Dataset Information

Clonal diversity and estimation of relative clone age: application to agrobiodiversity of yam (Dioscorea rotundata).

ABSTRACT:

Background

Clonal propagation is a particular reproductive system found in both the plant and animal kingdoms, from human parasites to clonally propagated crops. Clonal diversity provides information about plant and animal evolutionary history, i.e. how clones spread, or the age of a particular clone. In plants, this could provide valuable information about agrobiodiversity dynamics and more broadly about the evolutionary history of a particular crop. We studied the evolutionary history of yam, Dioscorea rotundata. In Africa, Yam is cultivated by tuber clonal propagation.

Results

We used 12 microsatellite markers to identify intra-clonal diversity in yam varieties. We then used this diversity to assess the relative ages of clones. Using simulations, we assessed how Approximate Bayesian Computation could use clonal diversity to estimate the age of a clone depending on the size of the sample, the number of independent samples and the number of markers. We then applied this approach to our particular dataset and showed that the relative ages of varieties could be estimated, and that each variety could be ranked by age.

Conclusions

We give a first estimation of clone age in an approximate Bayesian framework. However the precise estimation of clone age depends on the precision of the mutation rate. We provide useful information on agrobiodiversity dynamics and suggest recurrent creation of varietal diversity in a clonally propagated crop.

SUBMITTER: Scarcelli N

PROVIDER: S-EPMC3832681 | biostudies-literature | 2013 Nov

REPOSITORIES: biostudies-literature

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Publications

Clonal diversity and estimation of relative clone age: application to agrobiodiversity of yam (Dioscorea rotundata).

Scarcelli Nora N Couderc Marie M Baco Mohamed N MN Egah Janvier J Vigouroux Yves Y

BMC plant biology 20131113

<h4>Background</h4>Clonal propagation is a particular reproductive system found in both the plant and animal kingdoms, from human parasites to clonally propagated crops. Clonal diversity provides information about plant and animal evolutionary history, i.e. how clones spread, or the age of a particular clone. In plants, this could provide valuable information about agrobiodiversity dynamics and more broadly about the evolutionary history of a particular crop. We studied the evolutionary history ...[more]

PMID: 24219837

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Project description:Yam (Dioscorea spp.) is a major food security crop for millions of resource-poor farmers, particularly in West Africa. Soil mineral deficiency is the main challenge in yam production, especially with the dwindling of fallow lands for the indigenous nutrient supply. Cultivars tolerant to available low soil nutrients and responsive to added nutrient supply are viable components of an integrated soil fertility management strategy for sustainable and productive yam farming systems in West Africa. This study's objective was to identify white Guinea yam (D. rotundata) genotypes adapted to available low soil nutrients and responsive to externally added nutrient supply. Twenty advanced breeding lines and a local variety (Amula) were evaluated under contrasting soil fertility, low to expose the crop to available low soil nutrient supply and high to assess the crop response to added mineral fertilizer (NPK) input at Ibadan, Nigeria. The genotypes expressed differential yield response to low soil fertility (LF) stress and added fertilizer input. Soil fertility susceptibility index (SFSI) ranged from 0.64 to 1.34 for tuber yield and 0.60 to 1.30 for shoot dry weight. The genotypes R034, R041, R050, R052, R060, R100, and R125 combined lower SFSI with a low rate of reduction in tuber yield were identified as tolerant to LF stress related to the soil mineral deficiency. Likewise, the genotypes R109, R119, and R131 showed high susceptibility to soil fertility level and/or fertilizer response. Genotypes R025 and R034 had the tuber yielding potential twice of that the local variety under low soil nutrient conditions. Shoot dry weight and tuber yield showed a positive correlation both under low and high soil fertility conditions (r = 0.69 and 0.75, respectively), indicating the vigor biomass may be a morphological marker for selecting genotypes of white Guinea yam for higher tuber yield. Our results highlight genotypic variation in the tolerance to low soil nutrients and mineral fertilizer response in white Guinea yam to exploit through breeding and genetic studies to develop improved genotypes for low and high input production systems in West Africa.

Project description:Yams are economic and medicinal crops with a long growth cycle, spanning between 9-11 months due to their prolonged tuber dormancy. Tuber dormancy has constituted a major constraint in yam production and genetic improvement. In this study, we performed non-targeted comparative metabolomic profiling of tubers of two white yam genotypes, (Obiaoturugo and TDr1100873), to identify metabolites and associated pathways that regulate yam tuber dormancy using gas chromatography-mass spectrometry (GC-MS). Yam tubers were sampled between 42 days after physiological maturity (DAPM) till tuber sprouting. The sampling points include 42-DAPM, 56-DAPM, 87DAPM, 101-DAPM, 115-DAPM, and 143-DAPM. A total of 949 metabolites were annotated, 559 in TDr1100873 and 390 in Obiaoturugo. A total of 39 differentially accumulated metabolites (DAMs) were identified across the studied tuber dormancy stages in the two genotypes. A total of 27 DAMs were conserved between the two genotypes, whereas 5 DAMs were unique in the tubers of TDr1100873 and 7 DAMs were in the tubers of Obiaoturugo. The differentially accumulated metabolites (DAMs) spread across 14 major functional chemical groups. Amines and biogenic polyamines, amino acids and derivatives, alcohols, flavonoids, alkaloids, phenols, esters, coumarins, and phytohormone positively regulated yam tuber dormancy induction and maintenance, whereas fatty acids, lipids, nucleotides, carboxylic acids, sugars, terpenoids, benzoquinones, and benzene derivatives positively regulated dormancy breaking and sprouting in tubers of both yam genotypes. Metabolite set enrichment analysis (MSEA) revealed that 12 metabolisms were significantly enriched during yam tuber dormancy stages. Metabolic pathway topology analysis further revealed that six metabolic pathways (linoleic acid metabolic pathway, phenylalanine metabolic pathway, galactose metabolic pathway, starch and sucrose metabolic pathway, alanine-aspartate-glutamine metabolic pathways, and purine metabolic pathway) exerted significant impact on yam tuber dormancy regulation. This result provides vital insights into molecular mechanisms regulating yam tuber dormancy.

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Dataset Information

Clonal diversity and estimation of relative clone age: application to agrobiodiversity of yam (Dioscorea rotundata).

Background

Results

Conclusions

Publications

Clonal diversity and estimation of relative clone age: application to agrobiodiversity of yam (Dioscorea rotundata).

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