Berkshire Breeds Research Articles

Differences in Immune Characteristics and Related Gene Expression in Spleen among Ningxiang, Berkshire Breeds and Their Hybrid Pigs.

To investigate the differential immunology in Ningxiang and Berkshire pigs and their F1 offspring (F1 offspring), physiological and biochemical indicators in the plasma and spleen were analyzed. Then, transcriptomic analysis of the spleen identified 1348, 408, and 207 differentially expressed genes (DEGs) in comparisons of Ningxiang vs. Berkshire, Berkshire vs. F1 offspring, and Ningxiang vs. F1 offspring, respectively. In Ningxiang vs. Berkshire pigs, the gene ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated that the DEGs included CD163, MARCO, CXCL14, CCL19, and PPBP, which are associated with immunity. GO and KEGG analyses were also conducted comparing F1 offspring and their parents. The DEGs, including BPIFB1, HAVCR2, CD163, DDX3X, CCR5, and ITGB3, were enriched in immune-related pathways. Protein-protein interaction (PPI) analysis indicated that the EGFR and ITGA2 genes were key hub genes. In conclusion, this study identifies significant immune DEGs in different pig breeds, providing data to support the exploration of breeding strategies for disease resistance in local and crossbred pig populations.

Haplogroup of the modern lines of hybrid pigs

The aim. The study was conducted to characterize the genetic diversity of hybrid pigs (Large White×Landrace)×Maxgro in Ukraine. Method. DNA isolation was performed from bristle samples using Chelex-100 ion exchange resin and epithelial tissue from the ear of pigs by the sorbent method. The results. The results of DNA typing of hybrid pigs (Large White×Landrace)×Maxgro from LLC "Hlobynskyi Svynocomplex" are presented. Using PCR-RFLP analysis of the polymorphism of the D-loop section, 7 mitochondrial haplotypes were determined – N, C, O, G, D, E, K. In the studied sample of pigs (n=50), the concentration of haplotypes as a percentage is determined. It was found that mitochondrial haplotypes C (24 %) were found to be characteristic of Landrace pigs, Hampshire, Wales, a wild pig (Ukraine, Poland, France); haplotype O (12%) – inherent in a wild pig and Landrace breed (Sweden); haplotype G (12 %) – peculiar to Wales breed, a wild pig (Italy, France); haplotype N (28%) is characteristic of the Large White breed of pigs, representatives are carriers of the Asian type. It is worth noting that the Asian haplotype N is characteristic of the Asian wild pig and Berkshire breed. The presented data on the hybridization of mitochondrial genomes of Asian and European origin are the basis for the creation of modern lines of hybrid pigs along the maternal line. Haplotype N refers to haplogroup A(D), and haplotypes C, O, G belong to haplogroup E. It is completely uncertain that haplotypes D (10 %), E (6 %), K (8 %) belong to haplogroup A(D). According to the results obtained, haplogroup E in hybrid pigs is dominant, however, it is haplogroup A that is the predecessor of haplogroup E. We assume opinions that pigs of the Large White breed with haplotype N, D, E, K – contain aboriginal genetic resources. Pigs with haplotype D, E, K – are the result of hybridization with European wild boars. Over time, this led to the almost complete disappearance of the primary Middle Eastern ancestors in the nuclear genomes of European domesticated pigs. The speculation that traditional seasonal cattle breeding, annual long-distance migrations that have occurred in the past, and commercial trade in nucleuses explain the observatory pattern of favorable gene flow among hybrid pigs. Conclusions. The results obtained during the study of the mitochondrial genome of hybrid pigs improved the understanding of matrilineal origin and phylogeographic model of distribution of genetic diversity of cross-border pig breeds (Large White×Landrace)×Maxgro in Ukraine. We came to the conclusion that natural selection acts very weakly on the single nucleotide polymorphism that led to the formation of the haplogroup of cross-border breeds of pigs that are found today. The obtained results of the study are evidence that European pig breeds consist of pigs with Asian and non-Asian mitochondria, some of which were formed from closely related maternal ancestors. The work was carried out with the support of the National Academy of Agrarian Sciences of Ukraine 31.01.00.07.F. "To study the pleiotropic effect of genes whose SNPs are used in markerassociated selection of pigs." SR No. 0121U109838. Key words: hybrid pigs, (Large White×Landrace)×Maxgro, mtDNA, D-loop, haplotype, haplogroup, PCR-PDRF.

RESULTS OF INTRODUCTORY CROSSBREEDING OF BELARUSIAN BLACK-AND-WHITE AND BERKSHIRE PIGS

The article presents the results of using the Berkshire breed in the introductory crossbreeding with the Belarusian Black-and-White breed. The resulting two-breed pedigree pigs of new genotypes were evaluated in terms of their own productivity and
 underwent genetic testing for 12 STR-loci. It has been established that the use of the Berkshire breed reduces the prolificacy of the Belarusian Black-and-White sows by 0.8 heads. At the same time, the growth rate and viability of crossbred suckling piglets were high. Two-breed replacement young animals and their age-mates of the Belarusian Black-and-White breed had the same level of self-development. The ancestors of
 four lines in the Belarusian Black-and-White breed were selected from the boars tested. A microsatellite analysis of purebred and crossbred animals was performed according to lineage affiliation. Private alleles were determined in animals of the created lines Azart 1796 and Abrus 239.

Differential expression patterns of myogenic regulatory factors in the postnatal longissimus dorsi muscle of Jeju Native Pig and Berkshire breeds along with their co-expression with Pax7

Myogenic regulatory factors (MRFs) such as MyoD , Myf6 and Myf5 play a vital role in the growth and development of muscles. Jeju Native Pig (JNP) is the top ranker in Korea amongst the indigenous livestock reared for meat purpose. Few studies covering transcript abundance of the MRFs and related to their co-expression with Pax7 in JNP have been conducted. Despite having better quality pork, JNP does not have a comparative growth rate with respect to western breeds. Therefore, the present study was designed with the objective to study the relative transcript levels of MRFs in the postnatal myogenesis of longissimus dorsi muscles in JNP and Berkshire breeds. Relative transcript levels were analyzed by qRT-PCR and blot expression analysis through Western blotting. Immunocytochemistry was performed to analyze their expressions at cellular levels. ToppCluster aided in the analysis of gene ontology of biological processes. The quantitative transcript levels of MyoD and Pax7 were significantly ( P < 0.05) higher in Berkshire than in JNP. Myotube formation was observed under the co-expression of MyoD and Pax7. ToppCluster helped in the understanding of the linking of biological processes of the MRFs with the different signaling pathways. MyBPH had significantly ( P < 0.05) high transcript levels during the chosen age groups in JNP than Berkshire. The current study can be helpful in understanding the genetic basis for myogenesis in postnatal stage. Moreover, it can act as stepping stone for the identification of marker genes related to body growth and meat quality in JNP. How to cite: Sodhi SS, Sharma N, Ghosh M, et al. Differential expression patterns of myogenic regulatory factors in the postnatal longissimus dorsi muscle of Jeju Native Pig and Berkshire breeds along with their co-expression with Pax7. Electron J Biotechnol 2021;51. https://doi.org/10.1016/j.ejbt.2021.03.001

Detection of copy number variation of alpha amylase genes in domestic pigs (Sus scrofa domesticus) and wild boars (Sus scrofa)

Copy numbers of alpha amylase genes (AMY), which encode starch-digesting enzymes, are markedly increased in modern humans and domesticated dogs as an adaptive evolutionary mechanism in response to increased consumption of starch-rich foods acquired either by farming or domestication. In this study, we surveyed total AMY gene copy numbers in 150 domestic pigs (50 pigs of Berkshire breed, 50 of Landrace breed, and 50 of Large White breed) and 51 wild boars (30 Sus scrofa leucomystax and 21 S. s. riukiuanus) to identify whether the gene copy number has changed during the domestication of pigs. The relative copy number of AMY genes was measured using a quantitative polymerase chain reaction (qPCR) and it varied from 2.7 to 10.8 per haploid genome among individuals. However, in the four remaining populations, excluding S. s. riukiuanus, the average copy number was approximately six, and no significant differences were observed between the three selected pig breeds and S. s. leucomystax wild boar. Conversely, S. s. riukiuanus had an average of 7.2 copies. The results indicating six AMY copies per haploid genome were consistent with the porcine genome reference sequence (Sscrofa11.1). These results suggest that there has been no significant increase in the AMY gene copy number during the domestication process of pigs.

Myogenic regulatory factors are key players in determining muscle mass and meat quality in Jeju native and Berkshire pigs.

BackgroundMeat from Jeju native pigs (JNPs) is highly popular among Korean consumers; however, the production efficiency is limited due to the low adult body weight. In contrast, the Berkshire breed, which has a genetic background closely related to Asian native pigs, gains weight more efficiently.ObjectivesThis study focused on the differential expression of genes related to muscle growth in postnatal myogenesis between Berkshire and JNPs, specifically the myogenic regulatory factor (MRF) genes (MyoD, Pax7, Myf5, Myf6 and MyBPH). The MRF family is primarily involved in the proliferation and development of muscle.MethodsQualitative reverse transcription‐polymerase chain reaction and western blot analyses revealed that expression of MyoD and Pax7 was significantly higher in Berkshire pigs than in JNPs. In addition, co‐expression of MyoD and Pax7 was observed in myotubes formed in cultured C2C12 cells. ToppCluster was used to elucidate the relationship between biological processes of the MRFs and muscle‐related signalling pathways.ResultsMyoD and Pax7 are factors essential for the activation of satellite cell during myogenesis. However, the mRNA and protein levels of MyBPH (which is responsible for meat quality, e.g. water content, colour and tenderness) are significantly higher in both 1‐day‐old piglets and adult JNPs than in Berkshire pigs.ConclusionsThis study provides a genetic understanding of myogenesis in the postnatal and adult stages of Berkshire pigs and JNPs. Moreover, these results will help identify marker genes related to muscle mass, growth performance and meat quality in indigenous Korean pig breeds.

Identification of Marbling Gene Loci in Commercial Pigs in Canadian Herds

A genome-wide association study (GWAS) was performed on the intramuscular fat percentage in pork chops in commercially available swine in Canada. The Duroc, Iberian, Lacombe, Berkshire, and Pietrain breeds were crossed with Large White sows, and their F1 offspring were ranked according to the intramuscular fat percentage (IMF %) obtained in their longissimus dorsi (LD) muscle loin chops. The ideal IMF % is considered to be &gt;3%, whereas the average is ~1.5% in North American pork. The genetics of the top 10% and bottom 10% from our sample population were analysed by using 80,000 single nucleotide polymorphism (SNP) microarrays in the GWAS. Our sample population had an average IMF % of 2.5 ± 0.7%, but some pork achieved &gt;7% IMF. GWAS analysis revealed SNP markers which were associated with the highest marbled pork chops on chromosomes 5, 7, and 16. Using the Sus scrofa/ susScr 11.1 map, we determined that the nearest genes were sarcospan (SSPN), Rh-associated glycoprotein (RHAG), and EGF-like fibronectin and laminin G (EGFLAM), which can be linked with muscular dystrophy disorders. We tested a subpopulation of Duroc-sired animals and found a different set of markers close to glycine receptor beta (GRLB) and potassium channel 3 (KCNJ3) on chromosomes 8 and 15. Based on our results, we could achieve pork with a good IMF of &gt;4% from animals commercially bred and raised to standard market weights of 110 kg. The choice of obtaining a good marbling line of pigs is not necessarily breed-specific, but it is line-specific.

Comparisons of meat quality and muscle fibre characteristics on multiple pig breeds and sexes using principal component analysis

Comprehensive understanding of the effect of pig breed and sex on meat quality and post-mortem muscle conditions will be necessary to estimate meat quality post mortem. In this study, we applied multiple regression and principal component analysis (PCA) using conventional meat quality traits and muscle fibre characteristics on six pig breeds and different sexes. A total of 1374 pigs from six breeds [Berkshire, Duroc, Landrace, Meishan, Yorkshire, and LYD (Landrace × Yorkshire sows with Duroc as terminal sires) crossbreed] belonging to three sexes (male, castrated male and female) were used in this study. Most of the muscle fibre characteristics showed moderate to high significant correlations with conventional meat quality traits. In particularly, the cross-sectional area (CSAF) of muscle fibres was strongly correlated with muscle pH values, water-holding capacity values and lightness (0.10 &lt; |r| &lt;0.26 and P &lt; 0.01). Multiple regression analysis by general linear model revealed that the effects of breed were significant on muscle pH24h, lightness, drip loss, and marbling score (P &lt; 0.01), whereas sex had no significant effect on meat quality. In the muscle fibre characteristics, the effects of breed and sex were significant on composition of area and density of muscle fibres (P &lt; 0.05). We observed that the Meishan breed was clearly inferior to other breeds, whereas the LYD or Berkshire breeds showed better meat quality and muscle fibre properties. Moreover, we observed clear separations between pig breeds based on the PCA, whereas the sexes in each breed presented a continuum cluster. In summary, we suggest that muscle pH24h, lightness, and drip loss are conventional meat quality traits that can be considered as quantitative factors important in estimating ultimate meat quality of pigs along with the CSAF of muscle fibres; we conclude that Meishan pigs have low meat quality, whereas Berkshire and LYD crossbred pigs have higher quality of pork.

An integrated in silico approach for functional and structural impact of non- synonymous SNPs in the MYH1 gene in Jeju Native Pigs.

BackgroundThis study was performed to identify the non- synonymous polymorphisms in the myosin heavy chain 1 gene (MYH1) association with skeletal muscle development in economically important Jeju Native Pig (JNP) and Berkshire breeds. Herein, we present an in silico analysis, with a focus on (a) in silico approaches to predict the functional effect of non-synonymous SNP (nsSNP) in MYH1 on growth, and (b) molecular docking and dynamic simulation of MYH1 to predict the effects of those nsSNP on protein-protein association.ResultsThe NextGENe (V 2.3.4.) tool was used to identify the variants in MYH1 from JNP and Berkshire using RNA seq. Gene ontology analysis of MYH1 revealed significant association with muscle contraction and muscle organ development. The 95 % confidence intervals clearly indicate that the mRNA expression of MYH1 is significantly higher in the Berkshire longissimus dorsi muscle samples than JNP breed. Concordant in silico analysis of MYH1, the open-source software tools identified 4 potential nsSNP (L884T, K972C, N981G, and Q1285C) in JNP and 1 nsSNP (H973G) in Berkshire pigs. Moreover, protein-protein interactions were studied to investigate the effect of MYH1 mutations on association with hub proteins, and MYH1 was found to be closely associated with the protein myosin light chain, phosphorylatable, fast skeletal muscle MYLPF. The results of molecular docking studies on MYH1 (native and 4 mutants) and MYLFP demonstrated that the native complex showed higher electrostatic energy (−466.5 Kcal mol−1), van der Walls energy (−87.3 Kcal mol−1), and interaction energy (−835.7 Kcal mol−1) than the mutant complexes. Furthermore, the molecular dynamic simulation revealed that the native complex yielded a higher root-mean-square deviation (0.2–0.55 nm) and lower root-mean-square fluctuation (approximately 0.08–0.3 nm) as compared to the mutant complexes.ConclusionsThe results suggest that the variants at L884T, K972C, N981G, and Q1285C in MYH1 in JNP might represent a cause for the poor growth performance for this breed. This study is a pioneering in-depth in silico analysis of polymorphic MYH1 and will serve as a valuable resource for further targeted molecular diagnosis and population-based studies conducted for improving the growth performance of JNP.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-016-0341-1) contains supplementary material, which is available to authorized users.

Genome-wide Association Study (GWAS) and Its Application for Improving the Genomic Estimated Breeding Values (GEBV) of the Berkshire Pork Quality Traits.

The missing heritability has been a major problem in the analysis of best linear unbiased prediction (BLUP). We introduced the traditional genome-wide association study (GWAS) into the BLUP to improve the heritability estimation. We analyzed eight pork quality traits of the Berkshire breeds using GWAS and BLUP. GWAS detects the putative quantitative trait loci regions given traits. The single nucleotide polymorphisms (SNPs) were obtained using GWAS results with p value <0.01. BLUP analyzed with significant SNPs was much more accurate than that with total genotyped SNPs in terms of narrow-sense heritability. It implies that genomic estimated breeding values (GEBVs) of pork quality traits can be calculated by BLUP via GWAS. The GWAS model was the linear regression using PLINK and BLUP model was the G-BLUP and SNP-GBLUP. The SNP-GBLUP uses SNP-SNP relationship matrix. The BLUP analysis using preprocessing of GWAS can be one of the possible alternatives of solving the missing heritability problem and it can provide alternative BLUP method which can find more accurate GEBVs.

Comparative transcriptomic analysis to identify differentially expressed genes in fat tissue of adult Berkshire and Jeju Native Pig using RNA-seq.

Pork is a major source of animal protein for humans. The subcutaneous, intermuscular and the intramuscular fat are the factors responsible for meat quality. RNA-seq is rapidly adopted for the profiling of the transcriptomes in the studies related to gene regulation. The discovery of differentially expressed genes (DEGs) between adult animals of Jeju Native Pig (JNP) and Berkshire breeds are of particular interest for the current study. RNA-seq was used to investigate the transcriptome profiling in the fat tissue. Sequence reads were obtained from Ilumina HiSeq2000 and mapped to the pig genome using Tophat2. Total 153 DEGs were identified and 71 among the annotated genes, have BLAST matches in the non- redundant database. Metabolic, immune response and protein binding are enriched pathways in the fat tissue. In our study, biological adhesion, cellular, developmental and multicellular organismal processes in fat were up-regulated in JNP as compare to Berkshire. Multicellular organismal process, developmental process, embryonic morphogenesis and skeletal system development were the most significantly enriched terms in fat of JNP and Berkshire breeds (p = 1.17E-04, 0.044, 3.47E-04 and 4.48E-04 respectively). COL10A1, COL11A2, PDK4 and PNPLA3 genes responsible for skeletal system morphogenesis and body growth were down regulated in JNP. This study is the first statistical analysis for the detection of DEGs from RNA-seq data generated from fat tissue sample. This analysis can be used as stepping stone to understand the difference in the genetic mechanisms that might influence the identification of novel transcripts, sequence polymorphisms, isoforms and noncoding RNAs.

バークシャー種における自然発情下での経腟採卵条件の検討

バークシャー種における自然発情下での経腟採卵条件の検討

Porcine insulin-like growth factor 1 (IGF1) gene polymorphisms are associated with body size variation

Previous studies have confirmed that insulin growth factor-1 (IGF1) plays important roles in growth and body size in humans and animals. However, whether single nucleotide polymorphisms (SNPs) within the IGF1 gene affects body size and growth in pigs has been unclear. We identified IGF1 SNPs among 5 pig breeds (Berkshire, Duroc, Landrace, Yorkshire and Korea Native Pig) and found that the G allele of SNP (c.G189A) was associated with higher body weight and was more predominant in western pig breeds, while the Korean Native Pig is the breed with the highest frequency of the A allele. Four haplotypes (–GA–, –GG–, –AG–, and –AA–) were constructed using the 2 identified SNPs. The GA haplotype was most frequently observed, except in the Berkshire breed. In addition, these SNPs and haplotypes were significantly associated with body size (final weight), average daily gain, and backfat thickness (P < 0.05) in 2 intercrossed F2 pig populations (KNP × YS F2 and KNP × LR F2). Furthermore, the major GA haplotype had a significant additive effect on body size and average daily gain. In conclusion, specific SNPs within the porcine IGF1 gene may contribute to the smaller body size and lower growth rate of Korea Native Pigs.

Comparison of Growth Performance of Antibiotic-free Yorkshire Crossbreds Sired by Berkshire, Large Black, and Tamworth Breeds Raised in Hoop Structures.

The objective of this study was to compare body weight, ADG, and feed:gain ratio of antibiotic-free pigs from Yorkshire dams and sired by Yorkshire (YY), Berkshire (BY), Large Black (LBY) or Tamworth (TY) boars. All the crossbred pigs in each of three trials were raised as one group from weaning to finishing in the same deep-bedded hoop, providing a comfortable environment for the animals which allowed rooting and other natural behaviors. Birth, weaning and litter weights were measured and recorded. From approximately 50 kg to market weight (125 kg), feed intake and body weights were recorded manually (body weight) or using a FIRE (Feed Intake Recording Equipment, Osborne Industries Inc. Osborne, Kansas) system with eight individual feeding stations. Feed intake data for 106 finishing pigs between 140 and 210 d of age and the resulting weights and feed conversion ratios were analyzed by breed type. Least square means for body weights (birth, weaning and to 240 d) were estimated with Proc Mixed in SAS 9.2 for fixed effects such as crossbreed and days of age within the sire breed. The differences within fixed effects were compared using least significant differences with DIFF option. Individual birth weights and weaning weights were influenced by sire breed (p<0.05). For birth weight, BY pigs were the lightest, TY and YY pigs were the heaviest but similar to each other and LBY pigs were intermediate. For weaning weights, BY and LBY pigs were heavier than TY and YY pigs. However, litter birth and weaning weights were not influenced by sire breed, and average daily gain was also not significantly different among breed types. Tamworth sired pigs had lower overall body weight gain, and feed conversion was lower in TY and YY groups than BY and LBY groups (p<0.05), however, number of observations was somewhat limited for feed conversion and for Tamworth pigs. Overall, no convincing differences among breed types were noted for this study, but growth performance in the outdoor environment was satisfactory.

Effects of variation in porcine MYOD1 gene on muscle fiber characteristics, lean meat production, and meat quality traits

Three single nucleotide polymorphisms (SNPs) in the porcine MYOD1 gene were used for association analysis and haplotype construction to evaluate the effects of their substitution. Four hundred and three pigs of Yorkshire and Berkshire breeds were used. The mRNA expression levels of MYOD1 were examined. The g.489C>T and g.1264C>A SNPs were significantly associated with several muscle fiber characteristics, the loin eye area, and lightness. Particularly, animals having hetero-genotypes of both sites showed good performance both in lean meat production and meat quality traits. The results of haplotype substitution were similar to the associations of individual SNPs. Moreover, the 2 SNPs had significant effects on mRNA expression. Therefore, the g.489C>T and g.1264C>A SNPs in MYOD1 may be meaningful DNA markers that can be used for improving important porcine economic traits.

Study on the Prolactin Receptor 3 (PRLR3) Gene and the Retinol-binding Protein 4 (RBP4) Gene as Candidate Genes for Production Traits in Berkshire Pigs.

To investigate the influence of the prolactin receptor 3 (PRLR3) gene and the retinol-binding protein 4 (RBP4) gene on the production traits of swine, genotyping was performed on 156 and 141 Berkshire pigs, respectively, that were carefully selected for economic traits. The frequencies of allele A in the PRLR3 locus and allele B in the RBP4 locus were 0.50 and 0.42, respectively. Neither locus was in the Hardy-Weinberg equilibrium. After a genotype was assigned to the individuals whose parents had the homozygous genotype, a statistical analysis was conducted for 291 pigs. The animals with the PRLR3 and RBP4 genotypes included 182 and 227 head, respectively. Even though the genotypic effects of PRLR3 (p<0.05) and RBP4 (p<0.01) had a significant influence on the pigs’ back fat thickness, the interaction of both genes was not highly significant in terms of the back fat thickness (p = 0.1235). While the estimated epistasis effects of aaBB and aaBb decreased the back fat thickness and reduced the growth rate, the effects of AAbb and aabb increased the growth rate. Despite the insignificant difference in the PRLR genotypes in terms of the days to 90 kg and the average daily gain, the back fat thickness showed a significant difference (p<0.05), and the additive effect of allele A and the dominant effect of the hetero-genotype were −0.377 and 1.206 mm, respectively. The RBP4 genotypes had a very significant effect (p<0.01) on the back fat thickness, the days to 90 kg, and the average daily gain. The additive effects of allele B of the RBP4 locus on the back fat thickness, the days to 90 kg, and the average daily gain were 0.70 mm, −1.3 days and 6.2 g, respectively. Moreover, the dominant effects of the heterozygote for those traits were 0.63 mm, 9.9 days and −45.0 g, respectively. Allele A of the PRLR3 locus favorably influenced the back fat thickness, the days to 90 kg of the body weight, and the average daily gain and its dominant effect unfavorably influenced those traits. Allele B of RBP4 showed an incremental growth rate and back fat thickness, which could lower the lean meat percentage in the carcass. The RBP4 hetero-genotype negatively affected the pork production. These results strongly imply that the selection of allele A of PRLR3 and allele B of RBP4 would produce highly productive pigs in the Berkshire breed. Careful selection of allele B of RBP4 is required because of the increase in the back fat thickness.

Association analysis of polymorphism in KIAA1717 , HUMMLC2B , DECR1 and FTO genes with meat quality traits of the Berkshire breed

Single nucleotide polymorphisms (SNPs) in KIAA1717, HUMMLC2B, DECR1, and FTO genes have been found to be associated with some pork meat quality traits. In this study, we discovered that, in addition to meat quality traits reported previously, SNPs in these genes also are significantly associated with other meat quality traits in the Berkshire breed. A total of 323 Berkshire pigs bred under the same conditions were used for meat quality evaluation and polymerase chain reaction-amplified genes with restriction endonucleases (PCR-RFLP) genotyping analyses. The association analysis of RFLP genotyping with meat quality traits revealed that the SNPs in these 4 genes have novel associations with multiple meat quality traits (p < 0.01 or p < 0.05); a SNP in KIAA1717 was associated with meat color (CIE L), backfat thickness, drip loss, water-holding capacity, and pH 24hr ; a SNP in HUMMLC2B was associated with chemical composition (collagen), drip loss, shear force, and pH 24hr ; a SNP in DECR1 was associated with meat color (CIE a and b) and backfat thickness; and a SNP in FTO was associated with meat color (CIE L, a and b), protein content, drip loss, and water-holding capacity. Taken collectively, our results suggest that these 4 SNPs may be used for marker-assisted selection as a genetic marker for meat quality traits in Berkshire pigs. Key words : Berkshire, genetic markers, meat quality, SNP

Association between polymorphisms of the heart fatty acid binding protein gene and intramuscular fat content, fatty acid composition, and meat quality in Berkshire breed

The objective of this study was to examine the relationship between polymorphisms of the heart fatty acid binding protein (H-FABP) gene and variation in intramuscular fat (IMF) content, fatty acid composition, and meat quality in Berkshire breed. We detected an association between IMF content and H-FABP HinfI restriction fragment length polymorphism (RFLP) genotype. The HH genotype showed the greatest IMF content among the genotype classes (P<0.05). Regarding meat quality traits, only drip loss was significantly different among the H-FABP HinfI RFLP genotype classes (P<0.01). In the case of fatty acid composition, the degree of saturation of fatty acids was greater in hh-genotype pigs than in HH and Hh genotypes. The H-FABP MspI RFLP genotype affected unsaturated fatty acid content, and the ratio of polyunsaturated fatty acid to saturated fatty acid (P<0.05), whereas the H-FABP HaeIII RFLP genotype had no effect on fatty acid characteristics.

Single nucleotide polymorphisms of the KIT and KITLG genes in pigs

ABSTRACTHere, we report the variability in the KIT tyrosine kinase receptor and its ligand KITLG genes by determining single nucleotide polymorphisms (SNPs) in 384 individuals including 11 pig breeds, two synthetic‐line cross pigs, two cross breeds, and one Japanese wild boar. SNPs and indels within the coding sequence regions of KITLG and KIT and their 5′‐flanking regions were detected by aligning sequences from eight pigs, and subsequently the SNPs were genotyped using matrix‐assisted laser desorption ionization time‐of‐flight mass spectrometry (MALDI TOF‐MS). Principal component analysis using allele frequencies in the SNP locus showed a distant relationship between Asian and Euro‐American pig groups, except for Berkshire and Tokyo X breeds. These breeds were located within the mid‐portion of the distribution in the first principal component. The Hampshire breed was distant from the other pig groups on the axis of the second principal component. Haplotype frequencies that were deduced using non‐synonymous substitutions of the KIT gene revealed the uniqueness of Landrace, Large White, Middle White, and three‐way cross pigs (LWD) and of the Hampshire breed. On the other hand, the haplotypes of KITLG and KIT detected in the Berkshire breed were prevalent in Asian pig groups. This tendency is different from that observed in other Euro‐American pig breeds.

Porcine MHC Class II Haplotype Divergence (35.15)

Abstract The swine major histocompatibility complex (MHC) located in SSC7, is a gene dense region with a role in antigen presentation and controlling immune responsiveness. Although highly polymorphic, serological approaches to identify and define alleles have been disappointing. To determine the extent of MHC polymorphisms of class II genes, DNA from divergent world breeds of unrelated pigs was analyzed for SNPs. Primers targeting exon 2 of DQB and DRB were shown to be locus specific and amplified both loci for each animal. Expression of exon 2 PCR amplicons for both genes was verified through sequence analysis revealing 30 haplotypes comprised of over 20 different alleles among the 9 breeds. Located within the two genes were a total of 24 polymorphic sites, 22 of these were located within the antigen recognition site (DRB had two in the alpha helix) where 17 of those were nonsynonymous substitutions (7 synonymous). The breeds analyzed were selected to represent geographic areas in order to determine if haplotype divergence correlated with location of origin. The first group was identified as “Asian” and included Meishan, Erhualian and Lanyu breeds. The second group represented the “British Isles” (Hampshire, Yorkshire and Berkshire breeds) and the third group was identified as “Continental” (Duroc, Large White, and Landrace breeds). Fewer breed specific alleles were observed in breeds selected for lower fat and longer carcasses. SNPs in DRB appear to be under positive Darwinian selection with a dN/dS value of 13 as opposed to DQB with a value of 1 (no selective pressure or purifying selection) To confirm expression of the PCR products and eliminate the possibility of pseudogenes, RT-PCR with primers from intron-exon boundaries were utilized and verified the absence of pseudogene amplification and revealed highest RNA expression in DRB especially in heart, bone marrow, lung, small intestine and lymph node.