Genome–Environment Associations, an Innovative Tool for Studying Heritable Evolutionary Adaptation in Orphan Crops and Wild Relatives

Frontiers in Genetics, Journal Year: 2022, Volume and Issue: 13

Published: Aug. 5, 2022

Leveraging innovative tools to speed up prebreeding and discovery of genotypic sources adaptation from landraces, crop wild relatives, orphan crops is a key prerequisite accelerate genetic gain abiotic stress tolerance in annual such as legumes cereals, many which are still species despite advances major row crops. Here, we review novel, interdisciplinary approach combine ecological climate data with evolutionary genomics under the paradigm new field study: genome–environment associations (GEAs). We first exemplify how GEA utilizes situ georeferencing genotypically characterized, gene bank accessions pinpoint genomic signatures natural selection. later discuss necessity update current models predict both regional- local- or micro-habitat–based mechanistic ecophysiological indices cutting-edge GWAS-type association models. Furthermore, account for polygenic adaptation, encourage community start gathering estimated adaptive values (GEAVs) prediction (GP) multi-dimensional machine learning (ML) The latter two should ideally be weighted by de novo GWAS-based estimates optimized scalable marker subset. end envisioning avenues make inferences more robust through merging high-resolution sources, environmental remote sensing summary statistics site frequency spectrum, epigenetic molecular functionality responsible plastic inheritance wild. Ultimately, believe that coupling predictions innovations will help capture hidden adaptations stresses based on germplasm resources assist responses change. “I shall endeavor find out nature’s forces act upon one another, what manner geographic environment exerts its influence animals plants. In short, I must about harmony nature” Alexander von Humboldt— Letter Karl Freiesleben, June 1799 .

Language: Английский

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Genetic Diversity and Population Structure of Sorghum [Sorghum Bicolor (L.) Moench] Accessions as Revealed by Single Nucleotide Polymorphism Markers

Frontiers in Plant Science, Journal Year: 2022, Volume and Issue: 12

Published: Jan. 5, 2022

Ethiopia is the center of origin for sorghum [Sorghum bicolor (L.) Moench], where distinct agro-ecological zones significantly contributed to genetic diversity crops. A large number landrace accessions have been conserved ex situ. Molecular characterization this diverse germplasm can contribute its efficient conservation and utilization in breeding programs. This study aimed investigate Ethiopian using gene-based single nucleotide polymorphism (SNP) markers. In total, 359 individuals representing 24 were genotyped 3,001 SNP The markers had moderately high information content (PIC = 0.24) gene (H 0.29), on average. revealed 48 loci that deviated from Hardy-Weinberg equilibrium with excess heterozygosity 13 presumed be under selection (P < 0.01). analysis molecular variance (AMOVA) determined 35.5% total variation occurred within 64.5% among accessions. Similarly, significant differentiations observed geographic regions peduncle shape-based groups. latter case, bent peduncles higher than those erect peduncles. More alleles are private found eastern region other country, suggesting a good situ status east. Cluster, principal coordinates (PCoA), STRUCTURE analyses accession clusters. Hence, crossbreeding genotypes different clusters evaluating their progenies desirable traits advantageous. exceptionally SB4 SB21 western an intriguing finding study, which merits further investigation.

Language: Английский

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The origins and spread of the opium poppy ( Papaver somniferum L.) revealed by genomics and seed morphometrics

Philosophical Transactions of the Royal Society B Biological Sciences, Journal Year: 2025, Volume and Issue: 380(1926)

Published: May 1, 2025

The opium poppy ( Papaver somniferum L.) is one of the most important plants in human history. It main source opiates used as analgesic medicines or psychotropic drugs, latter related to addiction problems, illegal trafficking and geopolitical issues. Poppyseed also cooking. prehistoric origins, domestication cultivation spread remain unresolved. Traditionally, setigerum has been considered wild ancestor with early presumed have occurred Western Mediterranean region, where autochthonous. Other theories suggest that may introduced by Southwest Asian farmers a weed. To investigate these hypotheses, we analysed 190 accessions from 15 species using genotype-by-sequencing geometric morphometric (GMM) techniques. Our analysis revealed only taxa genetically close can be better described subspecies . domesticated are, however, distinct Additionally, GMM seeds morphological differences between Some phenotypically exhibited intermediate genetic features, suggesting introgression events. Two major populations were found and, some extent, correspond seed form. These two reflect recent attempts breed varieties rich opiates, opposed for poppyseed production. This study supports idea began Mediterranean, progenitor, although are likely feral forms, which confound studies. article part theme issue ‘Unravelling domestication: multi-disciplinary perspectives on non-human relationships past, present future’.

Language: Английский

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Exploring the correlation between salt tolerance and yield: research advances and perspectives for salt-tolerant forage sorghum selection and genetic improvement

Planta, Journal Year: 2022, Volume and Issue: 255(3)

Published: Feb. 21, 2022

Some salt stress response mechanisms can translate into sorghum forage yield and thus act as targets for genetic improvement. Sorghum is a drought-tolerant cereal that widely grown in the vast Africa's arid semi-arid areas. Apart from drought, salinity major abiotic factor that, addition to natural causes, has been exacerbated by increased poor anthropological activities. The importance of crop saline areas yet be fully realized. Despite intraspecific variation tolerance, generally moderately salt-tolerant, its productivity soils remarkably limited. This due difficulty replicating optimal field conditions great heterogeneity distribution soil. As promising fodder areas, classic phenotype-based selection methods integrated with modern -omics breeding programs simultaneously address tolerance production. To enable future manipulation, selection, improvement high here, we explore potential positive correlations between reliable indices performance under at phenotypic genotypic level. We then role incorporating these linked traits propose mechanism studies.

Language: Английский

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Multi‐locus genome‐wide association study reveal genomic regions underlying root system architecture traits in Ethiopian sorghum germplasm

The Plant Genome, Journal Year: 2024, Volume and Issue: 17(2)

Published: Feb. 15, 2024

Abstract The identification of genomic regions underlying the root system architecture (RSA) is vital for improving crop abiotic stress tolerance. To improve sorghum ( Sorghum bicolor L. Moench) environmental tolerance, information on genetic variability and linked to RSA traits paramount. aim this study was, therefore, investigate common quantitative trait nucleotides (QTNs) via multiple methodologies identify in a panel 274 Ethiopian accessions. Multi‐locus genome‐wide association was conducted using 265,944 high‐quality single nucleotide polymorphism markers. Considering QTN detected by at least three different methods, total 17 reliable QTNs were found be significantly associated with angle, number, length, dry weight. Four chromosome SBI‐05, followed SBI‐01 SBI‐02 each. Among QTNs, 11 are colocated previously identified loci remaining six genome novel genes. A 118 genes these up‐ down‐streams QTNs. Moreover, five intragenic. These S5_8994835 (number nodal roots), S10_55702393 S1_56872999 (nodal angle), S9_1212069 S5_5667192 (root weight) intragenic Sobic.005G073101 , Sobic.010G198000 Sobic.001G273000 Sobic.009G013600 Sobic.005G054700 respectively. Particularly, responsible plant growth hormone‐induced RSA. may regulate development seedling stage. Further analysis might important explore structure sorghum.

Language: Английский

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Evaluating the Potential of Rhizobacterial Isolates Enhancing Sorghum's Abiotic Stress Tolerance: A Focus on Ethiopian Soil Isolates From Sorghum Root

Journal of Agronomy and Crop Science, Journal Year: 2025, Volume and Issue: 211(3)

Published: April 15, 2025

ABSTRACT Sorghum is an economically important crop for human consumption, animal feed and biomass production. However, its productivity affected by abiotic biotic stresses. Drought one of the major global problems due to alarming climate change. Plant growth‐promoting rhizobacteria (PGPR) help crops improve their resilience survival in water‐scarce environments. Therefore, present study aimed investigate potential rhizobacterial isolates sorghum tolerance drought other stress. The bacterial sample from different soil roots genotype was isolated locations Ethiopia using serial dilution techniques. biochemical properties these were evaluated. PGPR traits analysed under temperatures, pH, salinity Furthermore, isolates' performance evaluated four concentrations PEG (6000): (10%, 15%, 25% 32.6%), which induces osmotic stress reducing water availability, thus mimicking effects sorghum. PCR detection genes associated with stress, such as phosphate solubilisation, nitrogen fixation, ACC (1‐aminocyclopropane‐1‐carboxylate) deaminase phytohormone production performed designed primers. In addition, identification molecular characterisation PGPRs 16S ribosomal RNA (rRNA) gene‐specific Serial techniques resulted 210 isolates. Biochemical analysis revealed that 68 exhibited while 50 showed ability solubilise phosphate. amplification identified involved several isolates, suggesting they have tolerance. Among examined, nifH gene 16 acdS 10 pgg 21 these, Pseudomonas ms22 isolate a high promote growth greenhouse performance. our findings suggest harnessing could pave way environmentally friendly efficient agricultural practices conditions.

Language: Английский

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Genetic dissection of root architecture in Ethiopian sorghum landraces

Theoretical and Applied Genetics, Journal Year: 2023, Volume and Issue: 136(10)

Published: Sept. 16, 2023

Language: Английский

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Genetic diversity, population structure, and selection signature in Ethiopian sorghum [Sorghum bicolor L. (Moench)] germplasm

G3 Genes Genomes Genetics, Journal Year: 2021, Volume and Issue: 11(6)

Published: April 19, 2021

Abstract Ethiopia, the probable center of origin and diversity for sorghum [Sorghum bicolor L. (Moench)] with unique ecogeographic features, possesses a large number landraces that have not been well studied. Increased knowledge this diverse germplasm through large-scale genomic characterization may contribute understanding evolutionary biology, adequate use these valuable resources from origin. In study, we characterized genetic diversity, population structure selection signature in 304 accessions collected growing regions Ethiopia using genotyping-by-sequencing. We identified total 108,107 high-quality single-nucleotide polymorphism (SNPs) markers were evenly distributed across genome. The average gene among was high (He = 0.29). detected relatively low frequency rare alleles (26%), highlighting potential subsequent allele mining studies genome-wide association studies. Although found no evidence differentiation administrative (FST 0.02, P 0.12), cluster analyses showed clear six Ethiopian populations 0.28, 0.01) adapting to different environments. Analysis SNP between groups revealed 40 carrying signatures selection. These harbored candidate genes potentially involved variety biological processes, including abiotic stress tolerance, pathogen defense reproduction. Overall, level untapped improvement remains available patterns consistent divergent on range adaptive characteristics.

Language: Английский

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Validation of sorghum quality control (QC) markers across African breeding lines

The Plant Genome, Journal Year: 2024, Volume and Issue: 17(2)

Published: Feb. 26, 2024

Abstract Sorghum [ bicolor (L.) Moench] is a cereal crop of critical importance in the semi‐arid tropics, particularly Africa where it second only to maize ( Zea mays L.) by area cultivation. The International Crops Research Institute for Semi‐Arid Tropics sorghum breeding program Eastern and Southern largest region develops improved varieties target agro‐ecologies. Varietal purity correct confirmation new crosses are essential integrity efficiency program. We used 49 quality control (QC) kompetitive allele‐specific PCR single nucleotide polymorphism (SNP) markers genotype 716 lines. Note that 46 SNPs were polymorphic with top 10 most informative revealing information content (PIC), minor allele frequency (MAF), observed heterozygosity H o ) 0.37, 0.43, 0.02, respectively, explaining 45% genetic variance within first two principal components (PC). Thirty‐nine highly across 16 Burkina Faso lines, out which revealed average PIC, MAF, 0.36, 0.39, 0.05, respectively. Discriminant analysis done using 30 separated lines into five major clusters, three distinct. Six successfully confirmed hybridization between genotypes IESV240, KARIMTAMA1, F6YQ212, FRAMIDA. A set 10, 20, recommended routine QC applications. Future effort should focus on deployment these programs enhanced gain.

Language: Английский

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Exploring the genetic basis of anthracnose resistance in Ethiopian sorghum through a genome-wide association study

BMC Genomics, Journal Year: 2024, Volume and Issue: 25(1)

Published: July 8, 2024

Abstract Background Sorghum anthracnose is a major disease that hampers the productivity of crop globally. The caused by hemibiotrophic fungal pathogen Colletotrichum sublineola . identification anthracnose-resistant sorghum genotypes, defining resistance loci and underlying genes, their introgression into adapted cultivars are crucial for enhancing productivity. In this study, we conducted field experiments on 358 diverse accessions Ethiopian sorghum. Quantitative to was evaluated at locations characterized heavy natural infestation suitable screening. Results field-based screening identified 53 were resistant across locations, while 213 exhibited variable against local pathotypes. Genome-wide association analysis (GWAS) performed using response scores 329 83,861 single nucleotide polymorphisms (SNPs) generated through genotyping-by-sequencing (GBS). We 38 significantly associated with resistance. Interestingly, subset these harbor genes encoding receptor-like kinases (RLK), nucleotide-binding leucine-rich repeats (NLRs), stress-induced antifungal tyrosine kinase have been previously implicated in A SNP chromosome 4 (S04_66140995) two SNPs 2 (S02_75784037, S02_2031925), localized with-in coding region encode putative kinase, an F-Box protein, Xa21-binding RLK strongly also highly significant associations between three linked (Sobic.002G058400, Sobic.008G156600, Sobic.005G033400) orthologue widely known NLR protein (RPM1), Leucine Rich Repeat family Heavy Metal Associated domain-containing respectively. Other predicted immune Conclusions germplasm collections used present study genetically diverse. They potentially useful, yet undiscovered, alleles This supported novel enriched regulators such as NLRs, LRKs, LRK, proteins. genotypic data available offer valuable resource breeders effectively improve crop. genomic regions candidate can be design markers molecular breeding diseases

Language: Английский

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