Genetic evaluation for production and body size traits using different animal models in purebred-Duroc pigs

Duroc pigs are popular crossbred terminal sires, and accurate assessment of genetic parameters in the population can help to rationalize breeding programmes. The principle aim of this study were to evaluate the genetic parameters of production (birth weight, BW; age at 115 kg, AGE; feed conversion ratio, FCR) and body size (body length, BL; body height, BH; front cannon circumference, FCC) traits of Duroc pigs. The second objective was to analyze the fit of different genetic assessment models. The variance components and correlations of BW (28,348 records), AGE (28,335 records), FCR (11,135 records), BL (31,544 records), BH (21,862 records), and FCC (14,684 records) traits were calculated by using DMU and AIREMLF90 from BLUPF90 package. In the common environment model, the heritability of BW, AGE, FCR, BL, BH, and FCC traits were 0.17 ± 0.014, 0.30 ± 0.019, 0.28 ± 0.024, 0.16 ± 0.013, 0.14 ± 0.017, and 0.081 ± 0.016, with common litter effect values of 0.25, 0.20, 0.18, 0.23, 0.19, and 0.16, respectively. According to the results of the Akaike information criterion (AIC) calculations, models with smaller AIC values have a better fit. We found that the common environment model with litter effects as random effects for estimating genetic parameters had a better fit. In this Model, the estimated genetic correlations between AGE with BW, FCR, BL, BH, and FCC traits were −0.28 (0.040), 0.76 (0.038), −0.71 (0.036), −0.44 (0.060), and −0.60 (0.073), respectively, with phenotypic correlations of −0.17, 0.52, −0.22, −0.13 and −0.24, respectively. In our analysis of genetic trends for six traits in the Duroc population from 2012 to 2021, we observed significant genetic trends for AGE, BL, and BH. Particularly noteworthy is the rapid decline in the genetic trend for AGE, indicating an enhancement in the pig's growth rate through selective breeding. Therefore, we believe that some challenging-to-select traits can benefit from the genetic correlations between traits. By selecting easily measurable traits, they can gain from synergistic selection effects, leading to genetic progress. Conducting population genetic parameter analysis can assist us in devising breeding strategies

Exploring the Fecal Microbial Composition and Metagenomic Functional Capacities Associated With Feed Efficiency in Commercial DLY Pigs

Gut microbiota has indispensable roles in nutrient digestion and energy harvesting, especially in processing the indigestible components of dietary polysaccharides. Searching for the microbial taxa and functional capacity of the gut microbiome associated with feed efficiency (FE) can provide important knowledge to increase profitability and sustainability of the swine industry. In the current study, we performed a comparative analysis of the fecal microbiota in 50 commercial Duroc × (Landrace × Yorkshire) (DLY) pigs with polarizing FE using 16S rRNA gene sequencing and shotgun metagenomic sequencing. There was a different microbial community structure in the fecal microbiota of pigs with different FE. Random forest analysis identified 24 operational taxonomic units (OTUs) as potential biomarkers to improve swine FE. Multiple comparison analysis detected 8 OTUs with a significant difference or tendency toward a difference between high- and low-FE pigs (P < 0.01, q < 0.1). The high-FE pigs had a greater abundance of OTUs that were from the Lachnospiraceae and Prevotellaceae families and the Escherichia-Shigella and Streptococcus genera than low-FE pigs. A sub-species Streptococcus gallolyticus subsp. gallolyticus could be an important candidate for improving FE. The functional capacity analysis found 18 KEGG pathways and CAZy EC activities that were different between high- and low-FE pigs. The fecal microbiota in high FE pigs have greater functional capacity to degrade dietary cellulose, polysaccharides, and protein and may have a greater abundance of microbes that can promote intestinal health. These results provided insights for improving porcine FE through modulating the gut microbiome

Estimates of variance components and heritability using different animal models for growth, backfat, litter size and healthy birth ratio in Large White pigs

This study compared the estimates of variance components using various animal models for Large White pigs. The traits included three production traits, birth weight (BW), age at 100 kg (Age_100), and backfat thickness at 100 kg (BF_100), and two reproduction traits, number of total born (NTB) and the ratio of healthy births (RHB). Five models including or ignoring common litter environmental effects, maternal effects, and the direct-maternal covariance (σam) were used for this study. The results showed that the model including all terms, or including all terms except σam, yielded the best-fitting result. The direct variance and heritability were overestimated when the model ignored all previously listed effects, especially for production traits. When all terms were modeled, the direct heritability estimates (  ± standard error) were 0.038 ± 0.008, 0.216 ± 0.022, 0.416 ± 0.023, 0.066 ± 0.013, and 0.049 ± 0.007 for BW, Age_100, BF_100, NTB, and RHB, respectively. The common litter effects reached statistical significance for all traits, and maternal heritability reached statistical significance for three production traits. The direct-maternal correlations were negative for all traits but only reached statistical significance for BW. These results indicate that using a more complex model may result in more accurate estimation of variance components in Large White pigs.The accepted manuscript in pdf format is listed with the files at the bottom of this page. The presentation of the authors' names and (or) special characters in the title of the manuscript may differ slightly between what is listed on this page and what is listed in the pdf file of the accepted manuscript; that in the pdf file of the accepted manuscript is what was submitted by the author

Genetic Architecture of Feeding Behavior and Feed Efficiency in a Duroc Pig Population

Increasing feed efficiency is a major goal of breeders as it can reduce production cost and energy consumption. However, the genetic architecture of feeding behavior and feed efficiency traits remains elusive. To investigate the genetic architecture of feed efficiency in pigs, three feeding behavior traits (daily feed intake, number of daily visits to feeder, and duration of each visit) and two feed efficiency traits (feed conversion ratio and residual feed intake) were considered. We performed genome-wide association studies (GWASs) of the five traits using a population of 1,008 Duroc pigs genotyped with an Illumina Porcine SNP50K BeadChip. A total of 9 genome-wide (P < 1.54E-06) and 35 suggestive (P < 3.08E-05) single nucleotide polymorphisms (SNPs) were detected. Two pleiotropic quantitative trait loci (QTLs) on SSC 1 and SSC 7 were found to affect more than one trait. Markers WU_10.2_7_18377044 and DRGA0001676 are two key SNPs for these two pleiotropic QTLs. Marker WU_10.2_7_18377044 on SSC 7 contributed 2.16 and 2.37% of the observed phenotypic variance for DFI and RFI, respectively. The other SNP DRGA0001676 on SSC 1 explained 3.22 and 5.46% of the observed phenotypic variance for FCR and RFI, respectively. Finally, functions of candidate genes and gene set enrichment analysis indicate that most of the significant pathways are associated with hormonal and digestive gland secretion during feeding. This study advances our understanding of the genetic mechanisms of feeding behavior and feed efficiency traits and provide an opportunity for increasing feeding efficiency using marker-assisted selection or genomic selection in pigs

Dynamic miRNA Landscape Links Mammary Gland Development to the Regulation of Milk Protein Expression in Mice

Mammary gland morphology varies considerably between pregnancy and lactation status, e.g., virgin to pregnant and lactation to weaning. Throughout these critical developmental phases, the mammary glands undergo remodeling to accommodate changes in milk production capacity, which is positively correlated with milk protein expression. The purpose of this study was to investigate the microRNA (miRNA) expression profiles in female ICR mice’s mammary glands at the virgin stage (V), day 16 of pregnancy (P16d), day 12 of lactation (L12d), day 1 of forced weaning (FW1d), and day 3 of forced weaning (FW3d), and to identify the miRNAs regulating milk protein gene expression. During the five stages of testing, 852 known miRNAs and 179 novel miRNAs were identified in the mammary glands. Based on their expression patterns, the identified miRNAs were grouped into 12 clusters. The expression pattern of cluster 1 miRNAs was opposite to that of milk protein genes in mammary glands in all five different stages. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed that the predicted target genes of cluster 1 miRNAs were related to murine mammary gland development and lactation. Furthermore, fluorescence in situ hybridization (FISH) analysis revealed that the novel-mmu-miR424-5p, which belongs to the cluster 1 miRNAs, was expressed in murine mammary epithelial cells. The dual-luciferase reporter assay revealed that an important milk protein gene—β-casein (CSN2)—was regarded as one of the likely targets for the novel-mmu-miR424-5p. This study analyzed the expression patterns of miRNAs in murine mammary glands throughout five critical developmental stages, and discovered a novel miRNA involved in regulating the expression of CSN2. These findings contribute to an enhanced understanding of the developmental biology of mammary glands, providing guidelines for increasing lactation efficiency and milk quality

Effect of miR-143-3p from Extracellular Vesicles of Porcine Uterine Luminal Fluid on Porcine Trophoblast Cells

Extracellular vesicles (EVs) in uterine luminal fluid (ULF) can reportedly affect the proliferation and migration function of porcine trophoblast cells (PTr2 cells) by mediating the maternal–fetal exchange of information. miR-143-3p is considered a crucial miRNA in early pregnancy in mammals; however, little is currently known about how it regulates the function of PTr2 cells. This study aimed to investigate the effects of ssc-miR-143-3p in ULF-EVs on the function of PTr2 cells during porcine embryo implantation. The uptake of ULF-EVs by PTr2 cells was confirmed, which significantly increased the expression of ssc-miR-143-3p. Ssc-miR-143-3p was found to facilitate the proliferation and migration of PTr2 cells in the CCK-8, EdU and wound-closure assays, while the opposite findings were observed after the knockdown of ssc-miR-143-3p. Bioinformatics analysis and the luciferase reporter assay showed that glycerol-3 phosphate dehydrogenase 2 (GDP2) was directly targeted by miR-143-3p. Inhibition of miR-143-3p was validated in mice to inhibit embryo implantation. In summary, ssc-miR-143-3p in ULF-EVs affects the proliferation and migration of PTr2 cells by mediating GPD2, thereby affecting embryo implantation

Pig Coat Color Manipulation by <i>MC1R</i> Gene Editing

Black coat color in pigs is determined by the dominant E allele at the MC1R locus. Through comparing MC1R gene sequences between recessive e and dominant ED1 alleles, we identified four missense mutations that could affect MC1R protein function for eumelanin synthesis. With the aim of devising a genetic modification method for pig coat color manipulation, we mutated the e allele in the Duroc breed to the dominant ED1 allele using CRISPR-mediated homologous recombination for the four mutation substitutions at the MC1R locus. The MC1R-modified Duroc pigs generated using the allele replacement strategy displayed uniform black coat color across the body. A genotyping assay showed that the MC1R-modified Duroc pigs had a heterozygous ED1/e allele at the MC1R locus; in addition, the pigs remained in the Duroc genetic background. Our work offers a gene editing method for pig coat color manipulation, which could value the culture of new pig varieties meeting the needs of diversified market

The Ecological Value of Typical Agricultural Products: An Emergy-Based Life-Cycle Assessment Framework

Agri-products have an impact on food security, ecology protection, and crucial strategic deployment. With this respect, the economic value of agri-products should be paralleled with a non-monetary assessment of ecological value for humans. This study set up an emergy-based life-cycle assessment (Em-LCA) framework to calculate the ecosystem service (ES) and ecosystem dis-services (EDS) that was applied to six typical crops, exploring the implementation path of the agricultural eco-product value. The results showed the agriculture system mainly depends on non-renewable resources. EDS generated by China’s agri-products is higher than the ES provided by them. Nevertheless, there is a low correlation between the current price of agri-products and their greenness, but, economic value presents a rising trend with agri-product greenness increasing. Further to discussing effective approaches to sustainable agriculture, it can be seen that 1) sustainable agriculture will lead to increased greenness, but it is impossible to improve greenness indefinitely. 2) Improving greenness is an effective way to implement ecological value, another way to preserve and raise ecological value is to reduce EDS generation. 3) Reducing energy consumption leads to a decrease in EDS but it is not an appropriate way to achieve sustainable development. These findings provide meaningful suggestions for decision-makers to realize the ecological value of agri-products