Important candidate genes for abdominal fat content identified by linkage disequilibrium and fixation index information

Wei, Na; Yu, Jiaqiang; Xu, Zi-Chun; Zhang, Xinyang; Yang, Lili; Zhi, Cao; Li, Hui; Zhang, Hui

doi:10.3382/ps/pey426

Cited by 9 publications

(8 citation statements)

References 46 publications

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“…Population structure was assessed using MDS and phylogenetic tree analysis, which confirmed the effectiveness of the selection program and the different selection directions of the two lines. After long-term selection for the IMF content, the chromosome regions that harbor important genes for IMF deposition may exhibit different allele or haplotype frequencies [25]. The F ST is a commonly used method to detect selection signatures between lines or breeds in domestic animals [26,27] and could be used as an additional source of information in genomic selection analysis [28].…”

Section: Identified Genes and Pathways Related To Lipid Metabolism Bementioning

confidence: 99%

“…However, it is unavoidable to yield false signatures depending on a single approach. Na et al [25] tried to use F ST and hapFLK to explore selection signatures for chicken abdominal fat deposition, while there was no overlap between two methods. Therefore, the relative gene expression was used to verify the reliability of the results in this study.…”

Section: Necessity For Further Studiesmentioning

confidence: 99%

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Effect of Divergent Selection for Intramuscular Fat Content on Muscle Lipid Metabolism in Chickens

Liu

Cui

Xing

et al. 2019

Animals

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Simple Summary: Intramuscular fat is an important factor affecting meat quality and consumer acceptance. Appropriate increases in the intramuscular fat content contribute to the improvement of meat quality, and genetic selection is an effective method to increase the intramuscular fat content in chickens. In this study, chicken lines divergently selected for their intramuscular fat content were used to investigate the mechanisms behind differential intramuscular fat deposition. These results found in this study may contribute to the improvement of meat quality in chickens.Abstract: Intramuscular fat (IMF)-an important factor affecting meat quality-can be appropriately increased by genetic selection. Chicken lines divergently selected for IMF content were used in this study to investigate the mechanisms behind differential IMF deposition. Sixty 15th generation chickens were genotyped using the IASCHICK 55K single nucleotide polymorphism (SNP) chip. After quality control, 59 chickens and 36,893 SNPs were available for subsequent analysis. Population structure assessment indicated that the lines were genetically differentiated. Based on the top 1% paired fixation index values, three pathways were significantly (p < 0.05) enriched, and nine genes were considered candidate genes for differential IMF deposition. Differences between the lines in the expressions of representative genes involved in the above pathways were detected in 16th generation chickens. This study suggests that genetic selection for increased IMF in the pectoralis major muscle may enhance fatty acid synthesis, transport, and esterification, and reduce triglyceride hydrolysis. The peroxisome proliferator-activated receptor (PPAR) signaling pathway, glycerolipid metabolism, and fatty acid degradation pathway may have contributed to the differences in IMF deposition between the lines. These results contribute to the understanding of the genetic mechanisms behind IMF deposition, and the improvement of chicken meat quality.

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Section: Identified Genes and Pathways Related To Lipid Metabolism Bementioning

confidence: 99%

Section: Necessity For Further Studiesmentioning

confidence: 99%

Effect of Divergent Selection for Intramuscular Fat Content on Muscle Lipid Metabolism in Chickens

Liu

Cui

Xing

et al. 2019

Animals

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“…Therefore, controlling the excessive abdominal fat deposition is an important long-term goal of native chicken breeding. Over the past several decades, though a number of candidate genes and genetic variations that could potentially affect fat deposition have been identified by different genetic analysis approaches in various chicken populations ( Jin et al, 2017 ; Chen et al, 2019 ; Mu et al, 2019 ; Na et al, 2019 ; Xing et al, 2020 ; Zhou et al, 2020 ; Wang et al., 2021a ; Wang et al., 2021b ; Xing et al, 2021 ; Yuan and Lu, 2021 ), the mechanisms underlying the abdominal fat deposition still remain poorly understood in chickens.…”

Section: Introductionmentioning

confidence: 99%

GPNMB promotes abdominal fat deposition in chickens: genetic variation, expressional profile, biological function, and transcriptional regulation

et al. 2022

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“…Although the exact function or effect of the FAM234A (also known as ITFG3) gene was not entirely clear, it is shown to be of genome-wide significance for abdominal fat weight in chicken [106]. Previous studies revealed the mitochondrial ribosomal protein L28 (MRPL28) as an important gene for abdominal fat deposition in chicken [107] and as obesity-related gene in mice [108].…”

Section: Gene Content Of Significant Cnv Regionsmentioning

confidence: 99%

Identificação de CNVR associadas à qualidade de carcaça e carne em bovinos da raça Nelore

Andrade¹

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The proposal of the study was to identify structural variants in the genome, named as CNVs (copy number variations), and investigate the association of CNVRs (copy number variation regions) with carcass and meat quality traits in 658 Nellore bulls with evaluation of hot carcass weight (HCW), rib-eye area (REA), subcutaneous backfat thickness (SBT), meat tenderness (TD) after 7, 14 and 21 days of aging, intramuscular fat content (IFC) and intramuscular cholesterol content (ICC). Among those, 407 animals were genotyped with the Illumina Bovine beadchip HD ® (777,962 SNPs). The PennCNV software was used to identify CNVs, which were concatenated and associated with the traits of interest by the CNVRuler program. Finally, genes overlapping total or partially the significant CNVRs (p<0.05) were identified by the BioMart package from R software using the UMD3.1 version of the bovine genome. In total, 2,119 distinct CNVs, representing 1,248 single duplications, 5 double replications, 794 single deletions and 72 double deletions, were identified. The CNVs were condensed into 475 CNVRs, covering 2.29% of the bovine genome. Of those, 59 CNVRs were significantly associated with the analyzed traits. Some genes identified in the significant CNV regions showed putative pleiotropic effect on carcass and meat quality traits, being involved in biological processes related to the immune system, cellular membrane structure, ATP binding and olfactory receptors. The identification of CNVs along the bovine genome and the association of CNVRs with carcass and meat quality traits in Nellore cattle may improve our knowledge on the biological architecture of these complex traits. In addition to enabling the development of novel selection strategies.

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Important candidate genes for abdominal fat content identified by linkage disequilibrium and fixation index information

Cited by 9 publications

References 46 publications

Effect of Divergent Selection for Intramuscular Fat Content on Muscle Lipid Metabolism in Chickens

Effect of Divergent Selection for Intramuscular Fat Content on Muscle Lipid Metabolism in Chickens

GPNMB promotes abdominal fat deposition in chickens: genetic variation, expressional profile, biological function, and transcriptional regulation

Identificação de CNVR associadas à qualidade de carcaça e carne em bovinos da raça Nelore

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