scholarly journals Multi-strategy genome-wide association studies identify the DCAF16-NCAPG region as a susceptibility locus for average daily gain in cattle

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Wengang Zhang ◽  
Junya Li ◽  
Yong Guo ◽  
Lupei Zhang ◽  
Lingyang Xu ◽  
...  
Keyword(s):  
Association Studies ◽  
Average Daily Gain ◽  
Genome Wide Association ◽  
Susceptibility Locus ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Daily Gain

scholarly journals A meta-analysis of genome-wide association studies for average daily gain and lean meat percentage in two Duroc pig populations

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Shenping Zhou ◽  
Rongrong Ding ◽  
Fanming Meng ◽  
Xingwang Wang ◽  
Zhanwei Zhuang ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Growth And Development ◽  
Genetic Architecture ◽  
Association Studies ◽  
Meta Analysis ◽  
Average Daily Gain ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Daily Gain

Abstract Background Average daily gain (ADG) and lean meat percentage (LMP) are the main production performance indicators of pigs. Nevertheless, the genetic architecture of ADG and LMP is still elusive. Here, we conducted genome-wide association studies (GWAS) and meta-analysis for ADG and LMP in 3770 American and 2090 Canadian Duroc pigs. Results In the American Duroc pigs, one novel pleiotropic quantitative trait locus (QTL) on Sus scrofa chromosome 1 (SSC1) was identified to be associated with ADG and LMP, which spans 2.53 Mb (from 159.66 to 162.19 Mb). In the Canadian Duroc pigs, two novel QTLs on SSC1 were detected for LMP, which were situated in 3.86 Mb (from 157.99 to 161.85 Mb) and 555 kb (from 37.63 to 38.19 Mb) regions. The meta-analysis identified ten and 20 additional SNPs for ADG and LMP, respectively. Finally, four genes (PHLPP1, STC1, DYRK1B, and PIK3C2A) were detected to be associated with ADG and/or LMP. Further bioinformatics analysis showed that the candidate genes for ADG are mainly involved in bone growth and development, whereas the candidate genes for LMP mainly participated in adipose tissue and muscle tissue growth and development. Conclusions We performed GWAS and meta-analysis for ADG and LMP based on a large sample size consisting of two Duroc pig populations. One pleiotropic QTL that shared a 2.19 Mb haplotype block from 159.66 to 161.85 Mb on SSC1 was found to affect ADG and LMP in the two Duroc pig populations. Furthermore, the combination of single-population and meta-analysis of GWAS improved the efficiency of detecting additional SNPs for the analyzed traits. Our results provide new insights into the genetic architecture of ADG and LMP traits in pigs. Moreover, some significant SNPs associated with ADG and/or LMP in this study may be useful for marker-assisted selection in pig breeding.

PSXI-5 Genome-wide association study of feed efficiency in Russian Duroc boars

2021 ◽  
Vol 99 (Supplement_3) ◽  
pp. 247-247
Author(s):  
Anna A Belous ◽  
Alexander A Sermyagin ◽  
Natalia A Zinovieva
Keyword(s):  
Feed Intake ◽  
Feed Efficiency ◽  
Average Daily Gain ◽  
Genome Wide Association ◽  
Bile Acid Metabolism ◽  
Alternative Measure ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Conversion Rates ◽  
Daily Gain

Abstract The cost of fodder is the major part in expenditure in pork industry. In this regard, improving the feed efficiency is the main goal of breeding programs for the most of pig breeds. Residual feed intake (RFI) is an alternative measure for feed efficiency, which is accepted in different livestock species including pigs. RFI is defined as the difference between the observed and predicted feed intake based on average daily gain and (additionally) back fat thickness. Our aim was to find the candidate genes responsible for RFI in Russian Duroc boars. RFI values for individual boars (n = 766) were calculated using linear regression of daily feed intake on metabolic mid-test weight and average daily gain. The SNP genotyping was carried out using Porcine GGP HD BeadChip (GeneSeek/Neogene). After data quality control, performed in PLINK 1.9, 43,199 SNPs were selected for genome-wide association studies (GWAS). The average daily gain in studied boars was 957 g with variation in individual animals from 424 to 1508 g. Feed conversion rates averaged to 2.21 kg/kg with variation from 1.8 to 3.7 kg/kg. GWAS results showed the presence of 48 SNPs, which were significantly (P < 0.00001) associated with RFI, including 15 SNPs on SSC2, 9 SNP – SSC4, 2 SNPs – SSC6, 21 SNPs – SSC9, and 1 SNP – SSC17. A search for genes located within 0.4 Mb window (0.2 Mb down-stream to 0.2 Mb up-stream from identified SNP) revealed several putative candidates. Functional annotation of the obtained candidates showed the presence of genes involved in protein metabolism (ADAMTS2,UIMC1 on SSC2; NTNG1 on SSC4), regulation of glucose and bile acid metabolism (FGFR4 on SSC2), neuronal development (ENC1 on SSC2; NTRK1, MEF2D on SSC4), vitamin D and K pathways (BGLAP on SSC4). The study was funded by the Russian Ministry of Science and Higher Education No.0445-2019-0029.

scholarly journals Genome-wide association analysis identifies a meningioma risk locus at 11p15.5

2018 ◽  
Vol 20 (11) ◽  
pp. 1485-1493 ◽  
Author(s):  
Elizabeth B Claus ◽  
Alex J Cornish ◽  
Peter Broderick ◽  
Joellen M Schildkraut ◽  
Sara E Dobbins ◽  
...  
Keyword(s):  
Association Studies ◽  
Meta Analysis ◽  
Adult Brain ◽  
Genome Wide Association ◽  
Susceptibility Locus ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Risk Locus ◽  
Additional Support ◽  
Brain And Spinal Cord

Abstract Background Meningiomas are adult brain tumors originating in the meningeal coverings of the brain and spinal cord, with significant heritable basis. Genome-wide association studies (GWAS) have previously identified only a single risk locus for meningioma, at 10p12.31. Methods To identify a susceptibility locus for meningioma, we conducted a meta-analysis of 2 GWAS, imputed using a merged reference panel from the 1000 Genomes Project and UK10K data, with validation in 2 independent sample series totaling 2138 cases and 12081 controls. Results We identified a new susceptibility locus for meningioma at 11p15.5 (rs2686876, odds ratio = 1.44, P = 9.86 × 10–9). A number of genes localize to the region of linkage disequilibrium encompassing rs2686876, including RIC8A, which plays a central role in the development of neural crest-derived structures, such as the meninges. Conclusions This finding advances our understanding of the genetic basis of meningioma development and provides additional support for a polygenic model of meningioma.

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