African Yam Domestication: Evidences of Selection in Starch, Root and Photosynthesis Related Genes

One way to get insight into the domestication process of a plant is to study the genetic basis of adaptation by revealing signature of selection. In this study, we analyzed a tuber crop, the African yam (Dioscorea rotundata) and its two wild relatives, D. abyssinica a savannah species and D. praehensilis a forest species, using NGS technology. We sequenced a total of 30 yam accessions from Benin (West Africa), including 10 cultivated individuals and 10 individuals from each wild species. Using the D. rotundata transcriptome reference, we identified 30,8840 high quality SNPs in 23,136 contigs. Detection of selection approaches revealed 998 candidate contigs showing some evidence of selection in the cultivated yam. Interestingly, we found selection signature in the starch biosynthesis pathway as well as in a well-known root development gene. We also found selection in phototropism genes, suggesting that growth pattern between wild and cultivated yam might have been reshaped during domestication.

Key word: Adaptation, diversity, domestication, genomic of selection, yam