Chromosome evolution and the genetic basis of agronomically important traits in greater yam

The nutrient-rich tubers of the greater yam, Dioscorea alata L., provide food and income security for millions of people around the world. Despite its global importance, however, greater yam remains an orphan crop. Here, we address this resource gap by presenting a highly contiguous chromosome-scale genome assembly of D. alata combined with a dense genetic map derived from African breeding populations. The genome sequence reveals an ancient allotetraploidization in the Dioscorea lineage, followed by extensive genome-wide reorganization. Using the genomic tools, we find quantitative trait loci for resistance to anthracnose, a damaging fungal pathogen of yam, and several tuber quality traits. Genomic analysis of breeding lines reveals both extensive inbreeding as well as regions of extensive heterozygosity that may represent interspecific introgression during domestication. These tools and insights will enable yam breeders to unlock the potential of this staple crop and take full advantage of its adaptability to varied environments

Food quality profile of pounded yam and implications for yam breeding

Open Access ArticleBACKGROUND Assessment of the key preferred quality traits in pounded yam, a popularly consumed yam food product in West Africa, is often done through sensory evaluation. Such assessment is time-consuming and results may be biased. Therefore, there is a need to develop objective, high-throughput methods to predict the quality of consumer-preferred traits in pounded yam. This study focused on how key quality traits in pounded yam proposed to yam breeders were determined, measured by biophysical and biochemical methods, in order to shorten the breeding selection cycle through adoption of these methods by breeders. RESULTS Consumer tests and sensory quantitative descriptive analysis (QDA) validated that preferred priority quality traits in pounded yam were related to textural quality (smooth, stretchable, moldable, slightly sticky and moderately hard) and color (white, cream or light yellow). There were significant correlations between sensory textural quality attributes cohesiveness/moldability, hardness, and adhesiveness/stickiness, with textural quality measurements from instrumental texture profile analysis (TPA). Color measurement parameters (L*, a*, and b*) with chromameter agreed with that of sensory evaluation and can replace the sensory panel approach. The smoothness (R2 = 1.00), stickiness (R2 = 1.00), stretchability (R2 = 1.00), hardness (R2 = 0.99), and moldability (R2 = 0.53) of pounded yam samples can be predicted by the starch, amylose, and protein contents of yam tubers estimated by near-infrared spectroscopy. CONCLUSION TPA and Hunter colorimeter can be used as medium-high throughput methods to evaluate the textural quality and color of pounded yam in place of the sensory panelists

Notes for genera: basal clades of Fungi (including Aphelidiomycota, Basidiobolomycota, Blastocladiomycota, Calcarisporiellomycota, Caulochytriomycota, Chytridiomycota, Entomophthoromycota, Glomeromycota, Kickxellomycota, Monoblepharomycota, Mortierellomycota, Mucoromycota, Neocallimastigomycota, Olpidiomycota, Rozellomycota and Zoopagomycota)

Compared to the higher fungi (Dikarya), taxonomic and evolutionary studies on the basal clades of fungi are fewer in number. Thus, the generic boundaries and higher ranks in the basal clades of fungi are poorly known. Recent DNA based taxonomic studies have provided reliable and accurate information. It is therefore necessary to compile all available information since basal clades genera lack updated checklists or outlines. Recently, Tedersoo et al. (MycoKeys 13:1--20, 2016) accepted Aphelidiomycota and Rozellomycota in Fungal clade. Thus, we regard both these phyla as members in Kingdom Fungi. We accept 16 phyla in basal clades viz. Aphelidiomycota, Basidiobolomycota, Blastocladiomycota, Calcarisporiellomycota, Caulochytriomycota, Chytridiomycota, Entomophthoromycota, Glomeromycota, Kickxellomycota, Monoblepharomycota, Mortierellomycota, Mucoromycota, Neocallimastigomycota, Olpidiomycota, Rozellomycota and Zoopagomycota. Thus, 611 genera in 153 families, 43 orders and 18 classes are provided with details of classification, synonyms, life modes, distribution, recent literature and genomic data. Moreover, Catenariaceae Couch is proposed to be conserved, Cladochytriales Mozl.-Standr. is emended and the family Nephridiophagaceae is introduced

Quantification of heavy metal levels in local rice (Oryza sativa) consumed in Anambra State, Nigeria

Rice is a little solid seed which is the most requested grain crop. Injection of this crop while contaminated can cause harm to the human organs. For this reason, the urge to study the Quantification of heavy metals in rice grain arises. Four towns in Anambra State (Nzam, Omor, Otuocha, Ufuma) were sampled. In the samples of the rice, analysis of heavy metals were conducted using Atomic Absorbance Spectrophotometer to determine the heavy metals present in the samples and the mean levels of heavy metals found in rice grains were; For lead: 0.0078mg/kg (Nzam), 0.1250mg/kg (Omor), 0.2070mg/kg (Otuocha). For Arsenic: 14.8889mg/kg (Nzam), 12.8333mg/kg (Omor), 12.8889mg/kg (Otuocha), and 12.3333 mg/kg (Ufuma). For Zinc: 0.7110mg/kg (Nzam), 0.7474mg/kg (Omor), 1.5930mg/kg (Otuocha), and 0.2518 mg/kg (Ufuma). For Iron: 0.6390mg/kg (Nzam), 0.5352mg/kg (Omor), 0.6194mg/kg (Otuocha), and 0.5709mg/kg (Ufuma). For Manganese: 0.0578mg/kg (Nzam), 0.0104mg/kg (Omor), and 0.714mg/kg (Ufuma). For Nickel: 0.0756mg/kg (Ufuma). There is no observed level of Cd, Co, Cu and Cr in the rice grown in these four towns (Nzam, Omor, Otuocha, Ufuma). With the results gotten from this Analysis, some rice samples were within the acceptable limit set by FAO/WHO while some were not within the permissible limit and it is therefore recommended that these four towns should be monitored continuously

Role of Non-Structural Sugar Metabolism in Regulating Tuber Dormancy in White Yam (<i>Dioscorea rotundata</i>)

Changes in sugar composition occur continuously in plant tissues at different developmental stages. Tuber dormancy induction, stability, and breaking are very critical developmental transitions in yam crop production. Prolonged tuber dormancy after physiological maturity has constituted a great challenge in yam genetic improvement and productivity. In the present study, biochemical profiling of non-structural sugar in yam tubers during dormancy was performed to determine the role of non-structural sugar in yam tuber dormancy regulation. Two genotypes of the white yam species, one local genotype (Obiaoturugo) and one improved genotype (TDr1100873), were used for this study. Tubers were sampled at 42, 56, 87, 101, 115, and 143 days after physiological maturity (DAPM). Obiaoturugo exhibited a short dormant phenotype and sprouted at 101-DAPM, whereas TDr1100873 exhibited a long dormant phenotype and sprouted at 143-DAPM. Significant metabolic changes were observed in non-structural sugar parameters, dry matter, and moisture content in Obiaoturugo from 56-DAPM, whereas in TDr1100873, significant metabolic changes were observed from 101-DAPM. It was observed that the onset of these metabolic changes occurred at a point when the tubers of both genotypes exhibited a dry matter content of 60%, indicating that a dry matter content of 60% might be a critical threshold for white yam tuber sprouting. Non-reducing sugars increased by 9–10-fold during sprouting in both genotypes, which indicates their key role in tuber dormancy regulation in white yam. This result implicates that some key sugar metabolites can be targeted for dormancy manipulation of the yam crop