scholarly journals Genetic Analysis of Stem Diameter and Water Contents To Improve Sorghum Bioenergy Efficiency

2020 ◽  
Vol 10 (11) ◽  
pp. 3991-4000
Author(s):  
Wenqian Kong ◽  
Huizhe Jin ◽  
Valorie H. Goff ◽  
Susan A. Auckland ◽  
Lisa K. Rainville ◽  
...  
Keyword(s):  
Water Content ◽  
Plant Traits ◽  
Association Studies ◽  
Duplication Event ◽  
Stem Diameter ◽  
Biofuel Production ◽  
Genome Wide Association Studies ◽  
Energy Demands ◽  
Genome Wide ◽  
Genomic Regions

Biofuel made from agricultural products has the potential in contribute to a stable supply of fuel for growing energy demands. Some salient plant traits, such as stem diameter and water content, and their relationship to other important biomass-related traits are so far poorly understood. Here, we performed QTL mapping for three stem diameter and two water content traits in a S. bicolor BTx623 x IS3620c recombinant inbred line population of 399 genotypes, and validated the genomic regions identified using genome-wide association studies (GWAS) in a diversity panel of 354 accessions. The discovery of both co-localized and non-overlapping loci affecting stem diameter traits suggests that stem widths at different heights share some common genetic control, but also have some distinct genetic influences. Co-localizations of stem diameter and water content traits with other biomass traits including plant height, flowering time and the ‘dry’ trait, suggest that their inheritance may be linked functionally (pleiotropy) or physically (linkage disequilibrium). Water content QTL in homeologous regions resulting from an ancient duplication event may have been retained and continue to have related functions for an estimated 96 million years. Integration of QTL and GWAS data advanced knowledge of the genetic basis of stem diameter and water content components in sorghum, which may lead to tools and strategies for either enhancing or suppressing these traits, supporting advances toward improved quality of plant-based biomass for biofuel production.

Genome-Wide Association Studies (GWAS) for Traits Related to Fodder Quality and Biofuel in Sorghum: Progress and Prospects

2021 ◽  
Vol 28 ◽  
Author(s):  
Vinutha Kanuganahalli Somegowda ◽  
Laavanya Rayaprolu ◽  
Abhishek Rathore ◽  
Santosh Pandurang Deshpande ◽  
Rajeev Gupta
Keyword(s):  
Genetic Architecture ◽  
Association Studies ◽  
Current Status ◽  
Genome Wide Association Studies ◽  
Potential Candidate ◽  
Crop Species ◽  
Fodder Quality ◽  
Genome Wide ◽  
Genomic Regions ◽  
Model Crop

: The main focus of this review is to discuss the current status of the use of GWAS for fodder quality and biofuel owing to its similarity of traits. Sorghum is a potential multipurpose crop, popularly cultivated for various uses as food, feed fodder, and biomass for ethanol. Production of a huge quantity of biomass and genetic variation for complex sugars are the main motivation not only to use sorghum as fodder for livestock nutritionists but also a potential candidate for biofuel generation. Few studies have been reported on the knowledge transfer that can be used from the development of biofuel technologies to complement improved fodder quality and vice versa. With recent advances in genotyping technologies, GWAS became one of the primary tools used to identify the genes/genomic regions associated with the phenotype. These modern tools and technologies accelerate the genomic assisted breeding process to enhance the rate of genetic gains. Hence, this mini-review focuses on GWAS studies on genetic architecture and dissection of traits underpinning fodder quality and biofuel traits and their limited comparison with other related model crop species.

scholarly journals Genetics of COPD

2020 ◽  
Vol 82 (1) ◽  
pp. 413-431 ◽  
Author(s):  
Edwin K. Silverman
Keyword(s):  
Association Studies ◽  
Chronic Obstructive ◽  
Genome Wide Association Studies ◽  
Obstructive Pulmonary Disease ◽  
Functional Variants ◽  
Genome Wide ◽  
Antitrypsin Deficiency ◽  
Alpha 1 Antitrypsin Deficiency ◽  
Alpha 1 Antitrypsin ◽  
Genomic Regions

Although chronic obstructive pulmonary disease (COPD) risk is strongly influenced by cigarette smoking, genetic factors are also important determinants of COPD. In addition to Mendelian syndromes such as alpha-1 antitrypsin deficiency, many genomic regions that influence COPD susceptibility have been identified in genome-wide association studies. Similarly, multiple genomic regions associated with COPD-related phenotypes, such as quantitative emphysema measures, have been found. Identifying the functional variants and key genes within these association regions remains a major challenge. However, newly identified COPD susceptibility genes are already providing novel insights into COPD pathogenesis. Network-based approaches that leverage these genetic discoveries have the potential to assist in decoding the complex genetic architecture of COPD.

scholarly journals Gene-centric functional dissection of human genetic variation uncovers regulators of hematopoiesis

2018 ◽  
Author(s):  
Satish K Nandakumar ◽  
Sean K McFarland ◽  
Laura Marlene Mateyka ◽  
Caleb A Lareau ◽  
Jacob C Ulirsch ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Target Genes ◽  
Association Studies ◽  
Human Diseases ◽  
Genome Wide Association Studies ◽  
Loss Of Function ◽  
Genome Wide ◽  
Causal Variants ◽  
Genomic Regions

Genome-wide association studies (GWAS) have identified thousands of variants associated with human diseases and traits. However, the majority of GWAS-implicated variants are in non-coding genomic regions and require in depth follow-up to identify target genes and decipher biological mechanisms. Here, rather than focusing on causal variants, we have undertaken a pooled loss-of-function screen in primary hematopoietic cells to interrogate 389 candidate genes contained in 75 loci associated with red blood cell traits. Using this approach, we identify 77 genes at 38 GWAS loci, with most loci harboring 1-2 candidate genes. Importantly, the hit set was strongly enriched for genes validated through orthogonal genetic approaches. Genes identified by this approach are enriched in relevant biological pathways, allowing regulators of human erythropoiesis and blood disease modifiers to be defined. More generally, this functional screen provides a paradigm for gene-centric follow up of GWAS for a variety of human diseases and traits.

scholarly journals Recessive effects in cancer predisposition exposed by genome-wide and proteome-wide association studies

2020 ◽  
Author(s):  
Nadav Brandes ◽  
Nathan Linial ◽  
Michal Linial
Keyword(s):  
Cancer Risk ◽  
Large Scale ◽  
Association Studies ◽  
Cancer Predisposition ◽  
Small Scale ◽  
Cancer Type ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Cancer Types ◽  
Genomic Regions

AbstractThe characterization of germline genetic variation affecting cancer risk, known as cancer predisposition, is fundamental to preventive and personalized medicine. Current attempts to detect cancer predisposition genomic regions are typically based on small-scale familial studies or genome-wide association studies (GWAS) over dedicated case-control cohorts. In this study, we utilized the UK Biobank as a large-scale prospective cohort to conduct a comprehensive analysis of cancer predisposition using both GWAS and proteome-wide association study (PWAS), a method that highlights genetic associations mediated by functional alterations to protein-coding genes. We discovered 137 unique genomic loci implicated with cancer risk in the white British population across nine cancer types and pan-cancer. While most of these genomic regions are supported by external evidence, our results highlight novel loci as well. We performed a comparative analysis of cancer predisposition between cancer types, finding that most of the implicated regions are cancer-type specific. We further analyzed the role of recessive genetic effects in cancer predisposition. We found that 30 of the 137 cancer regions were recovered only by a recessive model, highlighting the importance of recessive inheritance outside of familial studies. Finally, we show that many of the cancer associations exert substantial cancer risk in the studied cohort, suggesting their clinical relevance.

scholarly journals Genetic stratification of depression by neuroticism: revisiting a diagnostic tradition

2019 ◽  
Vol 50 (15) ◽  
pp. 2526-2535 ◽  
Author(s):  
Mark J. Adams ◽  
David M. Howard ◽  
Michelle Luciano ◽  
Toni-Kim Clarke ◽  
Gail Davies ◽  
...  
Keyword(s):  
Association Studies ◽  
Genetic Correlations ◽  
Genome Wide Association Studies ◽  
Uk Biobank ◽  
Genome Wide ◽  
Artery Disease ◽  
Specific Association ◽  
Genetic Stratification ◽  
Genomic Regions ◽  
Genetic Contributions

AbstractBackgroundMajor depressive disorder and neuroticism (Neu) share a large genetic basis. We sought to determine whether this shared basis could be decomposed to identify genetic factors that are specific to depression.MethodsWe analysed summary statistics from genome-wide association studies (GWAS) of depression (from the Psychiatric Genomics Consortium, 23andMe and UK Biobank) and compared them with GWAS of Neu (from UK Biobank). First, we used a pairwise GWAS analysis to classify variants as associated with only depression, with only Neu or with both. Second, we estimated partial genetic correlations to test whether the depression's genetic link with other phenotypes was explained by shared overlap with Neu.ResultsWe found evidence that most genomic regions (25/37) associated with depression are likely to be shared with Neu. The overlapping common genetic variance of depression and Neu was genetically correlated primarily with psychiatric disorders. We found that the genetic contributions to depression, that were not shared with Neu, were positively correlated with metabolic phenotypes and cardiovascular disease, and negatively correlated with the personality trait conscientiousness. After removing shared genetic overlap with Neu, depression still had a specific association with schizophrenia, bipolar disorder, coronary artery disease and age of first birth. Independent of depression, Neu had specific genetic correlates in ulcerative colitis, pubertal growth, anorexia and education.ConclusionOur findings demonstrate that, while genetic risk factors for depression are largely shared with Neu, there are also non-Neu-related features of depression that may be useful for further patient or phenotypic stratification.

scholarly journals Identification of Loci Controlling the Dwarfism Trait in the White Sailfin Molly (Poecilia latipinna) Using Genome-Wide Association Studies Based on Genotyping-By-Sequencing

Genes ◽  
2019 ◽  
Vol 10 (6) ◽  
pp. 418
Author(s):  
Fan Shao ◽  
Jing Liu ◽  
Mengyuan Ren ◽  
Junying Li ◽  
Haigang Bao ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Association Studies ◽  
Genotyping By Sequencing ◽  
Genome Wide Association ◽  
Expression Level ◽  
Genome Wide Association Studies ◽  
Sailfin Molly ◽  
Genome Wide ◽  
Genomic Regions ◽  
Sailfin Mollies

Dwarfism is a condition defined by low harvest weight in fish, but also results in strange body figures which may have potential for the selective breeding of new ornamental fish strains. The objectives of this study are to reveal the physiological causes of dwarfism and identify the genetic loci controlling this trait in the white sailfin molly. Skeletons of dwarf and normal sailfin mollies were observed by X-ray radioscopy and skeletal staining. Genome-wide association studies based on genotyping-by-sequencing (n = 184) were used to map candidate genomic regions associated with the dwarfism trait. Quantitative real-time PCR was performed to determine the expression level of candidate genes in normal (n = 8) and dwarf (n = 8) sailfin mollies. We found that the dwarf sailfin molly has a short and dysplastic spine in comparison to the normal fish. Two regions, located at NW_015112742.1 and NW_015113621.1, were significantly associated with the dwarfism trait. The expression level of three candidate genes, ADAMTS like 1, Larp7 and PPP3CA, were significantly different between the dwarf and normal sailfin mollies in the hepatopancreas, with PPP3CA also showing significant differences in the vertebrae and Larp7 showing significant differences in the muscle. This study identified genomic regions and candidate genes associated with the dwarfism trait in the white sailfin molly and would provide a reference to determine dwarf-causing variations.

scholarly journals The UMOD Locus: Insights into the Pathogenesis and Prognosis of Kidney Disease

2017 ◽  
Vol 29 (3) ◽  
pp. 713-726 ◽  
Author(s):  
Olivier Devuyst ◽  
Cristian Pattaro
Keyword(s):  
Kidney Disease ◽  
Kidney Diseases ◽  
Association Studies ◽  
Biochemical Properties ◽  
Genome Wide Association Studies ◽  
Genetic Studies ◽  
Rare Mutations ◽  
Genome Wide ◽  
Genomic Regions ◽  
Insight Into

The identification of genetic factors associated with kidney disease has the potential to provide critical insights into disease mechanisms. Genome-wide association studies have uncovered genomic regions associated with renal function metrics and risk of CKD. UMOD is among the most outstanding loci associated with CKD in the general population, because it has a large effect on eGFR and CKD risk that is consistent across different ethnic groups. The relevance of UMOD for CKD is clear, because the encoded protein, uromodulin (Tamm–Horsfall protein), is exclusively produced by the kidney tubule and has specific biochemical properties that mediate important functions in the kidney and urine. Rare mutations in UMOD are the major cause of autosomal dominant tubulointerstitial kidney disease, a condition that leads to CKD and ESRD. In this brief review, we use the UMOD paradigm to describe how population genetic studies can yield insight into the pathogenesis and prognosis of kidney diseases.

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