Genome-Wide Detection of Copy Number Variations and Their Potential Association with Carcass and Meat Quality Traits in Pingliang Red Cattle.

Copy number variation (CNV) serves as a significant source of genetic diversity in mammals and exerts substantial effects on various complex traits. Pingliang red cattle, an outstanding indigenous resource in China, possess remarkable breeding value attributed to their tender meat and superior marbling quality. However, the genetic mechanisms influencing carcass and meat quality traits in Pingliang red cattle are not well understood. We generated a comprehensive genome-wide CNV map for Pingliang red cattle using the GGP Bovine 100K SNP chip. A total of 755 copy number variable regions (CNVRs) spanning 81.03 Mb were identified, accounting for approximately 3.24% of the bovine autosomal genome. Among these, we discovered 270 potentially breed-specific CNVRs in Pingliang red cattle, including 143 gains, 73 losses, and 54 mixed events. Functional annotation analysis revealed significant associations between these specific CNVRs and important traits such as carcass and meat quality, reproduction, exterior traits, growth traits, and health traits. Additionally, our network and transcriptome analysis highlighted CACNA2D1, CYLD, UBXN2B, TG, NADK, and ITGA9 as promising candidate genes associated with carcass weight and intramuscular fat deposition. The current study presents a genome-wide CNV map in Pingliang red cattle, highlighting breed-specific CNVRs, and transcriptome findings provide valuable insights into the underlying genetic characteristics of Pingliang red cattle. These results offer potential avenues for enhancing meat quality through a targeted breeding program.

Effect of Brachiaria decumbens as a novel supplementation on the production performance of broiler chickens.

The primary goal of this research was to elucidate the novel influence of Brachiaria decumbens supplementation on broiler chicken growth performance, nutritional digestibility, cecal microbiota, intestinal histomorphology, carcass characteristics, and meat quality. A total of 300 male day-old Ross 308 broiler chickens were randomly subjected to six different treatment groups having five replicates per treatment with 10 birds in each replicate. In treatment 1, broiler chickens were fed commercial diets with no added additives; in treatment 2, broiler chickens were offered commercial diets containing 100 mg/kg of the antibiotic oxytetracycline. However, in treatments 3, 4, 5, and 6, broiler chickens received similar commercial diets supplemented with 25 mg/kg, 50 mg/kg, 75 mg/kg, and 100 mg/kg of B. decumbens ground leaf powder, respectively, without antibiotics. Throughout the 42-day trial, the body weight gain and total feed intake for each replicate were recorded every week to determine the growth performance. Then, on 21th and 42nd day, ten broilers from each treatment (two in each replicate) were randomly selected and slaughtered to assess the digestibility of nutrients, histomorphology of the small intestine, the population of the cecal microbiota, carcass characteristics, as well as quality of both breast and drumstick muscle. There were differences (p < 0.05) in the growth performance, apparent ileal nutrient digestibility, intestinal histomorphology, carcass characteristics, and meat quality. Animals supplemented with 25 mg/kg of B. decumbens had higher growth performance and better ileal nutrient digestibility of protein, fiber, and ether extract, as well as higher villi height and carcass percentage with superior meat quality. Besides, the growth of E. faecalis during the starter phase was inhibited. In summary, B. decumbens supplementation at 25 mg/kg may be suggested as an optimal dose of as a prophylactic as well as an alternative for antibiotic growth promoter in stimulating the productivity of commercial broilers. This unconventional phytobiotic supplementation could be the key to replacing unnecessary antibiotics used in poultry feed.

Genetic parameter estimation for reproductive traits in QingYu pigs and comparison of carcass and meat quality traits to Berkshire×QingYu crossbred pigs.

OBJECTIVE: The QingYu pig is well known for its excellent meat quality attributes in Sichuan province, China. In order to improve its production efficiency, the determination of genetic factors contributing to quantifiable economic traits of livestock is important. Moreover, the cross-breeding of QingYu pigs with western breeds possessing strong growth attributes is an efficient way to improve the performance of this breed. METHODS: Here, the genetic parameters of several important reproductive traits of QingYu pigs were estimated, include total number born (TNB), number born alive, litter birth weight, individual birth weight, number of piglets weaned, litter weaning weight, and individual weaning weight. The data was analyzed using the ASReml 3.0 software (NSW Inc., Sydney, Australia). Furthermore, the effects of crossing Berkshire with QingYu (BQ) pigs on carcass and meat quality traits, as well as the effects of slaughter weight on carcass and meat quality of BQ were characterized. RESULTS: QingYu pigs exhibited superior reproductive traits. The TNB available to QingYu pigs was more than 8 per parity. The observed repeatability of the reproductive traits of the QingYu pigs was between 0.10 and 0.23. The significantly correlated genetic and phenotypic of reproduction traits were consistent. Interestingly, the BQ pigs exhibited improved carcass quality, with a significant increase in loin muscle area, lean percentage and reduction in sebum percentage. As a result, BQ had higher L45min, lower cooking scores, and lower drip loss. In addition, the loin muscle area, body length, and sebum percentage were significantly higher in 90 and 100 kg animals. Cooking loss showed a significant increase at 80 kg, and marbling increased significantly from 90 kg. CONCLUSION: The results of this study suggest that QingYu pigs exhibit excellent reproductive properties and heritability of these traits. Crossing with Berkshire is an efficient strategy to improve the carcass and meat quality of QingYu pigs for commercial operations. Furthermore, it appears as though the optimal slaughter weight of BQ pigs is at approximately 90 kg.

Potential of Endangered Local Donkey Breeds in Meat and Milk Production.

The problem of the erosion of animal genetic resources is evident in certain local donkey breeds, and their long-term sustainability can be achieved by economically repositioning them. To develop alternative and sustainable commercial programs, the meat and milk production characteristics of Istrian donkey and Littoral Dinaric donkey breeds were investigated. The meat production characteristics were examined in mature males, whose carcasses were dissected, and meat composition was determined using NIT spectrophotometry and gas chromatography. Milk yield and milk composition were determined in jennies in second or subsequent lactations by measuring milk volume and using infrared spectrometry and gas chromatography. Compared to the Littoral Dinaric donkey, the Istrian donkey has a higher carcass weight and dressing percentage (p < 0.001). The share of boneless meat in relation to live weight was 28.27% in the Istrian donkey and 26.18% in the Littoral Dinaric donkey. The absolute masses of primal cuts of meat in E, I, and II classes were significantly greater in Istrian donkeys than in Littoral Dinaric donkeys (p < 0.01), although the differences in the proportions of primal cuts were not significant. The breed did not have a significant impact on the color, pH, or meat composition. A significant influence of breed on milk yield, lactose, protein, and the fat content of milk was observed (p < 0.01). A significant influence of breed on the ratio of n-6/n-3 PUFA fatty acids in donkey milk was observed (p = 0.002). The values of the atherogenic and thrombogenic indexes were favorable, considering potential beneficial effects of donkey milk and meat on consumer health. The findings of this research suggest that local donkey breeds hold significant potential for meat and milk production, focusing on the uniqueness and quality of their products rather than the quantity of meat and milk they can produce.

Integrative Analysis Between Genome-Wide Association Study and Expression Quantitative Trait Loci Reveals Bovine Muscle Gene Expression Regulatory Polymorphisms Associated With Intramuscular Fat and Backfat Thickness.

Understanding the architecture of gene expression is fundamental to unravel the molecular mechanisms regulating complex traits in bovine, such as intramuscular fat content (IMF) and backfat thickness (BFT). These traits are economically important for the beef industry since they affect carcass and meat quality. Our main goal was to identify gene expression regulatory polymorphisms within genomic regions (QTL) associated with IMF and BFT in Nellore cattle. For that, we used RNA-Seq data from 193 Nellore steers to perform SNP calling analysis. Then, we combined the RNA-Seq SNP and a high-density SNP panel to obtain a new dataset for further genome-wide association analysis (GWAS), totaling 534,928 SNPs. GWAS was performed using the Bayes B model. Twenty-one relevant QTL were associated with our target traits. The expression quantitative trait loci (eQTL) analysis was performed using Matrix eQTL with the complete SNP dataset and 12,991 genes, revealing a total of 71,033 cis and 36,497 trans-eQTL (FDR < 0.05). Intersecting with QTL for IMF, we found 231 eQTL regulating the expression levels of 117 genes. Within those eQTL, three predicted deleterious SNPs were identified. We also identified 109 eQTL associated with BFT and affecting the expression of 54 genes. This study revealed genomic regions and regulatory SNPs associated with fat deposition in Nellore cattle. We highlight the transcription factors FOXP4, FOXO3, ZSCAN2, and EBF4, involved in lipid metabolism-related pathways. These results helped us to improve our knowledge about the genetic architecture behind important traits in cattle.

Magnolol additive improves carcass and meat quality of Linwu ducks by modulating antioxidative status.

Magnolol rich in Magnolia officinalis is a bioactive polyphenolic compound. The aim of this study was to clarify the effects of magnolol additive (MA) on carcass and meat quality, biochemical characteristics and antioxidative capacity of Linwu ducks, by comparing it to that of antibiotic additive (colistin sulphate, CS). A total of 275 49-d-old ducks were randomly assigned to 5 groups with 5 cages of 11 ducks each and fed by the diets supplemented with 0, 100, 200 and 300 mg of MA/kg and 30 mg of CS/kg for 3 weeks, respectively. The results revealed that MA administration not only increased dressed percentage (calculated as a percentage of live weight), percentage of breast muscle, leg muscle and lean meat (calculated as a percentage of eviscerated weight), but also remarkably increased a*45 min and pH45 min of leg muscle. Moreover, MA administration decreased the percentage of abdominal fat (calculated as a percentage of eviscerated weight), 45-min cooking loss, water loss rate of leg muscle, 45-min cooking loss and drip loss of breast muscle at 24 hr and 48 hr. Furthermore, MA administration enhanced the activities of superoxide dismutase and catalase in serum or liver, serum total antioxidant capacity and hepatic reduced glutathione concentration significantly, compared with the basal diet or CS group (p < .05). On the other hand, triglyceride, total cholesterol, aspartate aminotransferase, malondialdehyde, protein carbonyl and 8-hydroxy-2'-deoxyguanosine contents in serum and liver were significantly increased in Linwu ducks fed with CS, compared with MA groups (p < .05). Taken together, these data demonstrated that magnolol could effectively improve the carcass and meat quality of Linwu ducks by regulating the in vivo antioxidant status and would be a potential candidate to replace antibiotic.

Influence of Farm Management for Calves on Growth Performance and Meat Quality Traits Duration Fattening of Simmental Bulls and Heifers.

This study assessed the effects of farm management during rearing practices in the first months of a calf's life on growth performance and meat quality traits during the fattening period. A total of 48 Simmental calves were divided into two groups at a commercial cattle feedlot. In the first group were calves from the same farm and herd (n = 12 male and n = 12 female). The second group included calves from several different herds and farms (n = 12 male and n= 12 female). Calves were transferred to a feedlot and fed with a commercial feedlot ration at three to four months of age. The aim was to determine if identical fattening conditions at feedlot can reduce initial calf rearing differences between cattle during the fattening period. Bulls grew faster than heifers reaching higher total gain and showed significantly higher slaughter weight than heifers. Meat samples of heifers from the same herd had the highest intramuscular fat content and reddest color with significant differences among cattle groups. The most abundant fatty acid was oleic acid (C18:1), followed by palmitic (C16:0), stearic (C18:0), linoleic (C18:2), and myristic acid (C14:0). Meat samples of heifers from different herds were darkest with highest content of iron (Fe) with significant differences among cattle groups.

Implementation of different feeding regimes and flashing light in broiler chicks.

A 3 × 2 factorial arrangement was implemented to determine the performance of 450 Cobb broilers subjected to different feeding regimes with and without lighting programs. The chicks were divided into 3 groups according to the feeding regime (ad libitum, restricted, or intermittent), and each group was reared under one of two lighting programs (100% continuous light or 50% continuous light and 50% flashing light). The results showed that the broilers under the ad libitum and intermittent feeding regimes had superior body weight (BW) and average daily gain (ADG) values and the lowest feed conversion ratio (FCR) at 3 and 6 wk of age. Broilers exposed to flashing light and an intermittent feeding regime had the highest BW and ADG values and the lowest FCR. Birds exposed to intermittent feeding had the highest dressed carcass weight and the lowest heart weight. Broilers reared with flashing light had higher tenderness and juiciness values than the other groups. Broilers subjected to a restricted feeding regime and flashing light had the lowest abdominal fat values of all the groups. Tenderness and juiciness were significantly higher in broilers subjected to the ad libitum feeding regime × flashing light and the intermittent feeding regime × flashing light. Broilers fed an intermittent regime had the lowest spleen %, heterophil, heterophil to lymphocyte (H/L) ratio and body temperature values of all the groups, and broilers reared under the intermittent regime × flashing light had the lowest spleen %, H/L ratio and body temperature values. Non-significant differences in all health aspects (shank length, keel bone length, foot pad burns, breast blisters score, hock discoloration, and mortality) were observed among the experimental groups. In conclusion, intermittent and restricted feeding regimes and a flashing lighting program improved the FCR and did not produce any adverse effects on performance or physiological parameters. The results of this work show that intermittent feeding and flashing lighting programs are more beneficial to broiler management.

Evaluation of the four breeds in synthetic line of Jiaxing Black Pigs and Berkshire for meat quality traits, carcass characteristics, and flavor substances.

To investigate breed characteristics and the effect of hybridization of Jiaxing Black Pig (JBP) with Western breeds, the carcass and meat quality traits and flavor substances such as inosinic acids (IMP), intramuscular fat (IMF) in longissimus muscle (LM) from five breeds including JBP, Berkshire, Berkshire × JBP (BJBP), Duroc × Berkshire × JBP (DBJBP), Duroc × Landrace × JBP (DLJBP) were compared in this study. It was found that water holding capacity (WHC) of LM in JBP was significantly higher than that in the other strains (p < 0.01). Dressing out percentage and lean percentage of JBP were both significantly lower than those in the others (p < 0.01) in connection with their lighter carcass weight and higher subcutaneous fat percentage (p < 0.01). Heterosis was realized in DJBP, DBJBP, and DLJBP since their carcass weight, lean percentage, and loin eye muscle area (LEMA) were markedly higher when compared to JBP, whereas lower than those in Berkshire. Among the breeds, the content of IMF and IMP in the LM of JBP were the highest. These traits were also palpably improved in the crossbreds, especially for DBJBP, of which pork was considered outstanding for containing the most abundant essential amino acids (EAA) and total amino acids (TAA).

The effect of Piétrain sire on the performance of the progeny of two commercial dam breeds: a pig intervention study.

Genetic evaluation of Piétrain sires in Flanders occurs under standardized conditions, on test stations with fixed dam breeds, standardized diets and uniform management practices. As environmental conditions vary on commercial farms and differ from the test stations, this study aimed at understanding to what extent the sire, the dam breed and the interaction between both affects the translation of breeding values to practice. Dams of two commercial breeds were inseminated with semen from one of five different sires selected for contrasting breeding values (daily gain, feed conversion ratio and carcass quality). For each sire by dam breed combination, six pen replicates (with three gilts and three barrows per pen) were evaluated for growth performance from 9 weeks of age (20 kg) to slaughter (110 kg), and for carcass and meat quality. In our experimental setup, both sire and dam breed affected growth, carcass and meat quality traits. No significant sire×dam breed interactions on performance could be detected. Though a tendency for interaction on average daily feed intake between 20 and 110 kg (P=0.087), and on pork colour (lightness) (P=0.093) was present. In general, offspring of all tested sires behaved similarly in both dam breeds, indicating that estimated breeding values for Piétrain sires determined in one dam breed are representative in other dam breeds as well.

Genome-wide association study for carcass traits, fatty acid composition, chemical composition, sugar, and the effects of related candidate genes in Japanese Black cattle.

We performed a genome-wide association study (GWAS) and candidate gene analysis to: (i) evaluate the effectiveness of the GWAS in our small population by performing GWAS for carcass weight (CW) and fatty acid composition; (ii) detect novel candidate regions affecting non-CW carcass traits, chemical composition and sugar; and (iii) evaluate the association of the candidate genes previously detected in CW and fatty acid composition with other economically important traits. A total of 574 Japanese Black cattle and 40 657 Single nucleotide polymorphisms were used. In addition, candidate gene analyses were performed to evaluate the association of three CW-related genes and two fatty acid-related genes with carcass traits, fatty acid composition, chemical composition and sugar. The significant regions with the candidate genes were detected for CW and fatty acid composition, and these results showed that a significant region would be detectable despite the small sample size. The novel candidate regions were detected on BTA23 for crude protein and on BTA19 for fructose. CW-related genes associated with the rib-eye area and fatty acid composition were identified, and fatty acid-related genes had no relationship with other traits. Moreover, the favorable allele of CW-related genes had an unfavorable effect on fatty acid composition.

Association of PPARγ2 polymorphisms with carcass and meat quality traits in a Pietrain x Jinhua F2 population.

The PPARγ2 gene is a key regulator of both proliferation and preadipocyte differentiation in mammals. Herein its genotype and allele frequencies were analyzed using PCR-SSCP in eight pig breeds (N = 416). Two kinds of polymorphisms of the PPARγ2 gene were detected, including a previously reported shift SNP A177G (Met59Val) in exon 1 and a novel silent mutation G876A in exon 5. The results revealed that European pig breeds carry a higher allele A frequency at the A177G locus and a fixed GG genotype at the G876A locus. Allele A at the G876A locus was only found in Jinhua pigs. The association between haplotype (A177G/G876A) and carcass and meat quality traits was analyzed in a Pietrain x Jinhua F2 population (N = 248). The PPARγ2 gene was found to be significantly associated with backfat thickness at the shoulder (p < 0.05), 6-7(th) ribs (p < 0.01), last rib (p < 0.01), gluteus medius (p <0.05) and ham weight (p < 0.01). Significant effects of different haplotypes on ham weight and backfat thickness at the 6-7(th) ribs, last rib, and gluteus medius were also observed.

Association of PPARgama2 polymorphisms with carcass and meat quality traits in a Pietrain x Jinhua F2 population

The PPARγ2 gene is a key regulator of both proliferation and preadipocyte differentiation in mammals. Herein its genotype and allele frequencies were analyzed using PCR-SSCP in eight pig breeds (N = 416). Two kinds of polymorphisms of the PPARγ2 gene were detected, including a previously reported shift SNP A177G (Met59Val) in exon 1 and a novel silent mutation G876A in exon 5. The results revealed that European pig breeds carry a higher allele A frequency at the A177G locus and a fixed GG genotype at the G876A locus. Allele A at the G876A locus was only found in Jinhua pigs. The association between haplotype (A177G/G876A) and carcass and meat quality traits was analyzed in a Pietrain x Jinhua F2 population (N = 248). The PPARγ2 gene was found to be significantly associated with backfat thickness at the shoulder (p < 0.05), 6-7th ribs (p < 0.01), last rib (p < 0.01), gluteus medius (p <0.05) and ham weight (p < 0.01). Significant effects of different haplotypes on ham weight and backfat thickness at the 6-7th ribs, last rib, and gluteus medius were also observed.