Genetic relationships among Chinese pigs and other pig populations from Hunan Province, China

Molecular Design-Based Breeding: A Kinship Index-Based Selection Method for Complex Traits in Small Livestock Populations

Genomic selection (GS) techniques have improved animal breeding by enhancing the prediction accuracy of breeding values, particularly for traits that are difficult to measure and have low heritability, as well as reducing generation intervals. However, the requirement to establish genetic reference populations can limit the application of GS in pig breeds with small populations, especially when small populations make up most of the pig breeds worldwide. We aimed to propose a kinship index based selection (KIS) method, which defines an ideal individual with information on the beneficial genotypes for the target trait. Herein, the metric for assessing selection decisions is a beneficial genotypic similarity between the candidate and the ideal individual; thus, the KIS method can overcome the need for establishing genetic reference groups and continuous phenotype determination. We also performed a robustness test to make the method more aligned with reality. Simulation results revealed that compared to conventional genomic selection methods, the KIS method is feasible, particularly, when the population size is relatively small.

Effects of Dietary Fiber on Growth Performance, Nutrient Digestibility and Intestinal Health in Different Pig Breeds

To explore the effect of dietary fiber on growth performance and intestinal health in different pig breeds, forty Taoyuan and Duroc pigs (pure breeds) of 60 days of age were randomly divided into a 2 (diet) × 2 (breed) factorial experiment (n = 10), and fed with a basal diet (BD) or high-fiber diet (HFD). The trial lasted for 28 d, and results showed that the Taoyuan pigs had a higher average daily feed intake (ADFI) than the Duroc pigs (p < 0.05). The average daily gain (ADG) and digestibilities of gross energy (GE) and crude protein (CP) were higher in Taoyuan pigs than in the Duroc pigs under HFD feeding (p < 0.05). The HFD increased the superoxide dismutase (SOD) and catalase (CAT) activity in Taoyuan pigs (p < 0.05). Interestingly, Taoyuan pigs had a higher jejunal villus height and ratio of villus height to crypt depth (V/C) than the Duroc pigs. The HFD significantly improved the villus height and V/C ratio in duodenum and jejunum (p < 0.05). The HFD also increased the jejunal maltase and ileal sucrase activities in Duroc and Taoyuan pigs, respectively (p < 0.05). Taoyuan pigs had a higher expression level of duodenal fatty acid transport protein-1 (FATP-1) than the Duroc pigs (p < 0.05). Furthermore, the HFD acutely improved the expression levels of ileal SGLT-1 and GLUT-2, and the expression levels of jejunal occludin and claudin-1 in Taoyuan pigs (p < 0.05). Importantly, Taoyuan pigs had a higher colonic Bifidobacterium abundance than the Duroc pigs (p < 0.05). The HFD not only elevated the colonic Lactobacillus abundance and butyrate acid content in Taoyuan pigs, but also increased the acetic and propionic acid contents in both the pig breeds (p < 0.05). These results indicated a difference in dietary fiber (DF) utilization by the two pig breeds, and results may also suggest a beneficial character of DF in regulating intestinal health.

Mitochondrial DNA sequence and phylogenetic evaluation of geographically disparate Sus scrofa breeds

Next generation sequencing of mitochondrial DNA (mtDNA) facilitates studies into the metabolic characteristics of production animals and their relation to production traits. Sequence analysis of mtDNA from pure-bred swine with highly disparate production characteristics (Mangalica Blonde, Mangalica Swallow-bellied, Meishan, Turopolje, and Yorkshire) was initiated to evaluate the influence of mtDNA polymorphisms on mitochondrial function. Herein, we report the complete mtDNA sequences of five Sus scrofa breeds and evaluate their position within the phylogeny of domestic swine. Phenotypic traits of Yorkshire, Mangalica Blonde, and Swallow-belly swine are presented to demonstrate their metabolic characteristics. Our data support the division of European and Asian breeds noted previously and confirm European ancestry of Mangalica and Turopolje breeds. Furthermore, mtDNA differences between breeds suggest function-altering changes in proteins involved in oxidative phosphorylation such as ATP synthase 6 (MT-ATP6), cytochrome oxidase I (MT-CO1), cytochrome oxidase III (MT-CO3), and cytochrome b (MT-CYB), supporting the hypothesis that mtDNA polymorphisms contribute to differences in metabolic traits between swine breeds. Our sequence data form the basis for future research into the roles of mtDNA in determining production traits in domestic animals. Additionally, such studies should provide insight into how mtDNA haplotype influences the extreme adiposity observed in Mangalica breeds.

Characterization of the porcine transferrin gene (TF) and its association with disease severity following an experimental Actinobacillus pleuropneumoniae infection

Transferrin (TF)-mediated provision of iron is essential for a productive infection by many bacterial pathogens, and iron-depletion of TF is a first line defence against bacterial infections. Therefore, the transferrin (TF) gene can be considered a candidate gene for disease resistance. We obtained the complete DNA sequence of the porcine TF gene, which spans 40 kb and contains 17 exons. We identified polymorphisms on a panel of 10 different pig breeds. Comparative intra- and interbreed sequence analysis revealed 62 polymorphisms in the TF gene including one microsatellite. Ten polymorphisms were located in the coding sequence of the TF gene. Four SNPs (c.902A>T, c.980G>A, c.1417A>G, c.1810A>C) were predicted to cause amino acid exchanges (p.Lys301Ile, p.Arg327Lys, p.Lys473Glu, p.Asn604His). We performed association analyses using six selected TF markers and 116 pigs experimentally infected with Actinobacillus pleuropneumoniae serotype 7. The analysis showed breed-specific TF allele frequencies. In German Landrace, we found evidence for a possible association of the severity of A. pleuropneumoniae infection with TF genotypes.

Relationships among genetic makeup, active ingredient content, and place of origin of the medicinal plant Gastrodia tuber

Gastrodia tuber and its component gastrodin have many pharmacological effects. The chemical fingerprints and gastrodin contents of eight Gastrodia populations were determined, and the genomic DNA polymorphism of the populations was investigated. Genetic distance coefficients among the populations were calculated using the DNA polymorphism data. A dendrogram of the genetic similarities between the populations was constructed using the genetic distance coefficients. The results indicated that the genomic DNA of Gastrodia tubers was highly polymorphic; the eight populations clustered into three major groups, and the gastrodin content varied greatly among these groups. There were obvious correlations among genetic makeup, gastrodin content, and place of origin. The ecological environments in Guizhou and Shanxi may be conducive to evolution and to gastrodin biosynthesis, and more suitable for cultivation of Gastrodia tubers. These findings may provide a scientific basis for overall genetic resource management and for the selection of locations for cultivating Gastrodia tubers.