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Candidate genes

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Stratification of candidate genes for Parkinson’s disease using weighted proteinprotein interaction network analysis

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PD-GWAS candidate genes prioritization. Finally, we compared the ORFs with the proteins contributing to the enrichment of the PD-specific func- tional blocks: 19 genes were in cis-haplotypes defined. by LD r genes in LD r genes in LD r 2 ≥ 0.6, and 4 genes in LD r 2 ≥ 0.5 with the top SNP of a risk locus, respectively, leading to the prioritization of a total of 27 candidate genes within the 32 PD-loci (Fig. Ten/27 candidate genes (5 of which are also Mendelian.

Prioritizing candidate genes post-GWAS using multiple sources of data for mastitis resistance in dairy cattle

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To move from a list of candidate genes to a list of pu- tative causal genes, we needed biological evidence. Candidate genes with further biological support were accepted as putative causal genes. We con- firmed the full set of significant genes from the gene- based association with the DEGs from the RNA-seq data. All candidate genes within a QTL interval that had biological support and were significant in the joint ana- lysis were listed as putative causal genes..

Prioritizing candidate genes for fertility in dairy cows using gene-based analysis, functional annotation and differential gene expression

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Table 2 Candidate genes identified by gene-based analysis. Search for candidate genes. We proposed candidate genes for seven QTL identified in this study. In this list, some candidate genes are supported by literature reports of relevant biological functions re- lated to fertility in other species. A similar strategy to prioritize candidate genes have helped identify several candidate genes for mastitis. In the present study, we faced two chal- lenges like in our previous study [28].

Genome-wide association studies detects candidate genes for wool traits by resequencing in Chinese fine-wool sheep

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Genome-wide association studies detects candidate genes for wool traits by re-. Background: The quality and yield of wool determine the economic value of the fine-wool sheep. Therefore, discovering markers or genes relevant to wool traits is the cornerstone for the breeding of fine-wool sheep. A genome-wide association study (GWAS) was performed to detect the candidate genes for the eight wool traits..

Genome-wide association study reveals a QTL and strong candidate genes for umbilical hernia in pigs on SSC14

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For the homozygote haplotype 1, 80% of the animals. had hernia, and for the homozygote 12 51% had hernia, which may suggest a dominant effect of the haplotype, with the haplotype 1 as the risk allele. b Map of characterized genes in the QTL region and their orientation, based on information available from Ensembl, where candidate genes are indicated in red. The red triangle covers the SNPs in the candidate genes and they are all in complete LD.

Weighted single-step GWAS identified candidate genes associated with semen traits in a Duroc boar population

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Based on the literature (cited above), some of the identified candidate genes have been previously reported to be involved in mammal spermiogenesis, tes- tes functioning, and male fertility. Candidate genes. Simi- larly, in the study conducted by Marques et al., [9], where wssGWAS was also used, no overlapping regions were identified between large white and landrace boars..

Identification of genetic loci and candidate genes related to soybean flowering through genome wide association study

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The Illumina Infinium SoySNP50K BeadChip was used to genotype the popula- tion consisting of 309 early-maturing soybean germ- plasm resources, and ten candidate genes homologous to Arabidopsis flowering genes were identified near the peak SNPs associated with flowering time detected via GWAS [3]. Our studies provided an insight into the genetic architecture of soybean growth periods and the identified candidate markers and genes would be valuable for the marker-assisted selec- tion of soybean..

Selection of candidate genes controlling veraison time in grapevine through integration of meta-QTL and transcriptomic data

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Heritability and identification of QTLs and underlying candidate genes associated with the architecture of the grapevine cluster (Vitis vinifera L. New candidate genes for the fine regulation of the colour of grapes. Impedance of the grape berry cuticle as a novel phenotypic trait to estimate resistance to botrytis Cinerea. Refined mapping of the Pierce's disease resistance locus, PdR1, and sex on an extended genetic map of Vitis rupestris x V.

Genome-wide association analysis reveals genetic variations and candidate genes associated with salt tolerance related traits in Gossypium hirsutum

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Genome-wide association analysis reveals genetic variations and candidate genes associated with salt tolerance related traits in Gossypium hirsutum. It is therefore important to breed salt tolerance varieties which can help accelerate the improvement of cotton production. The development of molecular markers linked to causal genes has provided an effective and efficient approach for improving salt tolerance..

Genome-wide association and transcriptome studies identify candidate genes and pathways for feed conversion ratio in pigs

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Genes that are located in the identified QTL region and the 0.5 Mb flanking these loci were considered candidate genes for regulating FCR [8, 65]. The differentially expressed genes identified by RNA-seq and the genes located in the QTL region associated with FCR were input into the DAVID software to found the genes located in the same signaling pathway.. org/10.1186/s w..

Construction of the first high-density genetic linkage map and identification of seed yield-related QTLs and candidate genes in Elymus sibiricus, an important forage grass in Qinghai-Tibet Plateau

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Together, these results highlight the possibility for seed shattering candidate gene identification in E. QTLs on other genomic regions may provide new candidate genes for seed shattering in E. Candidate genes for seed shattering. In this study, we identified 15 potential seed shattering candidate genes involved plant hormone including abscisic acid (ABA), ethylene, auxin, gibberellin and jasmonic acid. these ABA-responsive genes may affect seed shattering [5, 8].

Linkage mapping and genome-wide association study reveals conservative QTL and candidate genes for Fusarium rot resistance in maize

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Combined linkage and association mapping reveals qtl and candidate genes for plant and ear height in maize

Multi-population GWAS and enrichment analyses reveal novel genomic regions and promising candidate genes underlying bovine milk fatty acid composition

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Table 2 Genomic regions associated with milk fatty acid traits in the multi-population analysis and suggested candidate genes Region a Start (Mbp) End (Mbp) Traits associated (and % of explained genetic variance) Candidate genes. In our study, more FA traits have been found to have sig- nificant associations with the DGAT1 and SCD1 regions than previous GWAS using different parts of the multi-population dataset used in the current analysis [8–11, 14].

Identification of stable QTLs and candidate genes involved in anaerobic germination tolerance in rice via high-density genetic mapping and RNA-Seq

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Of the 13 stable loci, three were newly identified in this study and 10 overlapped with previous reports whose candidate genes responsible for traits were un- known. To further narrow down the scope of candidate genes, the fragments per kilo base of exon per million frag- ments mapped value of 84 genes and the phenotypic value of the four traits (CL, CSA, CV and CD) at three phases were used to calculate the Pearson correlation coefficients in R software.

Breeding history and candidate genes responsible for black skin of Xichuan blackbone chicken

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Finally, we per- formed a functional enrichment analysis of the candidate genes, using Gene Ontology (GO) categories and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. To determine whether novel allelic variants located in the top 5% of Fst regions of the genome affect gene expres- sion, we utilized RNA-Seq to construct six cDNA libraries from black (BS) and yellow (YS) dorsal skin of a Xichuan black-bone chickens hybrid population.

Whole genome sequencing and comparative genomic analysis of oleaginous red yeast Sporobolomyces pararoseus NGR identifies candidate genes for biotechnological potential and ballistospores-shooting

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pararoseus NGR identifies candidate genes for biotechnological potential and. ballistospores-shooting. completeness (BUSCO alignment: 95.4%) and RNA-seq analysis (expressed genes: 98.68%) indicated the high-quality features of the current genome.

Analysis of pooled genome sequences from Djallonke and Sahelian sheep of Ghana reveals co-localisation of regions of reduced heterozygosity with candidate genes for disease resistance and adaptation to a tropical environment

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Twelve of the 37 low heterozygosity regions (NPR2, ABCG2, FGF5, MSRB3, PDK2, NF1, NFATC2, OR2AG1, PRLR, ABHD2, MITF, GLB1) were also reported in the top 0.1% of candidate genes identified in a previous genome-wide study for signatures of recent selection in Table 6 Candidate genes for tropical adaptation co-localised with regions of reduced heterozygosity in Djallonke and Sahelian sheep. DJ GNAI3 Melanogenesis (Thermo-tolerance) Kim et al., 2016. DJ LMLN Melanogenesis Kim et al., 2016.

A genome-wide association study reveals novel genomic regions and positional candidate genes for fat deposition in broiler chickens

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Besides that, the Manhattan plots of the SNP effects within the. 2, Additional files 6, 7, and 8) Table 3 List of candidate genes within the genomic windows associated with abdominal fat and skin traits that exhibited GO terms related to lipid metabolic processes in the TT Reference Population. In the QTL on GGA5 at 38 Mb we identified the Jun dimerization protein 2 (JDP2) gene. We identified PLCG1, HNF4A and FITM2 genes in the QTL on GGA20 at 5-Mb.

Transcriptome analysis uncovers the key pathways and candidate genes related to the treatment of Echinococcus granulosus protoscoleces with the repurposed drug pyronaridine

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Transcriptome analysis uncovers the key pathways and candidate genes related to the treatment of Echinococcus granulosus protoscoleces with the repurposed drug pyronaridine. Background: Cystic echinococcosis (CE) is a life-threatening zoonosis caused by the larval form of Echinococcus granulosus tapeworm.

Genome-wide association study identifies favorable SNP alleles and candidate genes for frost tolerance in pea

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Among the candidate genes highlighted at the identified FD-related loci, the results also encourage further attention to the presence of C-repeat Binding Factors (CBF) as potential genetic determinants of the frost tolerance locus on LG VI.. Full list of author information is available at the end of the article.