PublicationDate_xml | – month: 03 year: 2025 text: 2025-03-13 day: 13 |
| PublicationDecade | 2020 |
| PublicationPlace | England |
| PublicationPlace_xml | – name: England |
| PublicationTitle | Scientific reports |
| PublicationTitleAlternate | Sci Rep |
| PublicationYear | 2025 |
| SSID | ssj0000529419 |
| Score | 2.4663846 |
| Snippet | Flax (Linum usitatissimum L.) is one of the founder crops domesticated for oil and fiber uses in the Near-Eastern Fertile Crescent, but its domestication... |
| SourceID | proquest pubmed |
| SourceType | Aggregation Database Index Database |
| StartPage | 8731 |
| SubjectTerms | Crops, Agricultural - genetics Domestication Flax - genetics Genome, Plant Genotype Phylogeny Polymorphism, Single Nucleotide |
| Title | Flax domesticationprocesses as inferred from genome-wide SNP data |
| URI | https://www.ncbi.nlm.nih.gov/pubmed/40082459 https://www.proquest.com/docview/3177152076 |
| Volume | 15 |
| WOSCitedRecordID | wos001444877000015&url=https%3A%2F%2Fcvtisr.summon.serialssolutions.com%2F%23%21%2Fsearch%3Fho%3Df%26include.ft.matches%3Dt%26l%3Dnull%26q%3D |
| hasFullText | 1 |
| inHoldings | 1 |
| isFullTextHit | |
| isPrint | |
| journalDatabaseRights | – providerCode: PRVAON databaseName: Directory of Open Access Journals customDbUrl: eissn: 2045-2322 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0000529419 issn: 2045-2322 databaseCode: DOA dateStart: 20110101 isFulltext: true titleUrlDefault: https://www.doaj.org/ providerName: Directory of Open Access Journals – providerCode: PRVHPJ databaseName: ROAD: Directory of Open Access Scholarly Resources customDbUrl: eissn: 2045-2322 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0000529419 issn: 2045-2322 databaseCode: M~E dateStart: 20110101 isFulltext: true titleUrlDefault: https://road.issn.org providerName: ISSN International Centre – providerCode: PRVPQU databaseName: Biological Science Database customDbUrl: eissn: 2045-2322 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0000529419 issn: 2045-2322 databaseCode: M7P dateStart: 20110101 isFulltext: true titleUrlDefault: http://search.proquest.com/biologicalscijournals providerName: ProQuest – providerCode: PRVPQU databaseName: Health & Medical Collection customDbUrl: eissn: 2045-2322 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0000529419 issn: 2045-2322 databaseCode: 7X7 dateStart: 20110101 isFulltext: true titleUrlDefault: https://search.proquest.com/healthcomplete providerName: ProQuest – providerCode: PRVPQU databaseName: ProQuest Central customDbUrl: eissn: 2045-2322 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0000529419 issn: 2045-2322 databaseCode: BENPR dateStart: 20110101 isFulltext: true titleUrlDefault: https://www.proquest.com/central providerName: ProQuest – providerCode: PRVPQU databaseName: Publicly Available Content Database customDbUrl: eissn: 2045-2322 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0000529419 issn: 2045-2322 databaseCode: PIMPY dateStart: 20110101 isFulltext: true titleUrlDefault: http://search.proquest.com/publiccontent providerName: ProQuest – providerCode: PRVPQU databaseName: Science Database customDbUrl: eissn: 2045-2322 dateEnd: 99991231 omitProxy: false ssIdentifier: ssj0000529419 issn: 2045-2322 databaseCode: M2P dateStart: 20110101 isFulltext: true titleUrlDefault: https://search.proquest.com/sciencejournals providerName: ProQuest |
| link | http://cvtisr.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwtV3dixMxEB-8q8q9iN-eHyWCbyW6H9lN8ngndyh4ZdET6lPJJlkp2O3SbbX-906S3dqjHuiDL0NIlgTmtzv57SQzA_DK6gRJaCWo1cpSxlhJhUo0tVzHosryMgpJXD_w8VhMJrLoqgK2vpwAr2ux2cjmv0KNfQi2C539B7i3k2IHthF0lAg7yr8C_vyb2ozMYu7SZwR_XBOCAWzrisq421dLd-ncB5a4FK1zS3_MjB19GhejLlRty1f9p--vE_WnC1vA1956L-qv9HS26ztIMnd5KoR-vrbexrhk9BRJ1VWDmO0B33ZbY7DYe2Y3JFlvkQy4gD1cR0iGLbn7MGqpmXudM8c7WJcI_Gqy637oAAYJzySaqUHx_qL4snWbuYNJFssu_AnXfbO_6hHc7ue5_r_B84fLu3CnI_7kJAB2D27Y-j7cCqVAfz6AEwcb-TNsRLWkh4042MgObARhIw62h_D5_Ozy7TvalbegTRKnK9wAY50KlcusZJoLw4yMdFZxIU2ZyZxVwiJ_VJHGX3CTYRdjlclNrEwa25iZ9BEc1ovaPgGipbEVGm_BWOJKBJRCp6XKbMWiNCnj8hhe9mqYovlwZ0Kqtot1O0X6yJHCRTw_hsdBP9Mm5DmZ9kp8eu3IMzj6_Vo9h8PVcm1fwE39fTVrl0M44BPupRjC4PRsXHwcep8HyoukcJKjDAj_AgNqQ2M |
| linkProvider | ProQuest |
| openUrl | ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fsummon.serialssolutions.com&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Flax+domesticationprocesses+as+inferred+from+genome-wide+SNP+data&rft.jtitle=Scientific+reports&rft.au=Fu%2C+Yong-Bi&rft.date=2025-03-13&rft.eissn=2045-2322&rft.volume=15&rft.issue=1&rft.spage=8731&rft_id=info:doi/10.1038%2Fs41598-025-89498-9&rft_id=info%3Apmid%2F40082459&rft.externalDocID=40082459 |
| thumbnail_l | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=2045-2322&client=summon |
| thumbnail_m | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=2045-2322&client=summon |
| thumbnail_s | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=2045-2322&client=summon |