Genomic dissection of productivity, lodging, and morpho‐physiological traits in Eragrostis tef under contrasting water availabilities

Plants People Planet, Journal Year: 2024, Volume and Issue: unknown

Published: March 25, 2024

Societal Impact Statement Underutilized species (also known as orphan crops) present opportunities to increase crop diversity and food security. Such crops lack modern genetic tools knowledge facilitate efficient breeding approaches. A wide collection of tef ( Eragrostis (Zucc.) Trotter) genotypes was used identify genomic regions associated with productivity, lodging, morpho‐physiological traits under contrasting water availabilities. The obtained results are expected enhance improve productivity traditional cropping systems, thus improving farmers' livelihood Summary Tef E. is an allotetraploid (2n = 4x 40) C4 cereal crop, endemic Ethiopia mainly cultivated in the Horn Africa. characterized by high grain feed nutritional qualities resilience abiotic biotic stresses; thus, it holds great potential sustain nutrition security Africa other parts world. objective this study responses regimes, a basis for future improvement. panel genotyped 28,837 single nucleotide polymorphisms (SNPs) phenotyped along two seasons (2020 2021) well‐watered water‐limited treatments. genome‐wide association performed key breeding. total 107 SNPs were one or more studied traits, resulting 138 marker–trait associations (MTAs) detected both Of these, 22 than trait, showing either multiple trait (pleiotropic) environment both. particularly strong found between yield, time heading. These findings open new avenues further research on physiological mechanisms underlying major tef, well marker‐assisted drought‐resilient cultivars.

Language: Английский

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gosset: An R package for analysis and synthesis of ranking data in agricultural experimentation

SoftwareX, Journal Year: 2023, Volume and Issue: 22, P. 101402 - 101402

Published: May 1, 2023

To derive insights from data, researchers working on agricultural experiments need appropriate data management and analysis tools. ensure that workflows are reproducible can be applied a routine basis, programmatic tools needed. Such increasingly necessary for rank-based type of is generated in on-farm experimentation synthesis exercises, among others. address this need, we developed the R package gosset, which provides functionality models. The gosset facilitates preparation, modeling results presentation stages. It introduces novel functions not available existing packages analyzing ranking data. This paper demonstrates using case study decentralized trial common bean (Phaseolus vulgaris L.) varieties Nicaragua.

Language: Английский

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The role of omics in improving the orphan crop tef

Trends in Genetics, Journal Year: 2024, Volume and Issue: 40(5), P. 449 - 461

Published: April 9, 2024

Tef research has little benefited from omics due to neglect of the crop by global scientific community. However, few utilized tools showed promising results. Chromosome-scale assembly genome reveals evolution tef. The whole-genome sequencing drought-resurrecting Eragrostis nindensis and desiccation-sensitive curvula shows genes that play key roles in drought responses. A studies using have revealed differentially expressed genes, proteins, metabolites tef plants exposed drought. Molecular markers deciphered diversity germplasm collected diverse agroecologies Ethiopia. application targeting induced local lesions genomes resulted mutant lines with a semidwarf stature, which were later bred locally adapted high-yielding varieties. Genome editing 'Green Revolution' lodging-tolerant plant. or teff [Eragrostis (Zucc.) Trotter] is cereal indigenous Horn Africa, where it staple food for large population. popularity arises its resilience environmental stresses nutritional value. For many years, been considered an orphan crop, but recent initiatives across globe are helping unravel undisclosed potential. Advanced techniques directed toward exploration tef's aim increasing productivity. In this review, we report on most advances brought into spotlight international research. organism four sets chromosomes resulting hybridization two different species. systematic study similarities differences gene content structure whole genomes. group plant-specific TFs important plant growth, development, response biotic abiotic stresses. how cells control activity without changing DNA sequence. intergenic regions contribute biological processes. short phrase typically used represent individual components ontologies, unify representation product attributes all total amount contained one copy single complete genome. identifies associations between genetic called SNPs phenotype interest traits. field biology focusing structure, function, evolution, mapping, duplicated derived parental species related ancestry. mineral nutrient trace elemental composition identification quantification small molecules present systems. microbial communities suite genomic directly access their content. small, single-stranded, noncoding RNA containing 21–23 nucleotides. integrating analysis multiple datasets. evolve common ancestral speciation usually retained similar function collection sequences contains shared individuals (core genome) also able display sequence information unique each (variable genome). overall characteristics traits can see (its phenotype) fits know about (genomics) proteins (proteomics). diagram represents evolutionary relationships among organisms. plastid, extensively phylogenetic analyses. protein properties obtain view cellular processes at level. region associated specific trait varies within incorporate essentially permanent set recombination events inherited more inbred strains. type component copies pastes itself various locations converting back DNA. synonym, microsatellites; variable numbers tandem repeats constitute repetitive regions. methods transcriptomes cells. reverse-genetics approach traditional chemical mutagenesis followed high-throughput facilitate screening point mutations. bind transcription. transcripts, both coding noncoding, given entity such as cell, tissue, organism. TF family. binds

Language: Английский

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Genome-wide association analysis of tan spot disease resistance in durum wheat accessions from Tunisia

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

Published: Oct. 25, 2023

Background: Tunisia harbors a rich collection of unexploited durum wheat landraces ( Triticum ssp. ) that have been gradually replaced by elite cultivars since the 1970s. These represent an important potential source for broadening genetic background and introgression novel genes key traits, including disease resistance, into these cultivars. Methods: In this study, single nucleotide polymorphism (SNP) markers were used to investigate diversity population structure core 235 accessions consisting mainly landraces. The high phenotypic fungal pathogen Pyrenophora tritici-repentis (cause tan spot wheat) in allowed assessment resistance at adult plant stage under field conditions over three cropping seasons. A genome-wide association study (GWAS) was performed using 90k SNP array. Results: Bayesian analysis with 9191 polymorphic classified two groups, where groups 1 2 included 49.79% 31.49% accessions, respectively, while remaining 18.72% admixtures. Principal coordinate analysis, unweighted pair group method arithmetic mean neighbor-joining clustered five groups. Analysis molecular variance indicated 76% variation among individuals 23% between individuals. Genome-wide analyses identified 26 SNPs associated explained 8.1% 20.2% variation. located on chromosomes 1B (1 SNP), 2B (4 SNPs), 3A (2 3B 4A 4B 5A 5B 6A (5 6B 7B SNP). Four markers, one each 1B, 5A, 5B, coincided previously reported either or closely related SNPs. Eight as possible sources could be introgressed Conclusion: results highlighted significance 2B, genomic regions resistance.

Language: Английский

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Genomic, climatic, and cultural diversity of maize landraces from the Himalayan Kingdom of Bhutan

Plants People Planet, Journal Year: 2024, Volume and Issue: 6(4), P. 965 - 978

Published: May 1, 2024

Societal Impact Statement Bhutan is an ancient kingdom in the Himalayan range and one of most rugged, geodiverse, mountainous agricultural countries world. Historically secluded geographically isolated, a hotspot for agrobiodiversity where small‐scale agriculture supports livelihoods large share resident population. Here, Bhutanese maize explored to unlock its adaptation potential using genomics participatory variety selection combination with climate research. We show that traditional farmers maintain wealth diversity may support sustainable intensification cropping Himalayas beyond. Summary Bhutan, enshrouded Himalayas, hosts largely untapped harness genetic variation useful local climates user needs. we genotyped‐by‐sequencing 351 pooled samples ( Zea mays L.) landraces, entire collection National Gene Bank, comparing their genomic from other range. reconstructed historical projected climates, identifying areas future maladaptation. then run common garden experiment involving smallholder evaluation landraces' performance, aiming at identification quantitative trait nucleotides (QTNs) contributing adaptation, farmers' choice. found unique range, locus on Chromosome 5 differentiation three distinct clusters. portion current can be associated landscape cultivation southwest country negatively impacted by climates. also contribute improvement. A genome‐wide association study identified 117 QTNs climatic agronomic preferences. Our results landraces are source adaptation. integration genomics, science, methods speed up factors

Language: Английский

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Genomic Loci Associated with Grain Protein and Mineral Nutrients concentrations in Eragrostis tef under Contrasting Water Regimes

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

Published: Aug. 8, 2024

Climate change is becoming a global concern, threating agricultures capacity to meet the food and nutritional requirements of growing population. Underutilized crops present an opportunity address resilience climate deficiencies. Tef stress resilient cereal crop, producing gluten free grain high quality. However, knowledge lacking on tef diversity properties, their interaction with environmental conditions (e.g., water availability) underlying genomic loci. We assessed effect availability nutrient concentrations identify associated A collection 223 genotypes, subset panel 300, were grown in field under well watered limited 2021, phenotyped for protein mineral seed color. genome wide association study was conducted using 28,837 single nucleotide polymorphisms (SNPs) phenotypic data marker trait associations (MTAs). exhibited genetic significant influence environment. Protein most micronutrients more concentrated conditions, whereas macronutrients higher total 59 SNPs one or studied traits, resulting 65 MTAs detected both treatments, providing insights into basis nutrients. Five reflected multiple associations, four detecting same treatments (multiple environment effect), Zn K (pleiotropic effect). In addition, two pairs closely linked effects. While provide greater support integrity these MTAs, pleiotropic locus hints at common mechanism controlling ions. The identified shed new light architecture tefs properties enhance quality alongside drought resilience.

Language: Английский

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Multivariate analysis of phenotypic diversity elite bread wheat (Triticum aestivum L.) genotypes from ICARDA in Ethiopia

Heliyon, Journal Year: 2024, Volume and Issue: 10(16), P. e36062 - e36062

Published: Aug. 1, 2024

Wheat is an important crop for food security, providing a source of protein and energy the growing population in Ethiopia. However, both biotic abiotic factors limit national wheat productivity. The availability genetically diverse genotypes crucial developing new varieties that are high-yielding resilient to stress. Therefore, this field trial aimed assess phenotypic variation relationship among ICARDA-derived bread using multivariate analysis techniques. was conducted at three locations: Enewari, Wogere, Kulumsa alpha lattice design with two replications during main cropping seasons 2022 2023. Phenotypic data on eight agronomic traits severity yellow rust were collected R programming used analysis. Individual combined location variance showed significant differences (p ≤ 0.05) most studied traits. highest heritability genetic advance as percentage mean observed days heading (90.8, 21.29), plant height (72.4, 28.6), seeds per spike (61.7, 28), thousand kernel weight (61.9, 12), area under disease progress curve (67, 39.8), suggesting predominance additive gene action. Grain yield strong positive correlation maturity, height, length, spikelet spike, each location. Dendrogram phylogenetic tree methods group into four distinct clusters. Cluster II III had greatest inter-cluster distance, indicating higher diversity their genotypes. This study identified candidate superior performance, high grain traits, robust resistance rust, making them valuable current future breeding programs. Additionally, comprehensive dataset produced could facilitate identification variations influencing desirable through genome-wide association

Language: Английский

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Evaluation of Spring Season Local and Improved Rice Genotypes on Growth, Yield, and Yield Attributing Characters in Gorkha District, Nepal

Journal La Lifesci, Journal Year: 2024, Volume and Issue: 5(2), P. 109 - 125

Published: April 30, 2024

Rice cultivation faces challenges related to varietal selection, limiting the potential yield of spring rice crops. This study was conducted in Zone Gorkha, Nepal during season 2022 with aim evaluate growth, yield, and attributing characters different genotypes. The hypothesized that significant differences exist among genotypes terms their characters. experiment employed a one-factor randomized complete block design (RCBD) seven genotypes, including local varieties (Hardinath Hybrid 1, Chaite-5, CH 45, Salijudi) pipeline (IR16L1919, IR10N118, IR86515), replicated three times. Results indicated variations response similar growing conditions nutrient availability. Notably, 45 exhibited highest plant height (113.50 cm), while IR16L1619 demonstrated longest panicle length (28.56 cm) number effective tillers (23.10). also displayed leaves (97.27 leaves) leaf area index (8.00). Chaite-5 had flag (33.13 recorded grains per (270.10). Salijudi lowest sterility percentage (7.52 %), thousand grain weight (26.40). Moreover, superior performance (8.19 t/ha), straw (7.12 biological (15.25 t/ha). findings underscored genotype-specific responses environmental conditions, highlighting importance tailored selection for optimal productivity.

Language: Английский

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Characterization of Ancient Cereals Cultivated by Intensive and Organic Procedures for Elements Content

Published: June 7, 2024

According to their nutritional value, ability adapt the various environmental conditions, and versatility, cereals are among most cultivated plants in world. However, ongoing climate changes subject crops important stress that for some varieties leads high production losses. Therefore, selection of species more versatile adaptable different conditions can be important. characteristics not completely known, this is a priority before improve cultivation. The aim study characterize select potential suitable local value.

Language: Английский

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Landrace in situ (on-farm) conservation: European Union achievements

Biodiversity and Conservation, Journal Year: 2024, Volume and Issue: 33(10), P. 2709 - 2738

Published: July 9, 2024

Abstract This paper offers an insight on present status of on-farm conservation landrace diversity in the European Union. The review initially examines types materials that are object conservation, assesses current maintenance and reproduction within farms gardens, explores motivations drive ongoing efforts as a foundation for future enhancement identifies key actors involved their respective roles. Secondarily, it reviews Union policies provisions supporting crop fields, with particular focus regulations pertaining to commercialization seeds. Given availability propagation material remains primary constraint widespread dissemination landraces, also includes achievements constraints could be mitigated. discussion highlights how continue intensify development implementation agro-environmental seed well further collection, documentation, study promotion traditional farmers’ knowledge ̶ associated development, production utilization local products can improve situation. It is hoped model applied useful other regions world.

Language: Английский

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