YamOmics: A comprehensive data resource on yam multi-omics DOI Creative Commons
Jinding Liu,

Mengda Wang,

Yi Zhao

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Jan. 25, 2024

Abstract Yams (Dioscorea spp.) are a highly important class of horticultural crops, serving as staple food for millions people in Africa and contributing significantly to security. They also widely cultivated East Asia medicinal herbs, bringing substantial economic incomes. Diverse omics data play pivotal role advancing yam research breeding. However, these often scattered, lacking systematic organization analysis, which underscores the need centralized comprehensive management. In view this, we gathered extensive developed Yam Omics Database (YamOmics; https://biotec.njau.edu.cn/yamdb ). The database currently offers vast diverse range data, covering genomic, transcriptomic plastomic from 41 distinct species, along with detailed records genomic variants ∼1000 germplasms, gene expression profiles ∼200 samples. Additionally, features thorough annotations, encompassing aspects like genome synteny, ortholog groups, signaling pathways, families protein interactions. To support basic biology breeding research, it is equipped suite user-friendly online tools, including PCR primer design, CRISPR enrichment kinship analysis tools.

Language: Английский

The Dioscorea Genus (Yam)—An Appraisal of Nutritional and Therapeutic Potentials DOI Creative Commons
Jude Obidiegwu, Jessica B. Lyons, Cynthia Adaku Chilaka

et al.

Foods, Journal Year: 2020, Volume and Issue: 9(9), P. 1304 - 1304

Published: Sept. 16, 2020

The quest for a food secure and safe world has led to continuous effort toward improvements of global health systems. While the developed countries seem have these systems stabilized, some parts still face enormous challenges. Yam (Dioscorea species) is an orphan crop, widely distributed globally; contributed enormously security especially in sub-Saharan Africa because its role providing nutritional benefits income. Additionally, yam non-nutritional components called bioactive compounds, which offer numerous ranging from prevention treatment degenerative diseases. Pharmaceutical application diosgenin dioscorin, among other compounds isolated yam, shown more prospects recently. Despite embedded reports on therapeutic potentials been fragmented diversity within genus much confusion. An overview importance will harness crop meet potential towards combating hunger malnutrition, while improving health. This review makes conscious attempt provide regarding nutritional, compositions diversity. Insights how increase utilization greater impact are elucidated.

Language: Английский

Citations

187

Chromosome evolution and the genetic basis of agronomically important traits in greater yam DOI Creative Commons
Jessen V. Bredeson, Jessica B. Lyons, Ibukun O. Oniyinde

et al.

Nature Communications, Journal Year: 2022, Volume and Issue: 13(1)

Published: April 14, 2022

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

Language: Английский

Citations

65

Beyond a reference genome: pangenomes and population genomics of underutilized and orphan crops for future food and nutrition security DOI
Mark A. Chapman, Yuqi He, Meiliang Zhou

et al.

New Phytologist, Journal Year: 2022, Volume and Issue: 234(5), P. 1583 - 1597

Published: March 22, 2022

Summary Underutilized crops are, by definition, under‐researched compared to staple yet come with traits that may be especially important given climate change and the need feed a globally increasing population. These are often stress‐tolerant, this combined unique beneficial nutritional profiles. Whilst progress is being made generating reference genome sequences, in Tansley Review, we show how only very first step. We advocate going ‘beyond genome’ should priority, as it at stage one can identify specific genes adaptive alleles underpin valuable traits. sum up population genomic pangenomic approaches have led identification of stress‐ disease‐tolerant compare small number examples from underutilized crops. also demonstrate previously benefitted advances many breeding targets well studied This cross‐crop population‐level resequencing could lead an understanding genetic basis level investment crucial for fully value these before they lost.

Language: Английский

Citations

39

Integrating Omics and Gene Editing Tools for Rapid Improvement of Traditional Food Plants for Diversified and Sustainable Food Security DOI Open Access
Ajay Kumar,

Thattantavide Anju,

Sushil Kumar

et al.

International Journal of Molecular Sciences, Journal Year: 2021, Volume and Issue: 22(15), P. 8093 - 8093

Published: July 28, 2021

Indigenous communities across the globe, especially in rural areas, consume locally available plants known as Traditional Food Plants (TFPs) for their nutritional and health-related needs. Recent research shows that many TFPs are highly nutritious they contain health beneficial metabolites, vitamins, mineral elements other nutrients. Excessive reliance on mainstream staple crops has its own disadvantages. food nowadays considered important of future can act supplementary foods burgeoning global population. They also emergency situations such COVID-19 times pandemics. The current situation necessitates alternative sustainable production. To increase cultivation or improve traits TFPs, it is essential to understand molecular basis genes regulate some components resilience biotic abiotic stresses. integrated use modern omics gene editing technologies provide great opportunities better genetic superior nutrient content, climate-resilient adaptation local agroclimatic zones. Recently, realizing importance benefits scientists have shown interest prospection sequencing improvements, mainstreaming. Integrated genomics, transcriptomics, proteomics, metabolomics ionomics successfully used provided a comprehensive understanding gene-protein-metabolite networks. Combined tools led successful several TFPs. This suggests there ample scope improvement In this article, we highlight importance, progress towards valuable by techniques.

Language: Английский

Citations

44

Polyploidy before and after domestication of crop species DOI Creative Commons
Takashi Akagi,

Katharina Jung,

Kanae Masuda

et al.

Current Opinion in Plant Biology, Journal Year: 2022, Volume and Issue: 69, P. 102255 - 102255

Published: July 21, 2022

Recent advances in the genomics of polyploid species answer some long-standing questions about role polyploidy crop species. Here, we summarize current literature to reexamine scenarios which played a both before and after domestication. The prevalence can help explain environmental robustness agroecosystems. This review also clarifies molecular basis agriculturally advantageous traits crops, including yield increments cotton via subfunctionalization, modification separated sexuality selfing persimmon neofunctionalization, transition system nonfunctionalization combined with epistatic interaction between duplicated S-loci. rapid progress genetics is discussed along how this will facilitate functional studies understudied

Language: Английский

Citations

38

Variability and genetic merits of white Guinea yam landraces in Nigeria DOI Creative Commons
Paterne A. Agre, Alex Edemodu, Jude Obidiegwu

et al.

Frontiers in Plant Science, Journal Year: 2023, Volume and Issue: 14

Published: Feb. 6, 2023

Landraces represent a significant gene pool of African cultivated white Guinea yam diversity. They could, therefore, serve as potential donor important traits such resilience to stresses well food quality attributes that may be useful in modern breeding. This study assessed the pattern genetic variability, quantitative trait loci (QTLs), alleles, and merits landraces, which could exploited breeding for more sustainable production Africa.A total 86 landraces representing popular Nigeria alongside 16 elite clones were used this study. The genotyped using 4,819 DArTseq SNP markers profiled key productivity traits.Genetic population structure through admixture hierarchical clustering methods revealed presence three major groups. Genome-wide association scan identified thirteen associated with five traits, suggesting constitute source valuable genes traits. Further dissection their Genomic Prediction Cross Performance (GPCP) allowed identifying several high crossing merit multiple Thirteen genitors develop segregating progenies improve simultaneously desired gains Results provide insights into patterns local diversity can utilized desirable alleles interest Africa.

Language: Английский

Citations

12

Exploiting genetic and genomic resources to enhance productivity and abiotic stress adaptation of underutilized pulses DOI Creative Commons

Sangam L. Dwivedi,

Mark A. Chapman, Michael Abberton

et al.

Frontiers in Genetics, Journal Year: 2023, Volume and Issue: 14

Published: June 16, 2023

Underutilized pulses and their wild relatives are typically stress tolerant seeds packed with protein, fibers, minerals, vitamins, phytochemicals. The consumption of such nutritionally dense legumes together cereal-based food may promote global nutritional security. However, species deficient in a few or several desirable domestication traits thereby reducing agronomic value, requiring further genetic enhancement for developing productive, dense, climate resilient cultivars. This review article considers 13 underutilized focuses on germplasm holdings, diversity, crop-wild-crop gene flow, genome sequencing, syntenic relationships, the potential breeding transgenic manipulation, genetics tolerance traits. Recent progress has shown crop improvement security, example, basis stem determinacy fragrance moth bean rice bean, multiple abiotic horse gram tepary bruchid resistance lima low neurotoxin grass pea, photoperiod induced flowering anthocyanin accumulation adzuki have been investigated. Advances introgression to develop elite stocks pea β-ODAP (neurotoxin compound), Mungbean yellow mosaic India virus black using adaptation common genes from carried out. highlights wider programs introduce locally adapted de-domestication feralization evolution new variants these crops also highlighted.

Language: Английский

Citations

11

Integrated assessment of yam mosaic virus (YMV) resistance in wild-yam (Dioscorea spp.) interspecific cross progenies using field phenotyping, molecular and biotechnological approaches. DOI Creative Commons
Femi Patrick Oyedoyin, Olufisayo Kolade, Paterne A. Agre

et al.

Research Square (Research Square), Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 10, 2025

Abstract Yams (Dioscorea spp.) are important food crops for millions in tropical and subtropical regions. Yield loss due to Yam Mosaic Virus (YMV genus Potyvirus) has been reported have a high level of damage, especially on white Guinea yam (D. rotundata). Crop wild relatives often serve as potential sources alleles that absent many cultivated crop species, howevertheir source new disease resistance plants remains underexplored. Therefore, this study evaluated YMV interspecific hybrids derived from two specieses, Dioscorea abyssinica female parent praehensilis male parent, trait introgression. Sixty-five hybrid genotypes their parents (maternal-TDabwild paternal-TDPr 1018) were planted the field exposed natural infestation. Field phenotyping severity ratings (1- asymptomatic, 2- resistant, 3- moderately 4- susceptible 5- highly susceptible) combined with molecular analyses using three diagnostic SNP markers, Biotechnology tool ELISA, RT-PCR predict, detect quantify susceptibility patterns. Significant variability was observed, exhibiting wide range area under progress curve (AUDPC) values. Genotypes lowest AUDPC values (63) displayed enhanced resistance, while those higher (197–231) more susceptible, reflecting overall impact. The ELISA findings further revealed diverse responses among progenies parents. Two snpDR00160 snpDR00162, favourable resistant GG AA, respectively, allele TT marker snpDR00161 failed amplify across all progenies. Six (TDabp2101007, TDabp2101009, TDabp2101015, TDabp2101021, TDabp2101026, TDabp2101060) together -TDPr demonstrated putative phenotypic, molecular, biotechnological assessments, making them promising candidates breeding programs aimed at developing YMV-resistant cultivars. Word Count: 299

Language: Английский

Citations

0

MOLECULAR AND AGRO-MORPHOLOGICAL EVALUATIONS OF INTERSPECIFIC HYBRIDISATION IN TWO WILD YAMS (Dioscorea spp.) FOR GENETIC IMPROVEMENT. DOI
Femi Patrick Oyedoyin, Odunayo Joseph Olawuyi, Paterne A. Agre

et al.

Ecological Genetics and Genomics, Journal Year: 2025, Volume and Issue: unknown, P. 100345 - 100345

Published: March 1, 2025

Language: Английский

Citations

0

GENETIC VARIABILITY AND MULTI-TRAIT SELECTION FOR SUPERIOR TRAITS IN WILD YAM HYBRIDS DOI
Femi Patrick Oyedoyin, Odunayo Joseph Olawuyi, Paterne A. Agre

et al.

FUDMA Journal of Sciences, Journal Year: 2025, Volume and Issue: 9(3), P. 224 - 232

Published: March 31, 2025

The interspecific breeding of yams (Dioscorea spp.) for superior traits is hindered by the dioecious nature their flowers and low flowering frequency, despite potential wild to improve related cultivated varieties. However, genetic variability these yam species has yet be fully explored. This study investigated heritability estimates multi-trait selection hybrids derived from crosses between two species, Dioscorea abyssinica praehensilis. Field experiment was conducted on 65 using a partially replicated block design. With standard descriptors, data were collected phenotypic traits, including stem length, internode, plant vigour, tuber weight, width, thorniness, surface cracks. Heritability, advance variance components estimated quantify contribution trait variability. Analysis identified significant differences (p=0.00) among high observed in assessed, with weight showing highest genotypic (104%) (127%) variances. Heritability suggested strong length (74%), (67%) hairiness (65%), while shape (7%) width (9%) showed potential. Multi-trait Genotype Ideotype Distance Index (MGIDI) analysis further 8 high-performing hybrid accessions (TDabp2101010, TDabp2101013, TDabp2101030, TDabp2101042, TDabp2101046, TDabp2101050, TDabp2101052, TDabp2101055). These findings demonstrate introgression, thereby paving way development new cultivars providing valuable insights improvement programs.

Language: Английский

Citations

0