Longissimus lumborum muscle transcriptome analysis of Laiwu and Yorkshire pigs differing in intramuscular fat content

Chen, Wei; Fang, Guo-feng; Wang, Shou-dong; Wang, Hui; Zeng, Yongqing

doi:10.1007/s13258-017-0540-9

Cited by 27 publications

(30 citation statements)

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“…In our results (Fig. 8, Table III), fatty acid transport-related gene (ACSL1) (Ellis et al, 2010;Widmann et al, 2011), the first step of mitochondrial fatty acid β-oxidationrelated genes (ACADS, ACADM, ACADL, and ACADVL) (Puig-Oliveras et al, 2014;Chen et al, 2017;, the last three steps of mitochondrial fatty acid β-oxidation-related genes (HADHA and HADHB) (Zha et al, 2005), the last step of the mitochondrial fatty acid β-oxidation-related gene (ACCA2) (Doi et al, 2003;Zha et al, 2005), the gene involved in peroxisomal fatty acid oxidation (ACAA1) (Wu et al, 2013) and the rate-limiting genes of mitochondrial fatty acid β-oxidation (CPT1A and CPT1B) (Kim et al, 2000;Zhang et al, 2014;Qiu et al, 2017) were all highly expressed in the LD muscle of Large White pigs, and the fatty acid synthesis-related gene (SCD) had a low expression level in the Large White group. These results indicated that the Large White pig has stronger ability of fatty acid oxidation, which might lead to fatty acid degradation and low IMF content in the LD muscle of Large White pig breeds.…”

Section: Cpt1a Acadl Acsl1 Scd Acsbg1 Acadm Acaa1 Cpt1b Acsbgsupporting

confidence: 50%

“…PPAR signaling pathway has long been considered important for fatty acid metabolism and meat quality in mammals (He et al, 2013;Wang et al, 2016), genes of which are involved in three biological processes: lipogenesis, fatty acid transport and fatty acid oxidation, that have been reported to associate with IMF deposition. The DEGs we obtained from our experiment are all involved in the three biological processes: (1) fatty acid transport (FAT/CD36, FABP1, FABP3, FABP5, ACSL1, ACSBG2, and LPL) (Bonen et al, 2004;Campbell et al, 2004;Jiang and Li, 2006;Luo et al, 2009;Ellis et al, 2010;Liu et al, 2011;Serao et al, 2011;Widmann et al, 2011;Jeong et al, 2015;, (2) fatty acid oxidation (CPT1A, CPT1B, ACAA1, ACADM, and ACADL) (Kim et al, 2000;Zha et al, 2005;Wu et al, 2013;Puig-Oliveras et al, 2014;Zhang et al, 2014;Chen et al, 2017;Qiu et al, 2017;, (3) lipogenesis (SCD) (Wang et al, 2013(Wang et al, , 2015Ros-Freixedes et al, 2016). Compared with the Min pig group, four fatty acid transport-related genes (FAT/CD36, FABP1, ACSL1, and LPL) and five fatty acid oxidation-related genes (CPT1A, CPT1B, ACAA1, ACADM, and ACADL) were highly upregulated, and the lipogenesis-related gene (SCD) was downregulated in the Large White pig group (Fig.…”

Section: Discussionmentioning

confidence: 99%

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Antagonistic Probioticity of Novel Bacterial Isolates from Pakistan against Fish Pathogen Pseudomonas fluorescens in Labeo rohita Fingerlings

Chaudhary¹,

Ahmad²,

Akram³

et al. 2021

PJZ

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Section: Cpt1a Acadl Acsl1 Scd Acsbg1 Acadm Acaa1 Cpt1b Acsbgsupporting

confidence: 50%

Section: Discussionmentioning

confidence: 99%

Antagonistic Probioticity of Novel Bacterial Isolates from Pakistan against Fish Pathogen Pseudomonas fluorescens in Labeo rohita Fingerlings

Chaudhary¹,

Ahmad²,

Akram³

et al. 2021

PJZ

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“…LW is representative of a typical Shandong black pig. As it has fresh meat and a high proportion of intramuscular fat (Chen et al, 2017), it serves as a perfect model for tracking selection for fat deposition in muscle. We therefore investigated DSRs under selection between LW and the Western pig breeds.…”

Section: Discussionmentioning

confidence: 99%

Genetic Diversities and Differentially Selected Regions Between Shandong Indigenous Pig Breeds and Western Pig Breeds

Qin

et al. 2020

Front. Genet.

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Shandong indigenous pig breeds are an invaluable source of data on genetics in Chinese pigs. However, information on the genetic basis of these breeds remains limited. In this study, we used specific-locus amplified fragment sequencing to conduct whole-genome screening to investigate genetic diversity in Shandong indigenous breeds and Western pig breeds. The results showed that Duroc pigs (DD) had clear genetic relationships with Dapulian pigs (DPL; Fst = 0.4386) and Laiwu pigs (LW; Fst = 0.5134), and DPL and LW were relatively close genetically (Fst = 0.2334). In general, Shandong indigenous breeds showed greater genetic variety than the Western breeds. Both neighbor-joining trees and principal components analyses were able to differentiate the breeds, but population structure analyses indicated that the Western breeds genetically influenced the Shandong indigenous breeds to some extent. A total of 162 differentially selected regions (DSRs) with 841 genes and 157 DSRs with 707 genes were identified in DPL and LW, respectively. Gene annotation of the selected regions identified a series of genes regulating immunity and fat deposition. Our data confirm the rationality and accuracy of the current classification of pig breeds in Shandong province. Our results point to candidate genes in Shandong indigenous pig breeds and further promote the importance of follow-up research on functional verification.

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“…Laiwu pig is an invaluable Chinese indigenous pig breed, and distributed mainly in Laiwu district, Shandong province of China. Laiwu pig has been well-known for its high proportion of intramuscular fat (IMF) [ 12 – 14 ]. The unique breed feature of Laiwu pigs has come about as a result of natural and artificial selection.…”

Section: Introductionmentioning

confidence: 99%

Genome-wide detection of selection signatures in Chinese indigenous Laiwu pigs revealed candidate genes regulating fat deposition in muscle

Chen

Wang

et al. 2018

BMC Genet

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BackgroundCurrently, genome-wide scans for positive selection signatures in commercial breed have been investigated. However, few studies have focused on selection footprints of indigenous breeds. Laiwu pig is an invaluable Chinese indigenous pig breed with extremely high proportion of intramuscular fat (IMF), and an excellent model to detect footprint as the result of natural and artificial selection for fat deposition in muscle.ResultIn this study, based on GeneSeek Genomic profiler Porcine HD data, three complementary methods, FST, iHS (integrated haplotype homozygosity score) and CLR (composite likelihood ratio), were implemented to detect selection signatures in the whole genome of Laiwu pigs. Totally, 175 candidate selected regions were obtained by at least two of the three methods, which covered 43.75 Mb genomic regions and corresponded to 1.79% of the genome sequence. Gene annotation of the selected regions revealed a list of functionally important genes for feed intake and fat deposition, reproduction, and immune response. Especially, in accordance to the phenotypic features of Laiwu pigs, among the candidate genes, we identified several genes, NPY1R, NPY5R, PIK3R1 and JAKMIP1, involved in the actions of two sets of neurons, which are central regulators in maintaining the balance between food intake and energy expenditure.ConclusionsOur results identified a number of regions showing signatures of selection, as well as a list of functionally candidate genes with potential effect on phenotypic traits, especially fat deposition in muscle. Our findings provide insights into the mechanisms of artificial selection of fat deposition and further facilitate follow-up functional studies.Electronic supplementary materialThe online version of this article (10.1186/s12863-018-0622-y) contains supplementary material, which is available to authorized users.

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Longissimus lumborum muscle transcriptome analysis of Laiwu and Yorkshire pigs differing in intramuscular fat content

Cited by 27 publications

References 29 publications

Antagonistic Probioticity of Novel Bacterial Isolates from Pakistan against Fish Pathogen Pseudomonas fluorescens in Labeo rohita Fingerlings

Antagonistic Probioticity of Novel Bacterial Isolates from Pakistan against Fish Pathogen Pseudomonas fluorescens in Labeo rohita Fingerlings

Genetic Diversities and Differentially Selected Regions Between Shandong Indigenous Pig Breeds and Western Pig Breeds

Genome-wide detection of selection signatures in Chinese indigenous Laiwu pigs revealed candidate genes regulating fat deposition in muscle

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