Dataset Information

The genome of African yam (Dioscorea cayenensis-rotundata complex) hosts endogenous sequences from four distinct Badnavirus species.

ABSTRACT: Several endogenous viral elements (EVEs) have been identified in plant genomes, including endogenous pararetroviruses (EPRVs). Here, we report the first characterization of EPRV sequences in the genome of African yam of the Dioscorea cayenensis-rotundata complex. We propose that these sequences should be termed 'endogenous Dioscorea bacilliform viruses' (eDBVs). Molecular characterization of eDBVs shows that they constitute sequences originating from various parts of badnavirus genomes, resulting in a mosaic structure that is typical of most EPRVs characterized to date. Using complementary molecular approaches, we show that eDBVs belong to at least four distinct Badnavirus species, indicating multiple, independent, endogenization events. Phylogenetic analyses of eDBVs support and enrich the current taxonomy of yam badnaviruses and lead to the characterization of a new Badnavirus species in yam. The impact of eDBVs on diagnosis, yam germplasm conservation and movement, and breeding is discussed.

SUBMITTER: Umber M

PROVIDER: S-EPMC6638810 | biostudies-literature | 2014 Oct

REPOSITORIES: biostudies-literature

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The genome of African yam (Dioscorea cayenensis-rotundata complex) hosts endogenous sequences from four distinct Badnavirus species.

Umber Marie M Filloux Denis D Muller Emmanuelle E Laboureau Nathalie N Galzi Serge S Roumagnac Philippe P Iskra-Caruana Marie-Line ML Pavis Claudie C Teycheney Pierre-Yves PY Seal Susan E SE

Molecular plant pathology 20140415 8

Several endogenous viral elements (EVEs) have been identified in plant genomes, including endogenous pararetroviruses (EPRVs). Here, we report the first characterization of EPRV sequences in the genome of African yam of the Dioscorea cayenensis-rotundata complex. We propose that these sequences should be termed 'endogenous Dioscorea bacilliform viruses' (eDBVs). Molecular characterization of eDBVs shows that they constitute sequences originating from various parts of badnavirus genomes, resultin ...[more]

PMID: 24605894

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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:Yam (Dioscorea spp.) is of great importance to food security, especially in West Africa. However, the loss of soil fertility due to dwindling fallow lands with indigenous nutrient supply poses a challenge for yam cultivation. This study aimed to determine shoot and tuber biomass and nutrient use efficiency of white Guinea yam (Dioscorea rotundata) grown under low- and high-NPK conditions. Six white Guinea yam genotypes were used in field experiments conducted at Ibadan, Nigeria. Experiments were conducted with low soil NPK conditions with zero fertilizer input and high soil NPK conditions with mineral fertilizer input. Differences in response to soil NPK conditions, nutrient uptake, and nutrient use efficiency (apparent nutrient recovery efficiency) were observed among the tested genotypes. The genotypes TDr1499 and TDr1649, with high soil fertility susceptibility index (SFSI>1) and an increase in shoot and tuber biomass with fertilizer input, were recognized as susceptible to soil NPK conditions. There was a marked difference in apparent nutrient recovery efficiency; however, there was no varietal difference in physiological efficiency. Differences in apparent nutrient recovery efficiency among genotypes affected the fertilizer response (or susceptibility to soil NPK conditions) and the nutrient uptake. In contrast, the genotype TDr2029, with SFSI<1 and low reduction in shoot and tuber production between non-F and +F conditions, was recognized as a less susceptible genotype to soil NPK status. It was revealed that NPK fertilization did not reduce tuber dry matter content, regardless of genotype differences in susceptibility to soil NPK conditions. Hence, this could be helpful to farmers because it implies that yield can be increased without reducing tuber quality through a balanced application of soil nutrients. Our results highlight genotypic variation in sensitivity to the soil NPK availability, nutrient uptake, and nutrient use efficiency white Guinea yam. Differences in susceptibility to soil NPK conditions could be due to the genotypic variations in nutrient recovery efficiency white Guinea yam. Our findings could contribute to breeding programs for the development of improved white Guinea yam varieties that enhance productivity in low soil fertility conditions with low and high-input farming systems.

Dataset Information

The genome of African yam (Dioscorea cayenensis-rotundata complex) hosts endogenous sequences from four distinct Badnavirus species.

Publications

The genome of African yam (Dioscorea cayenensis-rotundata complex) hosts endogenous sequences from four distinct Badnavirus species.

Similar Datasets

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