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Yang L, Yuan F, Rong L, Cai J, Yang S, Jia Z, Li S. Transcriptomic and Metabolomic Profile Analysis of Muscles Reveals Pathways and Biomarkers Involved in Flavor Differences between Caged and Cage-Free Chickens. Foods 2022; 11:foods11182890. [PMID: 36141015 PMCID: PMC9498551 DOI: 10.3390/foods11182890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/04/2022] [Accepted: 09/15/2022] [Indexed: 12/03/2022] Open
Abstract
The cage-free system has gained a lot of interest in recent years because it can offer chickens more freedom and is easier to manage compared with free-range rearing systems, but few studies have focused on the effect of the cage-free rearing system on meat quality and flavor. In this study, 44 Jianghan chickens were reared in caged or cage-free systems to explore the effect of different rearing systems on meat-eating quality. Sensory evaluation of cooked muscles showed that the leg muscle aroma, juiciness, and flavor intensity significantly improved by the cage-free rearing. The cage-free hens had significantly lower body weight, abdominal fat percentage, and meat fat content, but higher meat moisture content. The cage-free group had brighter breast muscle and redder leg muscle color 24 h after slaughter. Transcriptomic and metabolomic profile analysis of the leg muscle samples showed that the cage-free rearing changed biosynthesis pathways associated with glycogen metabolism, lipid and fatty acid biosynthesis and transport, muscle cellular type, and cellular components, which were related to raw meat quality. Different rearing systems also resulted in differences in glycolipid metabolism, lipid metabolism, and altered levels of intramuscular fat content and other flavor precursors. Pathways such as glycerolipid metabolism, adipocytokine signaling, and metabonomic pathways such as linoleic acid, glycerophospholipid, arginine, proline, and β-alanine metabolism may be responsible for the meat quality and flavor change.
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Affiliation(s)
- Liubin Yang
- College of Food Sciences & Technology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Fang Yuan
- College of Food Sciences & Technology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China
| | - Li Rong
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinping Cai
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Sendong Yang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Zijia Jia
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Shijun Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Smart Farming for Agricultural Animals, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
- Correspondence: ; Tel.: +86-27-8728-2091; Fax: +86-27-8728-0408
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The Potential Role of MYOM1 and ATGL Genes in Pig Production Improvement. ANNALS OF ANIMAL SCIENCE 2021. [DOI: 10.2478/aoas-2020-0102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Abstract
In the present study, two missense variants within ATGL (rs331307082) and MYOM1 (rs326001585) genes were tested for their potential usage as genetic markers related to pig production traits. The genotyping was performed on 519 pigs representing 990 synthetic sire line. The association analysis indicated that ATGL gene affected the panel of fattening parameters (test daily gain, age at slaughter), meatiness traits (meat percentage in the carcasses; the weight of loin, ham and primary cuts, and loin eye area), and meat quality characteristics (water exudation). In turn, MYOM1 polymorphism was related to loin weight, the weight of primary cuts and weight of loin backfat. Pigs with AA genotype were characterized by significantly higher loin and primary cut weights compared to opposite homozygotes GG (P<0.05). The observed differences were 2.29 kg and 1.2 kg, respectively. Moreover, despite higher meatiness, AA animals together with AG were characterized by lower weight of loin backfat (P<0.05) and average backfat thickness (P<0.1) compared to GG pigs. The MYOM1 polymorphism did not affect pork quality traits. The results allowed us to propose the new genetic markers which may be used in pig selection to obtain appropriate meatiness and fatness level in carcasses without decreasing meat quality.
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Piórkowska K, Żukowski K, Ropka-Molik K, Tyra M. Detection of genetic variants between different Polish Landrace and Puławska pigs by means of RNA-seq analysis. Anim Genet 2018; 49:215-225. [PMID: 29635698 DOI: 10.1111/age.12654] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/07/2018] [Indexed: 02/06/2023]
Abstract
Variant calling analysis based on RNA sequencing data provides information about gene variants. RNA-seq is cheaper and faster than is DNA sequencing. However, it requires individual hard filters during data processing due to post-transcriptional modifications such as splicing and RNA editing. In the present study, RNA-seq transcriptome data on two Polish pig breeds (Puławska, PUL, n = 8, and Polish Landrace, PL, n = 8) were included. The pig breeds are significantly different with regard to meat qualities such as texture, water exudation, growth traits and fat content in carcasses. A total of 2451 significant mutations were identified by a chi square tests, and functional analysis was carried out using Panther, KEGG and Kobas. Interesting missense gene variants and mutations located in regulatory regions were found in a few genes related to fatty acid metabolism and lipid storage such as ACSL5, ALDH3A2, FADS1, SCD, PLA2G12A and ATGL. A validation of mutational influences on pig traits was performed for ALDH3A2, ATGL, PLA2G12A and MYOM1 variants using association analysis including 215 pigs of the PL and PUL breeds. The ALDH3A2ENSSSCT00000019636.2:c.470T>C polymorphism was found to affect the weight of the ham and loin eye area. In turn, an ENSSSCT00000004091.2:c.2836G>A MYOM1 mutation, which could be implicated in myofibrillar network organisation, had an effect on meatiness and loin texture parameters. The study aimed to estimate the usefulness of RNA-seq results for a purpose other than differentially expressed gene analysis. The analysis performed indicated interesting gene variants that could be used in the future as markers during selection.
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Affiliation(s)
- K Piórkowska
- Department of Animal Molecular Biology, National Research Institute of Animal Production, 32-083, Balice, Poland
| | - K Żukowski
- Department of Cattle Breeding, National Research Institute of Animal Production, 32-083, Balice, Poland
| | - K Ropka-Molik
- Department of Animal Molecular Biology, National Research Institute of Animal Production, 32-083, Balice, Poland
| | - M Tyra
- Department of Pig Breeding, National Research Institute of Animal Production, 32-083, Balice, Poland
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Thekkoot DM, Young JM, Rothschild MF, Dekkers JCM. Genomewide association analysis of sow lactation performance traits in lines of Yorkshire pigs divergently selected for residual feed intake during grow-finish phase. J Anim Sci 2017; 94:2317-31. [PMID: 27285909 DOI: 10.2527/jas.2015-0258] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Lactation is an economically and biologically important phase in the life cycle of sows. Short generation intervals in nucleus herds and low heritability of traits associated with lactation along with challenges associated with collecting accurate lactation performance phenotypes emphasize the importance of using genomic tools to examine the underlying genetics of these traits. We report the first genomewide association study (GWAS) on traits associated with lactation and efficiency in 2 lines of Yorkshire pigs that were divergently selected for residual feed intake during grow-finish phase. A total of 862 farrowing records from 2 parities were analyzed using a Bayesian whole genome variable selection model (Bayes B) to locate 1-Mb regions that were most strongly associated with each trait. The GWAS was conducted separately for parity 1 and 2 records. Marker-based heritabilities ranged from 0.03 to 0.39 for parity 1 traits and from 0.06 to 0.40 for parity 2 traits. For all traits studied, around 90% of genetic variance came from a large number of genomic regions with small effects, whereas genomic regions with large effects were found to be different for the same trait measured in parity 1 and 2. The highest percentage of genetic variance explained by a 1-Mb window for each trait ranged from 0.4% for feed intake during lactation to 4.2% for back fat measured at farrowing in parity 1 sows and from 0.2% for lactation feed intake to 5.4% for protein mass loss during lactation in parity 2 sows. A total of thirteen 1-Mb nonoverlapping windows were found to explain more than 1.5% of genetic variance for either a single trait or across multiple traits. These 1-Mb windows were on chromosomes 2, 3, 6, 7, 8, 11, 14, 15, 17, and 18. The major positional candidate genes within 1 Mb upstream and downstream of these windows were , (SSC2), (SSC6) (SSC7), (SSC8), (SSC11), (SSC14), (SSC17). Further validation studies on larger populations are required to validate these findings and to improve our understanding of the biology and complex genetic architecture of traits associated with sow lactation performance.
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Dai L, Chu X, Lu F, Xu R. Detection of four polymorphisms in 5' upstream region of PNPLA2 gene and their associations with economic traits in pigs. Mol Biol Rep 2016; 43:1305-1313. [PMID: 27565982 DOI: 10.1007/s11033-016-4068-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 08/22/2016] [Indexed: 12/16/2022]
Abstract
As an important triglyceride hydrolase in mammalian cells, patatin-like phospholipase domain-containing 2 (PNPLA2) predominantly performs the first step in triglyceride hydrolysis. The objective of this study was to detect and evaluate the effects of mutations in the 5' upstream region of porcine PNPLA2 gene with fat deposition and carcass traits. Four single nuclear polymorphisms were identified, including g.161969 T>C, g.161962 A>G, g.161953 C>G and g.161904 G>T, and subsequently genotyped in five pure breeds. Three haplotypes were constructed, including H1(CGGT), H2(TACG) and H3(CACT), which were the most abundant haplotypes in Duroc (0.75), Landrace (0.78) and Chinese indigenous breeds (>0.73), respectively. Duroc individuals with the H1H1 diplotype always exhibited the lowest feed conversion ratio (FCR) (P < 0.05), while H2H2 had the thickest backfat thickness (P < 0.05). Landrace individuals with H2H3 had lower backfat thickness (P < 0.05), higher muscle thickness (P < 0.05) and estimated lean meat percentage (P < 0.05) than those with diplotype H2H2 and H3H3. Luciferase assay indicated pGL3-basic-H2 had the highest activity and pGL3-basic-H1 had the lowest activity in driving reporter gene transcription in HEK293 cells in vitro. In H1 haplotype, two GR binding sites and an ERα binding site were predicted to be introduced. While in H2 and H3, there were other transcriptional factor binding sites predicted in H2 and H3, such as Sp1, AP-2 and CAC-binding proteins, which were broadly expressed transcription factors and capable of contributing to basal promoter activity. The reduced basal promoter activity of H1 may be due to the lack of inducement for GR and ERα binding sites in HEK293 cells. The identified functional polymorphisms provide new evidence of PNPLA2 as an important candidate gene for fat deposition and carcass traits in pigs.
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Affiliation(s)
- Lihe Dai
- Key Laboratory of Animal Genetics and Breeding of Zhejiang Province, Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, People's Republic of China
| | - Xiaohong Chu
- Key Laboratory of Animal Genetics and Breeding of Zhejiang Province, Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, People's Republic of China
| | - Fuzeng Lu
- Key Laboratory of Animal Genetics and Breeding of Zhejiang Province, Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, People's Republic of China
| | - Ruhai Xu
- Key Laboratory of Animal Genetics and Breeding of Zhejiang Province, Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, People's Republic of China.
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Jiang Y, Cen W, Xing S, Chen J, Xu H, Wen A, Zhu L, Tang G, Li M, Jiang A, Li X. Tissue expression pattern and polymorphism of G0S2 gene in porcine. Gene 2014; 539:173-9. [PMID: 24487091 DOI: 10.1016/j.gene.2014.01.058] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2013] [Revised: 12/06/2013] [Accepted: 01/22/2014] [Indexed: 11/17/2022]
Abstract
Adipose triglyceride lipase (ATGL), catalyzing the initial step of hydrolysis of triacylglycerol (TAG) in adipocytes, has been known to be inhibited by G0/G1 switch protein 2 (G0S2). In this study, we determined tissue expression pattern and polymorphism of G0S2 gene in porcine. The results showed that the G0S2 transcript levels were very high in the liver and, to a lesser degree, in adipose tissues of greater omentum and suet fat; and low G0S2 transcript levels were observed in other tissues. A comparative study on the transcript levels between ATGL and G0S2 genes showed that ATGL transcript levels were high in all six adipose tissues, but negligible in the liver. Higher transcript levels were obtained for sows in adipose tissues of the inner layer of subcutaneous fat and suet fat, but higher expression values were found for boars in the liver, spleen, and stomach. 19 single nucleotide polymorphisms (SNPs), including 4 nonsynonymous SNPs (g.-307A>T, g.-394C>G, g.-565G>A, and g.-566T>C), were found in porcine G0S2 genomic DNA. Association analyses showed that the g.-565G>A and g.-742T>A SNPs were associated with back fat thickness (BFT). In conclusion, G0S2 mRNAs are abundantly expressed in porcine liver and adipose tissues of greater omentum and suet fat, and sex affects porcine G0S2 tissue transcript levels; meanwhile, the genetic diversity of porcine G0S2 gene is abundant and 2 SNPs are a genetic factor affecting BFT.
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Affiliation(s)
- Yanzhi Jiang
- College of Life and Basic Sciences, Sichuan Agricultural University, Ya'an City 625014, China.
| | - Wangmin Cen
- College of Life and Basic Sciences, Sichuan Agricultural University, Ya'an City 625014, China
| | - Shuhua Xing
- College of Life and Basic Sciences, Sichuan Agricultural University, Ya'an City 625014, China
| | - Jianning Chen
- College of Life and Basic Sciences, Sichuan Agricultural University, Ya'an City 625014, China
| | - Huaming Xu
- College of Life and Basic Sciences, Sichuan Agricultural University, Ya'an City 625014, China
| | - Anxiang Wen
- College of Life and Basic Sciences, Sichuan Agricultural University, Ya'an City 625014, China
| | - Li Zhu
- College of Animal Science and Technology, Sichuan Agricultural University, Ya'an City 625014, China
| | - Guoqing Tang
- College of Animal Science and Technology, Sichuan Agricultural University, Ya'an City 625014, China
| | - Mingzhou Li
- College of Animal Science and Technology, Sichuan Agricultural University, Ya'an City 625014, China
| | - Anan Jiang
- College of Animal Science and Technology, Sichuan Agricultural University, Ya'an City 625014, China
| | - Xuewei Li
- College of Animal Science and Technology, Sichuan Agricultural University, Ya'an City 625014, China.
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cDNA Cloning and Characterization of Adipose Triglyceride Lipase Gene in Zebra Finch (Taeniopygia guttata) and Java Sparrow (Padda oryzivora). DNA Cell Biol 2011; 30:461-8. [DOI: 10.1089/dna.2010.1168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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