Genome-Wide Association Study and Identification of Candidate Genes for Intramuscular Fat Fatty Acid Composition in Ningxiang Pigs

Zeng, Qinghua; Gao, Hu; Yin, Shishu; Peng, Yinglin; Yang, Fang; Fu, Yawei; Deng, Xiaoxiao; Chen, Yue; Hou, Xiaohong; Wang, Qian; Jin, Zhao; Song, Gang; He, Jun; Yin, Yulong; Xu, Kang

doi:10.3390/ani13203192

Cited by 4 publications

(1 citation statement)

References 60 publications

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“…Moreover, PRKG1 knockout mice have decreased triglyceride stores in brown adipose tissue [41]. In pigs, a GWAS on fatty acid composition in 691 Ningxiang pigs revealed that PRKG1 was associated with saturated fatty acid traits [42]. According to RNA-Seq analysis, PRKG1 exhibits differential expression between high and low fatty acid composition groups in the muscle [43].…”

Section: Patterns Of Selection Signaturesmentioning

confidence: 99%

Identification of Copy Number Variations and Selection Signatures in Wannan Spotted Pigs by Whole Genome Sequencing Data: A Preliminary Study

Zhang,

Jiang,

et al. 2024

Animals

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Copy number variation (CNV) is an important structural variation used to elucidate complex economic traits. In this study, we sequenced 25 Wannan spotted pigs (WSPs) to detect their CNVs and identify their selection signatures compared with those of 10 Asian wild boars. A total of 14,161 CNVs were detected in the WSPs, accounting for 0.72% of the porcine genome. The fixation index (Fst) was used to identify the selection signatures, and 195 CNVs with the top 1% of the Fst value were selected. Eighty genes were identified in the selected CNV regions. Functional GO and KEGG analyses revealed that the genes within these selected CNVs are associated with key traits such as reproduction (GAL3ST1 and SETD2), fatty acid composition (PRKG1, ACACA, ACSL3, UGT8), immune system (LYZ), ear size (WIF1), and feed efficiency (VIPR2). The findings of this study contribute novel insights into the genetic CNVs underlying WSP characteristics and provide essential information for the protection and utilization of WSP populations.

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Section: Patterns Of Selection Signaturesmentioning

confidence: 99%

Identification of Copy Number Variations and Selection Signatures in Wannan Spotted Pigs by Whole Genome Sequencing Data: A Preliminary Study

Zhang,

Jiang,

et al. 2024

Animals

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Transcriptomic profiling of backfat and muscle in Lijiang pigs with divergent body size across growth stages

Fang,

Luo,

Jin

et al. 2024

Sci Rep

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Backfat thickness is an important economic trait that affects pork quality and flavor. The Lijiang pig (LJP), a local breed in Yunnan province, China, exhibits variations in growth and body composition. However, the molecular basis for these variations is unclear. This study aimed to analyze transcriptome profiles of backfat at different growth stages in LJP with discrepant body size: two months (M2), four months, and six months. Firstly, we analyzed the gene expression differences and discovered a significantly highest number of differentially expressed genes (DEGs) at the M2 stage. Secondly, we identified four gene profiles with reverse expression trends in LJP populations with different body sizes, and the related genes mainly associated with immune response functionality. Thirdly, we observed a lower correlation in LJP with large body size at the M2 stage, with a specific enrichment of DEGs with high genetic differentiation related to neural activity. Finally, we correlated transcriptome profiles of muscle and backfat and discovered the lowest correlation at the M2 stage. Highly correlated genes exhibited more significant differences and were prominently enriched for immune response processes. This study unveils candidate genes linked to backfat growth in LJP, emphasizing the specificity of the early growth stage of backfat. Supplementary Information The online version contains supplementary material available at 10.1038/s41598-024-78054-6.

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Candidate genes associated with fatty acid compositions in north American Atlantic salmon (Salmo salar)

Langille,

Juárez,

Prieto

et al. 2024

BMC Genomics

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Fatty acids are a requirement for normal development, however, since humans are unable to de novo produce essential fatty acids, they must be obtained from diet. Atlantic salmon is a major dietary source of nutritious and digestible fatty acids. Here, we set out to uncover the genomic basis of individual fatty acids and indices (saturated fatty acids, monounsaturated fatty acids, polyunsaturated fatty acids, n-3, and n-6) in 208 North American Atlantic salmon, to understand selection potential toward increasing relative quantities of essential fatty acids and to identify candidate genes for future research. Total n-6 (pro-inflammatory) was higher than total n-3 (anti-inflammatory) fatty acids with a ratio of 1 : 1.31 (n-3 : n-6). Heritability of fatty acids ranged from 0 to 0.99, however, most fatty acids and indices had moderate to high heritabilities (ranged from 0.20 to 0.88), implying that selection for improvement of traits could be possible. We found the same significant markers on chromosome 23 (based on false discovery rate thresholds of 2.0e-6 and suggestive significant thresholds of 2.0e-5 in Manhattan plots) in four fatty acids (γ-linoleic acid, stearidonic acid, dihimo-γ-linolenic acid, and eicosatrienoic acid), where three genes (sin3b, acbd6, and fads2) are known to be involved in lipid metabolism. These genes, fads2 in particular, would all make ideal candidates for future functional studies. In addition, there were four fatty acids with loci over the suggestive significant threshold with a variety of markers on different chromosomes (lauric acid, stearic acid, eicosatetraenoic acid (ETA), and docosadienoic acid), with associated genes that had relevant functions to fatty acids or adipose cells in general.

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Genome-Wide Association Study and Identification of Candidate Genes for Intramuscular Fat Fatty Acid Composition in Ningxiang Pigs

Cited by 4 publications

References 60 publications

Identification of Copy Number Variations and Selection Signatures in Wannan Spotted Pigs by Whole Genome Sequencing Data: A Preliminary Study

Identification of Copy Number Variations and Selection Signatures in Wannan Spotted Pigs by Whole Genome Sequencing Data: A Preliminary Study

Transcriptomic profiling of backfat and muscle in Lijiang pigs with divergent body size across growth stages

Candidate genes associated with fatty acid compositions in north American Atlantic salmon (Salmo salar)

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