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Objective: The aim of the study was to evaluate the influence of gene polymorphisms and nongenetic factors on the somatic cell score (SCS) in the milk of Holstein (n = 148) and Simmental (n = 73) cows and their crosses (n = 6).Methods: The SCS was calculated by the formula SCS = log2(SCC/100,000)+3, where SCC is the somatic cell count. Polymorphisms in the casein alpha S1 (CSN1S1), beta-casein (CSN2), kappa-casein (CSN3), beta-lactoglobulin (LGB), acyl-CoA diacylglycerol transferase 1 (DGAT1), leptin (LEP), fatty acid synthase (FASN), stearoyl CoA desaturase 1 (SCD1), and 1-acylglycerol-3-phosphate O-acyltransferase 6 (AGPAT6) genes were genotyped, and association analysis to the SCS in the cow’s milk was performed. Further, the impact of breed, farm, year, month of the year, lactation stage and parity on the SCS were analysed. Phenotype correlations among SCS and milk constituents were computed by Pearson correlation coefficients.Results: Only CSN2 genotypes A1/A2 were found to have significant association with the SCS (p

Objective: Runs of homozygosity (ROH) are contiguous lengths of homozygous genotypes that can reveal inbreeding levels, selection pressure, and mating schemes. In this study, ROHs were evaluated in Wannan Black pigs to assess the inbreeding levels and the genome regions with high ROH frequency.Methods: In a previous study, we obtained 501.52 GB of raw data from resequencing (10×) of the genome and identified 21,316,754 single-nucleotide variants in 20 Wannan Black pig samples. We investigated the number, length, and frequency of ROH using resequencing data to characterize the homozygosity in Wannan Black pigs and identified genomic regions with high ROH frequencies.Results: In this work, 1,813 ROHs (837 ROHs in 100 to 500 kb, 449 ROHs in 500 to 1,000 kb, 527 ROHs in >1,000 kb) were identified in all samples, and the average genomic inbreeding coefficient (FROH) in Wannan Black pigs was 0.5234. Sixty-one regions on chromosomes 2, 3, 7, 8, 13, 15, and 16 harbored ROH islands. In total, 105 genes were identified in 42 ROH islands, among which some genes were related to production traits.Conclusion: This is the first study to identify ROH across the genome of Wannan Black pigs, the Chinese native breed of the Anhui province. Overall, Wannan Black pigs have high levels of inbreeding due to the influence of ancient and recent inbreeding due to the genome. These findings are a reliable resource for future studies and contribute to save and use the germplasm resources of Wannan Black pigs.

Objective: Growth hormone (GH) and insulin-like growth factor I (IGF-I) play a critical role in animal growth rates. We aimed to investigate the effect of GH and IGF-I genotypes on body weight (BW), dominance, and gene expression in slow-growing chickens at different ages.Methods: A total of 613 Korat chickens (KRs) were bred and divided into three groups by genotype – A1A1, A1A3, and A3A3 for GH and AA, AC, and CC for IGF-I. Chickens were weighed every two weeks, and liver and breast muscle tissues were collected at 10 weeks of age. Genetic parameters of KRs were estimated using ASReml software. The GH and IGF-I mRNA levels were measured by quantitative polymerase chain reaction. Significant differences between traits were analyzed using the generalized linear model.Results: A significant effect of GH genotypes on BW was found at most ages, and the A1A1 genotype had the highest value of BW. Compared with the A3A3 genotype, the A1A1 and A1A3 genotypes showed a higher dominance effect at 0 and 2 weeks, and genotype A1A1 had the highest value of dominance at 8 weeks of age. A difference in GH mRNA levels between genotypes was detected in breast muscle at 6 weeks and in the liver tissue at 2 weeks. In the case of IGF-I gene, the AA genotype had the highest BW at the beginning of life. Significant differences in BW dominance were found at 2 weeks. However, IGF-I mRNA levels were not different among genotypes in both breast muscles and liver tissues.Conclusion: Our results revealed that GH and IGF-I influence growth, but may not be involved in heterosis. GH can be used as a marker gene in selection programs for growth because the homozygous genotype (A1A1) had the highest BW at all ages. The IGF-I is not a useful marker gene for selection programs.

Objective: Owing to the lack of a breeding index for efficient and quick fertility evaluations of Holstein bulls when using traditional or genome-wide detection methods, this study aimed to determine whether in vitro fertilization (IVF) could be used as an indicator of conception rate of artificial insemination (AI).Methods: Conventional and sexed frozen semen from nine bulls were used for IVF and AI.Results: The IVF and AI conception rates of each bull were confirmed to be positively correlated between the conventional frozen and sexed frozen semen. The correlation coefficient R values of nine bulls between IVF and AI methods were 0.73 and 0.97 for the conventional frozen and sexed frozen semen, respectively. The average conception rate of three bulls undergoing AI was 69.5% and 64.2%, 61.8% and 58.8%, and 48.2% and 46.2% in first-, second-, and third-born cows when conventional frozen and sexed frozen semen were used, respectively, which showed a positive correlation with the fertilization rate in the same parity. We propose an evaluation standard to assess the fertilization ability of bulls based on their IVF test results, which is categorized into three grades: grade one, normal fertility bull with an AI conception rate of 40%±5% and IVF rate of 45% to 60%; grade two, higher fertility bull with an AI conception rate of 50%±5% and IVF rate of 61% to 80%; and grade three, highest fertility bull with an AI conception rate of 60%±5% and IVF rate of >80%.Conclusion: These findings reveal that IVF results can be used as a breeding index for bulls to evaluate their AI conception ability, which may shorten the time required to select bulls for breeding.

Objective: Microminipig (MMP) is a miniature pig with an extra small body size for experimental use. In the present study, the occurrence of stillbirths and their genetic association with swine leukocyte antigen (SLA) class II haplotypes were evaluated in a population of MMPs.Methods: The occurrences of stillbirth and genetic association with SLA class II haplotypes using 483 stillborn and 2,246 live piglets, and their parents were compared among the three groups of newborn piglet litters; an all stillborn (AS) group consisting of only stillborn piglet litters, a partial stillborn (PS) group consisting of stillborn and live piglet litters, and an all alive (AA) group consisting of only live piglet litters.Results: The incidence of stillborn piglets was 483/2,729 (17.7%). Distributions of litter sizes, numbers of stillborn piglets in a litter, parities, and gestation periods were distinct among the three groups. The frequencies of low resolution haplotype (Lr)-0.7 or Lr-0.23 were higher in the AS group than in the PS or AA groups. In sires, the frequency of Lr-0.7 associated with the AS group was significantly higher in the AS group than with the AA group. In dams, the frequency of Lr-0.23 was significantly higher in the AS group than in the PS or AA groups, whereas the frequency of Lr-0.7 was not significantly different.Conclusion: The incidence of stillborn piglets in MMPs appears to be higher than those in other pig breeds. Several traits related with stillbirths such as the number of stillborn piglets and parities of the AS group were different from those of the PS and AA groups. Specific SLA class II haplotypes were associated significantly with a high incidence of stillbirths and could be used as genetic markers to adopt breeding strategies to lower the rate of stillbirth in MMPs.

Objective: This study investigates the expression patterns of toll-like receptors (TLRs) and intracellular mediators in horse muscle cells after exercise, and the relationship between TLRS expression in stressed horse muscle cells and immune cell migration toward them.Methods: The expression patterns of the TLRs (TLR2, TLR4, and TLR8) and downstream signaling pathway-related genes (myeloid differentiation primary response 88 [MYD88]; activating transcription factor 3 [ATF3]) are examined in horse tissues, and horse peripheral blood mononuclear cells (PBMCs), polymorphonuclear cells (PMNs) and muscles in response to exercise, using the quantitative reverse transcription-polymerase chain reaction (qPCR). Expressions of chemokine receptor genes, i.e., C-X-C motif chemokine receptor 2 (CXCR2) and C-C motif chemokine receptor 5 (CCR5), are studied in PBMCs and PMNs. A horse muscle cell line is developed by transfecting SV-T antigen into fetal muscle cells, followed by examination of muscle-specific genes. Horse muscle cells are treated with stressors, i.e., cortisol, hydrogen peroxide (H2O2), and heat, to mimic stress conditions in vitro, and the expression of TLR4 and TLR8 are examined in stressed muscle cells, in addition to migration activity of PBMCs toward stressed muscle cells.Results: The qPCR revealed that TLR4 message was expressed in cerebrum, cerebellum, thymus, lung, liver, kidney, and muscle, whereas TLR8 expressed in thymus, lung, and kidney, while TLR2 expressed in thymus, lung, and kidney. Expressions of TLRs, i.e., TLR4 and TLR8, and mediators, i.e., MYD88 and ATF3, were upregulated in muscle, PBMCs and PMNs in response to exercise. Expressions of CXCR2 and CCR5 were also upregulated in PBMCs and PMNs after exercise. In the muscle cell line, TLR4 and TLR8 expressions were upregulated when cells were treated with stressors such as cortisol, H2O2, and heat. Migration of PBMCs toward stressed muscle cells was increased by exercise and oxidative stresses, and combinations of these. Treatment with methylsulfonylmethane (MSM), an antioxidant on stressed muscle cells, reduced migration of PBMCs toward stressed muscle cells.Conclusion: In this study, we have successfully cultured horse skeletal muscle cells, isolated horse PBMCs, and established an in vitro system for studying stress-related gene expressions and function. Expression of TLR4, TLR8, CXCR2, and CCR5 in horse muscle cells was higher in response to stressors such as cortisol, H2O2, and heat, or combinations of these. In addition, migration of PBMCs toward muscle cells was increased when muscle cells were under stress, but inhibition of reactive oxygen species by MSM modulated migratory activity of PBMCs to stressed muscle cells. Further study is necessary to investigate the biological function(s) of the TLR gene family in horse muscle cells.

Objective: With the rapid development of proteomics sequencing and RNA sequencing technology, multi-omics analysis has become a current research hotspot. Our previous study indicated that Xinjiang brown cattle have better meat quality than Kazakh cattle. In this study, Xinjiang brown cattle and Kazakh cattle were used as the research objects.Methods: Proteome sequencing and RNA sequencing technology were used to analyze the proteome and transcriptome of the longissimus dorsi muscle of the two breeds of adult steers (n = 3).Results: In this project, 22,677 transcripts and 1,874 proteins were identified through quantitative analysis of the transcriptome and proteome. By comparing the identified transcriptome and proteome, we found that 1,737 genes were identified at both the transcriptome and proteome levels. The results of the study revealed 12 differentially expressed genes and proteins: troponin I1, crystallin alpha B, cysteine, and glycine rich protein 3, phosphotriesterase-related, myosin-binding protein H, glutathione s-transferase mu 3, myosin light chain 3, nidogen 2, dihydropyrimidinase like 2, glutamate-oxaloacetic transaminase 1, receptor accessory protein 5, and aspartoacylase. We performed functional enrichment of these differentially expressed genes and proteins. The Kyoto encyclopedia of genes and genomes results showed that these differentially expressed genes and proteins are enriched in the fatty acid degradation and histidine metabolism signaling pathways. We performed parallel reaction monitoring (PRM) verification of the differentially expressed proteins, and the PRM results were consistent with the sequencing results.Conclusion: Our study provided and identified the differentially expressed genes and proteins. In addition, identifying functional genes and proteins with important breeding value will provide genetic resources and technical support for the breeding and industrialization of new genetically modified beef cattle breeds.

Objective: The aim was to characterize the genetic diversity evolution of the registered Mexican Charolais cattle population by pedigree analysis. Methods: Data consisted of 331,390 pedigree records of animals born from 1934 to 2018. Average complete generation equivalent, generation interval, effective population size (Ne), and effective numbers of founders (fe), ancestors (fa), and founder genomes (Ng) were calculated for seven five-year periods. The inbreeding coefficient was calculated per year of birth, from 1984 to 2018, whereas the gene contribution of the most influential ancestors was calculated for the latter period. Results: Average complete generation equivalent consistently increased across periods, from 4.76, for the first period (1984 through 1988), to 7.86, for the last period (2014 through 2018). The inbreeding coefficient showed a relative steadiness across the last seventeen years, oscillating from 0.0110 to 0.0145. During the last period, the average generation interval for the father-offspring pathways was nearly 1 yr. longer than that of the mother-offspring pathways. The effective population size increased steadily since 1984 (105.0) and until 2013 (237.1), but showed a minor decline from 2013 to 2018 (233.2). The population displayed an increase in the fa since 1984 and until 2008; however, showed a small decrease during the last decade. The effective number of founder genomes increased from 1984 to 2003, but revealed loss of genetic variability during the last fifteen years (from 136.4 to 127.7). The fa:fe ratio suggests that the genetic diversity loss was partially caused by formation of genetic bottlenecks in the pedigree; in addition, the Ng:fa ratio indicates loss of founder alleles due to genetic drift. The most influential ancestor explained 1.8% of the total genetic variability in the progeny born from 2014 to 2018. Conclusion: Inbreeding, Ne, fa, and Ng are rather beyond critical levels; therefore, the current genetic status of the population is not at risk.

Objective: Ovarian follicular development, which dependent on the proliferation and differentiation of granulosa cells (GCs), is a complex biological process in which miRNA plays an important role. Our previous study showed that miR-458b-5p is associated with ovarian follicular development in chicken. The detailed function and molecular mechanism of miR-458b-5p in GCs is unclear.Methods: The luciferase reporter assay was used to verify the targeting relationship between miR-458b-5p and catenin beta-1 (CTNNB1), which is an important transcriptional regulatory factor of the Wnt/β-catenin pathway. The cell counting kit-8 (CCK-8) assay, flow cytometry with propidium iodide (PI) and annexin V-fluorescein isothiocyanate (FITC) labeling were applied to explore the effect of miR-458b-5p on proliferation, cell cycle and apoptosis of chicken GCs. Quantitative real-time polymerase chain reaction and Western blot were used to detect the mRNA and protein expression levels.Results: We demonstrated that the expression of miR-458b-5p and CTNNB1 showed the opposite relationship in GCs and theca cells of hierarchical follicles. The luciferase reporter assay confirmed that CTNNB1 is the direct target of miR-458b-5p. Using CCK-8 assay and flow cytometry with PI and Annexin V-FITC labeling, we observed that transfection with the miR-458b-5p mimics significantly reduced proliferation and has no effects on apoptosis of chicken GCs. In addition, miR-458b-5p decreased the mRNA and protein expression of CD44 molecule and matrix metallopeptidase 7, which are the downstream effectors of CTNNB1 in Wnt/β-Catenin pathway and play functional roles in cell proliferation.Conclusion: Taken together, the data indicate that miR-458b-5p regulates ovarian GCs proliferation through Wnt/β-catenin signaling pathway by targeting CTNNB1, suggesting that miR-458b-5p and its target gene CTNNB1 may potentially play a role in chicken ovarian follicular development.

Objective: A comprehensive study was conducted to study the effects of partition of variance on accuracy of genetic parameters and genetic trends of economic traits in Vanaraja male line/project directorate-1 (PD-1) chicken.Methods: Variance component analysis utilizing restricted maximum likelihood animal model was carried out with five generations data to delineate the population status, direct additive, maternal genetic, permanent environmental effects, besides genetic trends and performance of economic traits in PD-1 chickens. Genetic trend was estimated by regression of the estimated average breeding values (BV) on generations.Results: The body weight (BW) and shank length (SL) varied significantly (p≤0.01) among the generations, hatches and sexes. The least squares mean of SL at six weeks, the primary trait was 77.44±0.05 mm. All the production traits, viz., BWs, age at sexual maturity, egg production (EP) and egg weight were significantly influenced by generation. Model four with additive, maternal permanent environmental and residual effects was the best model for juvenile growth traits, except for zero-day BW. The heritability estimates for BW and SL at six weeks (SL6) were 0.20±0.03 and 0.17±0.03, respectively. The BV of SL6 in the population increased linearly from 0.03 to 3.62 mm due to selection. Genetic trend was significant (p≤0.05) for SL6, BW6, and production traits. The average genetic gain of EP40 for each generation was significant (p≤0.05) with an average increase of 0.38 eggs per generation. The average inbreeding coefficient was 0.02 in PD-1 line.Conclusion: The population was in ideal condition with negligible inbreeding and the selection was quite effective with significant genetic gains in each generation for primary trait of selection. The animal model minimized the over-estimation of genetic parameters and improved the accuracy of the BV, thus enabling the breeder to select the suitable breeding strategy for genetic improvement.

Objective: Initial consequence of inbreeding is inbreeding depression which impairs the performance of growth, production, health, fertility and survival traits in different animal breeds and populations. The effect of inbreeding on economically important traits should be accurately estimated. The effect of inbreeding depression on growth traits in sheep has been reported in many breeds. Based on this, the main objective of the present research was to evaluate the impact of inbreeding on some growth traits of Iranian Baluchi sheep breed using quantile regression model.Methods: Pedigree and growth traits records of 13,633 Baluchi lambs born from year 1989 to 2016 were used in this research. The traits were birth weight, weaning weight, six-month weight, nine-month weight, and yearling weight. The contribution, inbreeding and co-ancestry software was used to calculate the pedigree statistics and inbreeding coefficients. To evaluate the impact of inbreeding on different quantiles of each growth trait, a series of quantile regression models were fitted using QUANTREG procedure of SAS software. Annual trend of inbreeding was also estimated fitting a simple linear regression of lamb’s inbreeding coefficient on the birth year.Results: Average inbreeding coefficient of the population was 1.63 percent. Annual increase rate of inbreeding of the flock was 0.11 percent (p

Objective: Considering the importance of dairy farming and the negative effects of heat stress, more tolerant genotypes need to be identified. The objective of this study was to investigate the effect of heat stress via temperature-humidity index (THI) and diurnal temperature variation (DTV) in the genetic evaluations for daily milk yield of Holstein dairy cattle, using random regression models.Methods: The data comprised 94,549 test-day records of 11,294 first parity Holstein cows from Brazil, collected from 1997 to 2013, and bioclimatic data (THI and DTV) from 18 weather stations. Least square linear regression models were used to determine the THI and DTV thresholds for milk yield losses caused by heat stress. In addition to the standard model (SM, without bioclimatic variables), THI and DTV were combined in various ways and tested for different days, totaling 41 models.Results: The THI and DTV thresholds for milk yield losses was THI = 74 (–0.106 kg/d/THI) and DTV = 13 (–0.045 kg/d/DTV). The model that included THI and DTV as fixed effects, considering the two-day average, presented better fit (–2logL, Akaike information criterion, and Bayesian information criterion). The estimated breeding values (EBVs) and the reliabilities of the EBVs improved when using this model.Conclusion: Sires are re-ranking when heat stress indicators are included in the model. Genetic evaluation using the mean of two days of THI and DTV as fixed effect, improved EBVs and EBVs reliability.

Objective: Vanin1 (VNN1) is a pantetheinase that can catalyze the hydrolysis of pantetheine to produce pantothenic acid and cysteamine. Our previous studies showed that VNN1 is specifically expressed in chicken liver. In this study, we aimed to investigate the roles of peroxisome proliferators activated receptor α (PPARα) and miRNA-181a-5p in regulating VNN1 gene expression in chicken liver.Methods: 5′-RACE was performed to identify the transcription start site of chicken VNN1. JASPAR and TFSEARCH were used to analyze the potential transcription factor binding sites in the promoter region of chicken VNN1 and miRanda was used to search miRNA binding sites in 3′ untranslated region (3′UTR) of chicken VNN1. We used a knock-down strategy to manipulate PPARα (or miRNA-181a-5p) expression levels in vitro to further investigate its effect on VNN1 gene transcription. Luciferase reporter assays were used to explore the specific regions of VNN1 targeted by PPARα and miRNA-181a-5p.Results: Sequence analysis of the VNN1 promoter region revealed several transcription factor-binding sites, including hepatocyte nuclear factor 1α (HNF1α), PPARα, and CCAAT/enhancer binding protein α. GW7647 (a specific agonist of PPARα) increased the expression level of VNN1 mRNA in chicken primary hepatocytes, whereas knockdown of PPARα with siRNA increased VNN1 mRNA expression. Moreover, the predicted PPARα-binding site was confirmed to be necessary for PPARα regulation of VNN1 gene expression. In addition, the VNN1 3′UTR contains a sequence that is completely complementary to nucleotides 1 to 7 of miRNA-181a-5p. Overexpression of miR-181a-5p significantly decreased the expression level of VNN1 mRNA.Conclusion: This study demonstrates that PPARα is an important transcriptional activator of VNN1 gene expression and that miRNA-181a-5p acts as a negative regulator of VNN1 expression in chicken hepatocytes.

Objective: The objectives of the current study were to study the main environmental factors affecting birth weight (BW) and weaning weight (WW), estimate variance components, genetic parameters and genetic trend and to evaluate the variability and relationships among breeding value of BW and WW using principal components analysis (PCA).Methods: A total of 16,370 records were collected from 8,271 buffalo calves. Genetic parameters and breeding values were estimated using a bivariate animal model which includes direct, maternal and permanent maternal effects. These estimates were standardized and used in PCA.Results: The direct heritability estimates were 0.06 and 0.41 for BW and WW, respectively whereas direct maternal heritability values were 0.03 and 0.14, respectively. Proportions of variance due to permanent environmental effects of dam were 0.455 and 0.280 for BW and WW respectively. The genetic correlation between BW and WWs was weak approaching zero, but the maternal correlation was 0.26. The first two principal components (PC1 and PC2) were estimated utilizing the standardized breeding values according to Kaiser method. The total variance explained by the first two PCs was 71.17% in which 45.91% and 25.25% were explained by PC1 and PC2, respectively. The direct breeding values of BW were related to PC2 but those of WW and maternal breeding values of BW and WWs were associated with PC1.Conclusion: The results of genetic parameters and PCA indicate that BW and WWs were not genetically correlated and improving growth traits of Egyptian buffaloes could be achieved using WW without any adverse effect by BW.

Objective: Tibetan pigs, an excellent species unique to China, face serious threats, which in turn affects the development and utilization of the outstanding advantages of plateau hypoxia adaptability and reduces their genetic diversity. Therefore, a discussion of measures to conserve this genetic resource is necessary. The method, based on genetic diversity, genetic divergence and total genetic contribution rate of population, reflects the priority conservation order and varies depending on the three different purposes of conservation.Methods: We analyzed mitochondrial DNA control region (D-loop) variation in 1,201 individuals from nine Tibetan pig populations across five provinces and downloaded 564 mtDNA D-loop sequences from three indigenous pig breeds in Qinghai, Sichuan, and Yunnan Provinces distributed near the Tibetan pigs.Results: We analyzed three different aspects: Changdu Tibetan pigs have the highest genetic diversity, and from the perspective of genetic diversity, the priority conservation is Changdu Tibetan pigs. Hezuo Tibetan pigs have the highest genetic contribution, so the priority conservation is Hezuo Tibetan pigs in the genetic contribution aspect. Rkaze Tibetan pigs were severely affected by indigenous pig breeds, so if considering from the perspective of introgression, the priority conservation is Rkaze Tibetan pigs.Conclusion: This study evaluated genetic diversity and comprehensively assessed conservation priority from three different aspects in nine Tibetan pig populations.

Objective: This study assessed genomic prediction accuracies based on different selection methods, evaluation procedures, training population (TP) sizes, heritability (h2) levels, marker densities and pedigree error (PE) rates in a simulated Korean beef cattle population.Methods: A simulation was performed using two different selection methods, phenotypic and estimated breeding value (EBV), with an h2 of 0.1, 0.3, or 0.5 and marker densities of 10, 50, or 777K. A total of 275 males and 2,475 females were randomly selected from the last generation to simulate ten recent generations. The simulation of the PE dataset was modified using only the EBV method of selection with a marker density of 50K and a heritability of 0.3. The proportions of errors substituted were 10%, 20%, 30%, and 40%, respectively. Genetic evaluations were performed using genomic best linear unbiased prediction (GBLUP) and single-step GBLUP (ssGBLUP) with different weighted values. The accuracies of the predictions were determined.Results: Compared with phenotypic selection, the results revealed that the prediction accuracies obtained using GBLUP and ssGBLUP increased across heritability levels and TP sizes during EBV selection. However, an increase in the marker density did not yield higher accuracy in either method except when the h2 was 0.3 under the EBV selection method. Based on EBV selection with a heritability of 0.1 and a marker density of 10K, GBLUP and ssGBLUP_0.95 prediction accuracy was higher than that obtained by phenotypic selection. The prediction accuracies from ssGBLUP_0.95 outperformed those from the GBLUP method across all scenarios. When errors were introduced into the pedigree dataset, the prediction accuracies were only minimally influenced across all scenarios.Conclusion: Our study suggests that the use of ssGBLUP_0.95, EBV selection, and low marker density could help improve genetic gains in beef cattle.

Objective: An initial RNA-Sequencing study revealed that UDP-galactose-4-epimerase (GALE) was one of the most promising candidates for milk protein concentration in Chinese Holstein cattle. This enzyme catalyzes the interconversion of UDP-galactose and UDP-glucose, an important step in galactose catabolism. To further validate the genetic effect of GALE on milk protein traits, genetic variations were identified, and genotypes-phenotypes associations were performed.Methods: The entire coding region and the 5’-regulatory region (5’-UTR) of GALE were re-sequenced using pooled DNA of 17 unrelated sires. Association studies for five milk production traits were performed using a mixed linear animal model with a population encompassing 1,027 Chinese Holstein cows.Results: A total of three variants in GALE were identified, including two novel variants (g.2114 A>G and g.2037 G>A) in the 5’-UTR and one previously reported variant (g.3836 G>C) in an intron. All three single nucleotide polymorphisms (SNPs) were associated with milk yield (pC.Conclusion: Overall, our findings provided new insights into the polymorphic variations in bovine GALE gene and their associations with milk protein concentration. The data indicate their potential uses for marker-assisted breeding or genetic selection schemes.

Objective: The objective of this study was to estimate the genetic parameters and trends for milk, fat, and protein yields in the first three lactations of Thai dairy cattle using a 3-trait,- 3-lactation random regression test-day model.Methods: Data included 168,996, 63,388, and 27,145 test-day records from the first, second, and third lactations, respectively. Records were from 19,068 cows calving from 1993 to 2013 in 124 herds. (Co) variance components were estimated by Bayesian methods. Gibbs sampling was used to obtain posterior distributions. The model included herd-year-month of testing, breed group-season of calving-month in tested milk group, linear and quadratic age at calving as fixed effects, and random regression coefficients for additive genetic and permanent environmental effects, which were defined as modified constant, linear, quadratic, cubic and quartic Legendre coefficients.Results: Average daily heritabilities ranged from 0.36 to 0.48 for milk, 0.33 to 0.44 for fat and 0.37 to 0.48 for protein yields; they were higher in the third lactation for all traits. Heritabilities of test-day milk and protein yields for selected days in milk were higher in the middle than at the beginning or end of lactation, whereas those for test-day fat yields were high at the beginning and end of lactation. Genetics correlations (305-d yield) among production yields within lactations (0.44 to 0.69) were higher than those across lactations (0.36 to 0.68). The largest genetic correlation was observed between the first and second lactation. The genetic trends of 305-d milk, fat and protein yields were 230 to 250, 25 to 29, and 30 to 35 kg per year, respectively.Conclusion: A random regression model seems to be a flexible and reliable procedure for the genetic evaluation of production yields. It can be used to perform breeding value estimation for national genetic evaluation in the Thai dairy cattle population.

Objective: Eggshells with a uniform color and intensity are important for egg production because many consumers assess the quality of an egg according to the shell color. In the present study, we evaluated the influence of dominant effects on the variations in eggshell color after 32 weeks in a crossbred population.Methods: This study was conducted using 7,878 eggshell records from 2,626 hens. Heritability was estimated using a univariate animal model, which included inbreeding coefficients as a fixed effect and animal additive genetic, dominant genetic, and residuals as random effects. Genetic correlations were obtained using a bivariate animal model. The optimal diagnostic criteria identified in this study were: L* value (lightness) using a dominance model, and a* (redness), and b* (yellowness) value using an additive model.Results: The estimated heritabilities were 0.65 for shell lightness, 0.42 for redness, and 0.60 for yellowness. The dominance heritability was 0.23 for lightness. The estimated genetic correlations were 0.61 between lightness and redness, –0.84 between lightness and yellowness, and –0.39 between redness and yellowness.Conclusion: These results indicate that dominant genetic effects could help to explain the phenotypic variance in eggshell color, especially based on data from blue-shelled chickens. Considering the dominant genetic variation identified for shell color, this variation should be employed to produce blue eggs for commercial purposes using a planned mating system.

Objective: This study evaluated the effect of pedigree errors (PEs) on the accuracy of estimated breeding value (EBV) and genetic gain for carcass traits in Korean Hanwoo cattle.Methods: The raw data set was based on the pedigree records of Korean Hanwoo cattle. The animals’ information was obtained using Hanwoo registration records from Korean animal improvement association database. The record comprised of 46,704 animals, where the number of the sires used was 1,298 and the dams were 38,366 animals. The traits considered were carcass weight (CWT), eye muscle area (EMA), back fat thickness (BFT), and marbling score (MS). Errors were introduced in the pedigree dataset through randomly assigning sires to all progenies. The error rates substituted were 5%, 10%, 20%, 30%, 40%, 50%, 60%, 70%, and 80%, respectively. A simulation was performed to produce a population of 1,650 animals from the pedigree data. A restricted maximum likelihood based animal model was applied to estimate the EBV, accuracy of the EBV, expected genetic gain, variance components, and heritability (h2) estimates for carcass traits. Correlation of the simulated data under PEs was also estimated using Pearson’s method.Results: The results showed that the carcass traits per slaughter year were not consistent. The average CWT, EMA, BFT, and MS were 342.60 kg, 78.76 cm2, 8.63 mm, and 3.31, respectively. When errors were introduced in the pedigree, the accuracy of EBV, genetic gain and h2 of carcass traits was reduced in this study. In addition, the correlation of the simulation was slightly affected under PEs.Conclusion: This study reveals the effect of PEs on the accuracy of EBV and genetic parameters for carcass traits, which provides valuable information for further study in Korean Hanwoo cattle.

Objective: Muscle fiber types, numbers and area are crucial aspects associated with meat production and quality. However, there are few studies of pig muscle fibre traits in terms of the detection power, false discovery rate and confidence interval precision of whole-genome quantitative trait loci (QTL). We had previously performed genome scanning for muscle fibre traits using 183 microsatellites and detected 8 significant QTLs in a White Duroc× Erhualian F2 population. The confidence intervals of these QTLs ranged between 11 and 127 centimorgan (cM), which contained hundreds of genes and hampered the identification of QTLs. A whole-genome sequence imputation of the population was used for fine mapping in this study.Methods: A whole-genome sequences association study was performed in the F2 population. Genotyping was performed for 1,020 individuals (19 F0, 68 F1, and 933 F2). The whole-genome variants were imputed and 21,624,800 single nucleotide polymorphisms (SNPs) were identified and examined for associations to 11 longissimus dorsi muscle fiber traits.Results: A total of 3,201 significant SNPs comprising 7 novel QTLs showing associations with the relative area of fiber type I (I_RA), the fiber number per square centimeter (FN) and the total fiber number (TFN). Moreover, one QTL on pig chromosome 14 was found to affect both FN and TFN. Furthermore, four plausible candidate genes associated with FN (kinase non-catalytic C-lobe domain containing [KNDC1]), TFN (KNDC1), and I_RA (solute carrier family 36 member 4, contactin associated protein like 5, and glutamate metabotropic receptor 8) were identified.Conclusion: An efficient and powerful imputation-based association approach was utilized to identify genes potentially associated with muscle fiber traits. These identified genes and SNPs could be explored to improve meat production and quality via marker-assisted selection in pigs.

Objective: Cattle were some of the first animals domesticated by humans for the production of milk, meat, etc. Long noncoding RNA (lncRNA) is defined as longer than 200 bp in non-protein coding transcripts. lncRNA is known to function in regulating gene expression and is currently being studied in a variety of livestock including cattle. The purpose of this study is to analyze the characteristics of lncRNA according to sex in Hanwoo cattle.Methods: This study was conducted using the skeletal muscles of 9 Hanwoo cattle include bulls, steers and cows. RNA was extracted from skeletal muscle of Hanwoo. Sequencing was conducted using Illumina HiSeq2000 and mapped to the Bovine Taurus genome. The expression levels of lncRNAs were measured by DEGseq and quantitative trait loci (QTL) data base was used to identify QTLs associated with lncRNA. The python script was used to match the nearby genesResults: In this study, the expression patterns of transcripts of bulls, steers and cows were identified. And we identified significantly differentially expressed lncRNAs in bulls, steers and cows. In addition, characteristics of lncRNA which express differentially in muscles according to the sex of Hanwoo were identified. As a result, we found differentially expressed lncRNAs according to sex were related to shear force and body weight.Conclusion: This study was classified and characterized lncRNA which differentially expressed by sex in Hanwoo cattle. We believe that the characterization of lncRNA by sex of Hanwoo will be helpful for future studies of the physiological mechanisms of Hanwoo cattle.

Objective: Evidence from previous reports indicates that pig domestication in East Asia mainly occurred in the Mekong region and the middle and downstream regions of the Yangtze River. Further research identified two new origin centers for domestic pigs in the Tibetan Plateau and the islands of Southeast Asia. However, due to the small sample size of Tibetan pigs, details of the origin and spread of Tibetan pigs has not yet been established.Methods: We analyzed mitochondrial DNA control region (D-loop) variation in 1,201 individuals from nine Tibetan pig populations across five provinces. Comprehensive Tibetan pig samples were taken to perform the most detailed analysis of Tibetan pigs to date.Results: The result indicate that Rkaze pigs had the lowest level of diversity, while Changdu pigs had the highest diversity. Interestingly, these two populations were both in the Tibetan Plateau area. If we calculate diversity in terms of each province, the Tibetan Plateau area had the lowest diversity, while the Chinese province of Gansu had the highest diversity. Diversity gradient analysis of major haplotypes suggested three domestication centers of Tibetan pigs in the Tibetan Plateau and the Chinese provinces of Gansu and Yunnan.Conclusion: We found two new domestication centers for Tibetan pigs. One is in the Chinese province of Gansu, which lies in the upstream region of the Yellow River, and the other is in the Chinese province of Yunnan.

Objective: Apoptosis of ovarian granulosa cells (GCs) affects mammalian follicular development and fecundity. This study aimed to explore the regulatory relationship between microRNA-26a (miR-26a) and the 3β-hydroxysteroid-Δ24-reductase gene (DHCR24) gene in porcine follicular granular cells (pGCs), and to provide empirical data for the development of methods to improve the reproductive capacity of pigs.Methods: The pGCs were transfected with miR-26a mimic, miR-26a inhibitor and DHCR24-siRNA in vitro. The cell apoptosis rate of pGCs was detected by the flow cytometry. The secretion levels of estradiol (E2) and progesterone (P) in pGCs were detected by enzymelinked immunosorbent assay. Double luciferase validation system was used to detect the binding sites between miR-26a and DHCR24 3′-UTR region. Qualitative real-time polymerase chain reaction and Western blotting were used to verify the DHCR24 mRNA and protein expression in pGCs, respectively, after transfecting with miR-26a mimic and miR-26a inhibitor.Results: Results showed that enhancement of miR-26a promoted apoptosis, and inhibited E2 and P secretion in pGCs. Meanwhile, inhibition of DHCR24 also upregulated the Caspase-3 expression, reduced the BCL-2 expression, promoted pGCs apoptosis, and inhibited E2 and P secretion in pGCs. There were the binding sites of miR-26a located within DHCR24 3′-UTR. Up-regulation of miR-26a inhibited DHCR24 mRNA and protein expression in pGCs.Conclusion: This study demonstrates that miR-26a can promote cell apoptosis and inhibit E2 and P secretion by inhibiting the expression of DHCR24 in pGCs.

Objective This study examined the effects of divergence in residual feed intake (RFI) on expression profiles of key genes related to lipid transport in the liver and duodenal epithelium and their associations with feed efficiency traits in meat-type ducks. Methods A total of 1,000 male ducks with similar body weight (1,042.1±87.2 g) were used in this study, and their individual RFI was calculated from 21 to 42 d of age. Finally, the 10 highest RFI (HRFI) and 10 lowest RFI (LRFI) ducks were chosen for examining the expression of key genes related to lipid transport in the liver and duodenal epithelium using quantitative polymerase chain reaction. Results In the liver, expression levels of albumin (ALB), CD36 molecule (CD36), fatty acid hydroxylase domain containing 2 (FAXDC2), and choline kinase alpha (CHKA) were significantly higher in LRFI ducks than in HRFI ducks (p

Objective: This study was conducted to test the efficiency of genomic selection for milk production traits in a Korean Holstein cattle population.Methods: A total of 506,481 milk production records from 293,855 animals (2,090 heads with single nucleotide polymorphism information) were used to estimate breeding value by single step best linear unbiased prediction.Results: The heritability estimates for milk, fat, and protein yields in the first parity were 0.28, 0.26, and 0.23, respectively. As the parity increased, the heritability decreased for all milk production traits. The estimated generation intervals of sire for the production of bulls (LSB) and that for the production of cows (LSC) were 7.9 and 8.1 years, respectively, and the estimated generation intervals of dams for the production of bulls (LDB) and cows (LDC) were 4.9 and 4.2 years, respectively. In the overall data set, the reliability of genomic estimated breeding value (GEBV) increased by 9% on average over that of estimated breeding value (EBV), and increased by 7% in cows with test records, about 4% in bulls with progeny records, and 13% in heifers without test records. The difference in the reliability between GEBV and EBV was especially significant for the data from young bulls, i.e. 17% on average for milk (39% vs 22%), fat (39% vs 22%), and protein (37% vs 22%) yields, respectively. When selected for the milk yield using GEBV, the genetic gain increased about 7.1% over the gain with the EBV in the cows with test records, and by 2.9% in bulls with progeny records, while the genetic gain increased by about 24.2% in heifers without test records and by 35% in young bulls without progeny records.Conclusion: More genetic gains can be expected through the use of GEBV than EBV, and genomic selection was more effective in the selection of young bulls and heifers without test records.

Objective: The objective of this study was to measure the special expression pattern of lipid metabolism genes and investigate the molecular mechanisms underlying intramuscular fat (IMF) deposition in Longissimus dorsi muscle of Laiwu pigs.Methods: Thirty-six pigs (Laiwu n = 18; Duroc×Landrace×Yorkshire n = 18) were used for the measurement of the backfat thickness, marbling score, IMF content, and expression of lipid metabolism genes.Results: Significant correlations were found between IMF content and the mRNA expression of lipid metabolism genes. Of the 14 fat deposition genes measured, fatty acid synthase (FASN) showed the strongest correlation (r = 0.75, p = 0.001) with IMF content, and of the 6 fat removal genes, carnitine palmitoyl transferase 1B (CPT1B) exhibited the greatest negative correlation (r = –0.66, p = 0.003) with IMF content in Laiwu pig. Multiple regression analysis showed that CPT1B, FASN, solute carrier family 27 member 1 (SLC27A1), and fatty acid binding protein 3 (FABP3) contributed 38% of the prediction value for IMF content in Laiwu pigs. Of these four variables, CPT1B had the greatest contribution to IMF content (14%) followed by FASN (11%), SLC27A1 (9%), and FABP3 (4%).Conclusion: Our results indicate that the combined effects of an upregulation in fat deposition genes and downregulation in fat removal genes promotes IMF deposition in Laiwu pigs.

Objective Testicular growth and development are strongly influenced by androgen. Although both testis weight and plasma testosterone level are inherited traits, the interrelationship between them is not fully established. Males of DDD/Sgn (DDD) mice are known to have extremely heavy testes and very high plasma testosterone level among inbred mouse strains. We dissected the genetic basis of testis weight and analyzed the potential influence of plasma testosterone level in DDD mice. Methods Quantitative trait loci (QTL) mapping of testis weight was performed with or without considering the influence of plasma testosterone level in reciprocal F2 intercross populations between DDD and C57BL/6J (B6) mice, thereby assessing the influence of testosterone on the effect of testis weight QTL. Candidate genes for testis weight QTL were investigated by next-generation sequencing analysis. Results Four significant QTL were identified on chromosomes 1, 8, 14, and 17. The DDD-derived allele was associated with increased testis weight. The F2 mice were then divided into two groups according to the plasma testosterone level (F2 mice with relatively “low” and “high” testosterone levels), and QTL scans were again performed. Although QTL on chromosome 1 was shared in both F2 mice, QTL on chromosomes 8 and 17 were identified specifically in F2 mice with relatively high testosterone levels. By whole-exome sequencing analysis, we identified one DDD-specific missense mutation Pro29Ser in alpha tubulin acetyltransferase 1 (Atat1). Conclusion Most of the testis weight QTL expressed stronger phenotypic effect when they were placed on circumstance with high testosterone level. High testosterone influenced the QTL by enhancing the effect of DDD-derived allele and diminishing the effects of B6-derived allele. Since Pro29Ser was not identified in other inbred mouse strains, and since Pro29 in Atat1 has been strongly conserved among mammalian species, Atat1 is a plausible candidate for testis weight QTL on chromosome 17.

Objective A genome-based best linear unbiased prediction (GBLUP) method was applied to evaluate accuracies of genomic estimated breeding value (GEBV) of carcass and reproductive traits in Berkshire, Duroc and Yorkshire populations in Korean swine breeding farms. Methods The data comprised a total of 1,870, 696, and 1,723 genotyped pigs belonging to Berkshire, Duroc and Yorkshire breeds, respectively. Reference populations for carcass traits consisted of 888 Berkshire, 466 Duroc, and 1,208 Yorkshire pigs, and those for reproductive traits comprised 210, 154, and 890 dams for the respective breeds. The carcass traits analyzed were backfat thickness (BFT) and carcass weight (CWT), and the reproductive traits were total number born (TNB) and number born alive (NBA). For each trait, GEBV accuracies were evaluated with a GEBV BLUP model and realized GEBVs. Results The accuracies under the GBLUP model for BFT and CWT ranged from 0.33–0.72 and 0.33–0.63, respectively. For NBA and TNB, the model accuracies ranged 0.32 to 0.54 and 0.39 to 0.56, respectively. The realized accuracy estimates for BFT and CWT ranged 0.30 to 0.46 and 0.09 to 0.27, respectively, and 0.50 to 0.70 and 0.70 to 0.87 for NBA and TNB, respectively. For the carcass traits, the GEBV accuracies under the GBLUP model were higher than the realized GEBV accuracies across the breed populations, while for reproductive traits the realized accuracies were higher than the model based GEBV accuracies. Conclusion The genomic prediction accuracy increased with reference population size and heritability of the trait. The GEBV accuracies were also influenced by GEBV estimation method, such that careful selection of animals based on the estimated GEBVs is needed. GEBV accuracy will increase with a larger sized reference population, which would be more beneficial for traits with low heritability such as reproductive traits.

Objective Sow longevity is important for efficient and profitable pig farming. Recently, there has been an increasing interest in social genetic effect (SGE) of pigs on stress-tolerance and behavior. The present study aimed to estimate genetic correlations among average daily gain (ADG), stayability (STAY), and number of piglets born alive at the first parity (NBA1) in Korean Yorkshire pigs, using a model including SGE. Methods The phenotypic records of ADG and reproductive traits of 33,120 and 11,654 pigs, respectively, were evaluated. The variances and (co) variances of the studied traits were estimated by a multi-trait animal model applying the Bayesian with linear-threshold models using Gibbs sampling. Results The direct and SGEs on ADG had a significantly negative (-0.30) and neutral (0.04) genetic relationship with STAY, respectively. In addition, the genetic correlation between the social effects on ADG and NBA1 tended to be positive (0.27), unlike the direct effects (-0.04). The genetic correlation of the total effect on ADG with that of STAY was negative (-0.23) but non-significant, owing to the social effect. Conclusion These results suggested that total genetic effect on growth in the SGE model might reduce the negative effect on sow longevity because of the growth potential of pigs. We recommend including social effects as selection criteria in breeding programs to obtain satisfactory genetic changes in both growth and longevity.

Objective The present study was to investigate the association of polymorphisms in exon-9 of the bone morphogenetic protein receptor-1B (BMPR-1B) gene (C864T) with litter size in 240 Dorset, 232 Mongolian, and 124 Small Tail Han ewes. Methods Blood samples were collected from 596 ewes and genomic DNA was extracted using the phenol: chloroform extraction method. The 304-bp amplified polymerase chain reaction product was analyzed for polymorphism by single-strand conformation polymorphism method. The genotypic frequency and allele frequency of BMPR-1B gene exon-9 were computed after sequence alignment. The χ2 independence test was used to analyze the association of genotypic frequency and litter size traits with in each ewe breed, where the phenotype was directly treated as category. Results The results indicated two different banding patterns AA and AB for this fragment, with the most frequent genotype and allele of AA and A. Calculated Chi-square test for BMPR-1B gene exon-9 was found to be more than that of p value at the 5% level of significance, indicating that the population under study was in Hardy-Weinberg equilibrium for all ewes. The χ2 independence test analyses indicated litter size differences between genotypes was not the same for each breed. The 304-bp nucleotide sequence was subjected to BLAST analysis, and the C864T mutation significantly affected litter size in singletons, twins and multiples. The heterozygosity in exon-9 of BMPR-1B gene could increase litter size for all the studied ewes. Conclusion Consequently, it appears that the polymorphism BMPR-1B gene exon-9 detected in this study may have potential use in marker assisted selection for litter size in Dorset, Mongolian, and Small Tail Han ewes.

Objective Intramuscular fat (IMF) content plays an important role in meat quality. Identification of single nucleotide polymorphisms (SNPs) and genes related to pig IMF, especially using pig populations with high IMF content variation, can help to establish novel molecular breeding tools for optimizing IMF in pork and unveil the mechanisms that underlie fat metabolism. Methods We collected muscle samples of 453 Chinese Lulai black pigs, measured IMF content by Soxhlet petroleum-ether extraction method, and genotyped genome-wide SNPs using GeneSeek Genomic Profiler Porcine HD BeadChip. Then a genome-wide association study was performed using a linear mixed model implemented in the GEMMA software. Results A total of 43 SNPs were identified to be significantly associated with IMF content by the cutoff p

Objective The inhibitory leukocyte immunoglobulin-like receptors (LILRBs) play an important role in innate immunity. The present study represents the first description of the cloning and structural and functional analysis of LILRB1 and LILRB3 isolated from two genetically disparate chicken lines. Methods Chicken LILRB1-3 genes were identified by bioinformatics approach. Expression studies were performed by transfection, quantitative polymerase chain reaction. Signal transduction was analyzed by western blots, immunoprecipitation and flow cytometric. Cytokine levels were determined by enzyme-linked immunosorbent assay. Results Amino acid homology and phylogenetic analyses showed that the homologies of LILRB1 and LILRB3 in the chicken line 6.3 to those proteins in the chicken line 7.2 ranged between 97%-99%, while homologies between chicken and mammal proteins ranged between 13%-19%, and 13%-69%, respectively. Our findings indicate that LILRB1 and LILRB3 subdivided into two groups based on the immunoreceptor tyrosine-based inhibitory motifs (ITIM) present in the transmembrane domain. Chicken line 6.3 has two ITIM motifs of the sequence LxYxxL and SxYxxV while line 7.2 has two ITIM motifs of the sequences LxYxxL and LxYxxV. These motifs bind to SHP-2 (protein tyrosine phosphatase, non-receptor type 11) that plays a regulatory role in immune functions. Moreover, our data indicate that LILRB1 and LILRB3 associated with and activated major histocompatibility complex (MHC) class I and β2-microglobulin and induced the expression of transporters associated with antigen processing, which are essential for MHC class I antigen presentation. This suggests that LILRB1 and LILRB3 are transcriptional regulators, modulating the expression of components in the MHC class I pathway and thereby regulating immune responses. Furthermore, LILRB1 and LILRB3 activated Janus kinase2/tyrosine kinase 2 (JAK2/TYK2); signal transducer and activator of transcription1/3 (STAT1/3), and suppressor of cytokine signaling 1 genes expressed in Macrophage (HD11) cells, which induced Th1, Th2, and Th17 cytokines. Conclusion These data indicate that LILRB1 and LILRB3 are innate immune receptors associated with SHP-2, MHC class I, β2-microglobulin, and they activate the Janus kinase/signal transducer and activator of transcription signaling pathway. Thus, our study provides novel insights into the regulation of immunity and immunopathology.

Objective The Shanghai Holstein cattle breed is susceptible to severe mastitis and other diseases due to the hot weather and long-term humidity in Shanghai, which is the main distribution centre for providing Holstein semen to various farms throughout China. Our objective was to determine the genetic mechanisms influencing economically important traits, especially diseases that have huge impact on the yield and quality of milk as well as reproduction. Methods In our study, we detected the structural variations of 1,092 Shanghai Holstein cows by using next-generation sequencing. We used the DELLY software to identify deletions and insertions, cn.MOPS to identify copy-number variants (CNVs). Furthermore, we annotated these structural variations using different bioinformatics tools, such as gene ontology, cattle quantitative trait locus (QTL) database and ingenuity pathway analysis (IPA). Results The average number of high-quality reads was 3,046,279. After filtering, a total of 16,831 deletions, 12,735 insertions and 490 CNVs were identified. The annotation results showed that these mapped genes were significantly enriched for specific biological functions, such as disease and reproduction. In addition, the enrichment results based on the cattle QTL database showed that the number of variants related to milk and reproduction was higher than the number of variants related to other traits. IPA core analysis found that the structural variations were related to reproduction, lipid metabolism, and inflammation. According to the functional analysis, structural variations were important factors affecting the variation of different traits in Shanghai Holstein cattle. Our results provide meaningful information about structural variations, which may be useful in future assessments of the associations between variations and important phenotypes in Shanghai Holstein cattle. Conclusion Structural variations identified in this study were extremely different from those of previous studies. Many structural variations were found to be associated with mastitis and reproductive system diseases; these results are in accordance with the characteristics of the environment that Shanghai Holstein cattle experience.

Objective The objective of this study was to investigate the genetic components of daily milk yield and to re-rank bulls in South Korea by estimated breeding value (EBV) under heat stress using the temperature-humidity index (THI). Methods This study was conducted using 125,312 monthly test-day records, collected from January 2000 to February 2017 for 19,889 Holstein cows from 647 farms in South Korea. Milk production data were collected from two agencies, the Dairy Cattle Genetic Improvement Center and the Korea Animal Improvement Association, and meteorological data were obtained from 41 regional weather stations using the Automated Surface Observing System (ASOS) installed throughout South Korea. A random regression model using the THI was applied to estimate genetic parameters of heat tolerance based on the test-day records. The model included herd-year-season, calving age, and days-in-milk as fixed effects, as well as heat tolerance as an additive genetic effect, permanent environmental effect, and direct additive and permanent environmental effect. Results Below the THI threshold (≤72; no heat stress), the variance in heat tolerance was zero. However, the heat tolerance variance began to increase as THI exceeded the threshold. The covariance between the genetic additive effect and the heat tolerance effect was −0.33. Heritability estimates of milk yield ranged from 0.111 to 0.176 (average: 0.128). Heritability decreased slightly as THI increased, and began to increase at a THI of 79. The predicted bull EBV ranking varied with THI. Conclusion We conclude that genetic evaluation using the THI function could be useful for selecting bulls for heat tolerance in South Korea.

Objective The progestogen-associated endometrial protein (PAEP) gene encodes the main whey protein in milk, β-lactoglobulin. The aim of the study was to investigate polymorphism in the PAEP gene and its association with milk yield, composition, and quality. Methods Test-day records for 782 dairy cows were analysed. A total of 10 single nucleotide polymorphisms (SNP) within the PAEP gene were investigated. The following parameters were recorded: milk yield (MY, kg/d), percent milk fat (%), protein (PP, %), dry matter (DMP, %) and lactose (LP, %), urea content (UC, mg/L) as well as natural logarithm for somatic cell count (LnSCC, ln). Effect on genomic estimated breeding values accuracy was evaluated with pedigree and single step model. Results Results show that only three SNPs were polymorphic, creating 5 composite genotypes: P1 to P5. Differences in MY between composite genotypes were noted in the two tested herds. Cows with P5 composite genotypes were characterised by the highest PP and LnSCC and the lowest LP and UC (p

Objective: The study aimed to evaluate the diversity of donkey populations by comparing with the diversity of Thoroughbred and Jeju Halla horses; identified breeding backgrounds can contribute to management and conservation of donkeys in South Korea.Methods: A total of 100 horse (50 Thoroughbreds and 50 Jeju Halla horses) and 79 donkeys samples were genotyped with 15 microsatellite markers (AHT4, AHT5, ASB2, ASB17, ASB23, CA425, HMS1, HMS2, HMS3, HMS6, HMS7, HTG4, HTG10, LEX3, and VHL20), to identify genetic diversity and relationships among horses and donkeys.Results: The observed number of alleles per locus ranged from 1 (ASB17, HMS1) to 14 (AHT5), with a mean value of 4.87, 8.00, and 5.87 in Thoroughbreds, Jeju Halla horses, and donkeys, respectively. Of the 15 markers, AHT4, AHT5, ASB23, CA425, HMS2, HMS3, HTG4, HTG10, and LEX3 loci had relatively high polymorphism information content (PIC) values (PIC>0.5) in these three populations. Mean levels of genetic variation were HE = 0.6721 and HO = 0.6600 in Thoroughbreds, HE = 0.7898 and HO = 0.7100 in Jeju Halla horses, and HE = 0.5635 and HO = 0.4861 in donkeys. Of the 15 loci in donkeys, three loci had negative inbreeding coefficients (FIS), with a moderate mean FIS (0.138). The FIS estimate for the HTG4 marker was highest (0.531) and HMS6 marker was lowest (–0.001). The total probability of exclusion value of 15 microsatellite loci was 0.9996 in donkeys.Conclusion: Genetic cluster analysis showed that the genetic relationship among 79 donkeys was generally consistent with pedigree records. Among the three breeds, donkeys and Thoroughbred horses formed clearly different groups, but the group of Jeju Halla horses overlapped with that of Thoroughbred horses, suggesting that the loci would be suitable for donkey parentage testing. Therefore, the results of this study are a valid tool for genetic study and conservation of donkeys.

Objective: FKBP prolyl isomerase 5 (FKBP5) has been shown to play an important role in metabolically active tissues such as skeletal muscle. However, the expression of FKBP5 in Muscovy duck tissues and its association with body weight are still unclear.Methods: In this study, real-time quantitative polymerase chain reaction was used to detect the expression of FKBP5 in different tissues of Muscovy duck at different growth stages. Further, single nucleotide polymorphisms (SNPs) were detected in the exon region of FKBP5 and were combined analyzed with the body weight of 334 Muscovy ducks.Results: FKBP5 was highly expressed in various tissues of Muscovy duck at days 17, 19, 21, 24, and 27 of embryonic development. In addition, the expression of FKBP5 in the tissues of female adult Muscovy ducks was higher than that of male Muscovy ducks. Besides, an association analysis indicated that 3 SNPs were related to body weight trait. At the g.4819252 A>G, the body weight of AG genotype was significantly higher than that of the AA and the GG genotype. At the g.4821390 G>A, the genotype GA was extremely significantly related to body weight. At the g.4830622 T>G, the body weight of TT was significantly higher than GG and TG.Conclusion: These findings indicate the possible effects of expression levels in various tissues and the SNPs of FKBP5 on Muscovy duck body weight trait. FKBP5 could be used as molecular marker for muscle development trait using early marker-assisted selection of Muscovy ducks.

Objective: The swine leukocyte antigen (SLA) gene group, which is closely linked and highly polymorphic, has important biomedical significance in the protection and utilization of germplasm resources. However, genetic polymorphism analyses of SLA microsatellite markers in Chinese miniature pigs are limited.Methods: Eighteen pairs of microsatellite primers were used to amplify the SLA regions of seven miniature pig breeds and three wild boar breeds (n = 346) from different regions of China. The indexes of genetic polymorphism, including expected heterozygosity (He), polymorphic information content (PIC), and haplotype, were analyzed. The genetic differentiation coefficient (Fst) and neighbor-joining methods were used for cluster analysis of the breeds.Results: In miniature pigs, the SLA I region had the highest numbers of polymorphisms, followed by the SLA II and SLA III regions; the region near the centromere had the lowest number of polymorphisms. Among the seven miniature pig breeds, Diannan small-ear pigs had the highest genetic diversity (PIC value = 0.6396), whereas the genetic diversity of the Hebao pig was the lowest (PIC value = 0.4330). The Fst values in the Mingguang small-ear, Diannan small-ear, and Yunnan wild boars were less than 0.05. According to phylogenetic cluster analysis, the South-China-type miniature pigs clustered into one group, among which Mingguang small-ear pigs clustered with Diannan small-ear pigs. Haplotype analysis revealed that the SLA I, II, and III regions could be constructed into 13, 7, and 11 common haplotypes, respectively.Conclusion: This study validates the high genetic diversity of the Chinese miniature pig. Mingguang small-ear pigs have close kinship with Diannan small-ear pigs, implying that they may have similar genetic backgrounds and originate from the same population. This study also provides a foundation for genetic breeding, genetic resource protection, and classification of Chinese miniature pigs.

Objective: This study was focused on the estimation of parameters of Wood’s model and description of the lactation curve using the cows which were lactated over 24 months on the first lactation.Methods: The database included 1,333 pure-bred dairy Simmental primiparous cows which lactated for 24 months (732 days). The initial dataset entering the procedure of assessment of parameters of Wood’s function included 35,826 milk yield records. Milk yield was recorded throughout lactation, with the earliest record taken on day 6 and the latest on day 1,348 of lactation. This dataset was used for the assessment of parameters a, b, c of Wood’s model using the non-linear statistical procedure. These parameters were estimated for different length of lactation. The assessed parameters were used for calculation of some characteristics of lactation curves.Results: The lowest value of a parameter (15.2317) of Wood’s model of lactation curve was found out in lactations up to 305 days long, contrary to b and c parameters which were highest in those lactations (0.1029 and 0.0015, respectively). The maximum value of a parameter (17.4329) was found out in lactations up to 640 days long, unlike b and c parameters which were minimal in those lactations (0.0603 and 0.0010, respectively).Conclusion: It can be concluded that the parameters of Wood’s model and the shape of lactation curve are changing with the growing number of milk yield records. Also, the assessed parameters revealed a significant milk production potential after 305 days of lactation.

Objective: In recent years, long noncoding RNAs (lncRNAs) have been identified in many species, and some of them have been shown to play important roles in muscle development and myogenesis. However, the differences in lncRNAs between Kazakh cattle and Xinjiang brown cattle remain undefined; therefore, we aimed to confirm whether lncRNAs are differentially expressed in the longissimus dorsi between these two types of cattle and whether differentially expressed lncRNAs regulate muscle differentiation.Methods: We used RNA-seq technology to identify lncRNAs in longissimus muscles from these cattle. The expression of lncRNAs were analyzed using StringTie (1.3.1) in terms of the fragments per kilobase of transcript per million mapped reads values of the encoding genes. The differential expression of the transcripts in the two samples were analyzed using the DESeq R software package. The resulting false discovery rate was controlled by the Benjamini and Hochberg’s approach. KOBAS software was utilized to measure the expression of different genes in Kyoto encyclopedia of genes and genomes pathways. We randomly selected eight lncRNA genes and validated them by quantitative reverse transcription polymerase chain reaction (RT-qPCR).Results: We found that 182 lncRNA transcripts, including 102 upregulated and 80 downregulated transcripts, were differentially expressed between Kazakh cattle and Xinjiang brown cattle. The results of RT-qPCR were consistent with the sequencing results. Enrichment analysis and functional annotation of the target genes revealed that the differentially expressed lncRNAs were associated with the mitogen-activated protein kinase, Ras, and phosphatidylinositol 3-kinase (PI3k)/Akt signaling pathways. We also constructed a lncRNA/mRNA coexpression network for the PI3k/Akt signaling pathway.Conclusion: Our study provides insights into cattle muscle-associated lncRNAs and will contribute to a more thorough understanding of the molecular mechanism underlying muscle growth and development in cattle.

Objective The purpose of this study was to investigate a single step genome-wide association study (ssGWAS) for identifying genomic regions affecting reproductive traits in Landrace and Large White pigs. Methods The traits included the number of pigs weaned per sow per year (PWSY), the number of litters per sow per year (LSY), pigs weaned per litters (PWL), born alive per litters (BAL), non-productive day (NPD) and wean to conception interval per litters (W2CL). A total of 321 animals (140 Landrace and 181 Large White pigs) were genotyped with the Illumina Porcine SNP 60k BeadChip, containing 61,177 single nucleotide polymorphisms (SNPs), while multiple traits single-step genomic BLUP method was used to calculate variances of 5 SNP windows for 11,048 Landrace and 13,985 Large White data records. Results The outcome of ssGWAS on the reproductive traits identified twenty-five and twenty-two SNPs associated with reproductive traits in Landrace and Large White, respectively. Three known genes were identified to be candidate genes in Landrace pigs including retinol binding protein 7, and ubiquitination factor E4B genes for PWL, BAL, W2CL, and PWSY and one gene, solute carrier organic anion transporter family member 6A1, for LSY and NPD. Meanwhile, five genes were identified to be candidate genes in Large White, two of which, aldehyde dehydrogenase 1 family member A3 and leucine rich repeat kinase 1, associated with all of six reproduction traits and three genes; retrotransposon Gag like 4, transient receptor potential cation channel subfamily C member 5, and LHFPL tetraspan subfamily member 1 for five traits except W2CL. Conclusion The genomic regions identified in this study provided a start-up point for marker assisted selection and estimating genomic breeding values for improving reproductive traits in commercial pig populations.

Objective The aim of this study was to estimate (co) variance components and genetic parameters for categorical carcass traits using Bayesian inference via mixed linear and threshold animal models in Anglonubian goats. Methods Data were obtained from Anglonubian goats reared in the Brazilian Mid-North region. The traits in study were body condition score, marbling in the rib eye, ribeye area, fat thickness of the sternum, hip height, leg perimeter, and body weight. The numerator relationship matrix contained information from 793 animals. The single- and two-trait analyses were performed to estimate (co) variance components and genetic parameters via linear and threshold animal models. For estimation of genetic parameters, chains with 2 and 4 million cycles were tested. An 1,000,000-cycle initial burn-in was considered with values taken every 250 cycles, in a total of 4,000 samples. Convergence was monitored by Geweke criteria and Monte Carlo error chain. Results Threshold model best fits categorical data since it is more efficient to detect genetic variability. In two-trait analysis the contribution of the increase in information and the correlations between traits contributed to increase the estimated values for (co) variance components and heritability, in comparison to single-trait analysis. Heritability estimates for the study traits were from low to moderate magnitude. Conclusion Direct selection of the continuous distribution of traits such as thickness sternal fat and hip height allows obtaining the indirect selection for marbling of ribeye.

Objective Non-synonymous single nucleotide polymorphisms (nsSNPs) were identified in Berkshire selective sweep regions and then were investigated to discover genetic nsSNP mechanisms that were potentially associated with Berkshire domestication and meat quality. We further used bioinformatics tools to predict damaging amino-acid substitutions in Berkshire-related nsSNPs. Methods nsSNPs were examined in whole genome resequencing data of 110 pigs, including 14 Berkshire pigs, generated using the Illumina Hiseq2000 platform to identify variations that might affect meat quality in Berkshire pigs. Results Total 65,550 nsSNPs were identified in the mapped regions; among these, 319 were found in Berkshire selective-sweep regions reported in a previous study. Genes encompassing these nsSNPs were involved in lipid metabolism, intramuscular fatty-acid deposition, and muscle development. The effects of amino acid change by nsSNPs on protein functions were predicted using sorting intolerant from tolerant and polymorphism phenotyping V2 to reveal their potential roles in biological processes that may correlate with the unique Berkshire meat-quality traits. Conclusion Our nsSNP findings confirmed the history of Berkshire pigs and illustrated the effects of domestication on generic-variation patterns. Our novel findings, which are generally consistent with those of previous studies, facilitated a better understanding of Berkshire domestication. In summary, we extensively investigated the relationship between genomic composition and phenotypic traits by scanning for nsSNPs in large-scale whole-genome sequencing data.

Objective This study aimed to screen and identify the target genes of miR-375 in pig Sertoli (ST) cells and to elucidate the effect of miR-375 on the proliferation of ST cells. Methods In this study, bioinformatics software was used to predict and verify miR-375 target genes. Quantitative polymerase chain reaction (PCR) was used to detect the relationship between miR-375 and its target genes in ST cells. Enzyme-linked immunosorbent assay (ELISA) of rearranged L-myc fusion (RLF) and hypoxia-induced gene domain protein 1A (HIGD1A) was performed on porcine ST cells, which were transfected with a miR-375 mimics and inhibitor to verify the results. Dual luciferase reporter gene assays were performed to assess the interactions among miR-375, RLF, and HIGD1A. The effect of miR-375 on the proliferation of ST cells was analyzed by CellTiter 96 AQueous One Solution Cell Proliferation Assay (MTS). Results Five possible target genes of miR-375, including RLF, HIGD1A, colorectal cancer associated 2, POU class 3 homeobox 1, and WW domain binding protein 1 like, were found. The results of quantitative PCR suggested that mRNA expression of RLF and HIGD1A had a negative correlation with miR-375, indicating that RLF and HIGD1A are likely the target genes of miR-375. The ELISA results revealed that RLF and HIGD1A were negatively correlated with the miR-375 protein level. The luminescence results for the miR-375 group co-transfected with wild-type RLF and HIGD1A vector were significantly lower than those of the miR-375 group co-transfected with the blank vector or mutant RLF and HIGD1A vectors. The present findings suggest that RLF and HIGD1A are target genes of miR-375 and that miR-375 inhibits ST cell proliferation according to MTS analysis. Conclusion It was speculated that miR-375 affects cell proliferation through its target genes, which play an important role in the development of testicular tissue.

Objective Present investigation was aimed to study the Single Nucleotide Variants of the luteinizing hormone beta (LHβ) gene and to analyze their association with the semen quality (fresh and post-thawed frozen semen) and luteinizing hormone (LH) concentrations in Murrah buffalo bulls. Methods Polymerase chain reaction–single stranded conformational polymorphism (PCR–SSCP) and Sanger sequencing method is used to study genetic variability in LHβ gene. LH assay was carried out using enzyme-linked immunosorbent assay method. A fixed general linear model was used to analyze association of single nucleotide polymorphism (SNP) of LHβ gene with semen quality in 109 and LH concentrations in 80 Murrah bulls. Results LHβ gene was found to be polymorphic. Total six SNPs were identified in LHβ gene g C356090A, g C356113T, g A356701G, g G355869A, g G356330C, and g G356606T. Single Stranded Conformational Polymorphism variants of pattern 2 of exon 1+pattern 2 of exon 2+pattern 1 of exon 3 had highly significant (p

Objective The purpose of this study was to investigate the genetic effects of six keratin (KRT) genes on the wool traits of 418 Chinese Merino (Xinjiang type) (CMXT) individuals. Methods To explore the effects and association of six KRT genes on sheep wool traits, The polymerase chain reaction-based single-strand conformation polymorphism (PCR-SSCP), DNA sequencing, and the gene pyramiding effect methods were used. Results We report 20 mutation sites (single-nucleotide polymorphisms) within the six KRT genes, in which twelve induced silent mutations; five induced missense mutations and resulted in Ile→Thr, Glu→Asp, Gly→Ala, Ala→Ser, Se→His; two were nonsense mutations and one was a same-sense mutation. Association analysis showed that two genotypes of the KRT31 gene were significantly associated with fiber diameter (p

Objective To determine the effects of genomic breeding values (GBV) and single nucleotide polymorphisms (SNP) on the total number of piglets born (TNB) in 3 pig breeds (Berkshire, Landrace, and Yorkshire). Methods After collecting genomic information (Porcine SNP BeadChip) and phenotypic TNB records for each breed, the effects of GBV and SNP were estimated by using single step best linear unbiased prediction (ssBLUP) method. Results The heritability estimates for TNB in Berkshire, Landrace, and Yorkshire breeds were 0.078, 0.107, and 0.121, respectively. The breeding value estimates for TNB in Berkshire, Landrace, and Yorkshire breeds were in the range of -1.34 to 1.47 heads, -1.79 to 1.87 heads, and -2.60 to 2.94 heads, respectively. Of sows having records for TNB, the reliability of breeding value for individuals with SNP information was higher than that for individuals without SNP information. Distributions of the SNP effects on TNB did not follow gamma distribution. Most SNP effects were near zero. Only a few SNPs had large effects. The numbers of SNPs with absolute value of more than 4 standard deviations in Berkshire, Landrace, and Yorkshire breeds were 11, 8, and 19, respectively. There was no SNP with absolute value of more than 5 standard deviations in Berkshire or Landrace. However, in Yorkshire, four SNPs (ASGA 0089457, ASGA0103374, ALGA0111816, and ALGA0098882) had absolute values of more than 5 standard deviations. Conclusion There was no common SNP with large effect among breeds. This might be due to the large genetic composition differences and the small size of reference population. For the precise evaluation of genetic performance of individuals using a genomic selection method, it may be necessary to establish the appropriate size of reference population.

Objective The study was designed to perform a genome-wide association (GWA) and partitioning of genome using Illumina's PorcineSNP60 Beadchip in order to identify variants and determine the explained heritability for the total number of teats in Yorkshire pig. Methods After screening with the following criteria: minor allele frequency, MAF≤0.01; Hardy-Weinberg equilibrium, HWE≤0.000001, a pair-wise genomic relationship matrix was produced using 42,953 single nucleotide polymorphisms (SNPs). A genome-wide mixed linear model-based association analysis (MLMA) was conducted. And for estimating the explained heritability with genome- or chromosome-wide SNPs the genetic relatedness estimation through maximum likelihood approach was used in our study. Results The MLMA analysis and false discovery rate p-values identified three significant SNPs on two different chromosomes (rs81476910 and rs81405825 on SSC8; rs81332615 on SSC13) for total number of teats. Besides, we estimated that 30% of variance could be explained by all of the common SNPs on the autosomal chromosomes for the trait. The maximum amount of heritability obtained by partitioning the genome were 0.22±0.05, 0.16±0.05, 0.10±0.03 and 0.08±0.03 on SSC7, SSC13, SSC1, and SSC8, respectively. Of them, SSC7 explained the amount of estimated heritability along with a SNP (rs80805264) identified by genome-wide association studies at the empirical p value significance level of 2.35E-05 in our study. Interestingly, rs80805264 was found in a nearby quantitative trait loci (QTL) on SSC7 for the teat number trait as identified in a recent study. Moreover, all other significant SNPs were found within and/or close to some QTLs related to ovary weight, total number of born alive and age at puberty in pigs. Conclusion The SNPs we identified unquestionably represent some of the important QTL regions as well as genes of interest in the genome for various physiological functions responsible for reproduction in pigs.

Objective The objective of the present study was to validate genes and genomic regions associated with carcass weight using a low-density single nucleotide polymorphism (SNP) Chip in Hanwoo cattle breed. Methods Commercial Hanwoo steers (n = 220) were genotyped with 20K GeneSeek genomic profiler BeadChip. After applying the quality control of criteria of a call rate ≥90% and minor allele frequency (MAF) ≥0.01, a total of 15,235 autosomal SNPs were left for genome-wide association (GWA) analysis. The GWA tests were performed using single-locus mixed linear model. Age at slaughter was fitted as fixed effect and sire included as a covariate. The level of genome-wide significance was set at 3.28×10−6 (0.05/15,235), corresponding to Bonferroni correction for 15,235 multiple independent tests. Results By employing EMMAX approach which is based on a mixed linear model and accounts for population stratification and relatedness, we identified 17 and 16 loci significantly (p