scholarly journals Comprehensive analysis and genome-wide association studies of biomass, chlorophyll, seed and salinity tolerance related traits in rice highlight genetic hotspots for crop improvement

2020 ◽  
Author(s):  
Md Nafis Ul Alam ◽  
G.M. Nurnabi Azad Jewel ◽  
Tomalika Azim ◽  
Zeba I. Seraj
Keyword(s):  
Candidate Genes ◽  
Sequence Data ◽  
Expression Profiles ◽  
Association Studies ◽  
Crop Improvement ◽  
Gene Expression Profiles ◽  
Fixed Effect Model ◽  
Specific Gene ◽  
Genome Wide Association Studies ◽  
Multiple Trait

AbstractFarmland is on the decline and worldwide food security is at risk. Rice is the staple of choice for over half the Earth’s people. To sustain current demands and ascertain a food secure future, substandard farmland affected by abiotic stresses must be utilized. For rapid crop improvement, a broader understanding of polygenic traits like stress tolerance and crop yield is indispensable. To this end, the hidden diversity of resilient and neglected wild varieties must be traced back to their genetic roots. In this study, we separately assayed 15 phenotypes in a panel of 176 diverse accessions predominantly comprised of local landraces from Bangladesh. We compiled high resolution sequence data for these accessions. We collectively studied the ties between the observed phenotypic differences and the examined additive genetic effects underlying these variations. We applied a sophisticated fixed effect model to associate phenotypes with genotypes on a genomic scale. Discovered QTLs were mapped to known genes. Candidate genes were sorted by tissue specific gene expression profiles and protein level consequence of existing polymorphisms. Our explorations yielded 17 QTLs related to various traits in multiple trait classes. 12 identified QTLs were equivalent to findings from previous studies. Integrative analysis assumes novel functionality for 21 candidate genes on multiple evidence levels. These findings will usher novel avenues for the bioengineering of high yielding crops of the future fortified with genetic defenses against abiotic stressors.

scholarly journals Novel QTLs for salinity tolerance revealed by genome-wide association studies of biomass, chlorophyll and tissue ion content in 176 rice landraces from Bangladesh

PLoS ONE ◽  
2021 ◽  
Vol 16 (11) ◽  
pp. e0259456
Author(s):  
Md Nafis Ul Alam ◽  
G. M. Nurnabi Azad Jewel ◽  
Tomalika Azim ◽  
Zeba I. Seraj
Keyword(s):  
Sequence Data ◽  
Association Studies ◽  
Crop Improvement ◽  
Fixed Effect Model ◽  
Genome Wide Association Studies ◽  
Multiple Trait ◽  
Phenotypic Differences ◽  
Rice Landraces ◽  
Genomic Scale ◽  
Additive Genetic Effects

Farmland is on the decline and worldwide food security is at risk. Rice is the staple of choice for over half the Earth’s people. To sustain current demands and ascertain a food secure future, substandard farmland affected by abiotic stresses must be utilized. For rapid crop improvement, a broader understanding of polygenic traits like stress tolerance and crop yield is indispensable. To this end, the hidden diversity of resilient and neglected wild varieties must be traced back to their genetic roots. In this study, we separately assayed 11 phenotypes in a panel of 176 diverse accessions predominantly comprised of local landraces from Bangladesh. We compiled high resolution sequence data for these accessions. We collectively studied the ties between the observed phenotypic differences and the examined additive genetic effects underlying these variations. We applied a fixed effect model to associate phenotypes with genotypes on a genomic scale. Discovered QTLs were mapped to known genes. Our explorations yielded 13 QTLs related to various traits in multiple trait classes. 10 identified QTLs were equivalent to findings from previous studies. Integrative analysis assumes potential novel functionality for a number of candidate genes. These findings will usher novel avenues for the bioengineering of high yielding crops of the future fortified with genetic defenses against abiotic stressors.

scholarly journals Proteomics as a Potential Tool for Identifying Biomarkers for Host Resistance to Cattle Tick

Proceedings ◽  
2020 ◽  
Vol 36 (1) ◽  
pp. 131
Author(s):  
Ali Raza ◽  
Peter James ◽  
Ala Tabor
Keyword(s):  
Gene Expression ◽  
Host Resistance ◽  
Serum Proteins ◽  
Expression Profiles ◽  
Association Studies ◽  
Gene Expression Profiles ◽  
Economic Losses ◽  
Effective Vaccine ◽  
Cattle Tick ◽  
Genome Wide Association Studies

The cattle tick, Rhiphicephalus microplus, and the diseases it transmits lead to massive economic losses to cattle industries in tropical and subtropical countries. The emergence of widespread resistance to acaricide drugs and the absence of an effective vaccine for tick control had led to genetic selection of host resistance as a method of choice for non-chemical control of cattle tick. Research to identify host genetic markers associated with tick susceptibility or resistance has been limited to the comparison of local breeds in specific geographic regions. Previous studies have also focused on gene expression profiles, localizing cellular and humoral immune responses, and genome-wide association studies (GWAS) to identify functional genetic variants associated with tick resistance/susceptibility. Given the fact that gene expression results and actual dynamics occurring at the protein level often do not correlate due to post-transcriptional, post-translational and degradation regulation, host proteomics may provide reliable biomarkers to assist in selection to support traditional breeding programs. The present study aims to investigate the variation in protein profiles among tick resistant and susceptible cattle following tick infestation. Preliminary findings suggest that different serum proteins exist between tick resistant and susceptible Santa Gertrudis cattle. This research is supported by Meat & Livestock Australia.

scholarly journals TWENTY-FOUR GENES ARE UPREGULATED IN PATIENTS WITH HYPOSPADIAS

2013 ◽  
Vol 16 (2) ◽  
pp. 39-43 ◽  
Author(s):  
R. Karabulut ◽  
Z. Turkyilmaz ◽  
K. Sonmez ◽  
G. Kumas ◽  
Sg. Ergun ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Profiles ◽  
Association Studies ◽  
Gene Expression Profiles ◽  
Ventral Surface ◽  
Genome Wide Association Studies ◽  
Expression Array ◽  
Large Patient ◽  
Expression Studies ◽  
Genome Wide

ABSTRACT Hypospadias is a congenital hypoplasia of the penis, with displacement of the urethral opening along the ventral surface, and has been reported to be one of the most common congenital anomalies, occurring in approximately 1:250 to 1:300 live births. As hypospadias is reported to be an easily diagnosed malformation at the crossroads of genetics and environment, it is important to study the genetic component in order to elucidate its etiology. In this study, the gene expression profiles both in human hypospadias tissues and normal penile tissues were studied by Human Gene Expression Array. Twentyfour genes were found to be upregulated. Among these, ATF3 and CYR61 have been reported previously. Other genes that have not been previously reported were also found to be upregulated: BTG2, CD69, CD9, DUSP1, EGR1, EIF4A1, FOS, FOSB, HBEGF, HNRNPUL1, IER2, JUN, JUNB, KLF2, NR4A1, NR4A2, PTGS2, RGS1, RTN4, SLC25A25, SOCS3 and ZFP36 (p <0.05). Further studies including genome-wide association studies (GWAS) with expression studies in a large patient group will help us for identifiying the candidate gene(s) in the etiology of hypospadias

scholarly journals A conditional multi-trait sequence GWAS discovers pleiotropic candidate genes and variants for sheep wool, skin wrinkle and breech cover traits

2021 ◽  
Vol 53 (1) ◽  
Author(s):  
Sunduimijid Bolormaa ◽  
Andrew A. Swan ◽  
Paul Stothard ◽  
Majid Khansefid ◽  
Nasir Moghaddar ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Genome Sequence ◽  
Sequence Data ◽  
Association Studies ◽  
Whole Genome Sequence ◽  
Genome Wide Association Studies ◽  
Whole Genome ◽  
Merino Wool ◽  
Causal Variants ◽  
Wool Proteins

Abstract Background Imputation to whole-genome sequence is now possible in large sheep populations. It is therefore of interest to use this data in genome-wide association studies (GWAS) to investigate putative causal variants and genes that underpin economically important traits. Merino wool is globally sought after for luxury fabrics, but some key wool quality attributes are unfavourably correlated with the characteristic skin wrinkle of Merinos. In turn, skin wrinkle is strongly linked to susceptibility to “fly strike” (Cutaneous myiasis), which is a major welfare issue. Here, we use whole-genome sequence data in a multi-trait GWAS to identify pleiotropic putative causal variants and genes associated with changes in key wool traits and skin wrinkle. Results A stepwise conditional multi-trait GWAS (CM-GWAS) identified putative causal variants and related genes from 178 independent quantitative trait loci (QTL) of 16 wool and skin wrinkle traits, measured on up to 7218 Merino sheep with 31 million imputed whole-genome sequence (WGS) genotypes. Novel candidate gene findings included the MAT1A gene that encodes an enzyme involved in the sulphur metabolism pathway critical to production of wool proteins, and the ESRP1 gene. We also discovered a significant wrinkle variant upstream of the HAS2 gene, which in dogs is associated with the exaggerated skin folds in the Shar-Pei breed. Conclusions The wool and skin wrinkle traits studied here appear to be highly polygenic with many putative candidate variants showing considerable pleiotropy. Our CM-GWAS identified many highly plausible candidate genes for wool traits as well as breech wrinkle and breech area wool cover.

scholarly journals cageminer: an R/Bioconductor package to prioritize candidate genes by integrating GWAS and gene coexpression networks

2021 ◽  
Author(s):  
Fabricio Almeida-Silva ◽  
Thiago M. Venancio
Keyword(s):  
Candidate Genes ◽  
Expression Profiles ◽  
Association Studies ◽  
Real Data ◽  
R Package ◽  
Genome Wide Association Studies ◽  
High Confidence ◽  
Data Set ◽  
Gene Coexpression ◽  
Coexpression Networks

Summary: Although genome-wide association studies (GWAS) identify variants associated with traits of interest, they often fail in identifying causative genes underlying a given phenotype. Integrating GWAS and gene coexpression networks can help prioritize high-confidence candidate genes, as the expression profiles of trait-associated genes can be used to mine novel candidates. Here, we present cageminer, the first R package to prioritize candidate genes through the integration of GWAS and coexpression networks. Genes are considered high-confidence candidates if they pass all three filtering criteria implemented in cageminer, namely physical proximity to SNPs, coexpression with known trait-associated genes, and significant changes in expression levels in conditions of interest. Prioritized candidates can also be scored and ranked to select targets for experimental validation. By applying cageminer to a real data set, we demonstrate that it can effectively prioritize candidates, leading to >99% reductions in candidate gene lists. Availability and implementation: The package is available at Bioconductor (http://bioconductor.org/packages/cageminer).

scholarly journals Whole-Genome Sequencing of the NARO World Rice Core Collection (WRC) as the Basis for Diversity and Association Studies

2020 ◽  
Vol 61 (5) ◽  
pp. 922-932 ◽  
Author(s):  
N Tanaka ◽  
M Shenton ◽  
Y Kawahara ◽  
M Kumagai ◽  
H Sakai ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Core Collection ◽  
Sequence Data ◽  
Association Studies ◽  
Crop Improvement ◽  
Heading Date ◽  
Principal Component ◽  
Genome Wide Association Studies ◽  
Whole Genome ◽  
Population Structure Analysis

Abstract Genebanks provide access to diverse materials for crop improvement. To utilize and evaluate them effectively, core collections, such as the World Rice Core Collection (WRC) in the Genebank at the National Agriculture and Food Research Organization, have been developed. Because the WRC consists of 69 accessions with a high degree of genetic diversity, it has been used for &gt;300 projects. To allow deeper investigation of existing WRC data and to further promote research using Genebank rice accessions, we performed whole-genome resequencing of these 69 accessions, examining their sequence variation by mapping against the Oryza sativa ssp. japonica Nipponbare genome. We obtained a total of 2,805,329 single nucleotide polymorphisms (SNPs) and 357,639 insertion–deletions. Based on the principal component analysis and population structure analysis of these data, the WRC can be classified into three major groups. We applied TASUKE, a multiple genome browser to visualize the different WRC genome sequences, and classified haplotype groups of genes affecting seed characteristics and heading date. TASUKE thus provides access to WRC genotypes as a tool for reverse genetics. We examined the suitability of the compact WRC population for genome-wide association studies (GWASs). Heading date, affected by a large number of quantitative trait loci (QTLs), was not associated with known genes, but several seed-related phenotypes were associated with known genes. Thus, for QTLs of strong effect, the compact WRC performed well in GWAS. This information enables us to understand genetic diversity in 37,000 rice accessions maintained in the Genebank and to find genes associated with different phenotypes. The sequence data have been deposited in DNA Data Bank of Japan Sequence Read Archive (DRA) (Supplementary Table S1).

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