Polymorphisms of candidate genes associated with meat quality and disease resistance in indigenous and exotic pig breeds of Vietnam

Abstract Shenxian pigs are the only local black pig of Hebei Province, and were listed in the Genetics of Livestock and Poultry Resources of China in 2016. This breed of pig is considered to be a valuable local pig germplasm genetic resource in China. When compared with other introduced pig breeds, the Shenxian pig breed is characterized with early sexual maturity, short oestrus intervals, large litter sizes, and good meat quality, which are all of good research significance. However, the Shenxian pig variety was previously declared extinct in 2004 due to the introduction of a large number of foreign pig breeds. In order to preserve and study the Shenxian pig breed, the Hebei Zhengnong Animal Husbandry Co., Ltd. was established in Hebei Province for the purpose of preserving the purified Shenxian pig strain. In the present study, in order to understand the genetic variations of Shenxian pigs, identify selected regions related to superior traits, and accelerate the breeding processes of Shenxian pigs, the whole genome of the Shenxian pigs was resequenced and compared with that of large white pigs. The goal was to explore the germplasm characteristics of Shenxian pigs.The results obtained in this research investigation revealed that the genetic relationships of the Shenxian pig breed were complex, and that sub-populations could be identified within the general population. A total of 23M SNP sites were obtained by whole genome resequencing, and 1,509 selected sites were obtained via bioinformatics analyses. It was determined after annotation that a total of 19 genes were enriched in three items of bioengineering, molecular function, and cell composition.During this research investigation, the aforementioned 19 genes were subjected to GO and KEGG analyses. Subsequently, the candidate genes related to cell proliferation were obtained (DMTF1 and WDR5), which were considered to possibly be related to the slow growth and development of Shenxian pigs. In addition, the candidate genes related to lactation were obtained (CSN2 and CSN3). However, no genes related to meat quality traits were successfully screened.

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Haplotype Block Analysis Reveals Candidate Genes and QTLs for Meat Quality and Disease Resistance in Chinese Jiangquhai Pig Breed

Frontiers in Genetics ◽

10.3389/fgene.2020.00752 ◽

2020 ◽

Vol 11 ◽

Author(s):

Favour Oluwapelumi Oyelami ◽

Qingbo Zhao ◽

Zhong Xu ◽

Zhe Zhang ◽

Hao Sun ◽

...

Keyword(s):

Disease Resistance ◽

Candidate Genes ◽

Meat Quality ◽

Haplotype Block

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Comparative adipose transcriptome analysis digs out genes related to fat deposition in two pig breeds

Scientific Reports ◽

10.1038/s41598-019-49548-5 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 4

Author(s):

Kai Xing ◽

Kejun Wang ◽

Hong Ao ◽

Shaokang Chen ◽

Zhen Tan ◽

...

Keyword(s):

Candidate Genes ◽

Signaling Pathway ◽

Meat Quality ◽

Differentially Expressed Genes ◽

Molecular Mechanisms ◽

Mapk Signaling ◽

Fat Deposition ◽

Differentially Expressed ◽

Integrated Analysis ◽

Pig Breeds

Abstract Fatness traits are important in pigs because of their implications for fattening efficiency, meat quality, reproductive performance and immunity. Songliao black pigs and Landrace pigs show important differences in production and meat quality traits, including fatness and muscle growth. Therefore, we used a high-throughput massively parallel RNA-seq approach to identify genes differentially expressed in backfat tissue between these two breeds (six pigs in each). An average of 37.87 million reads were obtained from the 12 samples. After statistical analysis of gene expression data by edgeR, a total of 877 differentially expressed genes were detected between the two pig breeds, 205 with higher expression and 672 with lower expression in Songliao pigs. Candidate genes (LCN2, CES3, DGKB, OLR1, LEP, PGM1, PCK1, ACACB, FADS1, FADS2, MOGAT2, SREBF1, PPARGC1B) with known effects on fatness traits were included among the DEGs. A total of 1071 lncRNAs were identified, and 85 of these lncRNAs were differentially expressed, including 53 up-regulated and 32 down-regulated lncRNAs, respectively. The differentially expressed genes and lncRNAs involved in glucagon signaling pathway, glycolysis/gluconeogenesis, insulin signaling pathway, MAPK signaling pathway and so on. Integrated analysis potential trans-regulating or cis-regulating relation between DEGs and DE lncRNAs, suggested lncRNA MSTRG.2479.1 might regulate the expressed level of VLDLR affecting porcine fat metabolism. These results provide a number of candidate genes and lncRNAs potentially involved in porcine fat deposition and provide a basis for future research on the molecular mechanisms underlying in fat deposition.

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Transcriptomic Profiling of Skeletal Muscle Reveals Candidate Genes Influencing Muscle Growth and Associated Lipid Composition in Portuguese Local Pig Breeds

Animals ◽

10.3390/ani11051423 ◽

2021 ◽

Vol 11 (5) ◽

pp. 1423

Author(s):

André Albuquerque ◽

Cristina Óvilo ◽

Yolanda Núñez ◽

Rita Benítez ◽

Adrián López-Garcia ◽

...

Keyword(s):

Candidate Genes ◽

Muscle Growth ◽

Rna Seq ◽

Next Generation Sequencing Technology ◽

Pig Breeds ◽

Nfkb Activation ◽

Main Gene ◽

Slow Type ◽

Longissimus Lumborum ◽

Generation Sequencing

Gene expression is one of the main factors to influence meat quality by modulating fatty acid metabolism, composition, and deposition rates in muscle tissue. This study aimed to explore the transcriptomics of the Longissimus lumborum muscle in two local pig breeds with distinct genetic background using next-generation sequencing technology and Real-Time qPCR. RNA-seq yielded 49 differentially expressed genes between breeds, 34 overexpressed in the Alentejano (AL) and 15 in the Bísaro (BI) breed. Specific slow type myosin heavy chain components were associated with AL (MYH7) and BI (MYH3) pigs, while an overexpression of MAP3K14 in AL may be associated with their lower loin proportion, induced insulin resistance, and increased inflammatory response via NFkB activation. Overexpression of RUFY1 in AL pigs may explain the higher intramuscular (IMF) content via higher GLUT4 recruitment and consequently higher glucose uptake that can be stored as fat. Several candidate genes for lipid metabolism, excluded in the RNA-seq analysis due to low counts, such as ACLY, ADIPOQ, ELOVL6, LEP and ME1 were identified by qPCR as main gene factors defining the processes that influence meat composition and quality. These results agree with the fatter profile of the AL pig breed and adiponectin resistance can be postulated as responsible for the overexpression of MAP3K14′s coding product NIK, failing to restore insulin sensitivity.

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Key Genes Regulating Skeletal Muscle Development and Growth in Farm Animals

Animals ◽

10.3390/ani11030835 ◽

2021 ◽

Vol 11 (3) ◽

pp. 835

Author(s):

Mohammadreza Mohammadabadi ◽

Farhad Bordbar ◽

Just Jensen ◽

Min Du ◽

Wei Guo

Keyword(s):

Skeletal Muscle ◽

Candidate Genes ◽

Meat Quality ◽

Muscle Development ◽

Muscle Growth ◽

Farm Animals ◽

Meat Production ◽

Skeletal Muscle Development ◽

Extrinsic Factors ◽

Myogenic Regulatory Factor

Farm-animal species play crucial roles in satisfying demands for meat on a global scale, and they are genetically being developed to enhance the efficiency of meat production. In particular, one of the important breeders’ aims is to increase skeletal muscle growth in farm animals. The enhancement of muscle development and growth is crucial to meet consumers’ demands regarding meat quality. Fetal skeletal muscle development involves myogenesis (with myoblast proliferation, differentiation, and fusion), fibrogenesis, and adipogenesis. Typically, myogenesis is regulated by a convoluted network of intrinsic and extrinsic factors monitored by myogenic regulatory factor genes in two or three phases, as well as genes that code for kinases. Marker-assisted selection relies on candidate genes related positively or negatively to muscle development and can be a strong supplement to classical selection strategies in farm animals. This comprehensive review covers important (candidate) genes that regulate muscle development and growth in farm animals (cattle, sheep, chicken, and pig). The identification of these genes is an important step toward the goal of increasing meat yields and improves meat quality.

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Transcriptome profiling analysis of muscle tissue reveals potential candidate genes affecting water holding capacity in Chinese Simmental beef cattle

Scientific Reports ◽

10.1038/s41598-021-91373-2 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Lili Du ◽

Tianpeng Chang ◽

Bingxing An ◽

Mang Liang ◽

Xinghai Duan ◽

...

Keyword(s):

Beef Cattle ◽

Candidate Genes ◽

Molecular Mechanism ◽

Meat Quality ◽

Relevant Literature ◽

Transcriptome Profiling ◽

Water Holding Capacity ◽

Potential Candidate ◽

Protein Protein Interaction ◽

Water Holding

AbstractWater holding capacity (WHC) is an important sensory attribute that greatly influences meat quality. However, the molecular mechanism that regulates the beef WHC remains to be elucidated. In this study, the longissimus dorsi (LD) muscles of 49 Chinese Simmental beef cattle were measured for meat quality traits and subjected to RNA sequencing. WHC had significant correlation with 35 kg water loss (r = − 0.99, p < 0.01) and IMF content (r = 0.31, p < 0.05), but not with SF (r = − 0.20, p = 0.18) and pH (r = 0.11, p = 0.44). Eight individuals with the highest WHC (H-WHC) and the lowest WHC (L-WHC) were selected for transcriptome analysis. A total of 865 genes were identified as differentially expressed genes (DEGs) between two groups, of which 633 genes were up-regulated and 232 genes were down-regulated. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment revealed that DEGs were significantly enriched in 15 GO terms and 96 pathways. Additionally, based on protein–protein interaction (PPI) network, animal QTL database (QTLdb), and relevant literature, the study not only confirmed seven genes (HSPA12A, HSPA13, PPARγ, MYL2, MYPN, TPI, and ATP2A1) influenced WHC in accordance with previous studies, but also identified ATP2B4, ACTN1, ITGAV, TGFBR1, THBS1, and TEK as the most promising novel candidate genes affecting the WHC. These findings could offer important insight for exploring the molecular mechanism underlying the WHC trait and facilitate the improvement of beef quality.

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Evaluation of candidate genes related to litter traits in Indian pig breeds

Reproduction in Domestic Animals ◽

10.1111/rda.13895 ◽

2021 ◽

Author(s):

Yoya Vashi ◽

Ankit Magotra ◽

Dipjyoti Kalita ◽

Santanu Banik ◽

Nihar R. Sahoo ◽

...

Keyword(s):

Candidate Genes ◽

Pig Breeds ◽

Litter Traits

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Microstructure of Longissimus Lumborum Muscle and Meat Quality of Native Polish Pig Breeds: Złotnicka Sp Otted and Puławska

Annals of Animal Science ◽

10.1515/aoas-2016-0029 ◽

2016 ◽

Vol 16 (4) ◽

pp. 1199-1210 ◽

Cited By ~ 5

Author(s):

Joanna Bogucka ◽

Wojciech Kapelański

Keyword(s):

Meat Quality ◽

The Other ◽

Type I ◽

Large White ◽

Pig Breeds ◽

Longissimus Lumborum ◽

Fattening Pigs

Abstract In 50 fattening pigs representing two Polish native breeds: 24 Złotnicka Spotted, 10 Puławska and 16 F1 ♀ (Polish Large White × Polish Landrace) × F1 ♂ (Duroc × Pietrain) crosses microstructure of muscle, carcass and meat quality were studied. Puławska pigs had the thickest backfat, but the loin eye area was smaller only in comparison to crossbreds. Compared to the Puławska breed, the meat of Złotnicka Spotted pigs was darker, which was associated with a greater percentage of type I fibres and a smaller percentage of type IIB fibres. Puławska pigs distinguished themselves from the other groups under study by the greatest density of fibres per mm2. Smaller diameter of type IIA and IIB fibres and higher total number of fibres were found in Puławska breed pigs compared to Złotnicka Spotted, despite the absence of differences in the loin eye area. Smaller thickness of the fibres favourably affects meat quality, and might be considered an indicator of a delicate structure of meat.

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A large-scale comparison of meat quality and intramuscular fatty acid composition among three Chinese indigenous pig breeds

Meat Science ◽

10.1016/j.meatsci.2020.108182 ◽

2020 ◽

Vol 168 ◽

pp. 108182

Author(s):

Yizhong Huang ◽

Lisheng Zhou ◽

Junjie Zhang ◽

Xianxian Liu ◽

Yifeng Zhang ◽

...

Keyword(s):

Fatty Acid Composition ◽

Fatty Acid ◽

Meat Quality ◽

Acid Composition ◽

Large Scale ◽

Pig Breeds

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Genome-wide analysis of expression QTL (eQTL) and allele-specific expression (ASE) in pig muscle identifies candidate genes for meat quality traits

Genetics Selection Evolution ◽

10.1186/s12711-020-00579-x ◽

2020 ◽

Vol 52 (1) ◽

Author(s):

Yan Liu ◽

Xiaolei Liu ◽

Zhiwei Zheng ◽

Tingting Ma ◽

Ying Liu ◽

...

Keyword(s):

Candidate Genes ◽

Meat Quality ◽

Quality Traits ◽

Q Value ◽

Specific Expression ◽

Allele Specific Expression ◽

Meat Quality Traits ◽

Genome Wide ◽

A Genome ◽

Allele Specific

Abstract Background Genetic analysis of gene expression level is a promising approach for characterizing candidate genes that are involved in complex economic traits such as meat quality. In the present study, we conducted expression quantitative trait loci (eQTL) and allele-specific expression (ASE) analyses based on RNA-sequencing (RNAseq) data from the longissimus muscle of 189 Duroc × Luchuan crossed pigs in order to identify some candidate genes for meat quality traits. Results Using a genome-wide association study based on a mixed linear model, we identified 7192 cis-eQTL corresponding to 2098 cis-genes (p ≤ 1.33e-3, FDR ≤ 0.05) and 6400 trans-eQTL corresponding to 863 trans-genes (p ≤ 1.13e-6, FDR ≤ 0.05). ASE analysis using RNAseq SNPs identified 9815 significant ASE-SNPs in 2253 unique genes. Integrative analysis between the cis-eQTL and ASE target genes identified 540 common genes, including 33 genes with expression levels that were correlated with at least one meat quality trait. Among these 540 common genes, 63 have been reported previously as candidate genes for meat quality traits, such as PHKG1 (q-value = 1.67e-6 for the leading SNP in the cis-eQTL analysis), NUDT7 (q-value = 5.67e-13), FADS2 (q-value = 8.44e-5), and DGAT2 (q-value = 1.24e-3). Conclusions The present study confirmed several previously published candidate genes and identified some novel candidate genes for meat quality traits via eQTL and ASE analyses, which will be useful to prioritize candidate genes in further studies.

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