- Background: After cereals, root and tuber crops are the main source of starch in the human diet. - But domestication of these root and tubers crops is also associated with gigantism of storage organs and changes of habitat.. - The genomic diversity in the cultivated species is roughly 30% less important than its wild relatives. - 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. - 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.. - One of the major changes in human history was the emer- gence of agricultural societies [1]. - The domestication process offers an interesting glimpse of the broad adapta- tion process and of the genetic basis of morphological and. - Today it is not clear if the knowledge we have of the process of domestication of cereal crops can be extrapolated to root and tuber crops.. - 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, 34394 Montpellier, France Full list of author information is available at the end of the article. - 2017 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0. - abyssinica is found in the wooded savanna areas while D. - Finally, the wild rela- tives of yam are vines which grow partly in the shade of their tutor tree, while cultivated yams grow in full sunlight. - This change of habitat might be associated with major adaptation.. - Using this dataset, we then scanned for selec- tion signature to pinpoint genes associated with domestication.. - We also performed SNP calling using the HaplotypeCaller in the Genome Analysis Toolkit (GATK) V . - Genetic structure was assessed using a least-squares optimization approach implemented in the sNMF pro- gram [27]. - To select the best K value, we used the minimum value of the cross entropy criterion [27]. - We also used the maximum likelihood structure approach imple- mented in the NgsAdmix program [28]. - rotundata and each of the wild species D.. - (2) The ratio of the cultivated genetic diversity divided by the mean diversity of the two wild relative species using π [29] and θ [30]. - (3) We estimated the differentiation index F ST [36] between the cultivated group and each of the two wild groups for each contig using vcftools v0.1.13 [35]. - Using the cutoff of the 1% top values, contigs with extreme F ST between the cultivated and both two wild relatives were selected as candidates. - The annotation of the candidate selected genes was retrieved from a previous study [24].. - Enrichment analysis for annotated candidate contigs First, all the candidate contigs annotated in the reference transcriptome were tested for enrichment of gene ontol- ogy (GO) molecular function terms. - Standard Fisher’s exact tests implemented in the R package TopGO [41]. - A low correlation was observed between the length of the contigs and the number of SNPs detected ( r = 0.34, p <. - Analysis of the population structure using sNMF led to three major genetic groups (Additional file 2: Figure S1), corresponding to the three species (Fig. - One individual (A3085) was cer- tainly misclassified in the field: it was recorded as D.. - abyssinica in the field but was genetically close to the D.. - The exact structuration was similarly found using the NgsAdmix approach, with only minor differences in the estimated proportion of admixture (Fig. - We compared nucleotide diversity π and the nucleo- tide polymorphism θ between the cultivated species and each of the wild species. - Contigs were searched for selection signatures using four different methods: Tajima’s D, marked reduction in the diversity in the cultivated samples, differentiation between wild and cultivated species, and principal com- ponent analysis. - (i) Tajima’s D in the cultivated yam showed a skewed distribution to positive values (Fig. - The distribution of Tajima’s values in the two wild species is centered on zero and consequently reflects a more global equilibrium between SNP occurrence and their frequencies (Additional file 2:. - total of 187 contigs were identified as potential candi- dates under selection in the cultivated sample.. - 1.34), a total of 232 contigs were identified as having an extremely low diversity in the cultivated sam- ple compared to their wild relatives, and were therefore considered as candidates. - We compared the candidate contigs with the available annotation of the yam transcriptome reference [24].. - In particular, among the genes annotated for the candidate genes, we identified five candidate contigs that were relevant in the light of yam domestication (Fig. - These five candidate contigs showed strong diversity loss in the cultivated group compared to the wild species (Additional file 2: Figure S7). - Two other genes were associated with the earliest stages of starch biosynthesis and storage i.e., genes coding for the sucrose synthase 4 [44] and the sucrose-phosphate syn- thase 1 [45]. - We also identified two genes associated with growth and phototropism, respectively : Ethylene In- sensitive 4 genes (EIN4) [46] and Phototropin 2 gene ( Phot2, [47]. - The set of GO terms found across these two enrichment tests was associated with dehydrogenase and oxidoreductase ( NADH DH ) activities (Fig. - 2 Summary of the different tests used to identify outlier contigs. - In the distribution of Tajima ’ s D value of the cultivated species (a), the red line indicates the 1% threshold used to consider contigs as candidates. - In the of reduction of nucleotide diversity π (b), the -log10 ( π c / π w ) for each contig is represented by one dot. - In the comparison of F ST. - between the cultivated and the two-wild species (c), each dot represents a contigs. - Finally, in the histogram of p-value (d), the peak of SNP close to zero indicates the presence of outliers. - Overall, despite the mode of reproduction of the culti- vated yam, both the diversity loss and the LD decay ob- served were similar to those in outcrossing crops.. - Among the contigs we identified, roughly 10% of the candidate contigs were commonly identified by a least two different methods used for detecting signa- tures of selection.. - Depending of the strength and the timing of selection, its resulting impact on diversity could differ. - So, the specificity of each test could lead to the discovery of only a small set of the same contigs by all different methods.. - Furthermore, signature of selection on two contigs could be associated with a single selection events one of them. - 3 Key genes associated with yam domestication. - 4 TreeMap view of the 10 most significant “ Go Terms ” identified. - In our study, we observed the selection of two genes involved in the production of sugar: SUS 4 and SPS1 . - In wheat, selection for increased starch content was associated with selection of SUS genes [62], and enhancing SUS ac- tivities also resulted in increasing starch content in maize [63]. - Yams are now grown in open fields, whereas its wild relatives grow as vines in the shade of tutor trees. - We observed strong signatures of selection in genes associated with physiological processes of regulation of photosynthesis for light tracking and for plant growth. - Beyond specific genes associated with the change from shade to light environment, we also found a significant enrichment of interesting gene ontology terms. - most significant GO terms observed were and oxidore- ductase activities associated with NADPH DH complex genes [64, 65]. - It plays a role in pro- tection against photo-oxidative stresses associated with the formation of reactive oxygen species (ROS) [68].. - In Brassica plants, the same NADH DH complex has also been reported to be associated with the domes- tication process [71]. - In this specific case, do- mestication was associated with a decrease in photosyn- thetic parameters under stress conditions in the cultivated species [71]. - The cultivated species D. - rotundata grows under full sunlight in the field. - We hypothesize that adaptation of the cultivated yam led to the selection of genes that enable efficient photo- synthesis with increasing light and heat intensity.. - Optimizing photosynthesis is also an important way to enhance production of carbohydrate, later stored as starch in the tuber.. - Selection in the early step of sugar biosynthesis is detected in yam, and previously detected in cereal. - More interestingly, drastic changes in habitat associated with domestication is certainly retraced in selection in photo- tropism genes. - Selection on dehydrogenase and oxidore- ductase activities associated with NADPH DH complex genes, was certainly the consequence of adaptation to optimize photosynthesis in full light. - List of the contigs detected as selected by at least one method. - Cross-entropy calculated using sNMF (Frichot et al., 2014) for K = 1 to 6. - Ten repetitions of the run were done. - Genetic diversity and selection in the maize starch pathway. - 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