Changes in the rhizosphere and root-associated bacteria community of white Guinea yam (Dioscorea rotundata Poir.) impacted by genotype and nitrogen fertilization
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SUBMITTER: Idowu A
PROVIDER: S-EPMC11252748 | biostudies-literature | 2024 Jun
REPOSITORIES: biostudies-literature
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Project description:Developing novel white Guinea yam (Dioscorea rotundata) varieties is constrained by the sparse, erratic, and irregular flowering behavior of most genotypes. We tested the effectiveness of nine agronomic and hormonal treatments to enhance flowering on D. rotundata under field conditions. Genotypes responded differently to flower-inducing treatments (p<0.001). Of the test treatments, pruning and silver thiosulfate (STS) were effective in increasing the number of spikes per plant and the flowering intensity on both sparse flowering and monoecious cultivars. STS and tuber removal treatments promoted female flowers on the monoecious variety while pruning and most treatments involving pruning favored male flowers. None of the treatments induced flowering on Danacha, a non-flowering yam landrace. Flower-enhancing treatments had no significant effect on flower fertility translated by the fruit set, since most treatments recorded fruit sets above the species' average crossability rate. Flower-enhancing techniques significantly influenced number of tubers per plant (p = 0.024) and tuber dry matter content (DMC, p = 0.0018) but did not significantly affect plant tuber yield. Nevertheless, treatments that could enhance substantially flowering intensity, such as pruning and STS, reduced tuber yield. DMC had negative associations with all flowering-related traits. This study provided insights into white yam flower induction and suggests promising treatments that can be optimized and used routinely to increase flowering in yam crop, without significantly affecting flower fertility and tuber yield.
| S-EPMC10593412 | biostudies-literature
Project description:BackgroundWhite Guinea yam (Dioscorea rotundata) is primarily a dioecious species with distinct male and female plants. Its breeding is constrained by sexual reproduction abnormalities, resulting in low success rates in cross-pollination. An accurate method for early detection of this plant's sex and compatible fertile parents at the seedling stage would improve levels of cross-pollination success in breeding. We used the genome-wide association studies (GWAS) to dissect the molecular basis of plant sex and cross-compatibility-related traits in a panel of 112 parental clones used in D. rotundata crossing blocks from 2010 to 2020.ResultsPopulation structure and phylogeny analyses using 8326 single nucleotide polymorphism (SNP) markers grouped the 112 white yam clones into three subpopulations. Using Multi-locus random-SNP-effect Mixed Linear Model, we identified three, one, and three SNP markers that were significantly associated with the average crossability rate (ACR), the percentage of high crossability (PHC), and the plant sex, respectively. In addition, five genes considered to be directly linked to sexual reproduction or regulating the balance of sex hormones were annotated from chromosomal regions controlling the assessed traits. This study confirmed the female heterogametic sex determination (ZZ/ZW) system proposed for D. rotundata.ConclusionsThis study provides valuable insights on the genomic control of sex identity and cross-pollination success in D. rotundata. It, therefore, opens an avenue for developing molecular markers for predicting plant sex and cross-pollination success at the early growth stage before field sex expression in this crop.
| S-EPMC9199169 | biostudies-literature
Project description:To meet the high demand for white Guinea yam, there is a need to develop and release improved varieties to farmers. Unfortunately, low rate of adoption of most of the improved yam varieties by both producers and consumers was observed. Information regarding agronomic characteristics and food qualities of popular white Guinea yam landraces with high market value are not available to establish minimum standards to be considered by breeding programs. To fill this gap, surveys using rural appraisal tools were carried out in 20 villages and 16 markets throughout Benin. Data on the agronomic performance suggested that for an improved variety to be adopted by Beninese farmers it should have a minimum yield of 4.16 ± 0.15 kg per mound, and average number of marketable tubers of 1.23 ± 0.05, a mean tuber length of 36.41 ± 1.22 cm, and a minimum diameter of 25.44 ± 1.16 cm. The sensorial attributes for boiled and pounded tubers of this improved variety should have minimum score of 3.16 for texture, 0.75 for softness, 3.75 for elasticity, and 1.34 for colour during the sensory evaluation. The improved variety must also have a minimum average severity score of 1.1 for yam mosaic virus disease, 1.33 for anthracnose and 1 for nematodes. Landraces Amoula, Laboko, and Djilaadja should be considered as the standard for yield, sensory attributes, and tolerance to pest and diseases while landraces Danwari, Kodjewe, Mondji, and Gnidou should be characterized as possessing good flowering and fruit setting capacities for breeding programs.
| S-EPMC9384998 | biostudies-literature
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.
| S-EPMC9597467 | biostudies-literature
Project description:Choosing superior parents with complementary trait values for hybridization and selecting variants with desired product profiles to release as a new cultivar are important breeding activities to progress genetic improvement in crops. This study assessed the genetic potential of 36 parental lines of white Guinea yam (Dioscorea rotundata) genotypes using multi-trait index-based factor analysis and ideotype design (FAI-BLUP). The experiment utilized 36 white yam genotypes laid out in a 6 × 6 triple lattice design with three replications and phenotyped for 18 agronomic and food quality traits. Findings showed significant differences among genotypes for all assessed traits. Fifteen traits had desired genetic gains, whereas stem diameter (-1.34%), and two starch property traits ((holding strength (-26.31%) and final paste viscosity (-3.33%)) had undesired selection gain. The FAI-BLUP index provided total genetic gains of 148.91% for traits desired for increase and -29.26% for those desired for decrease. Genotypes TDr08-21-2, TDr9518544, TDr9501932, TDr8902665 and Pampars were identified as top best candidate for simultaneous improvement of the measured traits in white yam breeding. The findings indicate the effectiveness of the FAI-BLUP index in identifying and selecting genotypes.
| S-EPMC9658037 | biostudies-literature
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.
| S-EPMC10223290 | biostudies-literature
Project description:Dioecy (distinct male and female individuals) and scarce to non-flowering are common features of cultivated yam (Dioscorea spp.). However, the molecular mechanisms underlying flowering and sex determination in Dioscorea are largely unknown. We conducted SuperSAGE transcriptome profiling of male, female and monoecious individuals to identify flowering and sex-related genes in white Guinea yam (D. rotundata), generating 20,236 unique tags. Of these, 13,901 were represented by a minimum of 10 tags. A total 88 tags were significantly differentially expressed in male, female and monoecious plants, of which 18 corresponded to genes previously implicated in flower development and sex determination in multiple plant species. We validated the SuperSAGE data with quantitative real-time PCR (qRT-PCR)-based analysis of the expression of three candidate genes. We further investigated the flowering patterns of 1938 D. rotundata accessions representing diverse geographical origins over two consecutive years. Over 85% of accessions were either male or non-flowering, less than 15% were female, while monoecious plants were rare. Intensity of flowering varied between male and female plants, with the former flowering more abundantly than the latter. Candidate genes identified in this study can be targeted for further validation and to induce regular flowering in poor to non-flowering cultivars. Findings of the study provide important inputs for further studies aiming to overcome the challenge of flowering in yams and to improve efficiency of yam breeding.
| S-EPMC6756524 | biostudies-literature
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.
| S-EPMC7934620 | biostudies-literature
Project description:White Guinea yam is mostly a dioecious outcrossing crop with male and female flowers produced on distinct plants. Fertile parents produce high fruit set in an open pollination polycross block, which is a cost-effective and convenient way of generating variability in yam breeding. However, the pollen parent of progeny from polycross mating is usually unknown. This study aimed to determine paternity in white Guinea yam half-sib progenies from polycross mating design. A total of 394 half-sib progenies from random open pollination involving nine female and three male parents was genotyped with 6602 SNP markers from DArTSeq platform to recover full pedigree. A higher proportion of expected heterozygosity, allelic richness, and evenness were observed in the half-sib progenies. A complete pedigree was established for all progenies from two families (TDr1685 and TDr1688) with 100% accuracy, while in the remaining families, paternity was assigned successfully only for 56 to 98% of the progenies. Our results indicated unequal paternal contribution under natural open pollination in yam, suggesting unequal pollen migrations or gene flow among the crossing parents. A total of 3.8% of progenies lacking paternal identity due to foreign pollen contamination outside the polycross block was observed. This study established the efficient determination of parental reconstruction and allelic contributions in the white Guinea yam half-sib progenies generated from open pollination polycross using SNP markers. Findings are useful for parental reconstruction, accurate dissection of the genetic effects, and selection in white Guinea yam breeding program utilizing polycross mating design.
| S-EPMC7238154 | biostudies-literature
Project description:Quantifying selection gains enables a more targeted assessment of breeding program effectiveness, highlighting opportunities for strategic improvement and optimized genetic advancement in white Guinea Yam. This study assessed genetic parameters and gain for key traits in a white Guinea yam (D. rotundata) breeding population. A total of 81 genotypes were evaluated for two seasons using a 9 × 9 lattice design with three replicates. Data was collected on yam mosaic virus disease severity, tuber yield and tuber dry content for genetic analysis. Broad sense heritability was generally high (> 60) for most of the traits. At the same time, the corresponding genetic advance as a percentage of the mean was exceptionally high (30.28-93.96%) for tuber yield, tuber flesh oxidation, average tuber weight and number of tubers per plant, suggesting additive genetic effects. A multi-trait selection index of the 5% highest performing genotypes revealed positive genetic gain for plant vigour, tuber length, and width, tuber weight per plant, average tuber weight and fresh tuber yield. The genetic gain was, however, negative for tuber dry matter content compared to the check varieties, necessitating a modification of the current breeding scheme such that post-harvest food quality is not sacrificed for tuber yield. Ranking of the breeding lines based on the multi-trait selection index identified four lines (TDr1700004_014, TDr1700004_113, TDr1700001_112 and TDr1700002_090) with high genetic merits for all the economic traits. These lines can be used as potential trait progenitors and evaluated further for possible release as new varieties. Our results decipher the genetic control and provide an overview of the performance of the breeding program for key traits in white Guinea yam.Supplementary informationThe online version contains supplementary material available at 10.1007/s10681-025-03467-x.
| S-EPMC11802673 | biostudies-literature