scholarly journals Genome-Wide Superior Alleles, Haplotypes and Candidate Genes Associated With Tolerance on Sodic-Dispersive Soils in Wheat (Triticum Aestivum L.)

2021 ◽  
Author(s):  
Darshan Lal Sharma ◽  
Roopali Bhoite ◽  
Karyn Reeves ◽  
Kerrie Forrest ◽  
Rosemary Smith ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Metal Ion ◽  
Stem Elongation ◽  
Wheat Yield ◽  
Ion Concentration ◽  
Yield Potential ◽  
Multiple Traits ◽  
Phenotypic Data ◽  
Genome Wide ◽  
Dispersive Soils

Abstract Sodic-dispersive soils have multiple subsoil constraints including poor soil structure, alkaline pH and subsoil toxic elemental ion concentration, affecting growth and development in wheat. Tolerance is required at all developmental stages to enhance wheat yield potential on such soils. An in-depth investigation of genome-wide associations was conducted using a field phenotypic data of 206 diverse Focused Identification of Germplasm Strategy (FIGS) wheat lines for two consecutive years from different sodic and non-sodic plots and the exome targeted genotyping by sequencing (tGBS) assay. A total of 39 quantitative trait SNPs (QTSs), including 18 haplotypes were identified on chromosome 1A, 1B, 1D, 2A, 2B, 2D, 3A, 3B, 5A, 5D, 6B, 7A, 7B, 7D for yield and yield-components tolerance. Among these, three QTSs had common associations for multiple traits, indicating pleiotropism and four QTSs had close associations for multiple traits, within 32.38 Mb. The overlapping metal ion binding (Mn, Ca, Zn and Al) and photosynthesis genes, and transcription factors (PHD-, Dof-, HTH myb-, BHLH-, PDZ_6-domain) identified are known to be highly regulated during germination, maximum stem elongation, anthesis, and grain development stages. The homozygous/biallelic SNPs having allele frequency above 30% were identified for yield and crop establishment/plants m-2. These SNPs correspond to HTH myb-type and BHLH transcription factors, brassinosteroid signaling pathway, kinase activity, ATP and chitin binding activity. These resources are valuable in haplotype-based breeding and genome editing to improve yield potential on sodic-dispersive soils.

scholarly journals Genome-wide superior alleles, haplotypes and candidate genes associated with tolerance on sodic-dispersive soils in wheat (Triticum aestivum L.)

2022 ◽  
Author(s):  
Darshan Lal Sharma ◽  
Roopali Bhoite ◽  
Karyn Reeves ◽  
Kerrie Forrest ◽  
Rosemary Smith ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Metal Ion ◽  
Stem Elongation ◽  
Wheat Yield ◽  
Yield Potential ◽  
Ion Binding ◽  
Metal Ion Binding ◽  
Multiple Traits ◽  
Genome Wide ◽  
Dispersive Soils

Abstract Key message The pleiotropic SNPs/haplotypes, overlapping genes (metal ion binding, photosynthesis), and homozygous/biallelic SNPs and transcription factors (HTH myb-type and BHLH) hold great potential for improving wheat yield potential on sodic-dispersive soils. Abstract Sodic-dispersive soils have multiple subsoil constraints including poor soil structure, alkaline pH and subsoil toxic elemental ion concentration, affecting growth and development in wheat. Tolerance is required at all developmental stages to enhance wheat yield potential on such soils. An in-depth investigation of genome-wide associations was conducted using a field phenotypic data of 206 diverse Focused Identification of Germplasm Strategy (FIGS) wheat lines for two consecutive years from different sodic and non-sodic plots and the exome targeted genotyping by sequencing (tGBS) assay. A total of 39 quantitative trait SNPs (QTSs), including 18 haplotypes were identified on chromosome 1A, 1B, 1D, 2A, 2B, 2D, 3A, 3B, 5A, 5D, 6B, 7A, 7B, 7D for yield and yield-components tolerance. Among these, three QTSs had common associations for multiple traits, indicating pleiotropism and four QTSs had close associations for multiple traits, within 32.38 Mb. The overlapping metal ion binding (Mn, Ca, Zn and Al) and photosynthesis genes and transcription factors (PHD-, Dof-, HTH myb-, BHLH-, PDZ_6-domain) identified are known to be highly regulated during germination, maximum stem elongation, anthesis, and grain development stages. The homozygous/biallelic SNPs having allele frequency above 30% were identified for yield and crop establishment/plants m−2. These SNPs correspond to HTH myb-type and BHLH transcription factors, brassinosteroid signalling pathway, kinase activity, ATP and chitin binding activity. These resources are valuable in haplotype-based breeding and genome editing to improve yield potential on sodic-dispersive soils.

scholarly journals Genomic Analysis of Vavilov’s Historic Chickpea Landraces Reveals Footprints of Environmental and Human Selection

2020 ◽  
Vol 21 (11) ◽  
pp. 3952 ◽  
Author(s):  
Alena Sokolkova ◽  
Sergey V. Bulyntsev ◽  
Peter L. Chang ◽  
Noelia Carrasquilla-Garcia ◽  
Anna A. Igolkina ◽  
...  
Keyword(s):  
Association Studies ◽  
Genomic Analysis ◽  
Phenotypic Traits ◽  
Genome Wide Association Studies ◽  
Nucleotide Polymorphisms ◽  
Multiple Traits ◽  
Phenotypic Data ◽  
Genome Wide ◽  
Bioclimatic Variables ◽  
Modern Breeding

A defining challenge of the 21st century is meeting the nutritional demands of the growing human population, under a scenario of limited land and water resources and under the specter of climate change. The Vavilov seed bank contains numerous landraces collected nearly a hundred years ago, and thus may contain ‘genetic gems’ with the potential to enhance modern breeding efforts. Here, we analyze 407 landraces, sampled from major historic centers of chickpea cultivation and secondary diversification. Genome-Wide Association Studies (GWAS) conducted on both phenotypic traits and bioclimatic variables at landraces sampling sites as extended phenotypes resulted in 84 GWAS hits associated to various regions. The novel haploblock-based test identified haploblocks enriched for single nucleotide polymorphisms (SNPs) associated with phenotypes and bioclimatic variables. Subsequent bi-clustering of traits sharing enriched haploblocks underscored both non-random distribution of SNPs among several haploblocks and their association with multiple traits. We hypothesize that these clusters of pleiotropic SNPs represent co-adapted genetic complexes to a range of environmental conditions that chickpea experienced during domestication and subsequent geographic radiation. Linking genetic variation to phenotypic data and a wealth of historic information preserved in historic seed banks are the keys for genome-based and environment-informed breeding intensification.

PAPER PRESENTED AT INTERNATIONAL WORKSHOP ON INCREASING WHEAT YIELD POTENTIAL, CIMMYT, OBREGON, MEXICO, 20–24 MARCH 2006 Genetic progress in yield potential in wheat: recent advances and future prospects

2007 ◽  
Vol 145 (1) ◽  
pp. 17-29 ◽  
Author(s):  
M. J. FOULKES ◽  
J. W. SNAPE ◽  
V. J. SHEARMAN ◽  
M. P. REYNOLDS ◽  
O. GAJU ◽  
...  
Keyword(s):  
Winter Wheat ◽  
Stem Elongation ◽  
Wheat Yield ◽  
Water Soluble ◽  
Physiological Traits ◽  
Yield Potential ◽  
Future Prospects ◽  
Genetic Gains ◽  
Recent Advances ◽  
The Uk

Knowledge of the changes in physiological traits associated with genetic gains in yield potential is essential to improve understanding of yield-limiting factors and to inform future breeding strategies. Recent advances in genetic yield potential and associated physiological changes in wheat (Triticum aestivum L.) are reviewed. Genetic gains in yield potential worldwide have been both positively correlated with harvest index (HI) and above-ground dry matter (AGDM), with more frequent reports of yield progress associated with biomass since about 1990. It is concluded that an important aim of future breeding will be the increase of biomass production while maintaining the present values of HI. In winter wheat recent biomass progress has been positively associated with pre-anthesis radiation-use efficiency (RUE) and water-soluble carbohydrate (WSC) content of stems at anthesis. Present results in two doubled-haploid (DH) populations show a positive linear relationship between stem WSC and grain yield in the UK environment. Results from various investigations worldwide in recent years have demonstrated that biomass increases have been associated with particular introductions of alien genes into wheat germplasm, e.g. the 1BL.1RS wheat-rye translocation and the 7DL.7Ag wheat-Agropyron elongatum translocation. Present results confirm a positive effect of 1BL.1RS on harvest biomass in two DH populations in the UK. The future prospects for identifying physiological traits to raise yield potential are considered with particular reference to winter wheat grown in northwestern Europe. It is proposed that optimized rooting traits, an extended stem-elongation phase, greater RUE, greater stem WSC storage and optimized ear morphology will be important for breeding progress in yield potential in future years.

scholarly journals How Well Can Multivariate and Univariate GWAS Distinguish Between True and Spurious Pleiotropy?

2021 ◽  
Vol 11 ◽  
Author(s):  
Samuel B. Fernandes ◽  
Kevin S. Zhang ◽  
Tiffany M. Jamann ◽  
Alexander E. Lipka
Keyword(s):  
Linkage Disequilibrium ◽  
Detection Rate ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Multiple Traits ◽  
Phenotypic Data ◽  
Future Studies ◽  
Genome Wide ◽  
Multivariate Gwas ◽  
Candidate Loci

Quantification of the simultaneous contributions of loci to multiple traits, a phenomenon called pleiotropy, is facilitated by the increased availability of high-throughput genotypic and phenotypic data. To understand the prevalence and nature of pleiotropy, the ability of multivariate and univariate genome-wide association study (GWAS) models to distinguish between pleiotropic and non-pleiotropic loci in linkage disequilibrium (LD) first needs to be evaluated. Therefore, we used publicly available maize and soybean genotypic data to simulate multiple pairs of traits that were either (i) controlled by quantitative trait nucleotides (QTNs) on separate chromosomes, (ii) controlled by QTNs in various degrees of LD with each other, or (iii) controlled by a single pleiotropic QTN. We showed that multivariate GWAS could not distinguish between QTNs in LD and a single pleiotropic QTN. In contrast, a unique QTN detection rate pattern was observed for univariate GWAS whenever the simulated QTNs were in high LD or pleiotropic. Collectively, these results suggest that multivariate and univariate GWAS should both be used to infer whether or not causal mutations underlying peak GWAS associations are pleiotropic. Therefore, we recommend that future studies use a combination of multivariate and univariate GWAS models, as both models could be useful for identifying and narrowing down candidate loci with potential pleiotropic effects for downstream biological experiments.

Use of agro-waste (Musa paradisiaca peels) as a sustainable biosorbent for toxic metal ions removal from contaminated water

2019 ◽  
Author(s):  
Chem Int
Keyword(s):  
Heavy Metal ◽  
Metal Ions ◽  
Contact Time ◽  
Metal Ion ◽  
Equilibrium Concentration ◽  
Ion Concentration ◽  
Contaminated Water ◽  
Musa Paradisiaca ◽  
Percentage Removal ◽  
Adsorbent Dose

A study of removal of heavy metal ions from heavy metal contaminated water using agro-waste was carried out with Musa paradisiaca peels as test adsorbent. The study was carried by adding known quantities of lead (II) ions and cadmium (II) ions each and respectively into specific volume of water and adding specific dose of the test adsorbent into the heavy metal ion solution, and the mixture was agitated for a specific period of time and then the concentration of the metal ion remaining in the solution was determined with Perkin Elmer Atomic absorption spectrophotometer model 2380. The effect of contact time, initial adsorbate concentration, adsorbent dose, pH and temperature were considered. From the effect of contact time results equilibrium concentration was established at 60minutes. The percentage removal of these metal ions studied, were all above 90%. Adsorption and percentage removal of Pb2+ and Cd2+ from their aqueous solutions were affected by change in initial metal ion concentration, adsorbent dose pH and temperature. Adsorption isotherm studies confirmed the adsorption of the metal ions on the test adsorbent with good mathematical fits into Langmuir and Freundlich adsorption isotherms. Regression correlation (R2) values of the isotherm plots are all positive (>0.9), which suggests too, that the adsorption fitted into the isotherms considered.

scholarly journals Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program

Nature ◽  
2021 ◽  
Vol 590 (7845) ◽  
pp. 290-299 ◽  
Author(s):  
Daniel Taliun ◽  
◽  
Daniel N. Harris ◽  
Michael D. Kessler ◽  
Jedidiah Carlson ◽  
...  
Keyword(s):  
Rare Variants ◽  
Sequence Data ◽  
Association Studies ◽  
Genotype Imputation ◽  
Genome Wide Association Studies ◽  
Phenotypic Data ◽  
Treatment And Prevention ◽  
Genome Wide ◽  
Diverse Backgrounds ◽  
Unmapped Reads

AbstractThe Trans-Omics for Precision Medicine (TOPMed) programme seeks to elucidate the genetic architecture and biology of heart, lung, blood and sleep disorders, with the ultimate goal of improving diagnosis, treatment and prevention of these diseases. The initial phases of the programme focused on whole-genome sequencing of individuals with rich phenotypic data and diverse backgrounds. Here we describe the TOPMed goals and design as well as the available resources and early insights obtained from the sequence data. The resources include a variant browser, a genotype imputation server, and genomic and phenotypic data that are available through dbGaP (Database of Genotypes and Phenotypes)1. In the first 53,831 TOPMed samples, we detected more than 400 million single-nucleotide and insertion or deletion variants after alignment with the reference genome. Additional previously undescribed variants were detected through assembly of unmapped reads and customized analysis in highly variable loci. Among the more than 400 million detected variants, 97% have frequencies of less than 1% and 46% are singletons that are present in only one individual (53% among unrelated individuals). These rare variants provide insights into mutational processes and recent human evolutionary history. The extensive catalogue of genetic variation in TOPMed studies provides unique opportunities for exploring the contributions of rare and noncoding sequence variants to phenotypic variation. Furthermore, combining TOPMed haplotypes with modern imputation methods improves the power and reach of genome-wide association studies to include variants down to a frequency of approximately 0.01%.

SUMMARY: PAPERS PRESENTED AT INTERNATIONAL WORKSHOP ON INCREASING WHEAT YIELD POTENTIAL, CIMMYT, OBREGON, MEXICO, 20–24 MARCH 2006 Challenges to international wheat improvement

2007 ◽  
Vol 145 (3) ◽  
pp. 223-227 ◽  
Author(s):  
M. P. REYNOLDS ◽  
P. R. HOBBS ◽  
H. J. BRAUN
Keyword(s):  
Management Practices ◽  
International Workshop ◽  
Green Revolution ◽  
Wheat Yield ◽  
Developed Countries ◽  
Yield Potential ◽  
Agronomic Practices ◽  
Agronomic Management ◽  
Genetically Improved ◽  
New Generation

Wheat is grown on 210 million ha throughout the world producing approximately 600 million tonnes of grain (10 year average; FAO 2005) and providing on average one fifth of the total calorific input of the world's population (FAO 2003). For some regions such as North Africa, Turkey and Central Asia, wheat provides half of total dietary energy intake. Of the cultivated wheat area, half is located in less developed countries where there have been steady increases in productivity since the green revolution, associated with genetic improvements in yield potential, resistance to diseases and adaptation to abiotic stresses (Reynolds & Borlaug 2006a, b) as well as better agronomic practices (Derpsch 2005). Nonetheless, challenges to wheat production are still considerable, especially in the developing world, not only because of increased demand but also because of the increased scarcity of water resources (Rosegrant 1997; WMO 1997), ever more unpredictable climates (Fischer et al. 2002), increased urbanization and loss of good quality land away from agriculture (Hobbs 2007), and decreased public sector investment in agriculture and rural affairs (Falcon & Naylor 2005). To meet demand in a sustainable way, more resources are required to breed a new generation of genetically improved cultivars as well as implement resource-conserving agronomic management practices.

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