Whole-genome re-sequencing reveals genome-wide variations between the peach variety Green No. 9 and its bud mutant Daifei

2021 ◽  
Author(s):  
Guixiang Li ◽  
Miao Li ◽  
Wei Liu ◽  
Xiaomin Dong ◽  
Xiaolan Gao ◽  
...  
Keyword(s):  
Genetic Basis ◽  
Anthocyanin Biosynthesis ◽  
Whole Genome ◽  
Genomic Variations ◽  
Sequencing Technologies ◽  
Genome Wide ◽  
Phenotypic Variations ◽  
Pathway Analyses ◽  
Variant Genes ◽  
Bud Mutant

Whole-genome sequencing technologies provide opportunities to further understand genetic variation among different varieties. Some related genes that are useful for the breeding process could be identified by sequencing technologies. In this study, two peach varieties, Green No. 9 and its bud mutant Daifei, were analyzed with whole-genome re-sequencing. Approximately 109 million total reads were generated, which covered ~89% of the peach reference genome. A total of 1143757 SNPs, 169827 InDels, 17132 SVs and 5040 CNVs were detected in Green No. 9 and Daifei. Variant genes were classified by GO and KEGG metabolic pathway analyses. Detected genes such as LOC18768059 (carbohydrate metabolism) and LOC18785045 (anthocyanin biosynthesis), were good candidate genes for exploring the phenotypic variations between Green No. 9 and Daifei. Green No. 9 and its bud mutant Daifei showed obvious differences in phenotypes and variant genetic loci. The detected genomic variations will contribute to explorations of important functional genes and to understanding the genetic basis of peach bud mutations.

Inherited skin disease

2020 ◽  
pp. 5602-5611
Author(s):  
Thiviyani Maruthappu ◽  
David P. Kelsell
Keyword(s):  
Genetic Basis ◽  
High Throughput Sequencing ◽  
Skin Diseases ◽  
Association Studies ◽  
Sequencing Technologies ◽  
Ectodermal Dysplasias ◽  
Genome Wide ◽  
Whole Exome ◽  
Common Skin ◽  
Immune Related Genes

Considerable advances in our understanding of inherited skin diseases have been made over the last decade as a result of high throughput sequencing technologies, including next generation sequencing and whole exome sequencing. The genetic basis of a myriad of monogenic epidermal disorders and syndromes including blistering diseases, ichthyoses, palmoplantar keratodermas, and the ectodermal dysplasias have now been elucidated. However, most patients referred from primary care to the dermatology clinic will be seeking treatment for a few common skin disorders such as psoriasis, eczema, and acne. The genetic basis of these disorders is rather more complex, but progress has been made through genome-wide association studies, which, for example, have linked susceptibility variants in the gene for filaggrin (FLG) and SPINK5 to atopic eczema, and IL23R and many other immune-related genes to psoriasis.

scholarly journals Genomics of coloration in natural animal populations

2017 ◽  
Vol 372 (1724) ◽  
pp. 20160337 ◽  
Author(s):  
Luis M. San-Jose ◽  
Alexandre Roulin
Keyword(s):  
Genetic Basis ◽  
High Throughput Sequencing ◽  
Model Species ◽  
Animal Coloration ◽  
Sequencing Technologies ◽  
Animal Populations ◽  
Genome Wide ◽  
General Relevance ◽  
Genetic Structures

Animal coloration has traditionally been the target of genetic and evolutionary studies. However, until very recently, the study of the genetic basis of animal coloration has been mainly restricted to model species, whereas research on non-model species has been either neglected or mainly based on candidate approaches, and thereby limited by the knowledge obtained in model species. Recent high-throughput sequencing technologies allow us to overcome previous limitations, and open new avenues to study the genetic basis of animal coloration in a broader number of species and colour traits, and to address the general relevance of different genetic structures and their implications for the evolution of colour. In this review, we highlight aspects where genome-wide studies could be of major utility to fill in the gaps in our understanding of the biology and evolution of animal coloration. The new genomic approaches have been promptly adopted to study animal coloration although substantial work is still needed to consider a larger range of species and colour traits, such as those exhibiting continuous variation or based on reflective structures. We argue that a robust advancement in the study of animal coloration will also require large efforts to validate the functional role of the genes and variants discovered using genome-wide tools. This article is part of the themed issue ‘Animal coloration: production, perception, function and application’.

scholarly journals RIdeogram: drawing SVG graphics to visualize and map genome-wide data on the idiograms

2019 ◽  
Author(s):  
Zhaodong Hao ◽  
Dekang Lv ◽  
Ying Ge ◽  
Jisen Shi ◽  
Dolf Weijers ◽  
...  
Keyword(s):  
Gc Content ◽  
R Package ◽  
Whole Genome ◽  
Data Mapping ◽  
Model Species ◽  
Chromosomal Distribution ◽  
Whole Genome Analysis ◽  
Sequencing Technologies ◽  
Genome Wide ◽  
Genome Wide Data

Background: Owing to the rapid advances in DNA sequencing technologies, whole genome from more and more species are becoming available at increasing pace. For whole-genome analysis, idiograms provide a very popular, intuitive and effective way to map and visualize the genome-wide information, such as GC content, gene and repeat density, DNA methylation distribution, etc. However, most available software programs and web servers are available only for a few model species, such as human, mouse and fly. As boundaries between model and non-model species are shifting, tools are urgently needs to generate idiograms for a broad range of species are needed to help better understanding fundamental genome characteristics. Results: The R package RIdeogram allows users to build high-quality idiograms of any species of interest. It can map continuous and discrete genome-wide data on the idiograms and visualize them in a heat map and track labels, respectively. Conclusion: The visualization of genome-wide data mapping and comparison allow users to quickly establish a clear impression of the chromosomal distribution pattern, thus making RIdeogram a useful tool for any researchers working with omics.

scholarly journals Comparative study of population genomic approaches for mapping colony-level traits

2018 ◽  
Author(s):  
Shani Inbar ◽  
Pnina Cohen ◽  
Tal Yahav ◽  
Eyal Privman
Keyword(s):  
Genetic Basis ◽  
Frequency Estimation ◽  
Whole Genome ◽  
Reduced Representation ◽  
Task Coordination ◽  
Population Genomic ◽  
Genome Wide ◽  
Alternative Approaches ◽  
Colony Level ◽  
And Task

AbstractSocial insect colonies exhibit colony-level phenotypes such as social immunity and task coordination, which are the sum of individual phenotypes. Mapping the genetic basis of such phenotypes requires associating the colony-level phenotype with the genotypes in the colony. In this paper, we examine alternative approaches to DNA extraction, library construction and sequencing for genome wide association (GWAS) studies of colony-level traits. We evaluate the accuracy of allele frequency estimation in sequencing a pool of individuals (pool-seq) from each colony in either whole-genome sequencing or reduced representation genomic sequencing. Based on empirical measurement of the experimental noise in sequencing DNA pools, we show that whole-genome pool-seq is more accurate than reduced representation pool-seq. We evaluate the power of the alternative approaches for detecting quantitative trait loci (QTL) of colony-level traits by using simulations that account for an environmental effect on the phenotype. Our results can inform experimental designs and enable optimizing the power of GWAS depending on budget, availability of samples and research goals. We conclude that for a given budget, sequencing un-normalized pools of individuals from each colony achieves greater QTL detection power.

scholarly journals The advent of genome-wide association studies for bacteria

2015 ◽  
Author(s):  
Peter E Chen ◽  
B Jesse Shapiro
Keyword(s):  
Genetic Architecture ◽  
Genetic Basis ◽  
Association Studies ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Bacterial Host ◽  
Sequencing Technologies ◽  
Genome Wide ◽  
Contrasting Method ◽  
Insight Into

Significant advances in sequencing technologies and genome-wide association studies (GWAS) have revealed substantial insight into the genetic architecture of human phenotypes. In recent years, the application of this approach in bacteria has begun to reveal the genetic basis of bacterial host preference, antibiotic resistance, and virulence. Here, we consider relevant differences between bacterial and human genome dynamics, apply GWAS to a global sample of Mycobacterium tuberculosis genomes to highlight the impacts of linkage disequilibrium, population stratification, and natural selection, and finally compare the traditional GWAS against phyC, a contrasting method of mapping genotype to phenotype based upon evolutionary convergence. We discuss strengths and weaknesses of both methods, and make suggestions for factors to be considered in future bacterial GWAS.

scholarly journals RIdeogram: drawing SVG graphics to visualize and map genome-wide data on the idiograms

2019 ◽  
Author(s):  
Zhaodong Hao ◽  
Dekang Lv ◽  
Ying Ge ◽  
Jisen Shi ◽  
Dolf Weijers ◽  
...  
Keyword(s):  
Gc Content ◽  
R Package ◽  
Whole Genome ◽  
Data Mapping ◽  
Model Species ◽  
Chromosomal Distribution ◽  
Whole Genome Analysis ◽  
Sequencing Technologies ◽  
Genome Wide ◽  
Genome Wide Data

Background: Owing to the rapid advances in DNA sequencing technologies, whole genome from more and more species are becoming available at increasing pace. For whole-genome analysis, idiograms provide a very popular, intuitive and effective way to map and visualize the genome-wide information, such as GC content, gene and repeat density, DNA methylation distribution, etc. However, most available software programs and web servers are available only for a few model species, such as human, mouse and fly. As boundaries between model and non-model species are shifting, tools are urgently needs to generate idiograms for a broad range of species are needed to help better understanding fundamental genome characteristics. Results: The R package RIdeogram allows users to build high-quality idiograms of any species of interest. It can map continuous and discrete genome-wide data on the idiograms and visualize them in a heat map and track labels, respectively. Conclusion: The visualization of genome-wide data mapping and comparison allow users to quickly establish a clear impression of the chromosomal distribution pattern, thus making RIdeogram a useful tool for any researchers working with omics.

scholarly journals Comprehensive Genome-Wide Association Analysis Reveals the Genetic Basis of Root System Architecture in Soybean

2020 ◽  
Vol 11 ◽  
Author(s):  
Waldiodio Seck ◽  
Davoud Torkamaneh ◽  
François Belzile
Keyword(s):  
Root System ◽  
System Architecture ◽  
Phenotypic Variation ◽  
Genetic Basis ◽  
Genome Wide Association Study ◽  
Primary Root ◽  
Root System Architecture ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Genome Wide

Increasing the understanding genetic basis of the variability in root system architecture (RSA) is essential to improve resource-use efficiency in agriculture systems and to develop climate-resilient crop cultivars. Roots being underground, their direct observation and detailed characterization are challenging. Here, were characterized twelve RSA-related traits in a panel of 137 early maturing soybean lines (Canadian soybean core collection) using rhizoboxes and two-dimensional imaging. Significant phenotypic variation (P < 0.001) was observed among these lines for different RSA-related traits. This panel was genotyped with 2.18 million genome-wide single-nucleotide polymorphisms (SNPs) using a combination of genotyping-by-sequencing and whole-genome sequencing. A total of 10 quantitative trait locus (QTL) regions were detected for root total length and primary root diameter through a comprehensive genome-wide association study. These QTL regions explained from 15 to 25% of the phenotypic variation and contained two putative candidate genes with homology to genes previously reported to play a role in RSA in other species. These genes can serve to accelerate future efforts aimed to dissect genetic architecture of RSA and breed more resilient varieties.

scholarly journals The Genetic Basis of Hypertriglyceridemia

2021 ◽  
Vol 23 (8) ◽  
Author(s):  
Germán D. Carrasquilla ◽  
Malene Revsbech Christiansen ◽  
Tuomas O. Kilpeläinen
Keyword(s):  
Genetic Basis ◽  
Association Studies ◽  
Cumulative Effect ◽  
Genome Wide Association Studies ◽  
Genetic Loci ◽  
Risk Variants ◽  
Genome Wide ◽  
Severe Hypertriglyceridemia ◽  
Increased Risk ◽  
Polygenic Scores

Abstract Purpose of Review Hypertriglyceridemia is a common dyslipidemia associated with an increased risk of cardiovascular disease and pancreatitis. Severe hypertriglyceridemia may sometimes be a monogenic condition. However, in the vast majority of patients, hypertriglyceridemia is due to the cumulative effect of multiple genetic risk variants along with lifestyle factors, medications, and disease conditions that elevate triglyceride levels. In this review, we will summarize recent progress in the understanding of the genetic basis of hypertriglyceridemia. Recent Findings More than 300 genetic loci have been identified for association with triglyceride levels in large genome-wide association studies. Studies combining the loci into polygenic scores have demonstrated that some hypertriglyceridemia phenotypes previously attributed to monogenic inheritance have a polygenic basis. The new genetic discoveries have opened avenues for the development of more effective triglyceride-lowering treatments and raised interest towards genetic screening and tailored treatments against hypertriglyceridemia. Summary The discovery of multiple genetic loci associated with elevated triglyceride levels has led to improved understanding of the genetic basis of hypertriglyceridemia and opened new translational opportunities.

scholarly journals Genomic basis of striking fin shapes and colours in the fighting fish

2021 ◽  
Author(s):  
Le Wang ◽  
Fei Sun ◽  
Zi Yi Wan ◽  
Baoqing Ye ◽  
Yanfei Wen ◽  
...  
Keyword(s):  
Evolutionary Biology ◽  
Association Studies ◽  
Regulatory Element ◽  
Regulatory Elements ◽  
Major Effect ◽  
Betta Splendens ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Phenotypic Variations ◽  
Genomic Basis

Abstract Resolving the genomic basis underlying phenotypic variations is a question of great importance in evolutionary biology. However, understanding how genotypes determine the phenotypes is still challenging. Centuries of artificial selective breeding for beauty and aggression resulted in a plethora of colors, long fin varieties, and hyper-aggressive behavior in the air-breathing Siamese fighting fish (Betta splendens), supplying an excellent system for studying the genomic basis of phenotypic variations. Combining whole genome sequencing, QTL mapping, genome-wide association studies and genome editing, we investigated the genomic basis of huge morphological variation in fins and striking differences in coloration in the fighting fish. Results revealed that the double tail, elephant ear, albino and fin spot mutants each were determined by single major-effect loci. The elephant ear phenotype was likely related to differential expression of a potassium ion channel gene, kcnh8. The albinotic phenotype was likely linked to a cis-regulatory element acting on the mitfa gene and the double tail mutant was suggested to be caused by a deletion in a zic1/zic4 co-enhancer. Our data highlight that major loci and cis-regulatory elements play important roles in bringing about phenotypic innovations and establish Bettas as new powerful model to study the genomic basis of evolved changes.

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