Out of Africa: The genomic footprints of Vietnamese Robusta coffee.
Vietnam is the main producer of Robusta (Coffea canephora) coffee, but faces several future agronomic challenges. These may be addressed through breeding for improved cultivars and more sustainable cropping systems. For such efforts to be successful and efficient, locally available genetic resources...
Saved in:
| Main Authors: | , , , , , , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2025-01-01
|
| Series: | PLoS ONE |
| Online Access: | https://doi.org/10.1371/journal.pone.0324988 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1850127113130082304 |
|---|---|
| author | Tram Vi Thi Nhu Le Philippe Cubry Viet Ha Phan Thi Tieu Oanh Dinh Thi Bich Ngoc Tran Van Toan Nguyen Claude Patrick Millet Jean-Léon Kambale Gba Kossia Manzan Karine Pascal Musoli Ucu Sumirat Jose Cassule Mahinga Piet Stoffelen Dapeng Zhang Pierre Marraccini Yves Vigouroux Ngan Giang Khong Valerie Poncet |
| author_facet | Tram Vi Thi Nhu Le Philippe Cubry Viet Ha Phan Thi Tieu Oanh Dinh Thi Bich Ngoc Tran Van Toan Nguyen Claude Patrick Millet Jean-Léon Kambale Gba Kossia Manzan Karine Pascal Musoli Ucu Sumirat Jose Cassule Mahinga Piet Stoffelen Dapeng Zhang Pierre Marraccini Yves Vigouroux Ngan Giang Khong Valerie Poncet |
| author_sort | Tram Vi |
| collection | DOAJ |
| description | Vietnam is the main producer of Robusta (Coffea canephora) coffee, but faces several future agronomic challenges. These may be addressed through breeding for improved cultivars and more sustainable cropping systems. For such efforts to be successful and efficient, locally available genetic resources must be understood. Indeed, while C. canephora exhibits high genetic diversity in its native tropical African forests, only a part of it contributed to the worldwide diffusion of Robusta. Here we traced the African origins of Robusta accessions cultivated in the Central Highlands of Vietnam. A total of 126 Robusta accessions from the Vietnam coffee germplasm collection were characterized, including historical, elite and local cultivated clones. Their genetic diversity and origins were inferred through comparisons with wild reference samples using a new set of 261 genome-wide SNPs. A core set of 45 accessions that maximize the genetic distance and allelic richness were identified for conservation and breeding priorities. Full genome sequencing of these individuals helped to closely trace the origins of chromosomal segments back to different, geographically-structured wild African genetic groups. All Vietnamese Robusta accessions displayed Congo Basin (ER group) origins, albeit to various extents. However, we also uncovered contribution from several other genetic groups, variously from the Guinean region (D), the central African Atlantic coast (AG), and Eastern CAR/Uganda (OB), in 31 hybrid individuals. These source groups have been widely used in crossbreeding to develop elite clones. In addition, using whole-genome sequencing data, we also identified various admixture patterns at the chromosome level among the hybrids, which might provide valuable information for selecting breeding materials. |
| format | Article |
| id | doaj-art-730e3a4e6c4443bc99fe08bb7e545594 |
| institution | OA Journals |
| issn | 1932-6203 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj-art-730e3a4e6c4443bc99fe08bb7e5455942025-08-20T02:33:44ZengPublic Library of Science (PLoS)PLoS ONE1932-62032025-01-01205e032498810.1371/journal.pone.0324988Out of Africa: The genomic footprints of Vietnamese Robusta coffee.Tram ViThi Nhu LePhilippe CubryViet Ha PhanThi Tieu Oanh DinhThi Bich Ngoc TranVan Toan NguyenClaude Patrick MilletJean-Léon KambaleGba Kossia Manzan KarinePascal MusoliUcu SumiratJose Cassule MahingaPiet StoffelenDapeng ZhangPierre MarracciniYves VigourouxNgan Giang KhongValerie PoncetVietnam is the main producer of Robusta (Coffea canephora) coffee, but faces several future agronomic challenges. These may be addressed through breeding for improved cultivars and more sustainable cropping systems. For such efforts to be successful and efficient, locally available genetic resources must be understood. Indeed, while C. canephora exhibits high genetic diversity in its native tropical African forests, only a part of it contributed to the worldwide diffusion of Robusta. Here we traced the African origins of Robusta accessions cultivated in the Central Highlands of Vietnam. A total of 126 Robusta accessions from the Vietnam coffee germplasm collection were characterized, including historical, elite and local cultivated clones. Their genetic diversity and origins were inferred through comparisons with wild reference samples using a new set of 261 genome-wide SNPs. A core set of 45 accessions that maximize the genetic distance and allelic richness were identified for conservation and breeding priorities. Full genome sequencing of these individuals helped to closely trace the origins of chromosomal segments back to different, geographically-structured wild African genetic groups. All Vietnamese Robusta accessions displayed Congo Basin (ER group) origins, albeit to various extents. However, we also uncovered contribution from several other genetic groups, variously from the Guinean region (D), the central African Atlantic coast (AG), and Eastern CAR/Uganda (OB), in 31 hybrid individuals. These source groups have been widely used in crossbreeding to develop elite clones. In addition, using whole-genome sequencing data, we also identified various admixture patterns at the chromosome level among the hybrids, which might provide valuable information for selecting breeding materials.https://doi.org/10.1371/journal.pone.0324988 |
| spellingShingle | Tram Vi Thi Nhu Le Philippe Cubry Viet Ha Phan Thi Tieu Oanh Dinh Thi Bich Ngoc Tran Van Toan Nguyen Claude Patrick Millet Jean-Léon Kambale Gba Kossia Manzan Karine Pascal Musoli Ucu Sumirat Jose Cassule Mahinga Piet Stoffelen Dapeng Zhang Pierre Marraccini Yves Vigouroux Ngan Giang Khong Valerie Poncet Out of Africa: The genomic footprints of Vietnamese Robusta coffee. PLoS ONE |
| title | Out of Africa: The genomic footprints of Vietnamese Robusta coffee. |
| title_full | Out of Africa: The genomic footprints of Vietnamese Robusta coffee. |
| title_fullStr | Out of Africa: The genomic footprints of Vietnamese Robusta coffee. |
| title_full_unstemmed | Out of Africa: The genomic footprints of Vietnamese Robusta coffee. |
| title_short | Out of Africa: The genomic footprints of Vietnamese Robusta coffee. |
| title_sort | out of africa the genomic footprints of vietnamese robusta coffee |
| url | https://doi.org/10.1371/journal.pone.0324988 |
| work_keys_str_mv | AT tramvi outofafricathegenomicfootprintsofvietnameserobustacoffee AT thinhule outofafricathegenomicfootprintsofvietnameserobustacoffee AT philippecubry outofafricathegenomicfootprintsofvietnameserobustacoffee AT viethaphan outofafricathegenomicfootprintsofvietnameserobustacoffee AT thitieuoanhdinh outofafricathegenomicfootprintsofvietnameserobustacoffee AT thibichngoctran outofafricathegenomicfootprintsofvietnameserobustacoffee AT vantoannguyen outofafricathegenomicfootprintsofvietnameserobustacoffee AT claudepatrickmillet outofafricathegenomicfootprintsofvietnameserobustacoffee AT jeanleonkambale outofafricathegenomicfootprintsofvietnameserobustacoffee AT gbakossiamanzankarine outofafricathegenomicfootprintsofvietnameserobustacoffee AT pascalmusoli outofafricathegenomicfootprintsofvietnameserobustacoffee AT ucusumirat outofafricathegenomicfootprintsofvietnameserobustacoffee AT josecassulemahinga outofafricathegenomicfootprintsofvietnameserobustacoffee AT pietstoffelen outofafricathegenomicfootprintsofvietnameserobustacoffee AT dapengzhang outofafricathegenomicfootprintsofvietnameserobustacoffee AT pierremarraccini outofafricathegenomicfootprintsofvietnameserobustacoffee AT yvesvigouroux outofafricathegenomicfootprintsofvietnameserobustacoffee AT ngangiangkhong outofafricathegenomicfootprintsofvietnameserobustacoffee AT valerieponcet outofafricathegenomicfootprintsofvietnameserobustacoffee |