Genomics of Yams, a Common Source of Food and Medicine in the Tropics

Mignouna, H.D.; Abang, Mathew M.; Asiedu, Robert

doi:10.1007/978-0-387-71219-2_23

Cited by 35 publications

(44 citation statements)

References 75 publications

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“…Yam production has been constrained owing to several abiotic and biotic factors that include diseases and pests, inadequate planting material, low yield potential, and decreasing soil fertility (Amusa et al 2003;Adegbite et al 2006). Despite the vitality of yam, its genetic improvement through conventional breeding has been hindered by the prolonged breeding cycle, dioecious and erratic flowering nature, poor seed setting, polyploidy, vegetative propagation through seed tubers and vine cuttings, and heterozygous genetic background (Mignouna et al 2008). So far, the application of genetic engineering to develop improved varieties has been limited by the absence of efficient protocols for regeneration and genetic transformation.…”

Section: Introductionmentioning

confidence: 99%

Plant regeneration from axillary bud derived callus in white yam (Dioscorea rotundata)

Rajesh

Tripathi

2016

Plant Cell Tiss Organ Cult

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Dioscorea rotundata, commonly known as white yam, is an important staple food crop widely cultivated in West Africa and provides food security to millions of people. Genetic improvements of this crop using the advanced biotechnology tools have been hampered hitherto by the recalcitrant nature of regeneration through somatic embryogenesis. Therefore, we have developed an efficient and reproducible system for plant regeneration via somatic embryogenesis. Explants of different types (immature leaf, node, stem internode, root segment, petiole, and axillary bud) of D. rotundata accession TDr 2436 were tested for their embryogenic potentials on Murashige and Skoog (MS) medium supplemented with various auxins (2,4-D, NAA, and picloram). Among all explants tested, axillary bud explants cultured on MS medium supplemented with picloram (0.5-12 mg/l) favored the production of calli. Maximum proliferation of calli (526 mg fresh weight/explant) was achieved on MS medium supplemented with picloram (0.5 mg/l), casein hydrolysate (600 mg/l), and proline (1 g/l). Histology analysis confirmed that the embryogenic calli produced on this medium were mixed with non-embryogenic calli. Transfer of calli on MS basal medium supplemented with activated charcoal (1 %) changed the color of calli to purple and promoted the production of somatic embryos (87 embryos/callus) as well as adventitious shoot buds. Furthermore, upon transfer to MS medium supplemented with BAP (0.4 mg/l), the embryos continued their differentiation and maturation and germinated into complete plantlets. The adventitious shoot buds produced multiple shoots on MS medium supplemented with BAP (0.4 mg/l). Well-developed germinated plantlets were acclimatized in the screen house with 90 % survivability. Histology studies confirmed that the regeneration of D. rotundata reported here followed dual regeneration pathways. The embryogenic calli regenerated through development of somatic embryos and germinated into complete plantlets, however non-embryogenic calli regenerated through organogenesis and developed multiple shoots. The developed protocol has potential for somatic hybridization, mass clonal propagation, and genetic transformation applications.

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Section: Introductionmentioning

confidence: 99%

Plant regeneration from axillary bud derived callus in white yam (Dioscorea rotundata)

Rajesh

Tripathi

2016

Plant Cell Tiss Organ Cult

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“…In West Africa, it is the second most important food crop after cassava by value and production (FAO, 2012;Scarcelli et al, 2006). It plays an essential role in food security and income generation for smallholders, particularly in West Africa which produces about 95% of the world's total yam production (Asiedu and Sartie, 2010;IITA, 2012;Mignouna et al, 2008). The white Guinea yam, Dioscorea rotundata, is the predominant yam species grown in this region, in contrast to other popular yam species such as D. alata and D. esculenta which predominate in the South Pacific (Kenyon et al, 2008 confused for a long time, and they have in the past few decades often been referred to collectively as members of the D. cayenensis-rotundata species complex (Dumont et al, 2006).…”

Section: Introductionmentioning

confidence: 99%

“…In West Africa, it is the second most important food crop after cassava by value and production (FAO, 2012;Scarcelli et al, 2006). It plays an essential role in food security and income generation for smallholders, particularly in West Africa which produces about 95% of the world's total yam production (Asiedu and Sartie, 2010; IITA, 2012;Mignouna et al, 2008 Several surveys on yam viruses suggest that badnaviruses are the most prevalent globally (Bousalem et al, 2009; Eni et al, 2008a, b;Galzi et al, 2013;Kenyon et al, 2008). Badnavirus particles were first reported in yam in association with a flexuous virus, causing internal brown spot disease in D. alata and D. cayenensis in the Caribbean (Harrison and Roberts, 1973;Mantell and Haque, 1978).…”

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confidence: 99%

The prevalence of badnaviruses in West African yams (Dioscorea cayenensis-rotundata) and evidence of endogenous pararetrovirus sequences in their genomes

et al. 2014

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A comparison of serological and nucleic acid techniques was used to investigate whether the PCRpositives were sequences amplified from badnavirus particles or putative endogenous badnavirus sequences in the yam genome. Protein A sandwich-enzyme-linked immunosorbent assay (PAS-ELISA) with badnavirus polyclonal antisera detected cross-reacting viral particles in only 60% (92 of 153) of the CIRAD collection samples analyzed, in contrast to the aforementioned 81% by PCR.Immunosorbent electron microscopy (ISEM) of virus preparations of a select set of 16 samples, representing different combinations of positive and negative PCR and PAS-ELISA results, identified bacilliform particles in 11 of these samples. Three PCR-positive yam samples from Burkina Faso (cv. Pilimpikou) were identified in which no viral particles were detected by either PAS-ELISA or ISEM.Southern hybridisation results using a yam badnavirus RT-RNaseH sequence (Gn155Dr) as probe, supported a lack of badnavirus particles in the cv. Pilimpikou and identified their equivalent sequences to be of plant genome origin. Probe Gn155Dr, however, hybridised to viral particles and plant genomic DNA in three D. rotundata samples from Guinea. These results represent the first data demonstrating the presence of integrated sequences of badnaviruses in yam. The implications of this for virus-indexing, and breeding and multiplication of seed yams are discussed. IntroductionYam (Dioscorea species) is the fourth most important food tuber crop in the world after potato, sweet potato, and cassava (FAO, 2012). In West Africa, it is the second most important food crop after cassava by value and production (FAO, 2012;Scarcelli et al., 2006). It plays an essential role in food security and income generation for smallholders, particularly in West Africa which produces about 95% of the world's total yam production (Asiedu and Sartie, 2010; IITA, 2012;Mignouna et al., 2008 Several surveys on yam viruses suggest that badnaviruses are the most prevalent globally (Bousalem et al., 2009; Eni et al., 2008a, b;Galzi et al., 2013;Kenyon et al., 2008). Badnavirus particles were first reported in yam in association with a flexuous virus, causing internal brown spot disease in D. alata and D. cayenensis in the Caribbean (Harrison and Roberts, 1973;Mantell and Haque, 1978). Two decades later yam badnaviruses were characterised by their nucleic acid and serological properties; particles isolated from D. alata and D. bulbifera were partially characterised and named informally as Dioscorea alata bacilliform virus (DaBV) and Dioscorea bulbifera bacilliform virus (DbBV) Phillips et al., 1999). These viruses were reported to induce leaf distortions and veinal chlorosis , although others found that often infected plants show no marked symptoms (Kenyon et al., 2008;Seal and Muller, 2007). Sensitive virus diagnostic tests are required to enable the identification of virus-free seed yams, and will underpin current efforts in West Africa to generate and multiply disease-free yam planting material (I...

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“…Our assembly offers a great opportunity to understand the evolution of yam and to elucidate some biological constraints inherent to yam including a long growth cycle, poor to non-flowering, polyploidy, vegetative propagation, and a heterozygous genetic background [33]. Yam improvement has been challenging due to these factors preventing the genetic study of important traits in yam [34].…”

Section: Discussionmentioning

confidence: 99%

High contiguity de novo genome sequence assembly of Trifoliate yam (Dioscorea dumetorum) using long read sequencing

Siadjeu

Pucker

Viehöver

et al. 2020

Preprint

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High contiguity de novo genome sequence assembly of 1 Trifoliate yam (Dioscorea dumetorum) using long read 2 sequencing 3 4 Abstract: The yam species Dioscorea dumetorum is one example of an orphan crop, not traded 17 internationally. Post-harvest hardening starts within 24 hours after harvesting and renders the tubers inedible.18 Genomic resources are required for trifoliate yam to improve breeding for non-hardening varieties and for 19 other traits. Here, we describe the sequencing of the D. dumetorum genome and the generation of a de novo 20 assembly together with a corresponding annotation. The two haplophases of this highly heterozygous genome 21 are separated to a large extent. The assembly represents 485 Mbp of the genome with an N50 of over 3.2 Mbp. 22 A total of 35,269 protein-encoding gene structures as well as 9,941 non-coding RNA genes were predicted and 23 functional annotations were assigned. 24 25

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Genomics of Yams, a Common Source of Food and Medicine in the Tropics

Cited by 35 publications

References 75 publications

Plant regeneration from axillary bud derived callus in white yam (Dioscorea rotundata)

Plant regeneration from axillary bud derived callus in white yam (Dioscorea rotundata)

The prevalence of badnaviruses in West African yams (Dioscorea cayenensis-rotundata) and evidence of endogenous pararetrovirus sequences in their genomes

High contiguity de novo genome sequence assembly of Trifoliate yam (Dioscorea dumetorum) using long read sequencing

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