Identification of candidate SNPs and genes associated with anti-RGNNV using GWAS in the red-spotted grouper, Epinephelus akaara

Background: Multiple Sclerosis (MS) is an inflammatory and demyelinating disease of the central nervous system, and genetic factors play an important role in its susceptibility. The expressions of many inflammatory genes implicated in MS are regulated by microRNA (miRNAs), whose function is to suppress the translation by pairing with miRNA Recognition Elements (MREs) present in the 3' untranslated region (3'UTR) of target mRNA. Recently, it has been shown that the Single Nucleotide Polymorphism (SNPs) present within the 3'UTR of mRNAs can affect the miRNA-mediated gene regulation and susceptibility to a variety of human diseases. Objective: The aim of this study was to analyze the SNPs within the 3'UTR of miRNA inflammatory target genes related to multiple sclerosis. Methods: By DisGeNET, dbGaP, Ovid, DAVID, Web of knowledge, and SNPs databases, 3'UTR genetic variants were identified in all inflammatory genes associated with MS. Also, miRNA's target prediction databases were used for predicting the miRNA binding sites. Results: We identified 125 SNPs with MAF>0.05 located in the binding site of the miRNA of 35 genes among 59 inflammatory genes related to MS. Bioinformatics analysis predicted 62 MRE-modulating SNPs and 59 MRE-creating SNPs in the 3'UTR of MSimplicated inflammatory genes. These candidate SNPs within miRNA binding sites of inflammatory genes can alter the miRNAs binding, and consequently lead to the mRNA gene regulation. Conclusion: Therefore, these miRNA and MRE-SNPs may play important roles in personalized medicine of MS, and hence, they would be valuable for further functional verification investigations.

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Uncovering genomic regions controlling plant architectural traits in hexaploid wheat using different GWAS models

Scientific Reports ◽

10.1038/s41598-021-86127-z ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Ali Muhammad ◽

Jianguo Li ◽

Weichen Hu ◽

Jinsheng Yu ◽

Shahid Ullah Khan ◽

...

Keyword(s):

Plant Height ◽

Genome Wide Association Study ◽

Flag Leaf ◽

Significant Snps ◽

Complex Trait ◽

Leaf Length ◽

Candidate Snps ◽

A Genome ◽

Multiple Environments ◽

Architectural Traits

AbstractWheat is a major food crop worldwide. The plant architecture is a complex trait mostly influenced by plant height, tiller number, and leaf morphology. Plant height plays a crucial role in lodging and thus affects yield and grain quality. In this study, a wheat population was genotyped by using Illumina iSelect 90K single nucleotide polymorphism (SNP) assay and finally 22,905 high-quality SNPs were used to perform a genome-wide association study (GWAS) for plant architectural traits employing four multi-locus GWAS (ML-GWAS) and three single-locus GWAS (SL-GWAS) models. As a result, 174 and 97 significant SNPs controlling plant architectural traits were detected by ML-GWAS and SL-GWAS methods, respectively. Among these SNP makers, 43 SNPs were consistently detected, including seven across multiple environments and 36 across multiple methods. Interestingly, five SNPs (Kukri_c34553_89, RAC875_c8121_1490, wsnp_Ex_rep_c66315_64480362, Ku_c5191_340, and tplb0049a09_1302) consistently detected across multiple environments and methods, played a role in modulating both plant height and flag leaf length. Furthermore, candidate SNPs (BS00068592_51, Kukri_c4750_452 and BS00022127_51) constantly repeated in different years and methods associated with flag leaf width and number of tillers. We also detected several SNPs (Jagger_c6772_80, RAC875_c8121_1490, BS00089954_51, Excalibur_01167_1207, and Ku_c5191_340) having common associations with more than one trait across multiple environments. By further appraising these GWAS methods, the pLARmEB and FarmCPU models outperformed in SNP detection compared to the other ML-GWAS and SL-GWAS methods, respectively. Totally, 152 candidate genes were found to be likely involved in plant growth and development. These finding will be helpful for better understanding of the genetic mechanism of architectural traits in wheat.

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Changes in expression of reproduction-related hormones in the brain and pituitary during early ovarian differentiation and development in the red spotted grouper Epinephelus akaara, with emphasis on FSHβ and LHβ

Aquaculture ◽

10.1016/j.aquaculture.2019.734497 ◽

2020 ◽

Vol 514 ◽

pp. 734497 ◽

Cited By ~ 1

Author(s):

Wen-gang Xu ◽

Soichiro Manabe ◽

Yuji Mushirobira ◽

Masaki Nagae ◽

Kiyoshi Soyano

Keyword(s):

Ovarian Differentiation ◽

Epinephelus Akaara ◽

The Brain

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A Linkage-Based Genome Assembly for the Mosquito Aedes albopictus and Identification of Chromosomal Regions Affecting Diapause

Insects ◽

10.3390/insects12020167 ◽

2021 ◽

Vol 12 (2) ◽

pp. 167

Author(s):

John H. Boyle ◽

Pasi M. A. Rastas ◽

Xin Huang ◽

Austin G. Garner ◽

Indra Vythilingam ◽

...

Keyword(s):

Linkage Map ◽

Aedes Albopictus ◽

Dna Sequences ◽

Genome Assembly ◽

Single Copy ◽

Health Concern ◽

Candidate Snps ◽

Single Location ◽

Asian Tiger ◽

Photoperiodic Diapause

The Asian tiger mosquito, Aedes albopictus, is an invasive vector mosquito of substantial public health concern. The large genome size (~1.19–1.28 Gb by cytofluorometric estimates), comprised of ~68% repetitive DNA sequences, has made it difficult to produce a high-quality genome assembly for this species. We constructed a high-density linkage map for Ae. albopictus based on 111,328 informative SNPs obtained by RNAseq. We then performed a linkage-map anchored reassembly of AalbF2, the genome assembly produced by Palatini et al. (2020). Our reassembled genome sequence, AalbF3, represents several improvements relative to AalbF2. First, the size of the AalbF3 assembly is 1.45 Gb, almost half the size of AalbF2. Furthermore, relative to AalbF2, AalbF3 contains a higher proportion of complete and single-copy BUSCO genes (84.3%) and a higher proportion of aligned RNAseq reads that map concordantly to a single location of the genome (46%). We demonstrate the utility of AalbF3 by using it as a reference for a bulk-segregant-based comparative genomics analysis that identifies chromosomal regions with clusters of candidate SNPs putatively associated with photoperiodic diapause, a crucial ecological adaptation underpinning the rapid range expansion and climatic adaptation of A. albopictus.

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Seawater activates l-amino acid oxidase from the serum of the red-spotted grouper Epinephelus akaara

Fish & Shellfish Immunology ◽

10.1016/j.fsi.2021.11.035 ◽

2021 ◽

Author(s):

Yoichiro Kitani ◽

Yuto Osaka ◽

Shoichiro Ishizaki

Keyword(s):

Amino Acid ◽

Acid Oxidase ◽

Amino Acid Oxidase ◽

Epinephelus Akaara

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PSXII-2 Identification of candidate SNPs associated with high prolificacy in Romanov sheep

Journal of Animal Science ◽

10.1093/jas/skab235.465 ◽

2021 ◽

Vol 99 (Supplement_3) ◽

pp. 254-255

Author(s):

Alexey V Shakhin ◽

Arsen V Dotsev ◽

Tatiana E Deniskova ◽

Gottfried Brem ◽

Natalia A Zinovieva

Keyword(s):

Higher Education ◽

Genetic Basis ◽

Reference Genome ◽

Unique Property ◽

Candidate Snps ◽

Merino Sheep ◽

Sheep Breeds ◽

Important Trait ◽

Very High ◽

Selection Of

Abstract Prolificacy is a very important trait in sheep. Romanov sheep, the well-known Russian sheep breed, are characterized by very high prolificacy; however, the genetic basis of this unique property of Romanov sheep is still unknown. It was reported that Ovine BMPR1B gene, located on the OAR6, is associated with prolificacy in several sheep breeds. The aim of our study was to identify candidate SNPs within BMPR1B gene, related to prolificacy. To achieve this goal, using NGS technology, we sequenced ovine BMPR1B gene in Romanov sheep (n = 6), which are characterized by high prolificacy (about 270 lambs per 100 ewes). The sequences of BMPR1B gene of Noire du Velay, Tan, Southdown and Australian Horned Merino sheep breeds as well as Asiatic mouflon (n = 1), which are characterized by significantly lower prolificacy (from 110 to 180 lambs per 100 ewes) were derived from publicly available sources and used for comparison. FST analysis performed in PLINK 1.9 program revealed 10 SNPs with values higher than 0.8. The majority of candidate SNPs under putative selection were localized in the region from 29,382,098 to 29,430,387 on OAR6 of Ovine reference genome (Oar_v3.1 (Ensembl release 98). Thus, we can suggest, that this region of the BMPR1B gene can be considered as the putative region, associated with high prolificacy of Romanov sheep. Additional studies will be needed to confirm the effect of identified candidate SNPs on prolificacy traits. The research results will be useful for artificial selection of sheep with higher prolific capacity, including the introduction of desired alleles in sheep populations using genome editing technologies. This work was supported by the Russian Ministry of Science and Higher Education No. 0445-2019-0024 and RFBR No. 20-516-56002.

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An Analytic Approach Using Candidate Gene Selection and Logic Forest to Identify Gene by Environment Interactions (G × E) for Systemic Lupus Erythematosus in African Americans

Genes ◽

10.3390/genes9100496 ◽

2018 ◽

Vol 9 (10) ◽

pp. 496 ◽

Cited By ~ 5

Author(s):

Bethany Wolf ◽

Paula Ramos ◽

J. Hyer ◽

Viswanathan Ramakrishnan ◽

Gary Gilkeson ◽

...

Keyword(s):

Systemic Lupus Erythematosus ◽

Lupus Erythematosus ◽

Secondhand Smoke ◽

Gene Selection ◽

Search Space ◽

Higher Order ◽

Candidate Snps ◽

Systemic Lupus ◽

Increased Risk ◽

Main Effects

Development and progression of many human diseases, such as systemic lupus erythematosus (SLE), are hypothesized to result from interactions between genetic and environmental factors. Current approaches to identify and evaluate interactions are limited, most often focusing on main effects and two-way interactions. While higher order interactions associated with disease are documented, they are difficult to detect since expanding the search space to all possible interactions of p predictors means evaluating 2p − 1 terms. For example, data with 150 candidate predictors requires considering over 1045 main effects and interactions. In this study, we present an analytical approach involving selection of candidate single nucleotide polymorphisms (SNPs) and environmental and/or clinical factors and use of Logic Forest to identify predictors of disease, including higher order interactions, followed by confirmation of the association between those predictors and interactions identified with disease outcome using logistic regression. We applied this approach to a study investigating whether smoking and/or secondhand smoke exposure interacts with candidate SNPs resulting in elevated risk of SLE. The approach identified both genetic and environmental risk factors, with evidence suggesting potential interactions between exposure to secondhand smoke as a child and genetic variation in the ITGAM gene associated with increased risk of SLE.

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Variants in the VCAM1 gene and risk for symptomatic stroke in sickle cell disease

Blood ◽

10.1182/blood-2001-12-0306 ◽

2002 ◽

Vol 100 (13) ◽

pp. 4303-4309 ◽

Cited By ~ 52

Author(s):

James G. Taylor VI ◽

Delia C. Tang ◽

Sharon A. Savage ◽

Susan F. Leitman ◽

Seth I. Heller ◽

...

Keyword(s):

Sickle Cell ◽

Critical Role ◽

Genome Project ◽

Monogenic Disease ◽

Candidate Snps ◽

Healthy Population ◽

Nucleotide Polymorphisms ◽

Coding Region ◽

A Cell ◽

The Human Genome Project

Stroke is a major cause of morbidity and mortality in sickle cell (SS) disease. Genetic risk factors have been postulated to contribute to this clinical outcome. The human genome project has substantially increased the catalog of variations in genes, many of which could modify the risk for manifestations of disease outcome in a monogenic disease, namely SS. VCAM1 is a cell adhesion molecule postulated to play a critical role in the pathogenesis of SS disease. We identified a total of 33 single nucleotide polymorphisms (SNPs) by sequencing the entire coding region, 2134 bp upstream of the 5′ end of the published cDNA, 217 bp downstream of the 3′ end of the cDNA, and selected intronic regions of the VCAM1 locus. Allelic frequencies for selected SNPs were determined in a healthy population. We subsequently analyzed 4 nonsynonymous coding, 2 synonymous coding, and 4 common promoter SNPs in a genetic association study of clinically apparent stroke in SS disease conducted in a cohort derived from a single institution in Jamaica (51 symptomatic cases and 51 matched controls). Of the 10 candidate SNPs analyzed in this pilot study, the variant allele of the nonsynonymous SNP, VCAM1 G1238C, may be associated with protection from stroke (odds ratio [OR] 0.35, 95% confidence interval [CI] 0.15-0.83, P = .04). Further study is required to confirm the importance of this variant inVCAM1 as a clinically useful modifier of outcome in SS disease.

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