Identification of Candidate Genes That Specifically Regulate Subcutaneous and Intramuscular Fat Deposition Using Transcriptomic and Proteomic Profiles in Dingyuan Pigs

Abstract Background: Subcutaneous fat and intramuscular fat (IMF) deposition are closely related to meat production and pork quality. The Dingyuan pig is a local pig breed in Anhui Province, China, that has great potential for fat deposition. Individuals with extreme subcutaneous fat and intramuscular fat content can be found in this breed, which provides a good study system for investigating the molecular mechanisms regulating these two types of fat deposit.Results: In this study, we used RNA-Seq and tandem mass tags-based proteomics to analyze the key pathways and genes that specifically regulate subcutaneous fat and intramuscular fat deposition in Dingyuan pigs. We identified 191 differentially expressed genes (DEGs) and 61 differentially abundant proteins (DAPs) in the high backfat thickness (HBF) and low backfat thickness (LBF) groups. In the high intramuscular fat and low intramuscular fat groups, we found 85 DEGs and 12 DAPs. The gene ontology and KEGG pathway enrichment analysis showed that the DEGs and DAPs in the backfat groups were mainly involved in various metabolic pathways, such as those related to carbohydrates, amino acids, esters, and fatty acids, whereas the DEGs and DAPs of the IMF groups were involved in a wide range of signaling pathways, including metabolic pathways, the insulin pathway, ketone body synthesis and degradation, longevity, and some disease-related pathways. Among the genes related to the metabolic pathways of carbohydrates, amino acids, esters, and fatty acids, we found 26 candidate genes that specifically regulate subcutaneous fat deposition and 7 genes that specifically regulate IMF deposition in Dingyuan pigs.Conclusion: Our data show that subcutaneous fat deposition and IMF deposition are regulated by the same genes, but there are also genes that specifically regulate these two fat depositions. Our data provide insights into the mechanisms of pig fat deposition.

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Identification of Candidate Genes that Specifically Regulate Subcutaneous and Intramuscular Fat Deposition Using Transcriptomic and Proteomic Profiles in Dingyuan Pigs

10.21203/rs.3.rs-754325/v1 ◽

2021 ◽

Author(s):

Pan Zhang ◽

Qinggang Li ◽

Yijing Wu ◽

Yawen Zhang ◽

Hao Zhang ◽

...

Keyword(s):

Amino Acids ◽

Fatty Acids ◽

Candidate Genes ◽

Metabolic Pathways ◽

Subcutaneous Fat ◽

Intramuscular Fat ◽

Fat Deposition ◽

Backfat Thickness ◽

Pathway Enrichment Analysis ◽

Wide Range

Abstract Background: Subcutaneous fat and intramuscular fat (IMF) deposition are closely related to meat production and pork quality. The Dingyuan pig is a local pig breed in Anhui Province, China, that has great potential for fat deposition. Individuals with extreme subcutaneous fat and intramuscular fat content can be found in this breed, which provides a good study system for investigating the molecular mechanisms regulating these two types of fat deposit.Results: In this study, we used RNA-Seq and tandem mass tags-based proteomics to analyze the key pathways and genes that specifically regulate subcutaneous fat and intramuscular fat deposition in Dingyuan pigs. We identified 191 differentially expressed genes (DEGs) and 61 differentially abundant proteins (DAPs) in the high backfat thickness (HBF) and low backfat thickness (LBF) groups. In the high intramuscular fat and low intramuscular fat groups, we found 85 DEGs and 12 DAPs. The gene ontology and KEGG pathway enrichment analysis showed that the DEGs and DAPs in the backfat groups were mainly involved in various metabolic pathways, such as those related to carbohydrates, amino acids, esters, and fatty acids, whereas the DEGs and DAPs of the IMF groups were involved in a wide range of signaling pathways, including metabolic pathways, the insulin pathway, ketone body synthesis and degradation, longevity, and some disease-related pathways. Among the genes related to the metabolic pathways of carbohydrates, amino acids, esters, and fatty acids, we found 26 candidate genes that specifically regulate subcutaneous fat deposition and 7 genes that specifically regulate IMF deposition in Dingyuan pigs.Conclusion: Our data show that subcutaneous fat deposition and IMF deposition are regulated by the same genes, but there are also genes that specifically regulate these two fat depositions. Our data provide insights into the mechanisms of pig fat deposition.

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Association of leptin genotype with growth performance, adipocyte cellularity, meat quality, and fatty acid profile in beef steers fed flaxseed or high-oleate sunflower seed diets with or without triticale dried distiller’s grains

Journal of Animal Science ◽

10.1093/jas/skaa104 ◽

2020 ◽

Vol 98 (4) ◽

Author(s):

Maolong L He ◽

Kim Stanford ◽

Michael E R Dugan ◽

Leigh Marquess ◽

Tim A McAllister

Keyword(s):

Fatty Acid ◽

Growth Performance ◽

Meat Quality ◽

Sunflower Seed ◽

Subcutaneous Fat ◽

Fat Deposition ◽

Beef Steers ◽

Distiller's Grains ◽

Fat Thickness ◽

Barley Silage

Abstract Leptin genotypes can be identified as homozygous normal (CC), homozygous mutant (TT), and heterozygous (CT) based on a single-nucleotide polymorphism in exon 2 of the leptin gene, which has been associated with feed intake and fat deposition in cattle. The experiment was designed as 2 × 2 × 2 factorial with three main factors: (1) genotype (CT or TT) and diets fed 2) with or without triticale dried distiller’s grains with solubles (DDG), and 3) with either flaxseed (FS) or high-oleate sunflower seed (SS). Evaluations included growth performance, subcutaneous fat deposition, adipocyte cellularity, meat quality, and fatty acid (FA) profile of various depots. Beef steers (n = 40, 459 ± 31 kg) of either CT or TT genotypes were housed in individual pens with ad libitum access to one of the four diets: 75% steam-rolled barley + 10% barley silage with 10% FS or SS (non-DDG diets, NDG) and 46.5% barley + 10% barley silage + 30% DDG, with 8.5% FS or SS, all on a dry matter basis. Growth performance, ultrasound subcutaneous fat thickness, rib eye area (REA), and plasma FA were measured prior to and during the finishing period. At slaughter, samples of subcutaneous fat, perirenal fat, and Longissimus thoracis (LT) muscle were collected for FA analysis and carcass and meat quality were measured. Compared with CT cattle, TT tended to have less (P = 0.06) C18:2-c9,t11 (rumenic acid) in plasma and subcutaneous fat and a greater proportion (P < 0.05) of C18:0 in subcutaneous, perirenal, and LT fat. Cattle with TT genotype also tended (P < 0.1) to have more total saturated and less unsaturated (USFA) and monounsaturated fats (MUFA) and had less (P = 0.04) linoleic acid in LT. Ultrasound fat thickness, REA, and average diameter of adipocytes in subcutaneous fat at 12 wk were not affected (P > 0.39) by genotype. Generally, carcass and meat quality were similar (P > 0.1) among diets, although adding FS tended to increase (P = 0.06) total USFA of subcutaneous fat including omega-3 FA (P < 0.001). For the high-fat diets evaluated, CT cattle would have more potential to produce beef with enhanced health benefits than would TT cattle.

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RNA-Seq Analysis Reveals Hub Genes Involved in Chicken Intramuscular Fat and Abdominal Fat Deposition During Development

Frontiers in Genetics ◽

10.3389/fgene.2020.01009 ◽

2020 ◽

Vol 11 ◽

Author(s):

Siyuan Xing ◽

Ranran Liu ◽

Guiping Zhao ◽

Lu Liu ◽

Martien A. M. Groenen ◽

...

Keyword(s):

Intramuscular Fat ◽

Abdominal Fat ◽

Fat Deposition ◽

Rna Seq ◽

Hub Genes ◽

Abdominal Fat Deposition

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Relationships among carcass quality characteristics between and within carcass quartering sites

Australian Journal of Agricultural Research ◽

10.1071/a96148 ◽

1998 ◽

Vol 49 (2) ◽

pp. 285 ◽

Cited By ~ 4

Author(s):

S. Baud ◽

C. M. Wade ◽

M. E. Goddard

Keyword(s):

Water Content ◽

Subcutaneous Fat ◽

Intramuscular Fat ◽

Quality Characteristics ◽

Carcass Quality ◽

Longissimus Muscle ◽

Fat Percentage ◽

Muscle Area ◽

Intermuscular Fat ◽

Fat Thickness

Carcass quality characteristics were measured on 511 steers of 4 breeds that were destined for the Japanese market. All steers had carcass measurements taken at the 10th/11th rib interface, while 103 steers had additional measurements made on the same characteristics at the 5th/6th rib interface. Australian marbling score, longissimus muscle area, intramuscular fat percentage, intramuscular water content, Japanese intermuscular fat thickness, Japanese subcutaneous fat thickness, Japanese rib thickness, and meat pH were measured in the study. These measurements allowed the phenotypic relationships between the different carcass quality traits measured at the 10th/11th rib interface to be calculated. Significant positive correlations were observed among measurements of carcass fatness, and significant negative correlations were observed between carcass fatness and carcass water content. Angus and Murray Grey cattle had higher levels of marbling and intramuscular fat than Hereford and Poll Hereford cattle The data enabled Australian, USDA, and Japanese marbling standards to be compared on the basis of intramuscular fat percentage determined by an ether extraction process. Differences between the same carcass characteristics taken at 5th/6th and 10/11th rib interfaces of the longissimus dorsi were estimated from the 103 steers measured at both sites. Correlations between the rib sites were high for marbling, intramuscular fat, and intramuscular water, but low for longissimus muscle area, intermuscular fat thickness, and pH.

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Meat Production in a Feedlot System of Zebu—Holstein Steers and Heifers with Dairy Genetics: Productive and Biological Analyses

The Scientific World JOURNAL ◽

10.1155/2014/371968 ◽

2014 ◽

Vol 2014 ◽

pp. 1-7 ◽

Cited By ~ 2

Author(s):

Gustavo Chamon de Castro Menezes ◽

Sebastião de Campos Valadares Filho ◽

José Reinaldo Mendes Ruas ◽

Edenio Detmann ◽

Arismar de Castro Menezes ◽

...

Keyword(s):

Body Weight ◽

Dry Matter ◽

Subcutaneous Fat ◽

The Body ◽

Biological Efficiency ◽

Meat Production ◽

Net Energy ◽

Productive Performance ◽

Subcutaneous Fat Thickness ◽

Fat Thickness

The aim of this study was to evaluate the productive and biological efficiency of steers and heifers from dairy genetics in a feedlot system in terms of meat production. Twenty-four steers and 24 heifers at 10 monthes of age, (3/4) Zebu × (1/4) Holstein were utilized. They were distributed over four feedlot times, 30, 60, 90, and 120 days with four replications for each sex, and were slaughtered at the end of each period. The productive and biological analyses were performed through comparative slaughter to determine the body composition. Heifers presented with greater intakes (P<0.05) of dry matter in grams per kg of body weight. Steers presented with a greater (P<0.05) final empty body weight, carcass gain, cold carcass weight, and meat proportion in the carcass; however, heifers presented with a greater subcutaneous fat thickness (P<0.05) and, consequently, a greater (P<0.05) fat proportion in the carcass. We conclude that steers are more efficient in their productive performance than heifers in a feedlot. For the finishing carcass fat cover, heifers need 90 days in the feedlot. The net energy requirements for maintenance are 67 kcal/EBW0.75/d, and the net requirements of energy (NEg) and protein (NPg) for gain can be estimated by the following equations:NEg(Mcal/d)=0.067×EBW0.75× EBG1.095andNPg=162×EBG-5.62×REfor the two sexes.

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Effects of dietary protein and β-agonist on growth and fat deposition in prepubertal lambs

Canadian Journal of Animal Science ◽

10.4141/cjas95-032 ◽

1995 ◽

Vol 75 (2) ◽

pp. 219-224 ◽

Cited By ~ 2

Author(s):

J. Zhang ◽

D. G. Grieve ◽

B. L. Coomber

Keyword(s):

Dietary Protein ◽

Subcutaneous Fat ◽

Fat Deposition ◽

Final Body Weight ◽

Target Weight ◽

Gland Weight ◽

Two Factors ◽

Subcutaneous Fat Thickness ◽

Fat Thickness ◽

Protein Treatment

Weaned female lambs were used to study the effects of dietary protein (15 or 20%) and β-agonist (L-644,969: 0 mg kg−1 or 1 mg kg−1) on fat deposition between weaning and puberty. Lambs were fed pelleted concentrate plus 200 g hay d−1 to achieve a target weight gain of 260 g d−1. The trial continued for 102 d with dietary protein treatment starting on day 1 and β-agonist starting on day 20. Comparisons were made between the two levels in each of the two factors when there was no interaction. Carcass fat was reduced by 19.1% (P < 0.01) and carcass protein was increased by 15.8% (P < 0.01) in lambs fed the β-agonist. Carcass fat and protein were not affected by dietary protein. There was a nonsignificant trend to lower kidney-pelvic fat and subcutaneous fat thickness with the β-agonist (P > 0.1). Treatment did not affect the total mammary-gland weight, expressed as a proportion of final body weight. Neither the diameter nor the number of fat cells in kidney–pelvic fat and the MGFP were affected by dietary protein or β-agonist. Results indicate that the β-agonist is effective in the control of fat deposition other than that in the MGFP in rapidly growing female lambs. However, there was no apparent effect of dietary protein on adipose tissues. Key words: Lambs, β-agonist, dietary protein, fat deposition

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Dietary effects on beef composition: II. Quantity and distribution of fat

The Journal of Agricultural Science ◽

10.1017/s0021859600022218 ◽

1969 ◽

Vol 72 (2) ◽

pp. 297-302 ◽

Cited By ~ 4

Author(s):

H. R. Johnson ◽

R. R. Garrigus ◽

R. D. Howard ◽

N. L. Firth ◽

R. B. Harrington ◽

...

Keyword(s):

Subcutaneous Fat ◽

Intramuscular Fat ◽

Fat Deposition ◽

Corn Silage ◽

Feeding Period ◽

Early Feeding ◽

Linear Measurements ◽

Cross Sectional ◽

Feeding Regimes ◽

Intermuscular Fat

SUMMARYStudies were conducted on the quantity and distribution of fat in 104 half-sib Angus steers which had received various combinations of hay, corn silage, and corn concentrate. Groups were slaughtered at live weights of 216, 284, 340, 409, and 454 kg. The weights of mesenteric, cod, pelvic, kidney and total excess carcass fat were determined. Four linear measurements of subcutaneous fat, three cross-sectional area measurements of intermuscular fat, and the intramuscular fat in seven muscles were observed. The results showed that the feeding regimes had marked influences on the quantity and location of fat, particularly during the early feeding period (216–340 kg live wt.). Feeding hay during this period generally resulted in less fat deposition than feeding corn silage, but the suppression of intramuscular fat deposition was not evident until the animals were subsequently fed higher energy rations to heavier weights (409 and 454 kg). The results indicated that it may be possible to design dietary regimens that suppress waste fat but allow intramuscular fat to be deposited.The results described above imply that one might influence the deposition of intramuscular fat by proper design of the diet in the early feeding period. Although this possibility exists, it is noted that quantities of chemically extractable fat are not identical with quantities of marbling fat and hence changes in the former may not alter the visible quality of the meat.

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Molecular Characterization of theGhrelinandGhrelin ReceptorGenes and Effects on Fat Deposition in Chicken and Duck

Journal of Biomedicine and Biotechnology ◽

10.1155/2009/567120 ◽

2009 ◽

Vol 2009 ◽

pp. 1-12 ◽

Cited By ~ 14

Author(s):

Q. Nie ◽

M. Fang ◽

L. Xie ◽

X. Peng ◽

H. Xu ◽

...

Keyword(s):

Crude Protein ◽

Subcutaneous Fat ◽

Abdominal Fat ◽

Fat Deposition ◽

Mrna Levels ◽

Crude Protein Content ◽

Subcutaneous Fat Thickness ◽

Fat Thickness ◽

Flanking Region

Ghrelin (GHRL) and its receptor (GHSR) are involved in various bioactivities. In this study, the complete cDNA and5′flanking region of the duckGHRL(dGHRL) gene and a 3717 bp fragment of the duckGHSR(dGHSR) gene were obtained. A total of 19, 8, 43, and 48 SNPs identified in 2751, 1358, 3671, and 3567 bp of the chickenGHRL(cGHRL), chickenGHSR(cGHSR),dGHRL, anddGHSRgenes, respectively. BothcGHRLanddGHRLwere expressed predominantly in the proventriculus, whereas the highest mRNA levels ofcGHSRanddGHSRwere detected in the breast muscle and pituitary. Association analysis showed that C-2047G, A-2355C, and A-2220C of thecGHRLgene were significantly associated with abdominal fat weight (AFW;P=.01), crude protein content of leg muscle (CPCLM;P=.02), and CPCLM (P=.0009), respectively. C-1459T of the cGHSR gene was also significantly associated with CPCLM (P=.0004). C-729T of dGHRL and A3427T of dGHSR were both significantly associated with subcutaneous fat thickness (SFT;P=.04). It was indicated by this study that theGHRLandGHSRgenes were related to fat deposition in both chicken and duck.

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