Genome-Wide Association Study Reveals the PLAG1 Gene for Knuckle, Biceps and Shank Weight in Simmental Beef Cattle

Song, Yifu; Xu, Lingyang; Chen, Yan; Zhang, Lupei; Gao, Huijiang; Zhu, Bo; Niu, Hong; Zhang, Wengang; Xia, Jiangwei; Gao, Xue; Li, Junya

doi:10.1371/journal.pone.0168316

Cited by 38 publications

(34 citation statements)

References 37 publications

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“…This region contains several widely known and well described genes, including the zinc finger protein Pleomorphic adenoma gene 1 ( PLAG1 ) gene. This region is of interest as previous GWAS studies have found significant associations between the PLAG1 gene, including surrounding genes, to have important associations with stature 30 , fertility 26 and beef production traits, such as carcass weight 26,31–33 . In the study by Fortes et al .…”

Section: Resultsmentioning

confidence: 99%

Sequencing the mosaic genome of Brahman cattle identifies historic and recent introgression including polled

Koufariotis

Hayes

Kelly³

et al. 2018

Sci Rep

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Brahman cattle have a Bos indicus and Bos taurus mosaic genome, as a result of the process used to create the breed (repeat backcrossing of Bos taurus females to Bos indicus bulls). With the aim of identifying Bos taurus segments in the Brahman genome at sequence level resolution, we sequenced the genomes of 46 influential Brahman bulls. Using 36 million variants identified in the sequences, we searched for regions close to fixation for Bos indicus or Bos taurus segments that were longer than expected by chance (from simulation of the breed formation history of Brahman cattle). Regions close to fixation for Bos indicus content were enriched for protein synthesis genes, while regions of higher Bos taurus content included genes of the G-protein coupled receptor family (including genes implicated in puberty, such as THRS). The region with the most extreme Bos taurus enrichment was on chromosome 14 surrounding PLAG1. The introgressed Bos taurus allele at PLAG1 increases stature and the high frequency of the allele likely reflects strong selection for the trait. Finally, we provide evidence that the polled mutation in Brahmans, a desirable trait under very strong recent selection, is of Celtic origin and is introgressed from Bos taurus.

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Section: Resultsmentioning

confidence: 99%

Sequencing the mosaic genome of Brahman cattle identifies historic and recent introgression including polled

Koufariotis

Hayes

Kelly³

et al. 2018

Sci Rep

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“…The XKR4 was associated with subcutaneous rump fat thickness, scrotal circumference, serum concentration of prolactin, and sexual precocity (Fortes et al, 2012a;Porto Neto et al, 2012;Bastin et al, 2014;Takada et al, 2018). PLAG1 has been implicated in the regulation of stature and weight (Littlejohn et al, 2012;Pryce et al, 2012;Song et al, 2016). This gene was associated with yearling weight in Australian Tropical Composite breeds (Porto-Neto et al, 2014).…”

Section: Discussionmentioning

confidence: 99%

Genomic Breed Composition of Selection Signatures in Brangus Beef Cattle

et al. 2020

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Cattle breeding routinely uses crossbreeding between subspecies (Bos taurus taurus and Bos taurus indicus) to form composite breeds, such as Brangus. These composite breeds provide an opportunity to identify recent selection signatures formed in the new population and evaluate the genomic composition of these regions of the genome. Using high-density genotyping, we first identified runs of homozygosity (ROH) and calculated genomic inbreeding. Then, we evaluated the genomic composition of the regions identified as selected (selective sweeps) using a chromosome painting approach. The genomic inbreeding increased at approximately 1% per generation after composite breed formation, showing the need of inbreeding control even in composite breeds. Three selected regions in Brangus were also identified as Angus selection signatures. Two regions (chromosomes 14 and 21) were identified as signatures of selection in Brangus and both founder breeds. Five of the 10 homozygous regions in Brangus were predominantly Angus in origin (probability >80%), and the other five regions had a mixed origin but always with Brahman contributing less than 50%. Therefore, genetic events, such as drift, selection, and complementarity, are likely shaping the genetic composition of founder breeds in specific genomic regions. Such findings highlight a variety of opportunities to better control the selection process and explore heterosis and complementarity at the genomic level in composite breeds.

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“…The HEPACAM2 gene was previously identified in a QTL region for mid-test metabolic weight (MMWT) in SimAngus on BTA4 [ 48 ]. The CHCHD7 gene on BTA14 is associated with CWT in the Hanwoo breed [ 11 ], with knuckle, biceps and shank trait in Chinese Simmental cattle [ 49 ], with carcass weight in Japanese Black steers [ 50 ], with back fat thickness and rump fat thickness in the Nellore breed [ 51 ], and with fat thickness and intramuscular fat in composite cattle [ 52 ]. The UBXN2B gene is associated with MMWT in SimAngus [ 48 ], and with carcass weight, carcass fat, and carcass conformation in Simmental [ 53 ].…”

Section: Discussionmentioning

confidence: 99%

Use of gene expression and whole-genome sequence information to improve the accuracy of genomic prediction for carcass traits in Hanwoo cattle

et al. 2020

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Background In this study, we assessed the accuracy of genomic prediction for carcass weight (CWT), marbling score (MS), eye muscle area (EMA) and back fat thickness (BFT) in Hanwoo cattle when using genomic best linear unbiased prediction (GBLUP), weighted GBLUP (wGBLUP), and a BayesR model. For these models, we investigated the potential gain from using pre-selected single nucleotide polymorphisms (SNPs) from a genome-wide association study (GWAS) on imputed sequence data and from gene expression information. We used data on 13,717 animals with carcass phenotypes and imputed sequence genotypes that were split in an independent GWAS discovery set of varying size and a remaining set for validation of prediction. Expression data were used from a Hanwoo gene expression experiment based on 45 animals. Results Using a larger number of animals in the reference set increased the accuracy of genomic prediction whereas a larger independent GWAS discovery dataset improved identification of predictive SNPs. Using pre-selected SNPs from GWAS in GBLUP improved accuracy of prediction by 0.02 for EMA and up to 0.05 for BFT, CWT, and MS, compared to a 50 k standard SNP array that gave accuracies of 0.50, 0.47, 0.58, and 0.47, respectively. Accuracy of prediction of BFT and CWT increased when BayesR was applied with the 50 k SNP array (0.02 and 0.03, respectively) and was further improved by combining the 50 k array with the top-SNPs (0.06 and 0.04, respectively). By contrast, using BayesR resulted in limited improvement for EMA and MS. wGBLUP did not improve accuracy but increased prediction bias. Based on the RNA-seq experiment, we identified informative expression quantitative trait loci, which, when used in GBLUP, improved the accuracy of prediction slightly, i.e. between 0.01 and 0.02. SNPs that were located in genes, the expression of which was associated with differences in trait phenotype, did not contribute to a higher prediction accuracy. Conclusions Our results show that, in Hanwoo beef cattle, when SNPs are pre-selected from GWAS on imputed sequence data, the accuracy of prediction improves only slightly whereas the contribution of SNPs that are selected based on gene expression is not significant. The benefit of statistical models to prioritize selected SNPs for estimating genomic breeding values is trait-specific and depends on the genetic architecture of each trait.

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Genome-Wide Association Study Reveals the PLAG1 Gene for Knuckle, Biceps and Shank Weight in Simmental Beef Cattle

Cited by 38 publications

References 37 publications

Sequencing the mosaic genome of Brahman cattle identifies historic and recent introgression including polled

Sequencing the mosaic genome of Brahman cattle identifies historic and recent introgression including polled

Genomic Breed Composition of Selection Signatures in Brangus Beef Cattle

Use of gene expression and whole-genome sequence information to improve the accuracy of genomic prediction for carcass traits in Hanwoo cattle

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