Yam genomics supports West Africa as a major cradle of crop domestication

Scarcelli, Nora; Cubry, Philippe; Akakpo, Roland; Thuillet, Anne-Céline; Obidiegwu, Jude; Baco, Mohamed Nasser; Otoo, Emmanuel; Sonké, Bonaventure; Dansi, Alexandre; Djèdatin, Gustave; Mariac, Cédric; Couderc, Marie; Causse, Sandrine; Alix, Karine; Chaïr, Hâna; Ochsenbein, F.; Vigouroux, Yves

doi:10.1126/sciadv.aaw1947

Cited by 79 publications

(83 citation statements)

References 41 publications

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“…To complement our result and to exactly replicate the previous report (28), fastsimcoal2 (33) used in the previous study (28) was also used to test these three models ({{A, P}, C}, {{C, P}, A}, and {{C, A}, P}). Until the step of SNP calling, we basically followed our own pipeline in supplementary text S3.2 based on the reference genome version 1 including the unanchored contigs (1) to be consistent with the previous study (28). The misclassified samples excluding hybrids were genetically reclassified by the admixture analysis following the previous study (28).…”

Section: S44 Inference Of the Evolutionary History Of Wild Dioscoreasupporting

confidence: 54%

“…In terms of the samples sequenced in the previous study (28), we only used the sequences whose species labels matched a species predicted by the admixture analysis in the previous study (28). Also, we removed the sequences which were labeled as hybrid in the previous study (28). Two sequences of D. alata for outgroup were downloaded from NCBI (Table SM11).…”

Section: Flow Cytometrymentioning

confidence: 99%

“…Until the step of SNP calling, we basically followed our own pipeline in supplementary text S3.2 based on the reference genome version 1 including the unanchored contigs (1) to be consistent with the previous study (28). The misclassified samples excluding hybrids were genetically reclassified by the admixture analysis following the previous study (28). The threshold of missing rate across all samples was set to 0.25 which was proposed in the previous study (28).…”

Section: S44 Inference Of the Evolutionary History Of Wild Dioscoreamentioning

confidence: 99%

“…The misclassified samples excluding hybrids were genetically reclassified by the admixture analysis following the previous study (28). The threshold of missing rate across all samples was set to 0.25 which was proposed in the previous study (28). The resulting SNPs through our pipeline were 87,672, which were less than the number of the analyzed SNPs in the coalescent simulation of the previous study (28).…”

Section: S44 Inference Of the Evolutionary History Of Wild Dioscoreamentioning

confidence: 99%

“…The threshold of missing rate across all samples was set to 0.25 which was proposed in the previous study (28). The resulting SNPs through our pipeline were 87,672, which were less than the number of the analyzed SNPs in the coalescent simulation of the previous study (28). Therefore, we skipped the down sampling of the SNPs to 100,000 unlike the previous study (28).…”

Section: S44 Inference Of the Evolutionary History Of Wild Dioscoreamentioning

confidence: 99%

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Genome analyses reveal the hybrid origin of the staple food crop white Guinea yam

Sugihara

Darkwa

Yaegashi

et al. 2020

Preprint

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White Guinea yam (Dioscorea rotundata) is an important staple tuber crop of West Africa. However, its origin remains unclear. In this study, we re-sequenced 336 accessions of white Guinea yam and compared them with the sequences of the wild Dioscorea species using an improved reference genome sequence of D. rotundata. Our results suggest a hybrid origin of white Guinea yam from crosses between the rainforest wild species D. praehensilis and the savannah-adapted D. abyssinica. We identified a higher genomic contribution from D. abyssinica in the sex chromosome of Guinea yam and an extensive introgression around the SWEETIE gene. Our findings point to a complex domestication scenario for Guinea yam and highlight the importance of wild species as gene donors for improvement of this crop through molecular breeding.

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Section: S44 Inference Of the Evolutionary History Of Wild Dioscoreasupporting

confidence: 54%

Section: Flow Cytometrymentioning

confidence: 99%

Section: S44 Inference Of the Evolutionary History Of Wild Dioscoreamentioning

confidence: 99%

Section: S44 Inference Of the Evolutionary History Of Wild Dioscoreamentioning

confidence: 99%

Section: S44 Inference Of the Evolutionary History Of Wild Dioscoreamentioning

confidence: 99%

See 3 more Smart Citations

Genome analyses reveal the hybrid origin of the staple food crop white Guinea yam

Sugihara

Darkwa

Yaegashi

et al. 2020

Preprint

View full text Add to dashboard Cite

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Looking beyond history: tracing the dispersal of the Malaysian complex of crops to Africa

Grimaldi

Andel

Denham

2022

American J of Botany

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In his 1959 book, Africa: Its Peoples and Their Culture History, George P. Murdock suggested that a Malaysian complex of crops dispersed to Africa in ancient times across the Indian Ocean along the Sabaean Lane. The Malaysian complex comprised bananas, sugarcane, taro, three yam species, rice, Polynesian arrowroot, breadfruit, coconut, areca palm, and betel leaf. Except for rice, arrowroot, and potentially taro, most of these crops were domesticated in the Island Southeast Asia-New Guinea region, from where they dispersed to Africa. Our reassessment of agronomic, archaeological, classical, genetic, and historical sources shows that we need to go beneath standard historical narratives to recover a much more ancient and complex history of crop introductions to Africa. Despite considerable uncertainty and fragmented research, we were able to conclude that the Malaysian complex of crops did not arrive in Africa as a complete assemblage at one time or along one route. Multiple lines of evidence suggest that these crops arrived in Africa at different times and followed different pathways of introduction to the continent.

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Demographic history was a formative mechanism of the genetic structure for the taste receptor TAS2R16 in human populations inhabiting Africa's Sahel/Savannah Belt

Kulichová

Mouterde

Mokhtar

et al. 2021

American Journal of Biological Anthropology

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Objectives: Mode of subsistence is an important factor influencing dietary habits and the genetic structure of various populations through differential intensity of gene flow and selection pressures. Previous studies suggest that in Africa Taste 2 Receptor Member 16 (TAS2R16), which encodes the 7-transmembrane receptor protein for bitterness, might also be under positive selection pressure.Methods: However, since sampling coverage of populations was limited, we created a new TAS2R16 population dataset from across the African Sahel/Savannah belt representing various local populations of differing subsistence modes, linguistic affiliations, and geographic provenience. We sequenced the TAS2R16 exon gene and analyzed 2250 haplotypes among 19 populations.Results: We found no evidence for selection as a driving force of genetic variation at this locus; instead, we discovered a highly significant correlation between TAS2R16 genetic and geographical distances based on provenience of the sampled populations, strongly suggesting that genetic drift most likely prevailed over positive selection at this specific locus. We also found significant correlations with other independent loci, mainly in sedentary farmers.Discussion: Our results do not support the notion that the genetic diversity of TAS2R16 in Sahelian populations was shaped by selective pressures. This could result from several alternative and not mutually exclusive mechanisms, of which the possibility that, due to the pleiotropic nature of TAS2R16, selective pressures on other traits could counterbalance those acting on bitter taste perception, or that the change of diet in the Neolithic generally relaxed selective pressure on this gene.

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Yam genomics supports West Africa as a major cradle of crop domestication

Cited by 79 publications

References 41 publications

Genome analyses reveal the hybrid origin of the staple food crop white Guinea yam

Genome analyses reveal the hybrid origin of the staple food crop white Guinea yam

Looking beyond history: tracing the dispersal of the Malaysian complex of crops to Africa

Demographic history was a formative mechanism of the genetic structure for the taste receptor TAS2R16 in human populations inhabiting Africa's Sahel/Savannah Belt

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