Genetic architecture of post-harvest tuber quality traits in bush yam (Dioscorea praehensilis Benth.) germplasm through association mapping
IntroductionBush yam (Dioscorea praehensilis Benth.) is an important semi-domesticated food crop in West Africa. Limited information on the genetic architecture and its poor post-harvest tuber quality traits significantly hinder its use as food and source of income. Hence, dissecting the genetics un...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2024-04-01
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| Series: | Frontiers in Horticulture |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fhort.2024.1373327/full |
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| author | Adeyinka S. Adewumi Adeyinka S. Adewumi Paul A. Asare Oluyemi Titilola Akintayo Idris I. Adejumobi Michael O. Adu Kingsley J. Taah Emmanuel Afutu Vincent A. Opoku Adekemi E. Stanley Selorm Akaba Jean M. Mondo Hapson Mushoriwa Paterne A. Agre |
| author_facet | Adeyinka S. Adewumi Adeyinka S. Adewumi Paul A. Asare Oluyemi Titilola Akintayo Idris I. Adejumobi Michael O. Adu Kingsley J. Taah Emmanuel Afutu Vincent A. Opoku Adekemi E. Stanley Selorm Akaba Jean M. Mondo Hapson Mushoriwa Paterne A. Agre |
| author_sort | Adeyinka S. Adewumi |
| collection | DOAJ |
| description | IntroductionBush yam (Dioscorea praehensilis Benth.) is an important semi-domesticated food crop in West Africa. Limited information on the genetic architecture and its poor post-harvest tuber quality traits significantly hinder its use as food and source of income. Hence, dissecting the genetics underlying the expression of its post-harvest tuber quality traits is essential for establishing proper breeding schemes.MethodsIn this study, 138 D. praehensilis accessions collected in Ghana were sequenced using Diversity Array Technology (DArTSeq). The materials were profiled for dry matter content (DMC), tuber flesh oxidation (TBOXI) and for tuber flesh hardness (TBhard) during two cropping seasons.Results and discussionDiversity assessment using population structure, principal component analysis and hierarchical clustering methods revealed the presence of three major groups. Six genetic models were used for the trait association analysis using multiple random locus mixed linear model (MrMLM). Sixteen SNP markers distributed across the yam genome were identified to be associated with the evaluated traits. The associated SNP markers displayed a phenotypic variance ranged from 4.22% in TBHard to 16.92% in TBOXI. A total 25 putative candidate genes were identified around the SNP markers. The putative genes were identified to play key roles in tuber bulking, oxidative browning and starch hydroxylase. This study provides a valuable insight on the genetics underlying tuber quality traits in bush yam and opens avenues for developing genomic resources to improve D. praehensilis. |
| first_indexed | 2024-04-24T12:30:52Z |
| format | Article |
| id | doaj.art-962491c465014b63a1566c892684cd91 |
| institution | Directory Open Access Journal |
| issn | 2813-3595 |
| language | English |
| last_indexed | 2024-04-24T12:30:52Z |
| publishDate | 2024-04-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Horticulture |
| spelling | doaj.art-962491c465014b63a1566c892684cd912024-04-08T04:43:58ZengFrontiers Media S.A.Frontiers in Horticulture2813-35952024-04-01310.3389/fhort.2024.13733271373327Genetic architecture of post-harvest tuber quality traits in bush yam (Dioscorea praehensilis Benth.) germplasm through association mappingAdeyinka S. Adewumi0Adeyinka S. Adewumi1Paul A. Asare2Oluyemi Titilola Akintayo3Idris I. Adejumobi4Michael O. Adu5Kingsley J. Taah6Emmanuel Afutu7Vincent A. Opoku8Adekemi E. Stanley9Selorm Akaba10Jean M. Mondo11Hapson Mushoriwa12Paterne A. Agre13Department of Crop Science, University of Cape Coast, University Post Office, Cape Coast, GhanaInternational Institute of Tropical Agriculture, Ibadan, NigeriaDepartment of Crop Science, University of Cape Coast, University Post Office, Cape Coast, GhanaÉcole Supérieure d’Agronomie - Université de Lomé (ESA-UL), Togo, GhanaInternational Institute of Tropical Agriculture, Ibadan, NigeriaDepartment of Crop Science, University of Cape Coast, University Post Office, Cape Coast, GhanaDepartment of Crop Science, University of Cape Coast, University Post Office, Cape Coast, GhanaDepartment of Crop Science, University of Cape Coast, University Post Office, Cape Coast, GhanaDepartment of Crop Science, University of Cape Coast, University Post Office, Cape Coast, GhanaInternational Institute of Tropical Agriculture, Ibadan, NigeriaDepartment of Agricultural Economics and Extension, University of Cape Coast, University Post Office, Cape Coast, GhanaDepartment of Crop Production, Université Evangélique en Afrique, Bukavu, Democratic Republic of CongoInternational Institute of Tropical Agriculture, Ibadan, NigeriaInternational Institute of Tropical Agriculture, Ibadan, NigeriaIntroductionBush yam (Dioscorea praehensilis Benth.) is an important semi-domesticated food crop in West Africa. Limited information on the genetic architecture and its poor post-harvest tuber quality traits significantly hinder its use as food and source of income. Hence, dissecting the genetics underlying the expression of its post-harvest tuber quality traits is essential for establishing proper breeding schemes.MethodsIn this study, 138 D. praehensilis accessions collected in Ghana were sequenced using Diversity Array Technology (DArTSeq). The materials were profiled for dry matter content (DMC), tuber flesh oxidation (TBOXI) and for tuber flesh hardness (TBhard) during two cropping seasons.Results and discussionDiversity assessment using population structure, principal component analysis and hierarchical clustering methods revealed the presence of three major groups. Six genetic models were used for the trait association analysis using multiple random locus mixed linear model (MrMLM). Sixteen SNP markers distributed across the yam genome were identified to be associated with the evaluated traits. The associated SNP markers displayed a phenotypic variance ranged from 4.22% in TBHard to 16.92% in TBOXI. A total 25 putative candidate genes were identified around the SNP markers. The putative genes were identified to play key roles in tuber bulking, oxidative browning and starch hydroxylase. This study provides a valuable insight on the genetics underlying tuber quality traits in bush yam and opens avenues for developing genomic resources to improve D. praehensilis.https://www.frontiersin.org/articles/10.3389/fhort.2024.1373327/fullSNP markerstrait association mappinggene annotationyamtrait discovery |
| spellingShingle | Adeyinka S. Adewumi Adeyinka S. Adewumi Paul A. Asare Oluyemi Titilola Akintayo Idris I. Adejumobi Michael O. Adu Kingsley J. Taah Emmanuel Afutu Vincent A. Opoku Adekemi E. Stanley Selorm Akaba Jean M. Mondo Hapson Mushoriwa Paterne A. Agre Genetic architecture of post-harvest tuber quality traits in bush yam (Dioscorea praehensilis Benth.) germplasm through association mapping Frontiers in Horticulture SNP markers trait association mapping gene annotation yam trait discovery |
| title | Genetic architecture of post-harvest tuber quality traits in bush yam (Dioscorea praehensilis Benth.) germplasm through association mapping |
| title_full | Genetic architecture of post-harvest tuber quality traits in bush yam (Dioscorea praehensilis Benth.) germplasm through association mapping |
| title_fullStr | Genetic architecture of post-harvest tuber quality traits in bush yam (Dioscorea praehensilis Benth.) germplasm through association mapping |
| title_full_unstemmed | Genetic architecture of post-harvest tuber quality traits in bush yam (Dioscorea praehensilis Benth.) germplasm through association mapping |
| title_short | Genetic architecture of post-harvest tuber quality traits in bush yam (Dioscorea praehensilis Benth.) germplasm through association mapping |
| title_sort | genetic architecture of post harvest tuber quality traits in bush yam dioscorea praehensilis benth germplasm through association mapping |
| topic | SNP markers trait association mapping gene annotation yam trait discovery |
| url | https://www.frontiersin.org/articles/10.3389/fhort.2024.1373327/full |
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