scholarly journals Adapting genotyping-by-sequencing and variant calling for heterogeneous stock rats

2019 ◽  
Author(s):  
Alexander F. Gileta ◽  
Jianjun Gao ◽  
Apurva S. Chitre ◽  
Hannah V. Bimschleger ◽  
Celine L. St. Pierre ◽  
...  
Keyword(s):  
Association Studies ◽  
Variant Calling ◽  
Genotyping By Sequencing ◽  
Genetic Maps ◽  
Genome Wide Association Studies ◽  
Nucleotide Polymorphisms ◽  
Heterogeneous Stock ◽  
Genotype Information ◽  
Genotype By Sequencing ◽  
Inbred Rat

ABSTRACTThe heterogeneous stock (HS) is an outbred rat population derived from eight inbred rat strains. HS rats are ideally suited for genome wide association studies; however, only a few genotyping microarrays have ever been designed for rats and none of them are currently in production. To address the need for an efficient and cost effective method of genotyping HS rats, we have adapted genotype-by-sequencing (GBS) to obtain genotype information at large numbers of single nucleotide polymorphisms (SNPs). In this paper, we have outlined the laboratory and computational steps we took to optimize double digest genotype-by-sequencing (ddGBS) for use in rats. We also evaluate multiple existing computational tools and explain the workflow we have used to call and impute over 3.7 million SNPs. We also compared various rat genetic maps, which are necessary for imputation, including a recently developed map specific to the HS. Using our approach, we obtained concordance rates of 99% with data obtained using data from a genotyping array. The principles and computational pipeline that we describe could easily be adapted for use in other species for which reliable reference genome sets are available.

scholarly journals Adapting Genotyping-by-Sequencing and Variant Calling for Heterogeneous Stock Rats

2020 ◽  
Vol 10 (7) ◽  
pp. 2195-2205 ◽  
Author(s):  
Alexander F. Gileta ◽  
Jianjun Gao ◽  
Apurva S. Chitre ◽  
Hannah V. Bimschleger ◽  
Celine L. St. Pierre ◽  
...  
Keyword(s):  
Association Studies ◽  
Variant Calling ◽  
Genotyping By Sequencing ◽  
Genetic Maps ◽  
Genome Wide Association Studies ◽  
Nucleotide Polymorphisms ◽  
Heterogeneous Stock ◽  
Genotype Information ◽  
Genotype By Sequencing ◽  
Inbred Rat

The heterogeneous stock (HS) is an outbred rat population derived from eight inbred rat strains. HS rats are ideally suited for genome wide association studies; however, only a few genotyping microarrays have ever been designed for rats and none of them are currently in production. To address the need for an efficient and cost effective method of genotyping HS rats, we have adapted genotype-by-sequencing (GBS) to obtain genotype information at large numbers of single nucleotide polymorphisms (SNPs). In this paper, we have outlined the laboratory and computational steps we took to optimize double digest genotype-by-sequencing (ddGBS) for use in rats. We evaluated multiple existing computational tools and explain the workflow we have used to call and impute over 3.7 million SNPs. We have also compared various rat genetic maps, which are necessary for imputation, including a recently developed map specific to the HS. Using our approach, we obtained concordance rates of 99% with data obtained using data from a genotyping array. The principles and computational pipeline that we describe could easily be adapted for use in other species for which reliable reference genome sets are available.

scholarly journals Characterization of cocaine addiction-like behavior in heterogeneous stock rats

2021 ◽  
Author(s):  
Giordano de Guglielmo ◽  
Lieselot Carrette ◽  
Marsida Kallupi ◽  
Molly Brennan ◽  
Brent Boomhower ◽  
...  
Keyword(s):  
Genetic Variability ◽  
Association Studies ◽  
Twin Studies ◽  
Progressive Ratio ◽  
Individual Variability ◽  
Genome Wide Association Studies ◽  
Nucleotide Polymorphisms ◽  
Heterogeneous Stock ◽  
Cocaine Use ◽  
Specific Effects

Twin studies suggest that approximately 50% of the vulnerability to cocaine use disorder is determined by genetic factors, but genome-wide association studies (GWAS) in humans have only begun to identify specific genes that confer this risk. The identification of a set of single nucleotide polymorphisms (SNPs) associated with increased vulnerability to develop compulsive cocaine use represents a major goal for understanding of the genetic risk factors to cocaine use disorder and facilitating the identification of novel druggable targets. Here we characterized addiction-like behaviors in heterogeneous stock (HS) rats, a unique outbred strain of rats characterized by high genetic variability that has been developed to mimic genetic variability in humans. HS rats were allowed to self-administer cocaine 6h/daily for 14 days. Animals were also screened for compulsive cocaine use, using progressive-ratio (PR) and responding despite adverse consequences (contingent foot shocks). To minimize cohort-specific effects, we used large cohorts (n = 46-60) and normalized the level of responding within cohorts using a Z-score. To take advantage of the three behaviors related to compulsive intake and further identify subjects that are consistently vulnerable vs. resilient to compulsive cocaine use we computed an Addiction index by averaging normalized responding (Z-scores) for the three behavioral tests. Results showed high individual variability between vulnerable and resilient rats that is likely to facilitate detection of gene variants associated with vulnerable vs. resilient individuals. Such data will have considerable translational value for designing pharmacogenetic studies in humans.

scholarly journals Genotyping-by-Sequencing-Based Genome-Wide Association Studies of Fusarium Wilt Resistance in Radishes (Raphanus sativus L.)

Genes ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 858
Author(s):  
O New Lee ◽  
Hyunjin Koo ◽  
Jae Woong Yu ◽  
Han Yong Park
Keyword(s):  
Fusarium Wilt ◽  
Association Studies ◽  
Genotyping By Sequencing ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Nucleotide Polymorphisms ◽  
Gwas Study ◽  
F2 Population ◽  
Genome Wide ◽  
Resistant Varieties

Fusarium wilt (FW) is a fungal disease that causes severe yield losses in radish production. The most effective method to control the FW is the development and use of resistant varieties in cultivation. The identification of marker loci linked to FW resistance are expected to facilitate the breeding of disease-resistant radishes. In the present study, we applied an integrated framework of genome-wide association studies (GWAS) using genotyping-by-sequencing (GBS) to identify FW resistance loci among a panel of 225 radish accessions, including 58 elite breeding lines. Phenotyping was conducted by manual inoculation of seedlings with the FW pathogen, and scoring for the disease index was conducted three weeks after inoculation during two constitutive years. The GWAS analysis identified 44 single nucleotide polymorphisms (SNPs) and twenty putative candidate genes that were significantly associated with FW resistance. In addition, a total of four QTLs were identified from F2 population derived from a FW resistant line and a susceptible line, one of which was co-located with the SNPs on chromosome 7, detected in GWAS study. These markers will be valuable for molecular breeding programs and marker-assisted selection to develop FW resistant varieties of R. sativus.

scholarly journals Genomic regions associated with herbicide tolerance in a worldwide faba bean (Vicia faba L.) collection

2022 ◽  
Vol 12 (1) ◽  
Author(s):  
Lynn Abou-Khater ◽  
Fouad Maalouf ◽  
Abdulqader Jighly ◽  
Alsamman M. Alsamman ◽  
Diego Rubiales ◽  
...  
Keyword(s):  
Protein Kinase ◽  
Faba Bean ◽  
Field Experiments ◽  
Core Protein ◽  
Association Studies ◽  
Herbicide Tolerance ◽  
Genotyping By Sequencing ◽  
Genome Wide Association Studies ◽  
Nucleotide Polymorphisms ◽  
Herbicide Treatments

AbstractWeeds represent one of the major constraints for faba bean crop. The identification of molecular markers associated with key genes imparting tolerance to herbicides can facilitate and fasten the efficient and effective development of herbicide tolerant cultivars. We phenotyped 140 faba bean genotypes in three open field experiments at two locations in Lebanon and Morocco against three herbicide treatments (T1 metribuzin 250 g ai/ha; T2 imazethapyr 75 g ai/ha; T3 untreated) and one in greenhouse where T1 and T3 were applied. The same set was genotyped using genotyping by sequencing (GBS) which yield 10,794 high quality single nucleotide polymorphisms (SNPs). ADMIXTURE software was used to infer the population structure which revealed two ancestral subpopulations. To identify SNPs associated with phenological and yield related traits under herbicide treatments, Single-trait (ST) and Multi-trait (MT) Genome Wide Association Studies (GWAS) were fitted using GEMMA software, showing 10 and 14 highly significant associations, respectively. Genomic sequences containing herbicide tolerance associated SNPs were aligned against the NCBI database using BLASTX tool using default parameters to annotate candidate genes underlying the causal variants. SNPs from acidic endochitinase, LRR receptor-like serine/threonine-protein kinase RCH1, probable serine/threonine-protein kinase NAK, malate dehydrogenase, photosystem I core protein PsaA and MYB-related protein P-like were significantly associated with herbicide tolerance traits.

scholarly journals Molecular Characterization of Global Finger Millet (Eleusine coracana, L. Gaertn) germplasm Reaction to Striga in Kenya

2018 ◽  
pp. 1-14
Author(s):  
Sirengo Peter Nyongesa ◽  
Wamalwa Dennis Simiyu ◽  
Oduor Chrispus ◽  
Odeny Damaris Achieng ◽  
Dangasuk Otto George
Keyword(s):  
Finger Millet ◽  
Association Studies ◽  
Block Design ◽  
Principal Component ◽  
Genotyping By Sequencing ◽  
Eleusine Coracana ◽  
Striga Hermonthica ◽  
Genome Wide Association Studies ◽  
Nucleotide Polymorphisms ◽  
Striga Resistance

Finger millet (Eleusine coracana, L. Gaertn) is an important food crop in Africa and Asia. The parasitic weed Striga hermonthica (Del.) Benth limits finger millet production through reduced yield in agro-ecologies where they exist. The damage of Striga to cereal crops is more severe under drought and low soil fertility. This study aims to determine genetic basis for reaction to Striga hermonthica among the selected germplasm of finger millets through genotyping by sequencing (GBS). One hundred finger millet genotypes were evaluated for reaction to Striga hermonthica infestation under field conditions at Alupe and Kibos in Western Kenya. The experiment was laid out in a randomized complete block design (RCBD) consisting of 10 x 10 square (triple lattice) under Striga (inoculated) and no Striga conditions and plant growth monitored to maturity after 110 days. All genotypes were genotyped by genotyping by sequencing (GBS) and data analyzed using the non-reference based Universal Network Enabled Analysis Kit (UNEAK) pipeline. Genome wide association studies (GWAS) were done to establish the association of detected Single Nucleotide Polymorphisms (SNPs) with Striga reaction based on field results. In molecular analysis 117,542 SNPs from raw GBS data used in GWAS revealed that markers TP 85424 and TP 88244 were associated with Striga resistance in the 95 genotypes. Principal Component Analysis revealed that the first and third component axes accounted for 2.5 and 8% of total variance respectively and the genotypes were distributed according to their reaction to Striga weed. Genetic diversity analysis grouped the 95 accessions into three major clusters containing; 32 (A), 56 (B), and 7 (C) genotypes.  All finger millet genotypes that showed high resistance to Striga in the field were from cluster B while the most susceptible genotypes were from clusters A and C. Results revealed genetic variation for Striga resistance in cultivated finger millet genotypes and hence the possibility of marker –assisted breeding for resistance to Striga.

scholarly journals Non-Mendelian inheritance of SNP markers reveals extensive chromosomal translocations in dioecious hops (Humulus lupulus L.)

2016 ◽  
Author(s):  
Dong Zhang ◽  
Nicholi J. Pitra ◽  
Mark C. Coles ◽  
Edward S. Buckler ◽  
Paul D. Matthews
Keyword(s):  
Candidate Genes ◽  
Association Studies ◽  
Genotyping By Sequencing ◽  
Mendelian Inheritance ◽  
Snp Markers ◽  
Genome Wide Association Studies ◽  
Nucleotide Polymorphisms ◽  
Genome Wide ◽  
Population Structures ◽  
Wild Accessions

AbstractGenome-wide meiotic recombination structures, sex chromosomes, and candidate genes for sex determination were discovered among Humulus spp. by application of a novel, high-density molecular marker system: ~1.2M single nucleotide polymorphisms (SNPs) were profiled with genotyping-by-sequencing (GBS) among 4512 worldwide accessions, including 4396 cultivars and landraces and 116 wild accessions of hops. Pre-qualified GBS markers were validated by inferences on families, population structures and phylogeny. Candidate genes discovered for several traits, including sex and drought stress-resistance, demonstrate the quality and utility of GBS SNPs for genome-wide association studies (GWAS) and Fst analysis in hops. Most importantly, pseudo-testcross mappings in F1 families delineated non-random linkage of Mendelian and non-Mendelian markers: structures that are indicative of unusual meiotic events which may have driven the evolution and cultivation of hops.

scholarly journals Regional genomic heritability mapping for agronomic traits in sugarcane

2020 ◽  
Author(s):  
Pedro Marcus Pereira Vidigal ◽  
Mehdi Momen ◽  
Paulo Mafra de Almeida Costa ◽  
Márcio Henrique Pereira Barbosa ◽  
Gota Morota ◽  
...  
Keyword(s):  
Agronomic Traits ◽  
Association Studies ◽  
Variant Calling ◽  
Breeding Population ◽  
Primary Concern ◽  
Genome Wide Association Studies ◽  
Nucleotide Polymorphisms ◽  
Genomic Heritability ◽  
Genomic Regions ◽  
Sugarcane Genome

AbstractBackgroundThe identification of genomic regions involved in agronomic traits is the primary concern for sugarcane breeders. Genome-wide association studies (GWAS) leverage the sequence variations to bridge phenotypes and genotypes. However, their effectiveness is limited in species with high ploidy and large genomes, such as sugarcane. As an alternative, a regional heritability mapping (RHM) method can be used to capture genetic signals that may be missed by GWAS by combining genetic variance from neighboring regions. We used RHM to screen the sugarcane genome aiming to identify regions with higher heritability associated with agronomic traits. We considered percentage of fiber in sugarcane bagasse (FB), apparent percentage of sugarcane sucrose (PC), tonnes of pol per hectare (TPH), and tonnes of stalks per hectare (TSH).MethodsSequence-capture data of 508 sugarcane (Saccharum spp.) clones from a breeding population under selection were processed for variant calling analysis using the sugarcane genome cultivar R570 as a reference. A set of 375,195 single nucleotide polymorphisms were selected after quality control. RHM was conducted by splitting the sugarcane genome into windows of 2 Mb length.ResultsWe selected the windows explaining > 20% of the total genomic heritability for TPH (64 windows - 5,654 genes) and TSH (72 windows - 6,050 genes), and > 15% for PC (16 windows - 1,517 genes) and FB (17 windows - 1,615 genes). The top five windows that explained the highest genomic heritability ranged from 20.8 to 24.6% for FB (629 genes), 18.0 to 22.0% for PC (452 genes), 53.8 to 66.0% for TPH (705 genes), and 59.5 to 67.4% for TSH (413 genes). The functional annotation of genes included in those top five windows revealed a set of genes that encode enzymes that integrate carbon metabolism, starch and sucrose metabolism, and phenylpropanoid biosynthesis pathways.ConclusionsThe selection of windows that explained the large proportions of genomic heritability allowed us to identify genomic regions containing a set of genes that are related to the agronomic traits in sugarcane. These windows spanned a region of 58.38Mb, which corresponds to 14.28% of the reference assembly in the sugarcane genome. We contend that RHM can be used as an alternative method for sugarcane breeders to reduce the complexity of the sugarcane genome.

scholarly journals Development of a 76k Alpaca (Vicugna pacos) Single Nucleotide Polymorphisms (SNPs) Microarray

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 291
Author(s):  
Marcos Calderon ◽  
Manuel J. More ◽  
Gustavo A. Gutierrez ◽  
Federico Abel Ponce de León
Keyword(s):  
Genetic Improvement ◽  
Association Studies ◽  
Fiber Quality ◽  
Genotyping By Sequencing ◽  
Economic Benefits ◽  
Genome Wide Association Studies ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Reduced Representation ◽  
Improvement Programs

Small farm producers’ sustenance depends on their alpaca herds and the production of fiber. Genetic improvement of fiber characteristics would increase their economic benefits and quality of life. The incorporation of molecular marker technology could overcome current limitations for the implementation of genetic improvement programs. Hence, the aim of this project was the generation of an alpaca single nucleotide polymorphism (SNP) microarray. A sample of 150 Huacaya alpacas from four farms, two each in Puno and Cerro de Pasco were used for SNP discovery by genotyping by sequencing (GBS). Reduced representation libraries, two per animal, were produced after DNA digestion with ApeK1 and double digestion with Pst1-Msp1. Ten alpaca genomes, sequenced at depths between 12× to 30×, and the VicPac3.1 reference genome were used for read alignments. Bioinformatics analysis discovered 76,508 SNPs included in the microarray. Candidate genes SNPs (302) for fiber quality and color are also included. The microarray SNPs cover 90.5% of the genome length with a density of about 39 ± 2.51 SNPs/Mb of DNA at an average interval of 26.45 ± 18.57 kbp. The performance was evaluated by genotyping 30 family trios and comparing them to their pedigrees, as well as comparing microarray to GBS genotypes. Concordance values of 0.93 and 0.94 for ApeK1 and Pst1-Msp1 generated SNPs were observed. Similarly, 290 fiber quality and color candidate gene SNPs were validated. Availability of this microarray will facilitate genome-wide association studies, marker-assisted selection and, in time, genomic selection.

scholarly journals Causal Association between Periodontitis and Parkinson’s Disease: A Bidirectional Mendelian Randomization Study

Genes ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 772
Author(s):  
João Botelho ◽  
Vanessa Machado ◽  
José João Mendes ◽  
Paulo Mascarenhas
Keyword(s):  
Parkinson’S Disease ◽  
Parkinson's Disease ◽  
Instrumental Variables ◽  
Mendelian Randomization ◽  
Association Studies ◽  
European Ancestry ◽  
Genome Wide Association Studies ◽  
Nucleotide Polymorphisms ◽  
Genetic Liability ◽  
Bidirectional Association

The latest evidence revealed a possible association between periodontitis and Parkinson’s disease (PD). We explored the causal relationship of this bidirectional association through two-sample Mendelian randomization (MR) in European ancestry populations. To this end, we used openly accessible data of genome-wide association studies (GWAS) on periodontitis and PD. As instrumental variables for periodontitis, seventeen single-nucleotide polymorphisms (SNPs) from a GWAS of periodontitis (1817 periodontitis cases vs. 2215 controls) and eight non-overlapping SNPs of periodontitis from an additional GWAS for validation purposes. Instrumental variables to explore for the reverse causation included forty-five SNPs from a GWAS of PD (20,184 cases and 397,324 controls). Multiple approaches of MR were carried-out. There was no evidence of genetic liability of periodontitis being associated with a higher risk of PD (B = −0.0003, Standard Error [SE] 0.0003, p = 0.26). The eight independent SNPs (B = −0.0000, SE 0.0001, p = 0.99) validated this outcome. We also found no association of genetically primed PD towards periodontitis (B = −0.0001, SE 0.0001, p = 0.19). These MR study findings do not support a bidirectional causal genetic liability between periodontitis and PD. Further GWAS studies are needed to confirm the consistency of these results.

scholarly journals Pharmacogenomics of Lithium Response in Bipolar Disorder

2021 ◽  
Vol 14 (4) ◽  
pp. 287
Author(s):  
Courtney M. Vecera ◽  
Gabriel R. Fries ◽  
Lokesh R. Shahani ◽  
Jair C. Soares ◽  
Rodrigo Machado-Vieira
Keyword(s):  
Bipolar Disorder ◽  
Association Studies ◽  
Mood Stabilizer ◽  
Genome Wide Association Studies ◽  
Nucleotide Polymorphisms ◽  
Non Coding Rna ◽  
Genome Wide ◽  
Lithium Response ◽  
Genetic Loading ◽  
Long Non Coding Rna

Despite being the most widely studied mood stabilizer, researchers have not confirmed a mechanism for lithium’s therapeutic efficacy in Bipolar Disorder (BD). Pharmacogenomic applications may be clinically useful in the future for identifying lithium-responsive patients and facilitating personalized treatment. Six genome-wide association studies (GWAS) reviewed here present evidence of genetic variations related to lithium responsivity and side effect expression. Variants were found on genes regulating the glutamate system, including GAD-like gene 1 (GADL1) and GRIA2 gene, a mutually-regulated target of lithium. In addition, single nucleotide polymorphisms (SNPs) discovered on SESTD1 may account for lithium’s exceptional ability to permeate cell membranes and mediate autoimmune and renal effects. Studies also corroborated the importance of epigenetics and stress regulation on lithium response, finding variants on long, non-coding RNA genes and associations between response and genetic loading for psychiatric comorbidities. Overall, the precision medicine model of stratifying patients based on phenotype seems to derive genotypic support of a separate clinical subtype of lithium-responsive BD. Results have yet to be expounded upon and should therefore be interpreted with caution.

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