Integrating Single-Step GWAS and Bipartite Networks Reconstruction Provides Novel Insights into Yearling Weight and Carcass Traits in Hanwoo Beef Cattle

Naserkheil, Masoumeh; Bahrami, Abolfazl; Lee, Deukhwan; Mehrban, Hossein

doi:10.3390/ani10101836

Cited by 22 publications

(21 citation statements)

References 98 publications

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“…Our findings were supported by results of ssGWAS which reveals major QTLs on chromosomes 6 and 14 for EMA, YW, and particularly for CW ( Figure S3 ), in which the improvement of the prediction accuracy using the WssGBLUP method was clear. The percentage of additive genetic variance explained on chromosome 14 (6) was 36% (4.56%) for CW, 9.39% (2.60%) for EMA, and 11.64% (9.05%) for YW, which was confirmed by the findings of the previous study [ 41 ]. The results of that study showed that some genomic regions on chromosome 14 were to influence CW, EMA, and YW, which indicated the same genes were controlling these traits [ 41 ].…”

Section: Discussionsupporting

confidence: 88%

“…The percentage of additive genetic variance explained on chromosome 14 (6) was 36% (4.56%) for CW, 9.39% (2.60%) for EMA, and 11.64% (9.05%) for YW, which was confirmed by the findings of the previous study [ 41 ]. The results of that study showed that some genomic regions on chromosome 14 were to influence CW, EMA, and YW, which indicated the same genes were controlling these traits [ 41 ].…”

Section: Discussionsupporting

confidence: 88%

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Genomic Prediction Using Alternative Strategies of Weighted Single-Step Genomic BLUP for Yearling Weight and Carcass Traits in Hanwoo Beef Cattle

Mehrban

Naserkheil

Lee

et al. 2021

Genes

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The weighted single-step genomic best linear unbiased prediction (GBLUP) method has been proposed to exploit information from genotyped and non-genotyped relatives, allowing the use of weights for single-nucleotide polymorphism in the construction of the genomic relationship matrix. The purpose of this study was to investigate the accuracy of genetic prediction using the following single-trait best linear unbiased prediction methods in Hanwoo beef cattle: pedigree-based (PBLUP), un-weighted (ssGBLUP), and weighted (WssGBLUP) single-step genomic methods. We also assessed the impact of alternative single and window weighting methods according to their effects on the traits of interest. The data was comprised of 15,796 phenotypic records for yearling weight (YW) and 5622 records for carcass traits (backfat thickness: BFT, carcass weight: CW, eye muscle area: EMA, and marbling score: MS). Also, the genotypic data included 6616 animals for YW and 5134 for carcass traits on the 43,950 single-nucleotide polymorphisms. The ssGBLUP showed significant improvement in genomic prediction accuracy for carcass traits (71%) and yearling weight (99%) compared to the pedigree-based method. The window weighting procedures performed better than single SNP weighting for CW (11%), EMA (11%), MS (3%), and YW (6%), whereas no gain in accuracy was observed for BFT. Besides, the improvement in accuracy between window WssGBLUP and the un-weighted method was low for BFT and MS, while for CW, EMA, and YW resulted in a gain of 22%, 15%, and 20%, respectively, which indicates the presence of relevant quantitative trait loci for these traits. These findings indicate that WssGBLUP is an appropriate method for traits with a large quantitative trait loci effect.

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Section: Discussionsupporting

confidence: 88%

Section: Discussionsupporting

confidence: 88%

Genomic Prediction Using Alternative Strategies of Weighted Single-Step Genomic BLUP for Yearling Weight and Carcass Traits in Hanwoo Beef Cattle

Mehrban

Naserkheil

Lee

et al. 2021

Genes

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“…This region also seems to be most significantly associated with carcass and growth traits in beef cattle (Magalhaes et al, 2016;Roberts, 2018;Zhang et al, 2019;Grigoletto et al, 2020). Positional candidate genes of FAM110B, UBXN2B, NSMAF, CYP7A1, SDCBP, and TOX have been previously reported to be associated with carcass weight in Hanwoo cattle (Lee et al, 2013;Bhuiyan et al, 2018;Naserkheil et al, 2020). For instance, Lee et al (2013) identified the six most significant SNPs associated with carcass weight in Hanwoo that were located in or nearby TOX, FAM110B, and SDCBP.…”

Section: Discussionmentioning

confidence: 96%

“…This method can also be extended to GWAS and controls the proportion of false positives by computing the posterior probability of association of a trait with each SNP or each window of consecutive SNPs. Numerous association studies have been carried out on growth and carcass traits in beef cattle using different GWAS approaches (Peters et al, 2012;Lee et al, 2013;Magalhaes et al, 2016;Weng et al, 2016;Roberts, 2018;Bedhane et al, 2019;Naserkheil et al, 2020). However, GWAS have not yet been conducted to identify significant genomic regions for carcass primal cut traits, which are highly relevant to Hanwoo cattle breeding.…”

Section: Introductionmentioning

confidence: 99%

Genome-wide Association Study for Carcass Primal Cut Yields Using Single-step Bayesian Approach in Hanwoo Cattle

et al. 2021

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The importance of meat and carcass quality is growing in beef cattle production to meet both producer and consumer demands. Primal cut yields, which reflect the body compositions of carcass, could determine the carcass grade and, consequently, command premium prices. Despite its importance, there have been few genome-wide association studies on these traits. This study aimed to identify genomic regions and putative candidate genes related to 10 primal cut traits, including tenderloin, sirloin, striploin, chuck, brisket, top round, bottom round, shank, flank, and rib in Hanwoo cattle using a single-step Bayesian regression (ssBR) approach. After genomic data quality control, 43,987 SNPs from 3,745 genotyped animals were available, of which 3,467 had phenotypic records for the analyzed traits. A total of 16 significant genomic regions (1-Mb window) were identified, of which five large-effect quantitative trait loci (QTLs) located on chromosomes 6 at 38–39 Mb, 11 at 21–22 Mb, 14 at 6–7 Mb and 26–27 Mb, and 19 at 26–27 Mb were associated with more than one trait, while the remaining 11 QTLs were trait-specific. These significant regions were harbored by 154 genes, among which TOX, FAM184B, SPP1, IBSP, PKD2, SDCBP, PIGY, LCORL, NCAPG, and ABCG2 were noteworthy. Enrichment analysis revealed biological processes and functional terms involved in growth and lipid metabolism, such as growth (GO:0040007), muscle structure development (GO:0061061), skeletal system development (GO:0001501), animal organ development (GO:0048513), lipid metabolic process (GO:0006629), response to lipid (GO:0033993), metabolic pathways (bta01100), focal adhesion (bta04510), ECM–receptor interaction (bta04512), fat digestion and absorption (bta04975), and Rap1 signaling pathway (bta04015) being the most significant for the carcass primal cut traits. Thus, identification of quantitative trait loci regions and plausible candidate genes will aid in a better understanding of the genetic and biological mechanisms regulating carcass primal cut yields.

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“…Some of which have been previously reported MS was also localized on Chr. 23 18 . In addition, there has been a population-related study of IMF in Wagyu cattle.…”

Section: Discussionmentioning

confidence: 99%

Investigation of genetic markers for intramuscular fat in the hybrid Wagyu cattle with bulked segregant analysis

Zhu

Han

Kang

et al. 2021

Sci Rep

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Abstractulked Segregant Analysis (BSA) is a rapid strategy for identifying genetic markers in specific regions of the phenotypical population and it has been widely used for QTLs mapping in smaller mixed F2 and F3 populations. We applied a modified BSA method to assessed genome-wide homozygous and heterozygous linkage patterns in the Chinese Wagyu Beef Cattle F2/F3 mixed population. Two overlapped regions from F2 and F3 populations on autosomes were found with high-density heterozygote alleles between high and low intramuscular fat groups. Regions from 24.8 M ~ 29.6 M of chromosome 23 were identified as most significantly correlated to the intramuscular fat in our samples. We also identified other 4 potential loci on chromosomes 5, 9, 15, and 21 correlated with Intramuscular fat. This study provided a novel low-cost method for QTLs mapping and identify molecular markers of phenotypical changes in a small mixed population.

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Integrating Single-Step GWAS and Bipartite Networks Reconstruction Provides Novel Insights into Yearling Weight and Carcass Traits in Hanwoo Beef Cattle

Cited by 22 publications

References 98 publications

Genomic Prediction Using Alternative Strategies of Weighted Single-Step Genomic BLUP for Yearling Weight and Carcass Traits in Hanwoo Beef Cattle

Genomic Prediction Using Alternative Strategies of Weighted Single-Step Genomic BLUP for Yearling Weight and Carcass Traits in Hanwoo Beef Cattle

Genome-wide Association Study for Carcass Primal Cut Yields Using Single-step Bayesian Approach in Hanwoo Cattle

Investigation of genetic markers for intramuscular fat in the hybrid Wagyu cattle with bulked segregant analysis

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