Production of polyunsaturated fatty acids in pork backfat fermented by Mucor circinelloides.

Pork backfat (PB) contains excessive saturated fatty acids (SFAs), but lacks polyunsaturated fatty acids (PUFAs). Excessive SFAs can be used as a substrate for the growth of certain microorganisms that convert them into PUFAs and monounsaturated fatty acids (MUFAs), and the added value of PB can be enhanced. In this study, Mucor circinelloides CBS 277.49 and Lactiplantacillus plantarum CGMCC 24189 were co-cultured for conversion of PB into fermented pork backfat (FPB) with high level of PUFAs. Our results showed that the content of γ-linolenic acid (GLA) and linoleic acid (LA) in the surface of FPB reached 9.04 ± 0.14 mg/g and 107.31 ± 5.16 mg/g for 7-day fermentation, respectively. To convert the internal SFAs of PB, ultrasound combined with papain was used to promote the penetrative growth of M. circinelloides into the internal PB, and the GLA level in the third layer of fat reached 2.58 ± 0.31 mg/g FPB. The internal growth of M. circinelloides in PB was promoted by adjusting the oxygen rate and ventilation rate through the wind velocity sensor. When the oxygen rate is 2 m/s and the ventilation rate is 18 m3/h, the GLA level in the third layer of fat reached 4.13 ± 1.01 mg/g FPB. To further improve the level of PUFAs in PB, FPB was produced by M. circinelloides at 18 °C. The GLA content on the surface of FPB reached 15.73 ± 1.13 mg/g FPB, and the GLA yield in the second and third layers of fat reached 8.68 ± 1.77 mg/g FPB and 6.13 ± 1.28 mg/g FPB, the LA yield in the second and third layers of fat reached 105.45 ± 5.01 mg/g FPB and 98.46 ± 4.14 mg/g FPB, respectively. These results suggested that excessive SFAs in PB can be converted into PUFAs and provided a new technique for improving PUFAs in FPB. KEY POINTS: • This article achieved the conversion of PUFAs in pork backfat by Mucor circinelloides CBS 277.49 and Lactiplantacillus plantarum CGMCC 24189. • This article solved the internal growth of M. circinelloides CBS277.49 in pork backfat by ultrasound combined with papain. • This article proposed an innovative of promoting the internal growth of M. circinelloides and increasing the PUFAs production by oxygen ventilation in pork backfat.

Genome-wide association studies for loin muscle area, loin muscle depth and backfat thickness in DLY pigs.

This study aimed at identifying genes associated with loin muscle area (LMA), loin muscle depth (LMD) and backfat thickness (BFT). We performed single-trait and multi-trait genome-wide association studies (GWASs) after genotyping 685 Duroc × (Landrace × Yorkshire) (DLY) pigs using the Geneseek Porcine 50K SNP chip. In the single-trait GWASs, we identified two, eight and two significant SNPs associated with LMA, LMD and BFT, respectively, and searched genes within the 1 Mb region near the significant SNPs with relevant functions as candidate genes. Consequently, we identified one (DOCK5), three (PID1, PITX2, ELOVL6) and three (CCR1, PARP14, CASR) promising candidate genes for LMA, LMD and BFT, respectively. Moreover, the multi-trait GWAS identified four significant SNPs associated with the three traits. In conclusion, the GWAS analysis of LMA, LMD and BFT in a DLY pig population identified several associated SNPs and candidate genes, further deepening our understanding of the genetic basis of these traits, and they may be useful for marker-assisted selection to improve the three traits in DLY pigs.

A prospective cohort study of factors associated with the digital cushion thickness in dairy cattle.

Key factors such as stage of lactation, parity and body fat reserves have been associated with the digital cushion thickness, however, there are discrepancies between the results of previously published studies. The objective of this study was to examine the association of stage of lactation, body fat reserves, parity, and lesion incidence with the digital cushion thickness (DCT) in a large cohort of intensively monitored cows. Across 4 UK farms, 2,352 cows were prospectively enrolled and assessed at 4 time points; before calving (T1-Precalving), immediately post-calving (T2-Calving), in early lactation (T3-Early) and late lactation (T4-Late). At each time point body condition score was recorded, the presence of sole lesions (sole ulcers and sole hemorrhage) and white line lesions were assessed by veterinarians, and an ultrasound image was taken to retrospectively measure the back-fat thickness in the pelvic (BFT) region and the digital cushion on the hind left lateral claw. Mixed effects multivariable linear regression models, with the cow as a random effect were fit to examine the association between explanatory variables and the DCT. Explanatory variables tested were farm, parity, stage of lactation, body condition score, BFT, height, the presence of a lesion at the time of measurement, the chronicity of a lesion during early lactation, predicted maximum daily milk yield and the rate of milk production rise in early lactation. Stage of lactation and farm were both associated with the DCT, however an interaction was present and this DCT pattern of change was farm dependent. Two distinct patterns emerged; one indicated the nadir to occur shortly after calving, the other indicated the nadir to occur during early lactation. Neither back fat thickness nor BCS were significantly associated with the DCT. Heifers displayed thinner digital cushions compared with multiparous cows, however, this effect was dependent on the stage of lactation, with heifers having a thinner digital cushion up until late lactation, by which time the DCT was commensurate with multiparous animals. Sole lesions and white line lesions at the time of measurement were associated with the DCT (sole lesion; Estimate: -0.07mm, 95% CI: -0.14-0.00, P = 0.039, white line lesion; Estimate: 0.28mm, 95% CI: 0.15-0.42, P < 0.001).

Genetic investigations on backfat thickness and body condition score in German Holstein cattle.

Up to now, little has been known about backfat thickness (BFT) in dairy cattle. The objective of this study was to investigate the lactation curve and genetic parameters for BFT as well as its relationship with body condition score (BCS) and milk yield (MKG). For this purpose, a dataset was analysed including phenotypic observations of 1929 German Holstein cows for BFT, BCS and MKG recorded on a single research dairy farm between September 2005 and December 2022. Additionally, pedigree and genomic information was available. Lactation curves were predicted and genetic parameters were estimated for all traits in first to third lactation using univariate random regression models. For BCS, lactation curves had nadirs at 94 DIM, 101 DIM and 107 DIM in first, second and third lactation. By contrast, trajectories of BFT showed lowest values later in lactation at 129 DIM, 117 DIM and 120 DIM in lactation numbers 1 to 3, respectively. Although lactation curves of BCS and BFT had similar shapes, the traits showed distinct sequence of curves for lactation number 2 and 3. Cows in third lactation had highest BCS, whereas highest BFT values were found for second parity animals. Average heritabilities were 0.315 ± 0.052, 0.297 ± 0.048 and 0.332 ± 0.061 for BCS in lactation number 1 to 3, respectively. Compared to that, BFT had considerably higher heritability in all lactation numbers with estimates ranging between 0.357 ± 0.028 and 0.424 ± 0.034. Pearson correlation coefficients between estimated breeding values for the 3 traits were negative between MKG with both BCS (r = -0.245 to -0.322) and BFT (r = -0.163 to -0.301). Correlation between traits BCS and BFT was positive and consistently high (r = 0.719 to 0.738). Overall, the results of this study suggest that BFT and BCS show genetic differences in dairy cattle, which might be due to differences in depletion and accumulation of body reserves measured by BFT and BCS. Therefore, routine recording of BFT on practical dairy farms could provide valuable information beyond BCS measurements and might be useful, for example, to better assess the nutritional status of cows.

Performance, nutrient utilization and meat quality traits in Bos indicus cattle: a meta-analysis examining the effect of residual feed intake.

This meta-analysis aims to investigate the effects of residual feed intake (RFI) phenotype on performance, nutrient utilization and meat quality traits in Zebu (Bos indicus) cattle. Twenty-three peer-reviewed publications with 37 treatment means were included in the dataset. Weighted mean difference analysis compared animals categorized into low RFI (more efficient) versus medium or high RFI (less efficient) groups. Data heterogeneity via meta-regression and subgroup analysis, considering variables such as animal age, sex class, experimental duration, RFI group, dietary concentrate, and estimated metabolizable energy intake were also explored. The predominant genetic group of cattle in the dataset was Nellore (89.18%), followed by Brahman (10.81%). More efficient animals (low RFI phenotype) exhibited less dry matter intake (DMI; P < 0.010) than medium or high RFI animals (-0.95 kg vs. -0.42 kg/d). Cattle dietary crude protein and fiber digestibility were consistent across RFI groups (P > 0.05), while dietary ether extract digestibility tended to decrease (P = 0.050) in low RFI animals (-13.20 g/kg DM). Low RFI animals tended to increased (P = 0.065) ribeye area (REA) compared to the high/medium RFI groups, while carcass backfat thickness (BFT) decreased (P = 0.042) compared to high/medium RFI groups. Moreover, there was an increase (P < 0.001) of 0.22 kg in Warner-Bratzler shear force (WBSF) and a reduction (P < 0.001) in the myofibrillar fragmentation index (MFI) in low RFI animals. Meat color parameters (lightness [L*] and yellowness [b*]) and visual marbling scores were consistent (P > 0.05) across RFI groups. In conclusion, Zebu cattle classified as efficient (low RFI) exhibited reduced DMI, which improves their feed efficiency. However, BFT and meat quality parameters such as tenderness (WBSF and MFI) and redness [a*] were compromised by low RFI phenotype, highlighting the challenge of enhancing feed efficiency and meat quality traits in Zebu cattle.

Genome-wide association study reveals a genomic region on SSC7 simultaneously associated with backfat thickness, skin thickness and carcass length in a Large White × Tongcheng advanced generation intercross resource population.

In order to identify important genetic markers associated with backfat thickness, skin thickness and carcass length, we first constructed Large White × Tongcheng (Chinese local breed), an advanced generation intercross population, then performed a genome-wide association study (GWAS) to reveal the key genomic region associated with these traits through whole genome sequencing. The GWAS results of backfat thickness, skin thickness and carcass length showed that all the most significant SNPs associated with these three traits were located on SSC7, and that 14.9, 27.0 and 21.1% of phenotypic variances were explained by these three SNPs, respectively. Through linkage disequilibrium analysis, we found that a 66.9 kb (30.23-30.31 Mb) genetic region was overlapped among these three traits, and that NUDT3 and HMGA1 were identified as major candidate genes for backfat thickness and carcass length, and GRM4 as a potential candidate gene for skin thickness. In addition, 13 highly linked SNPs significantly associated with the three traits were also identified in overlapped region, and three completely linked SNPs formed two haplotypes Q and q. The backfat thickness of individuals with the qq genotype was significantly lower than that of individuals with the QQ genotype, but their carcass length and skin thickness were significantly higher than those with the QQ genotype. Our detected candidate genes and SNPs will provide the foundation for genetic improvement of these three traits.

Association analysis of mitochondrial genome polymorphisms with backfat thickness in pigs.

Mitochondrial DNA (mtDNA) variations and associated effects on economic traits have been widely reported in farm animals, as these genetic polymorphisms can affect the efficiency of energy production and cell metabolism. In studies related to metabolism, the deposition of fat was highly correlated with mitochondria. However, the effect of mtDNA polymorphisms on porcine backfat thickness (BFT) remained unclear. In this study, 243 pigs were collected to analyse the relationship between BFT and mtDNA polymorphisms. There were considerable differences in BFT, ranging from 5 mm to 18 mm. MtDNA D-loop sequencing discovered 48 polymorphic sites. Association analysis revealed that 30 variations were associated with BFT (P < 0.05). The polymorphism m.794A > G showed the maximum difference in BFT between A and G carriers, which differed at ∼2.5 mm (P < 0.001). The 48 polymorphic sites generated 22 haplotypes (H1-H22), which clustered into 4 haplogroups (HG1-HG4). HG1 had a lower BFT value than other three haplogroups (P < 0.01), whereas H4 in HG1 exhibited the lowest BFT of all haplotypes analyzed (P < 0.01). The results of this study highlight an association between mtDNA polymorphisms and BFT, and suggest the potential application of mtDNA in pig molecular breeding practices.

Three novel simple sequence repeats (SSRs) identified by MALDI-TOF-MS method were associated with backfat in pig.

Backfat trait is an important economic trait and highly heritable, but difficult to evaluate. Thus, it is of great significance to explore optimal backfat thickness of pigs by using marker-assisted selection (MAS) to speed up its breeding process and improve economic efficiency. This study aimed to investigate the relationship between genetic variations (e.g., SSRs) and backfat of Qinghai Bamei pigs using MALDI-TOF Mass Spectrometry (MALDI-TOF-MS). Herein, five alternative SSR loci (namely V1, V2, V3, V4 and V5) were selected for subsequent detection. The results suggested that 3 (141-, 143- and 145-), 3 (128-, 130- and 132-), 2 (160- and 162-), 2 (136- and 139-) and 3 (170-, 184- and 192-) alleles of V1, V2, V3, V4 and V5 were found, respectively. Subsequent analysis showed that there was linkage equilibrium among five SSRs and Hap19 (13.1%) (141-/132-/160-/139-/192-) had the highest haplotype frequency. Among these five SSR loci, V1, V2 and V3 loci were significantly associated to the backfat of Qinghai Bamei sows. These findings enriched the study of SSRs in Qinghai Bamei pigs, and (AC)n (Chr15:85485851-85485995), (AC)n (Chr10:52724583-52724713) and (TG)n (Chr4:90732644-90732802) could be utilized as the candidate locus for MAS in pig industry.HIGHLIGHTSFive novel SSR loci was identified in pigs through MALDI-TOF MS.V1, V2 and V3 loci was were significantly associated to the backfat of pigs.

Impact of dietary supplementation with N-carbamoyl-aspartic acid on serum metabolites and intestinal microflora of sows.

BACKGROUND: N-Carbamoyl-aspartic acid (NCA) is a critical precursor for de novo biosynthesis of pyrimidine nucleotides. To investigate the cumulative effects of maternal supplementation with NCA on the productive performance, serum metabolites and intestinal microbiota of sows, 40 pregnant sows (∼day 80) were assigned into two groups: (1) the control (CON) and (2) treatment (NCA, 50 g t-1 NCA). RESULTS: Results showed that piglets from the NCA group had heavier birth weight than those in the CON group (P < 0.05). In addition, maternal supplementation with NCA decreased the backfat loss of sows during lactation (P < 0.05). Furthermore,16S-rRNA sequencing results revealed that maternal NCA supplementation decreased the abundance of Cellulosilyticum, Fournierella, Anaerovibrio, and Oribacterium genera of sows during late pregnancy (P < 0.05). Similarly, on the 14th day of lactation, maternal supplementation with NCA reduced the diversity of fecal microbes of sows as evidenced by significantly lower observed species, Chao1, and Ace indexes, and decreased the abundance of Lachnospire, Faecalibacterium, and Anaerovorax genera, while enriched the abundance of Catenisphaera (P < 0.05). Untargeted metabolomics showed that a total of 48 differentially abundant biomarkers were identified, which were mainly involved in metabolic pathways of arginine/proline metabolism, phenylalanine/tyrosine metabolism, and fatty acid biosynthesis, etc. CONCLUSION: Overall, the results indicated that NCA supplementation regulated intestinal microbial composition of sows and serum differential metabolites related to arginine, proline, phenylalanine, tyrosine, and fatty acids metabolism that may contribute to regulating the backfat loss of sows, and the birth weight and diarrhea rate of piglets. © 2022 Society of Chemical Industry.

Effect of non-starch polysaccharide enzyme supplementation with gradually reduced energy diet on growth performance, nutrient digestibility, lean meat percentage and backfat thickness of growing pigs.

This study was conducted with the objective of evaluating a way to reduce feed costs with better meat characteristics for growing pigs by supplementing non-starch polysaccharide enzyme (NSPE) in energy reduced diets. A total of 200 growing pigs [(Landrace × Yorkshire) × Duroc] weighing 22.94 ± 0.22 kg were divided into five dietary treatments, each with eight replication pens (three barrows and two gilts). The pigs were allotted in a completely randomised block design according to body weight and sex. The dietary treatments were: CON (control), basal diet (NE 2500 kcal); NSPE1, basal diet + 0.04% NSPE; NSPE2, (basal diet-20 kcal) + 0.04% NSPE; NSPE3, (basal diet-30 kcal) + 0.04% NSPE; NSPE4, (basal diet-50 kcal) + 0.04% NSPE. We have assessed growth performance, lean meat percentage (LMP) and backfat thickness at initial, Week 4 and 8. Apparent nutrient digestibility was assessed in Weeks 4 and 8. There was no significant difference (p > 0.05) among the groups on growth performance. In Week 8, gradual reduction of energy caused a linear reduction (p = 0.028) of backfat thickness and a linear increase (p < 0.05) of LMP. In addition, at Week 8, supplementation of NSPE enzyme showed improved digestibility of nitrogen (p < 0.05) and energy (p < 0.05) in the NSPE1 group than in the CON group. In short, gradual reduction of dietary energy supplemented with NSPE showed consistent growth performance through higher nutrient digestibility with positive changes in backfat thickness and LMP of growing pigs.

Impact of body condition on sow and litter performance, postpartum physiological, hematological, and biochemical parameters in Landlly crossbred pigs.

A total of 32 Landlly crossbred sows were categorized into three groups based on their body condition score (BCS) on the 90th day of gestation viz. low, moderate, and high body condition groups. BCS assessments were subsequently conducted on the 102nd day, at farrowing, and on the 7th, 17th, 27th, and 42nd day postpartum, along with measurements of ultrasonic backfat thickness and body weight. Key reproductive performance traits, including total number born (TNB) and alive (TLA), stillbirths, mummification, and litter weight at birth and weaning, were recorded. Several physiological, health, biochemical, and hematological parameters were also estimated at different lactation stages. Analysis of the data revealed that TNB, TLA (P<0.04), and weaned piglets (P<0.01), as well as litter weight at birth (P<0.08) and weaning (P<0.08), were significantly higher in the low BCS group. Meanwhile, the weaning to estrous interval (P<0.04) was optimized in the high and moderate BCS groups. However, sows with high body condition exhibited higher stillbirths and pre-weaning mortality. Additionally, the order of increasing body condition correlated with superior colostrum quality, characterized by higher IgG levels (P<0.02), and increased average milk yield during early and mid-lactation (P<0.03). A high occurrence of postpartum dysgalactia syndrome (PDS) was evident in obese sows (P<0.001). Moreover, a positive correlation was found between the body condition of sows at late gestation and cortisol concentration throughout lactation across the three BCS groups (P<0.0001). Furthermore, a strong positive correlation was observed between the postpartum serum concentration of T3 (thyroid hormone) (P<0.002) and the prepartum body condition of sows. Based on these findings, maintaining sows with a moderate body condition (BCS of 3) and a backfat thickness of 21 mm in the breeding herd is recommended for enhancing profitability and productivity at the farm level.

Meta-analysis of genome-wide association studies uncovers shared candidate genes across breeds for pig fatness trait.

BACKGROUND: Average backfat thickness (BFT) is a critical complex trait in pig and an important indicator for fat deposition and lean rate. Usually, genome-wide association study (GWAS) was used to discover quantitative trait loci (QTLs) of BFT in a single population. However, the power of GWAS is limited by sample size in a single population. Alternatively, meta-analysis of GWAS (metaGWAS) is an attractive method to increase the statistical power by integrating data from multiple breeds and populations. The aim of this study is to identify shared genetic characterization of BFT across breeds in pigs via metaGWAS.  RESULTS: In this study, we performed metaGWAS on BFT using 15,353 pigs (5,143 Duroc, 7,275 Yorkshire, and 2,935 Landrace) from 19 populations. We detected 40 genome-wide significant SNPs (Bonferroni corrected P < 0.05) and defined five breed-shared QTLs in across-breed metaGWAS. Markers within the five QTL regions explained 7 ~ 9% additive genetic variance and showed strong heritability enrichment. Furthermore, by integrating information from multiple bioinformatics databases, we annotated 46 candidate genes located in the five QTLs. Among them, three important (MC4R, PPARD, and SLC27A1) and seven suggestive candidate genes (PHLPP1, NUDT3, ILRUN, RELCH, KCNQ5, ITPR3, and U3) were identified. CONCLUSION: QTLs and candidate genes underlying BFT across breeds were identified via metaGWAS from multiple populations. Our findings contribute to the understanding of the genetic architecture of BFT and the regulating mechanism underlying fat deposition in pigs.

Genome-wide association study identifying genetic variants associated with carcass backfat thickness, lean percentage and fat percentage in a four-way crossbred pig population using SLAF-seq technology.

BACKGROUND: Carcass backfat thickness (BFT), carcass lean percentage (CLP) and carcass fat percentage (CFP) are important to the commercial pig industry. Nevertheless, the genetic architecture of BFT, CLP and CFP is still elusive. Here, we performed a genome-wide association study (GWAS) based on specific-locus amplified fragment sequencing (SLAF-seq) to analyze seven fatness-related traits, including five BFTs, CLP, and CFP on 223 four-way crossbred pigs. RESULTS: A total of 227, 921 highly consistent single nucleotide polymorphisms (SNPs) evenly distributed throughout the genome were used to perform GWAS. Using the mixed linear model (MLM), a total of 20 SNP loci significantly related to these traits were identified on ten Sus scrofa chromosomes (SSC), of which 10 SNPs were located in previously reported quantitative trait loci (QTL) regions. On SSC7, two SNPs (SSC7:29,503,670 and rs1112937671) for average backfat thickness (ABFT) exceeded 1% and 10% Bonferroni genome-wide significance levels, respectively. These two SNP loci were located within an intron region of the COL21A1 gene, which was a protein-coding gene that played an important role in the porcine backfat deposition by affecting extracellular matrix (ECM) remodeling. In addition, based on the other three significant SNPs on SSC7, five candidate genes, ZNF184, ZNF391, HMGA1, GRM4 and NUDT3 were proposed to influence BFT. On SSC9, two SNPs for backfat thickness at 6-7 ribs (67RBFT) and one SNP for CLP were in the same locus region (19 kb interval). These three SNPs were located in the PGM2L1 gene, which encoded a protein that played an indispensable role in glycogen metabolism, glycolysis and gluconeogenesis as a key enzyme. Finally, one significant SNP on SSC14 for CLP was located within the PLBD2 gene, which participated in the lipid catabolic process. CONCLUSIONS: A total of two regions on SSC7 and SSC9 and eight potential candidate genes were found for fatness-related traits in pigs. The results of this GWAS based on SLAF-seq will greatly advance our understanding of the genetic architecture of BFT, CLP, and CFP traits. These identified SNP loci and candidate genes might serve as a biological basis for improving the important fatness-related traits of pigs.

Non-contact detection method of pregnant sows backfat thickness based on two-dimensional images.

Since sow backfat thickness (BFT) is highly correlated with its service life and reproductive effectiveness, dynamic monitoring of BFT is a critical component of large-scale sow farm productivity. Existing contact measures of sow BFT have their problems including, high measurement intensity and sows' stress reaction, low biological safety, and difficulty in meeting the requirements for multiple measurements. This article presents a two-dimensional (2D) image-based approach for determining the BFT of pregnant sows when combined with the backfat growth rate (BGR). The 2D image features of sows extracted by convolutional neural networks (CNN) and the artificially defined phenotypic features of sows such as hip width, hip height, body length, hip height-width ratio, length-width ratio, and waist-hip ratio, were used respectively, combined with BGR, to construct a prediction model for sow BFT using support vector regression (SVR). Following testing and comparison, it was shown that using CNN to extract features from images could effectively replace artificially defined features, BGR contributed to the model's accuracy improvement. The CNN-BGR-SVR model performed the best, with R2 of 0.72 and mean absolute error of 1.21 mm, and root mean square error of 1.50 mm, and mean absolute percentage error of 7.57%. The results demonstrated that the CNN-BGR-SVR model based on 2D images was capable of detecting sow BFT, establishing a new reference for non-contact sow BFT detection technology.

Preliminary identification and analysis of differential RNA editing between higher and lower backfat thickness pigs using DNA-seq and RNA-seq data.

RNA editing is an essential post-transcriptional regulatory mechanism. However, few studies have investigated the functional RNA edits in the economic traits of livestock on a genome-wide scale. Pigs are one of the most important livestock species and their fat is the principal organ involved in the regulation of adipose deposition. Here, we used three full-sibling pairs, with each pair comprising a pig with higher backfat (BF) thickness and lower backfat thickness, to identify RNA editing events based on whole-genome and transcriptome sequencing data. A total of 60,903 non-redundant RNA editing sites with 59,472 (97.7%) A-to-G edits were detected using a revised bioinformatics pipeline. A specific sequence context with G preference was found one base downstream of the edited site, and the editing level was associated with the distribution of nucleotides across nearly sites. Moreover, the A-to-G editing sites mostly occurred in the pig-special short interspersed nuclear elements, Pre0_SS. Comparing the difference between pigs with higher BF and lower BF, we found 211 differentially edited sites (DESites). Functional enrichment analyses revealed a significant enrichment of genes containing DESites in terms of adipose deposition. The DESites located in the six adipose-related genes (SKP1, GSK3B, COL5A3, MDM4, NT5C2, and DENND2A) were selected as candidate RNA editing sites associated with adipose deposition, and thus require further evaluation. This study mined the potentially functional RNA editing sites in pig adipose tissue and indicated that RNA editing may play an important role in adipose deposition, which provides a new insight into the post-transcriptionally mediated regulation mechanism of fat development.

Identification of a missense variant in the porcine AGPAT gene family associated with intramuscular fat content through whole-genome sequencing.

The 1-acylglycerol-3-phosphate O-acyltransferases (AGPATs) are enzymes that catalyze the conversion of lysophosphatidic acid to phosphatidic acid, which is a precursor of triacylglycerol, the main fat reservoir in mammals. We used whole-genome sequencing of 205 pigs to identify 6639 genetic variants in the porcine AGPAT gene family. Of these, 166 common variants in the AGPAT5 gene had significant associations with fat content and composition traits. We preselected a missense single nucleotide polymorphism in exon 6 of AGPAT5 (rs196952262, A>G) for validation of its associations in 1034 pigs from the same Duroc line. The A allele showed a positive additive effect for intramuscular fat content (+1.12% ± 0.21, p < 0.001, for gluteus medius and +0.89% ± 0.33, p < 0.01, for longissimus). We also observed significant associations with fatty acid composition that were, at least in part, independent of the increased intramuscular fat. The A allele resulted in more monounsaturated fatty acids (+0.34% ± 0.15, p < 0.05, for longissimus) and a greater monounsaturated/polyunsaturated fatty acids ratio (+0.11 ± 0.04, p < 0.01, for gluteus medius and +0.13 ± 0.05, p < 0.05, for longissimus). The effect of the AGPAT5 variant on intramuscular fat was more noticeable in fatter pigs, and AGPAT5 interacts with other genes that affect overall fatness such as LEPR. AGPAT5 was the most expressed gene of the AGPAT family in pig skeletal muscle. This variant can be used as a marker in assisted selection for modulating pig fat deposition and fatty acid content.

Genome-wide association studies for growth-related traits in a crossbreed pig population.

Growth-related traits are important economic traits in the pig industry that directly influence pork production efficiency. To detect quantitative trait loci and candidate genes affecting growth traits, genome-wide association studies were performed for backfat thickness (BF) and loin muscle depth (LMD) in 370 Chuying-black pigs using Illumina PorcineSNP50 BeadChip array. We totally identified 14 BF-associated SNPs, which included 11 genome-wide SNPs (P < 1.39E-06) and 3 chromosome-wide suggestive SNPs (P < 2.79E-05) and for LMD, 9 SNPs surpassed the genome-wide significant threshold (P < 1.39E-06). These SNPs explained 30.33 and 27.51% phenotypic variance for BF and LMD respectively. Furthermore, 14 and 9 genes nearest to the significant SNPs were selected to be candidate genes, including MAGED1, GPHN, CCSER1, and GUCY2D for BF and PARM1, COL18A1, HSF5, and SCML2 genes for LMD. One significant SNP, which explained 6.07% of phenotypic variance for BF, mapped to a pleiotropic quantitative trait locus with a 494-kb interval. Together, the SNPs and candidate genes identified in this study will advance our understanding of the complex genetic architecture of BF and LMD traits, and they will also provide important clues for future implementation of a genomic selection program in Chuying-black pigs.

A further survey of the quantitative trait loci affecting swine body size and carcass traits in five related pig populations.

Breeding for good meat quality performance while maintaining large body size and desirable carcass traits has been the major challenge for modern swine selective breeding. To address this goal, in the present work we studied five related populations produced by two commercial breeds (Berkshire and Duroc) and two Chinese breeds (Licha black pig and Lulai black pig). A single-trait GWAS performed on 20 body size and carcass traits using a self-developed China Chip-1 porcine SNP50K BeadChip identified 11 genome-wide significant QTL on nine chromosomes and 22 suggestive QTL on 15 chromosomes. For the 11 genome-wide significant QTL, eight were detected in at least two populations, and the rest were population-specific and only mapped in Shanxia black pig. Most of the genome-wide significant QTL were pleiotropic; for example, the QTL around 75.65 Mb on SSC4 was associated with four traits at genome-wide significance level. After screening the genes within 50 kb of the top SNP for each genome-wide significant QTL, NR6A1 and VRTN were chosen as candidate genes for vertebrae number; PLAG1 and BMP2 were identified as candidate genes for body size; and MC4R was the strong candidate gene for body weight. The four genes have been reported as candidates for thoracic vertebrae number, lumbar vertebrae number, carcass length and body weight respectively in previous studies. The effects of VRTN on thoracic vertebrae number, carcass length and body length have been verified in Shanxia black pig. Therefore, the VRTN genotype could be used in gene-assisted selection, and this could accelerate genetic improvement of body size and carcass traits in Shanxia black pig.

Body status and blood metabolites profiles during resumption of postpartum ovarian activity in yak (Poephagus grunniens).

We examined the changes in body weight (BW), back-fat thickness (BFT) and blood metabolites in relation to postpartum (PP) ovarian activity status in twenty female yaks raised under semi-intensive system. BFT and ovarian activities, like follicle development, ovulation (OV) and corpus luteum (CL) development, were monitored from 4 to 15 weeks (wk) PP using ultrasonography. Resumption of ovarian activity was confirmed with ovulation of dominant follicle (DF) and subsequent CL development, and >1 ng/ml progesterone concentration in blood plasma sample after 1week of ovulation. Yaks were further classified as cyclic (with CL), acyclic (without CL), and cystic (with >25 mm follicular cyst; FC). Within 20 weeks PP, 60% yaks resumed cyclic ovarian activity, while 25% failed to initiate cycling activity, and 15% developed follicular cysts. In all categories of yak, BW gradually decreased (p < .05) till nadir; however, nadir reached earlier (p < .05) in acyclic yaks. BFT differed (p < .05) among the yak groups, but it tended to be higher in cyclic yaks as compared to acyclic and cystic. No difference (p > .05) in non-esterified fatty acids (NEFA) values was found among the different categories of yaks, whereas, beta-hydroxy butyrate (BHB) levels were higher in cystic animals as compared to acyclic and cyclic. Blood glucose levels decreased in all yaks during initial 2 weeks after calving. Our findings suggest that yaks with low BW, BFT and glucose levels, and higher BHB values were at risk of delayed resumption of ovarian activity and concomitant development of follicular cysts.

Fetal mortality associated with backfat thickness at first mating and first farrowing of the primiparous sows raised in a commercial herd in Thailand.

This study aimed to investigate the fetal mortality, including stillborn piglets (SB) and mummified fetuses (MM), in relation to backfat thickness both at first mating (MBF) and at first farrowing (FBF) in 200 primiparous sows accommodated in a commercial breeding herd in Thailand. Backfat thickness of all pigs was measured at P2 position using an A-mode ultrasonography. Based on MBF, the gilts were classified into four groups: MBF1 (≤12.0 mm), MBF2 (>12.0-15.0 mm), MBF3 (>15.0-18.0 mm), and MBF4 (>18.0 mm). According to FBF, the primiparous sows were categorized into four classes: FBF1 (≤15.0 mm), FBF2 (>15.0-18.0 mm), FBF3 (>18.0-21.0 mm), and FBF4 (>21.0 mm). At farrowing, 174 litters were examined for percentage of SB and MM. The results indicated that mean MBF and FBF were 16.7 ± 0.3 mm and 19.6 ± 0.3 mm, respectively. Based on MBF, the pigs in MBF1 significantly possessed higher percentage of MM (13.8 ± 4.5%) than others; meanwhile, SB percentage was not different among groups (P > 0.05). According to FBF, the pigs in FBF4 farrowed the highest percentage of SB (9.1 ± 3.2%) than others, whereas MM percentage was not different among classes (P > 0.05). In summary, backfat thickness of the gilts should be one of the parameters to pay more attention since it is related to fetal mortality of the primiparous sows. The farmers should monitor the backfat thickness not only at the first mating time, but also along the gestation period in order to minimize fetal mortality in the primiparous sows.