Cis-eQTLs in seven duck tissues identify novel candidate genes for growth and carcass traits.

BACKGROUND: Expression quantitative trait loci (eQTL) studies aim to understand the influence of genetic variants on gene expression. The colocalization of eQTL mapping and GWAS strategy could help identify essential candidate genes and causal DNA variants vital to complex traits in human and many farm animals. However, eQTL mapping has not been conducted in ducks. It is desirable to know whether eQTLs within GWAS signals contributed to duck economic traits. RESULTS: In this study, we conducted an eQTL analysis using publicly available RNA sequencing data from 820 samples, focusing on liver, muscle, blood, adipose, ovary, spleen, and lung tissues. We identified 113,374 cis-eQTLs for 12,266 genes, a substantial fraction 39.1% of which were discovered in at least two tissues. The cis-eQTLs of blood were less conserved across tissues, while cis-eQTLs from any tissue exhibit a strong sharing pattern to liver tissue. Colocalization between cis-eQTLs and genome-wide association studies (GWAS) of 50 traits uncovered new associations between gene expression and potential loci influencing growth and carcass traits. SRSF4, GSS, and IGF2BP1 in liver, NDUFC2 in muscle, ELF3 in adipose, and RUNDC1 in blood could serve as the candidate genes for duck growth and carcass traits. CONCLUSIONS: Our findings highlight substantial differences in genetic regulation of gene expression across duck primary tissues, shedding light on potential mechanisms through which candidate genes may impact growth and carcass traits. Furthermore, this availability of eQTL data offers a valuable resource for deciphering further genetic association signals that may arise from ongoing extensive endeavors aimed at enhancing duck production traits.

Genome-wide identification of quantitative trait loci and candidate genes for seven carcass traits in a four-way intercross porcine population.

BACKGROUND: Carcass traits are essential economic traits in the commercial pig industry. However, the genetic mechanism of carcass traits is still unclear. In this study, we performed a genome-wide association study (GWAS) based on the specific-locus amplified fragment sequencing (SLAF-seq) to study seven carcass traits on 223 four-way intercross pigs, including dressing percentage (DP), number of ribs (RIB), skin thinkness (ST), carcass straight length (CSL), carcass diagonal length (CDL), loin eye width (LEW), and loin eye thickness (LET). RESULTS: A total of 227,921 high-quality single nucleotide polymorphisms (SNPs) were detected to perform GWAS. A total of 30 SNPs were identified for seven carcass traits using the mixed linear model (MLM) (p < 1.0 × 10- 5), of which 9 SNPs were located in previously reported quantitative trait loci (QTL) regions. The phenotypic variation explained (PVE) by the significant SNPs was from 2.43 to 16.32%. Furthermore, 11 candidate genes (LYPLAL1, EPC1, MATN2, ZFAT, ZBTB10, ZNF704, INHBA, SMYD3, PAK1, SPTBN2, and ACTN3) were found for carcass traits in pigs. CONCLUSIONS: The GWAS results will improve our understanding of the genetic basis of carcass traits. We hypothesized that the candidate genes associated with these discovered SNPs would offer a biological basis for enhancing the carcass quality of pigs in swine breeding.

Comparative assessment of growth performance, heat resistance and carcass traits in four poultry genotypes reared in hot-humid tropical environment.

This study investigated the impact of heat stress on growth and carcass traits in four poultry genotypes-Giriraja, Country chicken, Naked Neck and Kadaknath reared in a hot and humid tropical environment. Birds from all genotypes had ad libitum access to feed and water while being challenged with consistently high environmental temperatures in the experimental shed. Daily diurnal meteorological data were recorded inside and outside the shed. The study specifically examined growth variables and carcass characteristics. Significant differences (p < 0.01) were observed in body weight and average daily gain at various intervals. Notably, feed intake showed significant differences (p < 0.01) across weeks, indicating interactions between genotypes and time intervals. The feed conversion ratio (FCR) varied significantly (p < 0.01), with the highest FCR recorded in the Kadaknath breed. Livability percentages were similar across groups, except for Giriraja, which had significantly lower livability (p < 0.01). Carcass traits, including dressing, wings, feathers and giblet percentages, showed significant differences among genotypes (p < 0.01). Hepatic mRNA expression of growth-related genes revealed numerical variations, with Naked Neck displaying the highest (p < 0.05) fold change in IGF-1 expression compared to other genotypes. The study recognized in the Naked Neck genotype to possess higher resilience in maintaining homoeostasis and uncompromised growth under heat stress, providing valuable insights for sustainable poultry farming in challenging environmental conditions.

A meta-analysis of the meat physicochemical parameters of broiler chickens fed insect-based diet.

A total of 23 studies were identified in a literature search performed in the Scopus, Science Direct and Google Scholar databases for meta-analysis. The criteria used include studies that were published from 2015 to 2023 and those reporting the effects of insect meal utilisation in poultry diets. Data on live weight (LW), carcass weight (CW), moisture, meat pH, lightness (L*), redness (a*), yellowness (b*), proximate composition (protein, fat and ash content) and shear force in broilers were subjected to OpenMEE software, and data were pooled using a random-effect model. Subgroup analysis and meta-regression were performed to ascertain the influence of dietary insect meals on the response of meat aspects and the source of heterogeneity, respectively, using the following moderators (insect species, dosage level, feeding duration and age at slaughter). The results indicated that dietary insect meal did not affect LW, CW, meat L*, pH, shear force, moisture, fat and ash content. In contrast, dietary insect meal increased the a* of the meat (standardised mean differences (SMDs) = 1.03; 95% confidence intervals (CIs) = 0.484-1.578; p ≤ 0.001), b* (SMD = 1.117; 95% CI = 0.334-1.90; p = 0.005), and meat protein content (SMD = 0.365; 95% CI = 0.031-0.7; p = 0.032). The subgroup analysis showed that insect meal dosage of ≤10% and age at slaughtered ≤35 days had improved the LW, CW and meat L*. In addition, the meat a*, protein and ash content were also influenced by insect species, dosage levels and age at slaughter. In conclusion, ≤10% of either Hermetia illucens or Tenebrio molitor can be included in broiler diets without compromising the LW, CW, meat pH, colour, shear force, moisture, fat and ash content in broilers. The study therefore indicated that insect meals have a bright future as an alternative protein source in poultry diets.

Cull guinea pigs: carcass and non-carcass traits in males and females compared to their fattening counterparts.

Culling of guinea pigs can provide a large number of animals per year for meat production, but little information is available in the scientific literature on the carcass characteristics and non-carcass components of these animals. The objective of this study was to evaluate the carcass and non-carcass characteristics of cull guinea pigs in comparison to their fattening counterparts. Forty-eight fattening (3 months-age, 24 females and 24 males) and forty-eight cull (14 months-age, 24 females and 24 males) guinea pigs were slaughtered and carcass yield, linear measurements, tissular composition, and non-carcass components were evaluated. In general, cull guinea pigs had higher carcass, tissue, and non-carcass component weights. Cull male and both female guinea pig groups had similar carcass yields. Cull animals had higher carcass and hind leg lengths, lumbar and thoracic circumferences, and carcass compactness than their young counterparts. However, a sex effect was found for leg compactness depending on whether they were fattened or cull. Tissue percentages values were similar between fattening and culling animals of the same sex. However, females had a higher percentage of fat tissue than males. Fattening females had the best muscle to bone ratio, followed by cull males. The non-carcass elements were more represented in fattening animals than in culls, probably due to an allometric growth of the viscera in relation to the rest of the body. In commercial and cooking terms, this information is valuable for producers and researchers who need to understand the factors that influence carcass characteristics of guinea pigs.

A 14-bp deletion in bovine EPAS1 gene is associated with carcass traits.

EPAS1 (Endothelial PAS Domain Protein 1) gene is well-known for its function in plateau hypoxia adaptability. It encodes HIF-2α, which involved in the induction of genes regulated by oxygen and then affects multiple physiological processes such as angiogenesis and energy metabolism. All of these indicate it may affect the development of animals. In this study, a 14-bp deletion in EPAS1 gene was uncovered in Shandong black cattle population (n = 502). Two genotypes (II and ID) were found and the frequency of the homozygous II genotype is higher than the heterozygous ID genotype. This population is consisted with HWE (p > 0.05). And more importantly, the 14-bp deletion was associated with outside flat (p = 0.003), brisket (p = 0.001), and knuckle (p = 0.032). These findings suggested that the 14-bp deletion is significantly associated with carcass traits, which could be served as a molecular marker applied to cow breeding.

Carcass traits, proximate composition, amino acid and fatty acid profiles, and mineral contents of meat from Cherry Valley, Chinese crested, and crossbred ducks.

Duck meat is known for its taste and high nutritive value. To preserve local genetic diversity while maintaining commercial viability, we obtained a crossbreed (CB) between high-performing Cherry Valley (CV) and traditional Chinese crested (CC) ducks. We compared carcass traits and meat quality characteristics of CB and parental breeds. Meat from the above ducks at their respective marketable ages was evaluated for proximate composition, amino acid and fatty acid profiles, and selected mineral content. The live weights, carcass weights, and breast muscle percentage of CB were higher than CC but lower than CV; the leg muscle of CB was lower than CV and CC. CB had higher intramuscular fat content than CV; its collagen content was lower than CC but higher than CV in breast and thigh muscles. Additionally, the saturated fatty acid content of CB muscle was lower than CV and higher than CC. CB contained more monounsaturated fatty acids than CV and CC. Zn content was higher in CB breast than CV and CC. CB, obtained by crossing CV and CC, has partial advantages over both the breeds suggesting that these characteristics aligned with standards to breed ducks with high-quality meat.

Effect of feed efficiency on growth performance, body composition, and fat deposition in growing Hu lambs.

The present study aimed to investigate the relationship between growth performance, body composition, and fat deposition factors, and feed efficiency in growing lambs. We measured average daily feed intake (ADFI) and body weight (BW) from 653 Hu sheep that were fed a pellet diet. The residual feed intake (RFI) not significantly genetic and phenotypic correlated with the metabolic body weight (MBW) and average daily gain (ADG), but it was significantly genetic and phenotypic correlated with ADFI and the feed conversion ratio (FCR) (p < 0.01). However, the FCR was significantly associated with growth traits (p < 0.01). With the same ADG, body fat deposition was greater in animals with low feed efficiency compared with high feed efficiency. Therefore, excessive fat deposition can affect the feed efficiency of the body, and organ weight and gut-weight have a greater impact on the feed efficiency of lambs. The reticulum stomach and jejunum of lambs with a low RFI were smaller compared with that in the high RFI, indicating that lambs with a low RFI have less intake and a higher absorption rate. Small organs, such as the liver, of lambs with high FE might be associated with low energy expenditure and slow metabolism. This study provides a new perspective to study the biological processes responsible for feed efficiency variation in lambs.

Cull cow carcass traits and risk of culling of Holstein cows and 3-breed rotational crossbred cows from Viking Red, Montbéliarde, and Holstein bulls.

Culled dairy cows represent a considerable source of meat production, but their carcasses may vary greatly in quality because of the wide variation in the age, stage of lactation, breed, body condition, and other characteristics of the cows at slaughter. However, the effect of crossbreeding on the value of culled cows has so far received little investigation. The aim of this observational study was to compare a range of carcass attributes of cull cows from 3-breed rotational crossbreeding using Viking Red, Montbéliarde (MO), and Holstein (HO) bulls with those of HO purebred cows. Data on 1,814 dairy cows were collected. Cows were reared together in one herd and slaughtered in 4 slaughterhouses. The carcass weight, fleshiness, and fatness scores, the total value, and the price (€/kg) of each cow carcass were recorded. The culling of a few cows in the sample (n = 86) was classified by the farm manager as "urgent" following a diagnosis of injury or sickness, and this information was recorded. Carcass traits were analyzed with a mixed model which included the fixed effects of parity, days in milk, genetic group (purebred HO, 787 cows, and crossbred cows, classified according to the breed of sire within crossbreds, with 309, 428, and 290 cows sired by Viking Red, MO, and HO bulls, respectively), and interactions, and the random effects of month × year of the date of slaughter, and slaughterhouse. Logistic regression was used to investigate the association of parity, days in milk and purebred or crossbred origin with unplanned, "urgent" culling compared with regular culling. Average carcass weight across genetic groups was 297 ± 65 kg, average price €2.03 ± 0.53/kg, and average value €631 ± 269. Compared with HO, crossbred carcasses were 7 to 12% heavier depending on the breed of sire, were graded + 0.12 to + 0.28 units higher for fleshiness and + 0.26 to + 0.30 units higher for fatness, and fetched an 8 to 11% higher price. As a consequence, compared with purebred HO, carcasses from crossbreds had 15 to 24% higher value (€84 to €133 more per cow), with crossbred cows sired by MO showing the greatest values. Moreover, compared with the HO cows, the crossbred cows had a 37% lower risk of being urgently removed from the herd, which raises welfare concerns and may reduce the salvage value of cull cows. Because cull cows represent a supplemental source of income for dairy farmers, the greater overall value of crossbred cull cows should be taken into account in evaluating the economic effectiveness of crossbreeding schemes.

Assessment of genomic breeding values and their accuracies for carcass traits in Jeju Black cattle using whole-genome SNP chip panels.

The objective of the present study was to evaluate the breeding value and accuracy of genomic estimated breeding values (GEBVs) of carcass traits in Jeju Black cattle (JBC) using Hanwoo steers and JBC as a reference population using the single-trait animal model. Our research included genotype and phenotype information on 19,154 Hanwoo steers with 1097 JBC acting as the reference population. Likewise, the test population consisted of 418 genotyped JBC individuals with no phenotypic records for those carcass traits. For estimating the accuracy of GEBV, we divided the entire population into three groups. Hanwoo and JBC make up the first group; Hanwoo and JBC, who has both the genotype and phenotypic records, are referred to as the reference (training) population, and JBC, who lacks phenotypic information is referred to as the test (validation) population. The second group consists of the JBC (without phenotype) as the test population and Hanwoo as a reference population with phenotype and genotypic data. The only JBCs in the third group are those who have genotypic and phenotypic data on them as a reference population but no phenotypic data on them as a test population. The single-trait animal model was used in all three groups for statistical purposes. The reference populations estimated heritabilities for carcass weight (CWT), eye muscle area (EMA), backfat thickness (BF), and marbling score (MS) as 0.30, 0.26, 0.26, and 0.34 for the Hanwoo steer and 0.42, 0.27, 0.26, and 0.48 for JBC. The average accuracy for carcass traits in Group 1 was 0.80 for the Hanwoo and JBC reference population compared with 0.73 for the JBC test population. Although the average accuracy for carcass traits in Group 2 was 0.80, it was 0.80 for the Hanwoo reference population and only 0.56 for the JBC test population. The average accuracy for the JBC reference and test populations was 0.68 and 0.50, respectively, when they were included in the accuracy comparison without the Hanwoo reference population. Groups 1 and 2 used Hanwoo as reference population, which led to a better average accuracy; however, Group 3 only used the JBC reference and test population, which led to a lower average accuracy. This might be due to the fact that Group 3 used a smaller reference size than the group that came before it and that the genetic makeup of the Hanwoo and JBC breeds differed. The GEBV accuracy for MS was higher than that of other traits across all three analysis groups, followed by CWT, EMA, and BF, which may be partially explained by the MS traits' higher heritability. This study suggests that in order to achieve more accuracy, a large reference population particular to a breed should be established. Therefore, to increase the accuracy of GEBV prediction and the genetic benefit from genomic selection in JBC, individual reference breeds, and large populations are required.

Sow-Offspring Diets Supplemented with Probiotics and Synbiotics Are Associated with Offspring's Growth Performance and Meat Quality.

Probiotics and synbiotics supplementation have been shown to play potential roles in animal production. The present study aimed to evaluate the effects of dietary probiotics and synbiotics supplementation to sows during gestation and lactation and to offspring pigs (sow-offspring) on offspring pigs' growth performance and meat quality. Sixty-four healthy Bama mini-pigs were selected and randomly allocated into four groups after mating: the control, antibiotics, probiotics, and synbiotics groups. After weaning, two offspring pigs per litter were selected, and four offspring pigs from two litters were merged into one pen. The offspring pigs were fed a basal diet and the same feed additive according to their corresponding sows, representing the control group (Con group), sow-offspring antibiotics group (S-OA group), sow-offspring probiotics group (S-OP group), and sow-offspring synbiotics group (S-OS group). Eight pigs per group were euthanized and sampled at 65, 95, and 125 d old for further analyses. Our findings showed that probiotics supplementation in sow-offspring diets promoted growth and feed intake of offspring pigs during 95-125 d old. Moreover, sow-offspring diets supplemented with probiotics and synbiotics altered meat quality (meat color, pH45min, pH24h, drip loss, cooking yield, and shear force), plasma UN and AMM levels, and gene expressions associated with muscle-fiber types (MyHCI, MyHCIIa, MyHCIIx, and MyHCIIb) and muscle growth and development (Myf5, Myf6, MyoD, and MyoG). This study provides a theoretical basis for the maternal-offspring integration regulation of meat quality by dietary probiotics and synbiotics supplementation.

Variation in Acetyl-CoA Carboxylase Beta Gene and Its Effect on Carcass and Meat Traits in Gannan Yaks.

Acetyl-CoA carboxylase beta (ACACB) is a functional candidate gene that impacts fat deposition. In the present study, we sequenced exon 37-intron 37, exon 46-intron 46, and intron 47 of yak ACACB using hybrid pool sequencing to search for variants and genotyped the gene in 593 Gannan yaks via Kompetitive allele-specific polymerase chain (KASP) reaction to determine the effect of ACACB variants on carcass and meat quality traits. Seven single nucleotide polymorphisms were detected in three regions. Eight effective haplotypes and ten diplotypes were constructed. Among them, a missense variation g.50421 A > G was identified in exon 37 of ACACB, resulting in an amino acid shift from serine to glycine. Correlation analysis revealed that this variation was associated with the cooking loss rate and yak carcass weight (p = 0.024 and 0.012, respectively). The presence of haplotypes H5 and H6 decreased Warner-Bratzler shear force (p = 0.049 and 0.006, respectively), whereas that of haplotypes H3 and H4 increased cooking loss rate and eye muscle area (p = 0.004 and 0.034, respectively). Moreover, the presence of haplotype H8 decreased the drip loss rate (p = 0.019). The presence of one and two copies of haplotypes H1 and H8 decreased the drip loss rate (p = 0.028 and 0.004, respectively). However, haplotype H1 did not decrease hot carcass weight (p = 0.011), whereas H3 increased the cooking loss rate (p = 0.007). The presence of one and two copies of haplotype H6 decreased Warner-Bratzler shear force (p = 0.014). The findings of the present study suggest that genetic variations in ACACB can be a preferable biomarker for improving yak meat quality.

Rice gluten meal as a substitute for soybean meal in the diets for growing rabbits.

The impacts of different dietary levels of rice gluten meal (RGM) on growth performance, digestibility, carcass characteristics, and blood traits of growing New Zealand White (NZW) rabbits were studied. One hundred and twenty, 6 weeks old weaned male rabbits (body weight; 682 [g] ± 23) were randomly allotted into four groups. The control diet contained 160 [g/kg] soybean meal (SBM), while the other three diets were obtained by replacing 40, 80, and 120 [g/kg] SBM with RGM (RGM40, RGM80, and RGM120, respectively). The results showed that RGM contained higher levels of dry matter (DM), crude protein (CP), ether extract (EE), ash, and gross energy than SBM. RGM contained a high level of arginine followed by leucine and valine as essential amino acids and high levels of glutamic, aspartic acid, and alanine as non-essential amino acids. The obtained results showed that the final body weight of rabbits fed diets containing 40, 80, and 120 [g/kg] RGM was higher than those fed the control diet. The daily weight gain of rabbits fed RGM diets increased (p < 0.05) by 10.50%, 6.50%, and 10.00%, respectively, compared to the control group. Rabbits fed RGM80 showed the highest (p < 0.05) digestibility of DM, organic matter (OM), EE, neutral detergent fibre (NDF), and acid detergent fibre (ADF) compared to the other tested levels. Rabbits fed RGM120 had the highest (p < 0.05) digestible energy (DE) and digestible crude protein (DCP) values. RGM inclusion levels of 40 and 80 [g/kg] increased (p < 0.05) plasma total protein and albumin compared to the control group. Rabbits fed a diet containing RGM40 had the highest (p < 0.05) globulin level. The highest (p < 0.05) plasma urea concentration level was measured in the rabbit group fed the RGM120 diet. Conclusively, RGM could be a valuable ingredient for growing rabbits, as at all the tested levels improved growth performance, digestibility, and nutritional values.

Effect on growth performance, carcass traits, and myostatin gene expression in Aseel chicken fed varied levels of dietary protein in isocaloric energy diets.

A study was conducted to assess the effect of feeding different crude protein (CP) levels with isocaloric metabolizable energy (ME) diets on growth performance, carcass traits, and myostatin (MSTN) gene expression of Aseel chicken during 0 to 16 weeks of age. A total of two hundred and ten day-old Aseel chickens were randomly allotted to seven dietary treatment groups. Each group had thirty chicks distributed into three replicates of ten chicks in each. Experimental diets were formulated to have varying levels of CP, viz. 18.5, 19.0, 19.5, 20.0, 20.5, 21.0, and 21.5%, with isocaloric energy of 2800 kcal ME/kg diets of mash feed fed to birds in a completely randomized design. Different CP levels had a significant effect (P < 0.05) on the body weight gain (BWG) of Aseel chicken. At the end of 16 weeks of age, the group fed 21% CP gained 223.53 g more than the lowest CP (18.5%)-fed group. The different CP levels did not significantly (P > 0.05) influenced the feed intake of all treatment groups, but numerically highest feed intake was observed in the lowest CP (18.5%)-fed group. However, significant differences in feed efficiency (FE) appeared from the 13th week only with the 21.0% CP-fed group showing the best FE until the 16th week (3.86 to 4.06). The maximum dressing % (70.61) was observed by the 21% CP-fed group. The CP 21% diet down-regulated the MSTN gene expression in breast muscle tissue to 0.07 folds when compared to the diet of CP 20%. The best economical coordinates for maximum performance for Aseel chicken appeared to be CP of 21% and ME of 2800 kcal/kg to achieve the best FE of 3.86 at the earliest age of 13 weeks. In conclusion, 21% CP in an isocaloric diet of 2800 kcal ME/kg, in Aseel chickens, would be optimum to improve the growth performance at maximum in terms of BWG and FE up to 16 weeks of age.

Meta-analysis of blood indices and production physiology of broiler chickens on dietary fermented cassava intervention.

The effects of dietary fermented cassava on the blood constituents and production parameters of broiler chickens have been reported with variable outcomes. Therefore, this investigation aimed to explore the impacts of dietary fermented cassava on growth traits, blood constituents, visceral organ, and carcass characteristics of broiler chickens. Four databases were searched for studies that assessed responses of broiler chickens dietary fermented cassava. Eleven articles were used for the investigation, and data generated were analysed using OpenMEE software. A random effects model was used, and effect sizes were presented as standardised mean difference (SMD) at a 95 % confidence interval (CI). Sources of heterogeneity were evaluated using the following modifiers: broiler strain used, cassava form, feeding duration, type of microbes used for the fermentation, and inclusion level of cassava. Results indicate that fermented cassava-based diets increased feed intake (SMD = 0.38; 95 % CI: 0.11, 0.65; P = 0.006), feed conversion ratio (SMD = 1.26; 95 % CI: 0.91, 1.61; P < 0.001), white blood cells (SMD = 1.26; 95 % CI: 0.54, 1.98; P < 0.001), total serum protein (SMD = 1.23; 95 % CI: 0.41, 2.05; P = 0.003), serum cholesterol (SMD = 0.43; 95 % CI: 0.01, 0.85; P = 0.050), serum creatinine (SMD = 2.53; 95 % CI: 0.53, 4.53; P = 0.013), and serum uric acid (SMD = 4.33; 95 % CI: 6.25, 2.41; P < 0.001), but lowered average daily gain and carcass yield, taking heterogeneity into account. Results reveal that studied modifiers were responsible for the inconsistent results among authors. In conclusion, dietary fermented cassava negatively influenced carcass yield, growth performance, and aspects of blood indices of broiler chickens, but did not affect abdominal fat content, visceral organ weights, and cut-part weights. However, more innovative research is needed to improve the feeding quality of cassava using other biotechnological tools in order to maximise its potential as an energy source in broiler chickens.

The comparison of two different plumage-color lines of Japanese quail (Coturnix japonica) disclosed a significant effect in increasing abdominal fat contents with increasing age.

This study aimed to investigate the characteristic differences between the white and brown-feathered Japanese quails, by evaluating the carcass traits and egg fat content, blood parameters, and intestinal histopathological features. A total of 1200 1-day-old Japanese quail chicks of two varieties (brown and white-feathered) were used in this study. Live body weight and feed intake were reordered every week. At the 4th week of age, 80 birds from each variety were slaughtered and carcass quality measurements and histopathological changes were recorded. After 6 weeks of age, eggs were collected, and egg quality was assessed. The results revealed that white-feathered quails had significantly heavier body weights and higher growth rates. At 4 weeks of age, females of the white-feather quail had significantly heavier slaughter, after de-feathering, and carcass weights. Remarkable variations between the studied quail varieties, with significant dominance of females in both varieties, at the level of water holding capacity, pH, and meat tenderness ascertained an obvious superiority of white-feathered quails compared to brown ones and indicated the higher tendency of the white quails for meat production. These results were linked with significant changes in biochemical profiles including lipids biomarkers, total protein, and Ca and phosphorus levels along with variations in the intestinal morphometry. It can be concluded that white-feathered quails had, in general, higher values of productivity compared with the brown-feathered ones during growing and laying periods.

Assessment of variations in productive performance of two different plumage color varieties of Japanese quail and their reciprocal crosses.

This study aimed to detect the phenotypic differences between the brown (BB) and white (WW) feathered quails and their reciprocal crosses (BW and WB) over two successive generations. The WW and cross quails, especially the BW, had the heaviest body weights, throughout the studied period, with significant variations between the two studied generations (P<0.05). Moreover, the WW and BW possessed the largest egg production during the F1, while in the F2, the BB had superiority among the studied quails with a prominent superiority of the F2 over the F1 (P<0.05). However, the F1 had higher egg weights than F2 with superiority of WW quails compared to the others (P<0.05). Also, the WW quails had the lowest lipid contents of the eggs. These phenotypic variations among the studied quails might be preliminarily explained by the results of the analyzed microsatellite markers despite the few markers used. The high variability among the BW and WB quails might be due to the larger number of alleles (NA and Ne) and the lower values of FIS with low heterozygosity levels (HO and He). Moreover, the BW and BB were the closest, while WB and WW were the farthest because of the high and low genetic identities and the high and low genetic distance between them, respectively. So the obtained results might introduce an initial scientific basis for evaluating and employing the genetic properties of BB, WW, BW, and WB quails in further genetic improvement program, and more microsatellite markers are recommended.

A composite strategy of genome-wide association study and copy number variation analysis for carcass traits in a Duroc pig population.

BACKGROUND: Carcass traits are important in pig breeding programs for improving pork production. Understanding the genetic variants underlies complex phenotypes can help explain trait variation in pigs. In this study, we integrated a weighted single-step genome-wide association study (wssGWAS) and copy number variation (CNV) analyses to map genetic variations and genes associated with loin muscle area (LMA), loin muscle depth (LMD) and lean meat percentage (LMP) in Duroc pigs. RESULTS: Firstly, we performed a genome-wide analysis for CNV detection using GeneSeek Porcine SNP50 Bead chip data of 3770 pigs. A total of 11,100 CNVs were detected, which were aggregated by overlapping 695 CNV regions (CNVRs). Next, we investigated CNVs of pigs from the same population by whole-genome resequencing. A genome-wide analysis of 21 pigs revealed 23,856 CNVRs that were further divided into three categories (851 gain, 22,279 loss, and 726 mixed), which covered 190.8 Mb (~ 8.42%) of the pig autosomal genome. Further, the identified CNVRs were used to determine an overall validation rate of 68.5% for the CNV detection accuracy of chip data. CNVR association analyses identified one CNVR associated with LMA, one with LMD and eight with LMP after applying stringent Bonferroni correction. The wssGWAS identified eight, six and five regions explaining more than 1% of the additive genetic variance for LMA, LMD and LMP, respectively. The CNVR analyses and wssGWAS identified five common regions, of which three regions were associated with LMA and two with LMP. Four genes (DOK7, ARAP1, ELMO2 and SLC13A3) were highlighted as promising candidates according to their function. CONCLUSIONS: We determined an overall validation rate for the CNV detection accuracy of low-density chip data and constructed a genomic CNV map for Duroc pigs using resequencing, thereby proving a value genetic variation resource for pig genome research. Furthermore, our study utilized a composite genetic strategy for complex traits in pigs, which will contribute to the study for elucidating the genetic architecture that may be influenced and regulated by multiple forms of variations.

Genome-wide association study for carcass traits in Hanwoo cattle using additional relatives' information of non-genotyped animals.

The aim of this study was to find significant genomic regions associated with carcass traits in Hanwoo cattle and to compare the benefit of using additional information from non-genotyped animals. Imputed whole-genome sequence data were used along with phenotypic data on 13 715 genotyped animals as well as phenotypes of 440 284 non-genotyped animals that were offspring of 454 genotyped sires. For carcass weight, 15 083 SNPs in 33 QTL regions and 313 candidate genes were identified. We found 410 SNPs in 17 QTL regions containing 122 candidate genes for back fat thickness. In total, 656 SNPs in 19 QTLs with 137 candidate genes for eye muscle area and 79 SNPs in 12 QTL regions with 77 candidate genes were identified for marbling score. The most important candidate genes included ZFAT, TG, PLAG1, CHCHD7, and TOX for carcass weight and eye muscle area, NOG for back fat thickness, and EVOVL5 for marbling score. This study showed that the use of phenotypic records on non-genotyped progeny along with imputed whole-genome sequence data increased the power of detecting new significant genomic regions.

Effects of slaughter age on carcass traits and meat quality of crossbred (Duroc × Landrace × Yorkshire) finishing pigs.

Thirty castrated Duroc × Landrace × Yorkshire (DLY) pigs were randomly divided into three groups and slaughtered at 180, 210, and 240 days of age, respectively. Here, we found that the live weight, carcass weight, carcass length, dressing percentage, eye muscle area, backfat deposit, muscle yellowness b* value, drip loss, and cooking loss increased significantly, and the muscle pH 45 min value decreased dramatically as the slaughter age of DLY pigs extended. Moreover, increasing the slaughter age of DLY pigs could obtain higher n-3 polyunsaturated fatty acid (PUFA) percentage, crude protein, essential amino acids (EAA) contents and EAA/NEAA level, and lower n-6/n-3 PUFA level and antioxidant capacity. Together, this study suggests that the older slaughter age improves the carcass traits and nutritional value of pork, but leads to a significant decrease in pork sensory quality in DLY finishing pigs.