Molecular basis of African yam domestication: Analyses of selection point to root development, starch biosynthesis, and photosynthesis related genes
Background: After cereals, root and tuber crops are the main source of starch in the human diet. Starch biosynthesis was certainly a significant target for selection during the domestication of these crops. But domestication of these root and tubers crops is also associated with gigantism of storage organs and changes of habitat. Results: We studied here, the molecular basis of domestication in African yam, Dioscorea rotundata. The genomic diversity in the cultivated species is roughly 30% less important than its wild relatives. Two percent of all the genes studied showed evidences of selection. Two genes associated with the earliest stages of starch biosynthesis and storage, the sucrose synthase 4 and the sucrose-phosphate synthase 1 showed evidence of selection. An adventitious root development gene, a SCARECROW-LIKE gene was also selected during yam domestication. Significant selection for genes associated with photosynthesis and phototropism were associated with wild to cultivated change of habitat. If the wild species grow as vines in the shade of their tree tutors, cultivated yam grows in full light in open fields. Conclusions: Major rewiring of aerial development and adaptation for efficient photosynthesis in full light characterized yam domestication.
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dig-cirad-fr-5856232024-01-29T00:33:25Z http://agritrop.cirad.fr/585623/ http://agritrop.cirad.fr/585623/ Molecular basis of African yam domestication: Analyses of selection point to root development, starch biosynthesis, and photosynthesis related genes. Akakpo Roland, Scarcelli Nora, Chaïr Hâna, Dansi Alexandre, Djedatin Gustave, Thuillet Anne-Céline, Rhoné Bénédicte, François Olivier, Alix Karine, Vigouroux Yves. 2017. BMC Genomics, 18:782, 9 p.https://doi.org/10.1186/s12864-017-4143-2 <https://doi.org/10.1186/s12864-017-4143-2> Molecular basis of African yam domestication: Analyses of selection point to root development, starch biosynthesis, and photosynthesis related genes Akakpo, Roland Scarcelli, Nora Chaïr, Hâna Dansi, Alexandre Djedatin, Gustave Thuillet, Anne-Céline Rhoné, Bénédicte François, Olivier Alix, Karine Vigouroux, Yves eng 2017 BMC Genomics F30 - Génétique et amélioration des plantes F70 - Taxonomie végétale et phytogéographie F50 - Anatomie et morphologie des plantes F60 - Physiologie et biochimie végétale Dioscorea génétique des populations domestication des plantes adaptation développement biologique système racinaire amidon biosynthèse métabolisme des glucides Dioscorea rotundata http://aims.fao.org/aos/agrovoc/c_2288 http://aims.fao.org/aos/agrovoc/c_34326 http://aims.fao.org/aos/agrovoc/c_36518 http://aims.fao.org/aos/agrovoc/c_117 http://aims.fao.org/aos/agrovoc/c_921 http://aims.fao.org/aos/agrovoc/c_16034 http://aims.fao.org/aos/agrovoc/c_7369 http://aims.fao.org/aos/agrovoc/c_928 http://aims.fao.org/aos/agrovoc/c_1299 http://aims.fao.org/aos/agrovoc/c_2298 Bénin http://aims.fao.org/aos/agrovoc/c_875 Background: After cereals, root and tuber crops are the main source of starch in the human diet. Starch biosynthesis was certainly a significant target for selection during the domestication of these crops. But domestication of these root and tubers crops is also associated with gigantism of storage organs and changes of habitat. Results: We studied here, the molecular basis of domestication in African yam, Dioscorea rotundata. The genomic diversity in the cultivated species is roughly 30% less important than its wild relatives. Two percent of all the genes studied showed evidences of selection. Two genes associated with the earliest stages of starch biosynthesis and storage, the sucrose synthase 4 and the sucrose-phosphate synthase 1 showed evidence of selection. An adventitious root development gene, a SCARECROW-LIKE gene was also selected during yam domestication. Significant selection for genes associated with photosynthesis and phototropism were associated with wild to cultivated change of habitat. If the wild species grow as vines in the shade of their tree tutors, cultivated yam grows in full light in open fields. Conclusions: Major rewiring of aerial development and adaptation for efficient photosynthesis in full light characterized yam domestication. article info:eu-repo/semantics/article Journal Article info:eu-repo/semantics/publishedVersion http://agritrop.cirad.fr/585623/1/Akakpo_et_al-2017-BMC_Genomics.pdf text Cirad license info:eu-repo/semantics/openAccess https://agritrop.cirad.fr/mention_legale.html https://doi.org/10.1186/s12864-017-4143-2 10.1186/s12864-017-4143-2 info:eu-repo/semantics/altIdentifier/doi/10.1186/s12864-017-4143-2 info:eu-repo/semantics/altIdentifier/purl/https://doi.org/10.1186/s12864-017-4143-2 info:eu-repo/semantics/dataset/purl/https://figshare.com/articles/journal_contribution/Additional_file_1_of_Molecular_basis_of_African_yam_domestication_analyses_of_selection_point_to_root_development_starch_biosynthesis_and_photosynthesis_related_genes/5497291 |
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F30 - Génétique et amélioration des plantes F70 - Taxonomie végétale et phytogéographie F50 - Anatomie et morphologie des plantes F60 - Physiologie et biochimie végétale Dioscorea génétique des populations domestication des plantes adaptation développement biologique système racinaire amidon biosynthèse métabolisme des glucides Dioscorea rotundata http://aims.fao.org/aos/agrovoc/c_2288 http://aims.fao.org/aos/agrovoc/c_34326 http://aims.fao.org/aos/agrovoc/c_36518 http://aims.fao.org/aos/agrovoc/c_117 http://aims.fao.org/aos/agrovoc/c_921 http://aims.fao.org/aos/agrovoc/c_16034 http://aims.fao.org/aos/agrovoc/c_7369 http://aims.fao.org/aos/agrovoc/c_928 http://aims.fao.org/aos/agrovoc/c_1299 http://aims.fao.org/aos/agrovoc/c_2298 http://aims.fao.org/aos/agrovoc/c_875 F30 - Génétique et amélioration des plantes F70 - Taxonomie végétale et phytogéographie F50 - Anatomie et morphologie des plantes F60 - Physiologie et biochimie végétale Dioscorea génétique des populations domestication des plantes adaptation développement biologique système racinaire amidon biosynthèse métabolisme des glucides Dioscorea rotundata http://aims.fao.org/aos/agrovoc/c_2288 http://aims.fao.org/aos/agrovoc/c_34326 http://aims.fao.org/aos/agrovoc/c_36518 http://aims.fao.org/aos/agrovoc/c_117 http://aims.fao.org/aos/agrovoc/c_921 http://aims.fao.org/aos/agrovoc/c_16034 http://aims.fao.org/aos/agrovoc/c_7369 http://aims.fao.org/aos/agrovoc/c_928 http://aims.fao.org/aos/agrovoc/c_1299 http://aims.fao.org/aos/agrovoc/c_2298 http://aims.fao.org/aos/agrovoc/c_875 |
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F30 - Génétique et amélioration des plantes F70 - Taxonomie végétale et phytogéographie F50 - Anatomie et morphologie des plantes F60 - Physiologie et biochimie végétale Dioscorea génétique des populations domestication des plantes adaptation développement biologique système racinaire amidon biosynthèse métabolisme des glucides Dioscorea rotundata http://aims.fao.org/aos/agrovoc/c_2288 http://aims.fao.org/aos/agrovoc/c_34326 http://aims.fao.org/aos/agrovoc/c_36518 http://aims.fao.org/aos/agrovoc/c_117 http://aims.fao.org/aos/agrovoc/c_921 http://aims.fao.org/aos/agrovoc/c_16034 http://aims.fao.org/aos/agrovoc/c_7369 http://aims.fao.org/aos/agrovoc/c_928 http://aims.fao.org/aos/agrovoc/c_1299 http://aims.fao.org/aos/agrovoc/c_2298 http://aims.fao.org/aos/agrovoc/c_875 F30 - Génétique et amélioration des plantes F70 - Taxonomie végétale et phytogéographie F50 - Anatomie et morphologie des plantes F60 - Physiologie et biochimie végétale Dioscorea génétique des populations domestication des plantes adaptation développement biologique système racinaire amidon biosynthèse métabolisme des glucides Dioscorea rotundata http://aims.fao.org/aos/agrovoc/c_2288 http://aims.fao.org/aos/agrovoc/c_34326 http://aims.fao.org/aos/agrovoc/c_36518 http://aims.fao.org/aos/agrovoc/c_117 http://aims.fao.org/aos/agrovoc/c_921 http://aims.fao.org/aos/agrovoc/c_16034 http://aims.fao.org/aos/agrovoc/c_7369 http://aims.fao.org/aos/agrovoc/c_928 http://aims.fao.org/aos/agrovoc/c_1299 http://aims.fao.org/aos/agrovoc/c_2298 http://aims.fao.org/aos/agrovoc/c_875 Akakpo, Roland Scarcelli, Nora Chaïr, Hâna Dansi, Alexandre Djedatin, Gustave Thuillet, Anne-Céline Rhoné, Bénédicte François, Olivier Alix, Karine Vigouroux, Yves Molecular basis of African yam domestication: Analyses of selection point to root development, starch biosynthesis, and photosynthesis related genes |
description |
Background: After cereals, root and tuber crops are the main source of starch in the human diet. Starch biosynthesis was certainly a significant target for selection during the domestication of these crops. But domestication of these root and tubers crops is also associated with gigantism of storage organs and changes of habitat. Results: We studied here, the molecular basis of domestication in African yam, Dioscorea rotundata. The genomic diversity in the cultivated species is roughly 30% less important than its wild relatives. Two percent of all the genes studied showed evidences of selection. Two genes associated with the earliest stages of starch biosynthesis and storage, the sucrose synthase 4 and the sucrose-phosphate synthase 1 showed evidence of selection. An adventitious root development gene, a SCARECROW-LIKE gene was also selected during yam domestication. Significant selection for genes associated with photosynthesis and phototropism were associated with wild to cultivated change of habitat. If the wild species grow as vines in the shade of their tree tutors, cultivated yam grows in full light in open fields. Conclusions: Major rewiring of aerial development and adaptation for efficient photosynthesis in full light characterized yam domestication. |
format |
article |
topic_facet |
F30 - Génétique et amélioration des plantes F70 - Taxonomie végétale et phytogéographie F50 - Anatomie et morphologie des plantes F60 - Physiologie et biochimie végétale Dioscorea génétique des populations domestication des plantes adaptation développement biologique système racinaire amidon biosynthèse métabolisme des glucides Dioscorea rotundata http://aims.fao.org/aos/agrovoc/c_2288 http://aims.fao.org/aos/agrovoc/c_34326 http://aims.fao.org/aos/agrovoc/c_36518 http://aims.fao.org/aos/agrovoc/c_117 http://aims.fao.org/aos/agrovoc/c_921 http://aims.fao.org/aos/agrovoc/c_16034 http://aims.fao.org/aos/agrovoc/c_7369 http://aims.fao.org/aos/agrovoc/c_928 http://aims.fao.org/aos/agrovoc/c_1299 http://aims.fao.org/aos/agrovoc/c_2298 http://aims.fao.org/aos/agrovoc/c_875 |
author |
Akakpo, Roland Scarcelli, Nora Chaïr, Hâna Dansi, Alexandre Djedatin, Gustave Thuillet, Anne-Céline Rhoné, Bénédicte François, Olivier Alix, Karine Vigouroux, Yves |
author_facet |
Akakpo, Roland Scarcelli, Nora Chaïr, Hâna Dansi, Alexandre Djedatin, Gustave Thuillet, Anne-Céline Rhoné, Bénédicte François, Olivier Alix, Karine Vigouroux, Yves |
author_sort |
Akakpo, Roland |
title |
Molecular basis of African yam domestication: Analyses of selection point to root development, starch biosynthesis, and photosynthesis related genes |
title_short |
Molecular basis of African yam domestication: Analyses of selection point to root development, starch biosynthesis, and photosynthesis related genes |
title_full |
Molecular basis of African yam domestication: Analyses of selection point to root development, starch biosynthesis, and photosynthesis related genes |
title_fullStr |
Molecular basis of African yam domestication: Analyses of selection point to root development, starch biosynthesis, and photosynthesis related genes |
title_full_unstemmed |
Molecular basis of African yam domestication: Analyses of selection point to root development, starch biosynthesis, and photosynthesis related genes |
title_sort |
molecular basis of african yam domestication: analyses of selection point to root development, starch biosynthesis, and photosynthesis related genes |
url |
http://agritrop.cirad.fr/585623/ http://agritrop.cirad.fr/585623/1/Akakpo_et_al-2017-BMC_Genomics.pdf |
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