African Yam Domestication: Analyses of Selection Pinpoint to Starch, Root and Photosynthesis Related Genes

Domestication is associated with major phenotypic changes. To understand the molecular basis of domestication one could assess selection signature at the whole genome scale. Here, we studied a tuber crop, the African yam (Dioscorea rotundata). This species has two closed wilds relatives with very specific ecological distribution: one is Dioscorea abyssinica found in the savanna, the other is Dioscorea praehensilis native from forest areas. We sequenced a sample of 30 yam accessions from Benin in West Africa, including 10 cultivated individuals and 10 individuals from each of its two putative wild parents. We identified 308840 high quality SNPs in 23,136 contigs. Detection of selection approaches allow to identify 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 gene, suggesting how at the molecular level, growth pattern between wild and cultivated yam might have been reshaped during domestication.

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