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Molecular basis of African yam domestication: analyses of selection point to root development, starch biosynthesis, and photosynthesis related genes

  • Akakpo, Roland1, 2, 3
  • Scarcelli, Nora1
  • Chaïr, Hana4
  • Dansi, Alexandre3
  • Djedatin, Gustave3
  • Thuillet, Anne-Céline1
  • Rhoné, Bénédicte1, 5
  • François, Olivier6
  • Alix, Karine2
  • Vigouroux, Yves1
  • 1 Institut de Recherche pour le Développement, Université de Montpellier, Unité Mixte de Recherche Diversité Adaptation et Développement des Plantes (UMR DIADE), 911, avenue Agropolis, Montpellier, 34394, France , Montpellier (France)
  • 2 Unité Mixte de Recherche Génétique Quantitative et Evolutive – Le Moulon, INRA – Univ. Paris-Sud – CNRS – AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, 91190, France , Gif-sur-Yvette (France)
  • 3 Université d’Abomey, Faculté des Sciences et Techniques de Dassa, Laboratoire de Biotechnologie, Ressources Génétiques et Amélioration des Espèces Animales et Végétales (BIORAVE), Dassa-Zoumè, Benin , Dassa-Zoumè (Benin)
  • 4 Centre International de la Recherche Agronomique pour le Développement, UMR AGAP, Montpellier, F-34398, France , Montpellier (France)
  • 5 Université Lyon 1, CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, Lyon, France , Lyon (France)
  • 6 Université de Grenoble, Grenoble, France , Grenoble (France)
Published Article
BMC Genomics
Springer (Biomed Central Ltd.)
Publication Date
Oct 12, 2017
DOI: 10.1186/s12864-017-4143-2
Springer Nature


BackgroundAfter 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.ResultsWe 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.ConclusionsMajor rewiring of aerial development and adaptation for efficient photosynthesis in full light characterized yam domestication.

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