| QTL Map Information |
|---|
| Chromosome: | 4 |
| QTL Peak Location: | n/a |
| QTL Span: | n/a
128.6-128.6 (Mbp) |
 |
Upper, "Suggestive": | n/a |
| Upper, "Significant": | n/a |
| Peak: | rs345095260 |
| Lower, "Significant": | n/a |
| Lower, "Suggestive": | n/a |
| Marker type: | SNP |
| Analysis type: | Association |
| Model tested: | n/a |
| Test base: | Genome-wise |
| Threshold significance level: | Significant |
 |
P_values | <0.05 | | Dominance effect: | n/a |
| Additive effect: | n/a |
| Associated Gene: | n/a |
| Cis/Trans acting type: |  |
| Links:
Edit |
Map view
|
| Extended information: |
|---|
| (none) |
User inputs on QTL #295731
Add your annotations
Add your comments
Report problems
|
| QTL Experiment in Brief |
|---|
| Animals: | Landrace, Yorkshire, Duroc*Erhualian, Duroc, Gottingen Mini*Duroc, Gottingen Mini*Yorkshire, Suhuai, Chuyinghei, Duroc*Landrace*Yorkshire, Meishan*Pietrain, Pietrain*Landrace, Pietrain*Yorkshire, Wild(EU)*Meishan, Wild(EU)*Pietrain pigs |
| Breeds associated:
|
| Design: | Animals were genotyped using either the Illumina Porcine SNP60K Bead Chip, or the GeneSeek Genomic Profiler (GGP) Porcine SNP80 BeadChip, or the GGP Procine SNP50 BeadChip, or the KPS Porcine Breeding Chip, or the GenoBaits Porcine SNP50K BeadChip, or low-coverage sequence. After imputing genotypes to the sequence level using a multi-breed genotype imputation reference panel, we kept 28,297,602 SNPs and conducted a comprehensive cross-population/breed meta-GWAS analysis for 232 pig complex traits. |
| Analysis: | We first conducted individual GWAS for each trait in each population. To enable individual GWAS from different populations to be comparable in the meta-analysis, we checked all summary-level GWAS results. We then performed meta-analyses on the cleaned individual GWAS results for each trait based on an inverse variance-weighted fixed effects model. |
| Software: | METAL, GCTA, MMAP, DMU, Beagle |
| Notes: | Fourteen of the 59 populations in this study used were previously analyzed data (PMID 34282453, 33372713, 35026054, 31296617, 34403536, 32719719, 34929285, and 31316554). |
| Links: | Edit |
| Reference |
|---|
| Authors: | Xu Z, Lin Q, Cai X, Zhong Z, Teng J, Li B, Zeng H, Gao Y, Cai Z, Wang X, Shi L, Wang X, Wang Y, Zhang Z, Lin Y, Liu S, Yin H, Bai Z, Wei C, Zhou J, Zhang W, Zhang X, Shi S, Wu J, Diao S, Liu Y, Pan X, Feng X, Liu R, Su Z, Chang C, Zhu Q, Wu Y, The PigGTEx Consortium, Zhou Z, Bai L, Li K, Wang Q, Pan Y, Xu Zhong, Peng X, Mei S, Mo D, Liu X, Zhang H, Yuan X, Liu Y, Liu G, Su G, Sahana G, Lund MS, Ma L, Xiang R, Shen X, Li P, Huang R, Ballester M, Piazuelo DC, Amills M, Clop A, Mortensen PK, Fredholm M, Tang G, Li M, Li X, Ding X, Li J, Chen Y, Zhang Q, Zhao Y, Zhao F, Fang L, Zhang Z |
| Affiliation: | State Key Laboratory of Swine & Poultry Breeding Industry, Natl. Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural Univ., Guangzhou, China |
| Title: | Integrating large-scale meta-GWAS and PigGTEx resources to decipher the genetic basis of 232 complex traits in pigs |
| Journal: | bioRxiv, 2024, |
| Links: |
No PubMed entry | Abstract | List all data
| Edit |
User inputs on reference #ISU0127
Add your comments
Note similar findings
Note contradictions
|
