18 research outputs found
Additional file 1: of Candidate genes for male and female reproductive traits in Canchim beef cattle
Significantly associated single nucleotide polymorphism (SNP) with scrotal circumference at 420Â days of age (SC420) after Bonferroni (B) and false discovery rate (FDR) correction at a chromosome-wise (CW) and genome-wide (GW) level. (DOCX 95Â kb
Additional file 4: Fig. S1. of Candidate genes for male and female reproductive traits in Canchim beef cattle
Linkage disequilibrium for scrotal circumference at 420Â d of age on chromosome 5. Fig. S2. Linkage disequilibrium for scrotal circumference at 420Â d of age on chromosome 9. Fig. S3. Linkage disequilibrium for scrotal circumference at 420Â d of age on chromosome 13. Fig. S4. Linkage disequilibrium for scrotal circumference at 420Â d of age on chromosome 14. Fig. S5. Linkage disequilibrium for scrotal circumference at 420Â d of age on chromosome 18. Fig. S6. Linkage disequilibrium for scrotal circumference at 420Â d of age on chromosome 21. (ZIP 1985Â kb
Additional file 1: of Strategies for genotype imputation in composite beef cattle
Average linkage disequilibrium (r2) by chromosome between adjacent markers
Additional file 2: of Candidate genes for male and female reproductive traits in Canchim beef cattle
Genome-wide (in bold) and chromosome-wise associations for scrotal circumference at 420 days of age. Gene symbols, SNP reference number, and chromosomes (Chr) and positions (Pos, in megabase) were obtained from NCBI website. Distances to gene (kilobase) are presented from 5′ to gene and 3′ to gene directions. If distance equals zero (0.00), the SNP is on intragenic region. P-values are presented as the minimum (Min) and maximum (Max) significance obtained from the generalized quasi-likelihood method. (DOCX 34 kb
Additional file 10: of Identification of putative regulatory regions and transcription factors associated with intramuscular fat content traits
R-squared values of linkage disequilibrium between each pair of hotspot eQTLs. (XLSX 54 kb
Additional file 14: of Identification of putative regulatory regions and transcription factors associated with intramuscular fat content traits
Top ten transcription factor binding sites (TFBSs) over-represented in promoter sequence of genes that were associated with RUNX1T1. (XLSX 54 kb
Additional file 5: of Identification of putative regulatory regions and transcription factors associated with intramuscular fat content traits
Variant effect annotation of cis-eQTLs by VEP tool. (XLSX 212 kb
Additional file 13: of Identification of putative regulatory regions and transcription factors associated with intramuscular fat content traits
Top ten transcription factor binding sites (TFBSs) over-represented in promoter sequence of genes that were associated with EGR4. (XLSX 49 kb
Additional file 6: of Identification of putative regulatory regions and transcription factors associated with intramuscular fat content traits
Variant effect annotation of trans-eQTLs by VEP tool. (XLSX 262 kb
Additional file 12: of Identification of putative regulatory regions and transcription factors associated with intramuscular fat content traits
Biological processes identified using the list of genes harbored within 2Â Mb cis (A), trans (B) and hotspot (C) eQTL regions as the input gene list file. The values shown in the pie chart are the percentage of genes classified to each GO term over the total number of genes in the list used. (DOCX 599 kb