Indigenous Pig Breeds Research Articles

Invited review: reproductive physiology in commercial and premium pig breeds – history of 30-year-long cooperation

Abstract. Cooperation of the Hungarian Research Institute for Animal Breeding and Nutrition (ATK) with the German Leibniz Institute for Farm Animal Biology (FBN) goes back many decades. In 1988 the two departments of reproductive biology began a joint project concerning on ovulation investigation in Landrace pigs. This joint project laid the foundation for further joint projects and has existed for almost 30 years. Over the years, the main focus has always been on the events of the female reproductive tract in pigs, i.e., follicular growth, ovulation, transport of gametes in the oviduct, fertilization and early embryonic development. Nearly all studies were done under in vivo circumstances and using different clinical and endocrinological methods, enabling us to obtain more profound knowledge of the dynamics of reproductive processes. Even results considered to be basic scientific achievements were available for utilization in the daily practice of porcine reproductive management. Since the end of the 1990s, the common projects have been gradually shifted to the physiology of the Hungarian indigenous pig breed Mangalica. Research partners were convinced that modern utilization of indigenous pig breeds would open new doors for premium pork production. In addition to the Mangalica breed, this principal was broadened to non-European fatty-type native pig breeds as well and resulted in long-term, intercontinental scientific cooperation.

Analysis of pedigree and inbreeding variation of Lithuanian indigenous wattle pigs

The objective of the study was to analyse the pedigree of pigs and to determine the level of their inbreeding, effective population size and interval between generations in the nucleus herd of restored and conserved Lithuanian indigenous wattle pig breed. The data of pedigree records on 329 Lithuanian indigenous wattle pigs were used for the analysis. The analysis was performed using the statistical programme PopReport. In the twelfth year of the restored population breeding, the completeness of pedigree in two first generations was 100%, in the third generation it was 99.1%, in the fourth generation 96.6%, in the fifth generation 93.6% and in the sixth generation it was 86.9%. The average interval between the generations was 3 years. From 2003 to 2013, the inbreeding coefficient of the introduced new generation increased by 10%. Due to the inbreeding increase in the last years the effective population size Ne of the nucleus decreased up to 12 and shows the general status of the whole population. The status of the breed remains critical-maintained.

Longissimus lumborum muscle transcriptome analysis of Laiwu and Yorkshire pigs differing in intramuscular fat content

The pig provides meat products for human consumption on a large scale. High-throughput sequencing technology provides a powerful approach for the characterization of the muscle transcriptome of pigs. Despite many studies using high-throughput technologies, the functional complexity of porcine muscle transcriptome is not fully elucidated. Therefore, the aim of this study was to gain insight into the longissimus lumborum muscle transcriptome between two pig breeds with distinct phenotypes, Laiwu pig, a Chinese indigenous pig breed, and Yorkshire pig, a Western breed. RNA-seq was applied to sample transcripts of the longissimus lumborum muscle between the two pig breeds to gain insights into whole-genome transcription profiles. For the Laiwu and Yorkshire libraries, we obtained a total of 40,498,476 and 59,072,892 high quality reads, respectively. Moreover, the resulting data set provided expression patterns for many annotated, predicted and novel pig genes. 178 significantly differentially expressed genes were identified between the Laiwu and Yorkshire pigs, with 98 up-regulated and 80 down-regulated genes in Laiwu pig compared with Yorkshire pig. Gene expression results of the RNA-seq data were validated by qRT-PCR for twelve genes. Genes that were differentially expressed were involved in lipid metabolism and were more highly expressed in Laiwu pigs. The present study provides a comprehensive view of differences in the muscle transcriptome between two pig phenotypes. These results expand our knowledge of the genes transcribed in the skeletal muscle of two breeds and provide a basis for future research of the molecular mechanisms underlying the phenotypic differences on meat quality.

Substantial hybridisation between wild boars (Sus scrofa scrofa) and East Balkan pigs (Sus scrofa f. domestica) in natural environment as a result of semi-wild rearing in Bulgaria

The East Balkan pig (EBP) is a traditional domestic pig breed in Bulgaria managed in semi-wild conditions and well-adapted to the continental climate and rearing on pastures. From the genetical and historical point of view it is important to preserve this ancient breed. However, over the last several years, a dramatic decline of EBP herds has been observed. Moreover, introgression between EBP and wild boar in Bulgaria (WBB) is very likely to have occurred. In this study we used a set of 10 microsatellites and the polymerase chain reaction–restriction fragment length polymorphism method on melanocortin-1 receptor (MC1R) polymorphisms to study the degree of hybridisation between WBB, EBP, and a commercial pig breed (CPB). MC1R results identified WBB-EBP hybrids and the analysis of the microsatellite data with a Bayesian assignment approach and the Discriminant Analysis of Principal Components revealed a low genetic differentiation between WBB and EBP and a high amount of introgression of WBB into EBP. A mentionable introgression of CPB into EBP was also revealed. It is apparent that the traditional rearing system of EBP, which is hundreds of years old, has led to a permanent hybridisation between WBB and EBP. In our opinion, the preservation of the semi-wild rearing system is a prerequisite for the conservation of this old, indigenous pig breed and its genetic composition, as the semi-wild rearing system allows the continuous introgression with WBB. Moreover, the introgression of commercial breeds into EBP or WBB should be prevented. Due to the bidirectional gene flow these hybridisation events would have negative consequences (i.e. loss of viability and adaptation) for the wild boars as well as for the indigenous pig breed.

Productivity of pigs of conservation breeds in terms of selected gene polymorphisms

The material for the analyses comprised blood samples collected from 65 Zlotnicka Spotted (Zlp) sows and 43 Zlotnicka White (Zlb) sows born and kept in two herds in Wielkopolska. While analysing reproductive, fattening and slaughter traits, information was collected on 290 litters, including 180 litters of Zlp sows and 110 litters of Zlb sows. Intravital measurements were taken using a Piglog 105 for the evaluation of the mean backfat thickness, lean meat content and loin eye thickness. The aim of the research was to determine the effect of selected genotypes on reproductive, fattening and carcass performance traits of the two indigenous pig breeds (Zlotnicka White and Zlotnicka Spotted), kept and bred in Poland. The frequency of RYR1 genotypes indicates that the number of animals with the RYRTT genotype carrying a mutation in the RYR1 gene was low in the Zlotnicka breeds. In the herd of Zlb sows, a statistically significant negative effect of the RYRCT genotype on piglet wastage up to 21 days of age was found. The highest wastage rate was recorded in the group of heterozygotes. The frequency of the genotypes indicates that the DD genotype typical of animals with polymorphism in the GH/MspI gene occurred rarely in the analysed population of the Zlotnicka breeds. A statistically significant effect of the GH/MspI genotype on litter weight at 21 days of age was observed in the population of the Zlb sows. The heaviest piglets were born to sows with the DD genotype, while the lightest piglets were born to sows with the CC genotype. The frequency of the LEP genotypes indicates that the number of animals with the TT genotype was very low in the population of the Zlb pigs. No animal with the TT genotype was found in the Zlp herd.

Coat colour phenotype of Qingyu pig is associated with polymorphisms of melanocortin receptor 1 gene.

ObjectiveQingyu pig, a Chinese indigenous pig breed, exhibits two types of coat colour phenotypes, including pure black and white with black spotting respectively. Melanocortin receptor 1 (MC1R) and agouti signaling protein (ASIP) are two widely reported pivotal genes that significantly affect the regulation of coat colour. The objectives of this study were to investigate whether the polymorphisms of these two genes are associated with coat colour and analyze the molecular mechanism of the coat colour separation in Qingyu pig.MethodsWe studied the phenotype segregation and used polymerase chain reaction amplification and Sanger sequencing to investigate the polymorphism of MC1R and ASIP in 121 Qingyu pigs, consisting of 115 black and 6 white with black spotted pigs.ResultsCoat colour of Qingyu pig is associated with the polymorphisms of MC1R but not ASIP. We only found 2 haplotypes, EQY and Eqy, based on the 13 observed mutations from MC1R gene. Among which, Eqy presented a recessive inheritance mode in black spotted Qingyu pigs. Further analysis revealed a g.462–463CC insertion that caused a frameshift mutation and a premature stop codon, thus changed the first transmembrane domain completely and lost the remaining six transmembrane domains. Altogether, our results strongly support that the variety of Qingyu pig’s coat colour is related to MC1R.ConclusionOur findings indicated that black coat colour in Qingyu pig was dominant to white with black spotted phenotype and MC1R gene polymorphism was associated with coat colour separation in Qingyu pig.

Profiles of colour, minerals, amino acids and fatty acids of musculus longissimus thoracis et lumborum of Ghungroo pigs

Carcass composition and meat quality were evaluated in Ghungroo, the first registered indigenous pig breed of India. Ghungroo pigs (16 gilts and 26 barrows) were slaughtered at the age of 10 months for evaluating the different parameters. Instrumental colour measurement indicated that the coordinates were in the following range: lightness (L*), 39.17 - 57.39; redness (a*, red ± green), 8.37 - 14.21; and yellowness (b*, yellow ± blue), 13.08 - 18.17. Haem iron content was significantly higher in barrows compared to gilts. The mineral contents in the musculus (M.) longissimus thoracis et lumborum were in the following range: potassium, 289 – 349 mg/100g; zinc, 0.58 – 0.91 mg/100g; copper, 0.13 – 0.17 mg/100g; manganese, 0.05 –0.06 mg/100g and magnesium, 4.72 –7.37 mg/ 100g. Significant differences were not observed in the concentration of any of the estimated amino acids between the sexes. Fatty acid profiling of M. longissimus thoracis et lumborum indicated that saturated and unsaturated fatty acids were in the range of 32.17 - 41.19% and 58.98 - 68.15%, respectively. Results further indicated a concentration of 0.88 – 1.73% omega-3 fatty acids; 19.95 - 27.23% omega-6 fatty acids and 14.52 - 23.47% essential fatty acids in the Ghungroo muscle tissues.

Genome-wide analysis of DNA methylation in obese, lean, and miniature pig breeds.

DNA methylation is a crucial epigenetic modification involved in diverse biological processes. There is significant phenotypic variance between Chinese indigenous and western pig breeds. Here, we surveyed the genome-wide DNA methylation profiles of blood leukocytes from three pig breeds (Tongcheng, Landrace, and Wuzhishan) by methylated DNA immunoprecipitation sequencing. The results showed that DNA methylation was enriched in gene body regions and repetitive sequences. LINE/L1 and SINE/tRNA-Glu were the predominant methylated repeats in pigs. The methylation level in the gene body regions was higher than in the 5′ and 3′ flanking regions of genes. About 15% of CpG islands were methylated in the pig genomes. Additionally, 2,807, 2,969, and 5,547 differentially methylated genes (DMGs) were identified in the Tongcheng vs. Landrace, Tongcheng vs. Wuzhishan, and Landrace vs. Wuzhishan comparisons, respectively. A total of 868 DMGs were shared by the three contrasts. The DMGs were significantly enriched in development- and metabolism-related biological processes and pathways. Finally, we identified 32 candidate DMGs associated with phenotype variance in pigs. Our research provides a DNA methylome resource for pigs and furthers understanding of epigenetically regulated phenotype variance in mammals.

RNA-Seq Analysis Reveals Genes Underlying Different Disease Responses to Porcine Circovirus Type 2 in Pigs

Porcine circovirus type 2 (PCV2), an economically important pathogen, causes postweaning multisystemic wasting syndrome (PMWS) and other syndrome diseases collectively known as porcine circovirus-associated disease (PCVAD). Previous studies revealed breed-dependent differences in porcine susceptibility to PCV2; however, the genetic mechanism underlying different resistance to PCV2 infection remains largely unknown. In this study, we found that Yorkshire × Landrace (YL) pigs exhibited serious clinical features typifying PCV2 disease, while the Laiwu (a Chinese indigenous pig breed, LW) pigs showed little clinical symptoms of the disease during PCV2 infection. At 35 days post infection (dpi), the PCV2 DNA copy in YL pigs was significantly higher than that in LW pigs (P < 0.05). The serum level of IL-4, IL-6, IL-8, IL-12 and TGF-β1 in LW pigs and TNF-α in YL pigs increased significantly at the early infected stages, respectively; while that of IL-10 and IFN-γ in YL pigs was greatly increased at 35 dpi. RNA-seq analysis revealed that, at 35 dpi, 83 genes were up-regulated and 86 genes were down-regulated in the lung tissues of LW pigs, while in YL pigs, the numbers were 187 and 18, respectively. In LW pigs, the differentially expressed genes (DEGs) were mainly involved in complement and coagulation cascades, metabolism of xenobiotics by cytochrome P450, RIG-I-like receptor signaling and B cell receptor signaling pathways. Four up-regulated genes (TFPI, SERPNC1, SERPNA1, and SERPNA5) that are enriched in complement and coagulation cascades pathway were identified in the PCV2-infected LW pigs, among which the mRNA expression of SERPNA1, as well as three genes including TGF-β1, TGF-β2 and VEGF that are regulated by SERPNA1 was significantly increased (P < 0.05). We speculate that higher expression of SERPNA1 may effectively suppress excessive inflammation reaction and reduce the pathological degree of lung tissue in PCV2-infected pigs. Collectively, our findings indicate that the susceptibility to PCV2 infection depends on a genetic difference between LW and YL pigs, and SERPNA1 likely plays an important role in the resistance of LW pigs to PCV2 infection.

Identification of genes in longissimus dorsi muscle differentially expressed between Wannanhua and Yorkshire pigs using RNA-sequencing.

Western commercial pig breeds have been intensively selected, resulting in a sizeable, rapid and efficient accretion of muscle but a reduction in meat quality. When compared with Western commercial pig breeds, Chinese indigenous pig breeds exhibited slower growth rates and reduced lean meat content but superior perceived meat quality. To study the factors that determine meat quality, we examined piglets of one Western commercial breed (Yorkshire) and one Chinese indigenous breed (Wannanhua) and sequenced the longissimus dorsi muscle using RNA-sequencing (RNA-seq). We analyzed their transcriptomes, focusing on identifying candidate genes that may influence porcine muscle growth, meat quality and adipose deposition. Gene Ontology functional enrichment and pathway enrichment analyses identified differentially expressed genes (DEGs) primarily associated with glycolytic metabolism, biological processes of muscle development and signaling pathways related to fatty acid metabolism, growth and carcass traits. This finding suggests that the DEGs may play important roles in determining meat quality traits. Quantitative real-time reverse transcription polymerase chain reaction confirmed the differential expression of 12 selected DEG. This study identified a number of novel candidate genes for porcine meat quality and carcass traits that merit further investigation to elucidate the molecular mechanisms responsible for muscle growth and fat deposition.

Carcass and pork quality traits of indigenous pure breeds (Mangalitsa, Moravka) and their crossbreads

Objective of this paper was to evaluate phenotypic variability of carcass side and pork quality traits of fatteners (male castrated and female heads). Investigation included 12 pigs per group of Mangalitsa (Genotype 1), Moravka (Genotype 2), cross-breed Mangalitsa with Moravka (Genotype 3) and cross-breed Moravka with Duroc boar (Genotype 4). Results show that Mangalitsa had lower daily gain (268 g) than other genotypes (p&lt;0.001). The greatest difference for fat thickness was determined between Genotype 1 and Genotype 4. As expected, the thinnest fat and maximum value for gain and depth of Musculus longissimus (ML) had the Genotype 4. The highest value for the ML surface was found in Genotype 4(47.52 cm2) whereas for the same trait in Mangalitsa the lowest value was observed (24.16 cm2). Mangalitsa had significantly lower L*, a* and b* values of ML compared with all other groups (p&lt;0.001). Considering the low production performance of indigenous pig breeds, crossbreeding with the Duroc breed will contribute a improvement of growth and carcass traits.

Identification of Genes Related to Growth and Lipid Deposition from Transcriptome Profiles of Pig Muscle Tissue.

Transcriptome profiles established using high-throughput sequencing can be effectively used for screening genome-wide differentially expressed genes (DEGs). RNA sequences (from RNA-seq) and microRNA sequences (from miRNA-seq) from the tissues of longissimus dorsi muscle of two indigenous Chinese pig breeds (Diannan Small-ear pig [DSP] and Tibetan pig [TP]) and two introduced pig breeds (Landrace [LL] and Yorkshire [YY]) were examined using HiSeq 2000 to identify and compare the differential expression of functional genes related to muscle growth and lipid deposition. We obtained 27.18 G clean data through the RNA-seq and detected that 18,208 genes were positively expressed and 14,633 of them were co-expressed in the muscle tissues of the four samples. In all, 315 DEGs were found between the Chinese pig group and the introduced pig group, 240 of which were enriched with functional annotations from the David database and significantly enriched in 27 Gene Ontology (GO) terms that were mainly associated with muscle fiber contraction, cadmium ion binding, response to organic substance and contractile fiber part. Based on functional annotation, we identified 85 DEGs related to growth traits that were mainly involved in muscle tissue development, muscle system process, regulation of cell development, and growth factor binding, and 27 DEGs related to lipid deposition that were mainly involved in lipid metabolic process and fatty acid biosynthetic process. With miRNA-seq, we obtained 23.78 M reads and 320 positively expressed miRNAs from muscle tissues, including 271 known pig miRNAs and 49 novel miRNAs. In those 271 known miRNAs, 20 were higher and 10 lower expressed in DSP-TP than in LL-YY. The target genes of the 30 miRNAs were mainly participated in MAPK, GnRH, insulin and Calcium signaling pathway and others involved cell development, growth and proliferation, etc. Combining the DEGs and the differentially expressed (DE) miRNAs, we drafted a network of 46 genes and 18 miRNAs for regulating muscle growth and a network of 15 genes and 16 miRNAs for regulating lipid deposition. We identified that CAV2, MYOZ2, FRZB, miR-29b, miR-122, miR-145-5p and miR-let-7c, etc, were key genes or miRNAs regulating muscle growth, and FASN, SCD, ADORA1, miR-4332, miR-182, miR-92b-3p, miR-let-7a and miR-let-7e, etc, were key genes or miRNAs regulating lipid deposition. The quantitative expressions of eight DEGs and seven DE miRNAs measured with real-time PCR certified that the results of differential expression genes or miRNAs were reliable. Thus, 18,208 genes and 320 miRNAs were positively expressed in porcine longissimus dorsi muscle. We obtained 85 genes and 18 miRNAs related to muscle growth and 27 genes and 16 miRNAs related to lipid deposition, which provided new insights into molecular mechanism of the economical traits in pig.

Targeted mutations in myostatin by zinc-finger nucleases result in double-muscled phenotype in Meishan pigs.

Myostatin (MSTN) is a dominant inhibitor of skeletal muscle development and growth. Mutations in MSTN gene can lead to muscle hypertrophy or double-muscled (DM) phenotype in cattle, sheep, dog and human. However, there has not been reported significant muscle phenotypes in pigs in association with MSTN mutations. Pigs are an important source of meat production, as well as serve as a preferred animal model for the studies of human disease. To study the impacts of MSTN mutations on skeletal muscle growth in pigs, we generated MSTN-mutant Meishan pigs with no marker gene via zinc finger nucleases (ZFN) technology. The MSTN-mutant pigs developed and grew normally, had increased muscle mass with decreased fat accumulation compared with wild type pigs, and homozygote MSTN mutant (MSTN−/−) pigs had apparent DM phenotype, and individual muscle mass increased by 100% over their wild-type controls (MSTN+/+) at eight months of age as a result of myofiber hyperplasia. Interestingly, 20% MSTN-mutant pigs had one extra thoracic vertebra. The MSTN-mutant pigs will not only offer a way of fast genetic improvement of lean meat for local fat-type indigenous pig breeds, but also serve as an important large animal model for biomedical studies of musculoskeletal formation, development and diseases.

Genetic diversity and population structure of six Chinese indigenous pig breeds in the Taihu Lake region revealed by sequencing data.

SummaryThe Chinese indigenous pig breeds in the Taihu Lake region are the most prolific pig breeds in the world. In this study, we investigated the genetic diversity and population structure of six breeds, including Meishan, Erhualian, Mi, Fengjing, Shawutou and Jiaxing Black, in this region using whole‐genome SNP data. A high SNP with proportions of polymorphic markers ranging from 0.925 to 0.995 was exhibited by the Chinese indigenous pigs in the Taihu Lake region. The allelic richness and expected heterozygosity also were calculated and indicated that the genetic diversity of the Meishan breed was the greatest, whereas that of the Fengjing breed was the lowest. The genetic differentiation, as indicated by the fixation index, exhibited an overall mean of 0.149. Both neighbor‐joining tree and principal components analysis were able to distinguish the breeds from each other, but structure analysis indicated that the Mi and Erhualian breeds exhibited similar major signals of admixture. With this genome‐wide comprehensive survey of the genetic diversity and population structure of the indigenous Chinese pigs in the Taihu Lake region, we confirmed the rationality of the current breed classification of the pigs in this region.

Transcriptome Analysis of Liangshan Pig Muscle Development at the Growth Curve Inflection Point and Asymptotic Stages Using Digital Gene Expression Profiling.

Animal growth curves can provide essential information for animal breeders to optimize feeding and management strategies. However, the genetic mechanism underlying the phenotypic differentiation between the inflection point and asymptotic stages of the growth curve is not well characterized. Here, we employed Liangshan pigs in stages of growth at the inflection point (under inflection point: UIP) and the two asymptotic stages (before the inflection point: BIP, after the inflection point: AIP) as models to survey global gene expression in the longissimus dorsi muscle using digital gene expression (DGE) tag profiling. We found Liangshan pigs reached maximum growth rate (UIP) at 163.6 days of age and a weight of 134.6 kg. The DGE libraries generated 117 million reads of 5.89 gigabases in length. 21,331, 20,996 and 20,139 expressed transcripts were identified BIP, UIP and AIP, respectively. Among them, we identified 757 differentially expressed genes (DEGs) between BIP and UIP, and 271 DEGs between AIP and UIP. An enrichment analysis of DEGs proved the immune system was strengthened in the AIP stage. Energy metabolism rate, global transcriptional activity and bone development intensity were highest UIP. Meat from Liangshan pigs had the highest intramuscular fat content and most favorable fatty acid composition in the AIP. Three hundred eighty (27.70%) specific expression genes were highly enriched in QTL regions for growth and meat quality traits. This study completed a comprehensive analysis of diverse genetic mechanisms underlying the inflection point and asymptotic stages of growth. Our findings will serve as an important resource in the understanding of animal growth and development in indigenous pig breeds.

Identification of a short interspersed repetitive element insertion polymorphism in the porcine MX1 promoter associated with resistance to porcine reproductive and respiratory syndrome virus infection.

The myxovirus resistance (Mx) proteins belong to the dynamin superfamily and are important for innate host defence against RNA viruses. In this study, we demonstrate that positive elements are present in the two promoter regions of -2713 to -2565 and -688 to -431 in the porcine MX1 gene. Sequencing and alignment of the amplified porcine MX1 gene promoter region identified a short interspersed repetitive element (SINE) insertion of 275 bp at site -547. At this site, allele B (an insertion of 275 bp) is dominant in Chinese indigenous pig breeds but has a workable minor allele frequency in western lean-type pig breeds. Luciferase activity was compared between promoters with and without the insertion of the 275-bp fragment in transiently transfected MARC-145 cells. The insertion of the 275-bp fragment increased the luciferase activity significantly (P < 0.05) both prior to and post-porcine reproductive and respiratory syndrome (PRRS) virus inoculation. These results suggest that the SINE insertion polymorphism at site -547 of the MX1 gene promoter region is a potential DNA marker for PRRS resistance in pigs.

Dynamic transcriptome profiles of skeletal muscle tissue across 11 developmental stages for both Tongcheng and Yorkshire pigs.

BackgroundThe growth and development of skeletal muscle directly impacts the quantity and quality of pork production. Chinese indigenous pig breeds and exotic species vary greatly in terms of muscle production and performance traits. We present transcriptome profiles of 110 skeletal muscle samples from Tongcheng (TC) and Yorkshire (YK) pigs at 11 developmental periods (30, 40, 55, 63, 70, 90, and 105 days of gestation, and 0, 1, 3, and 5 weeks of age) using digital gene expression on Solexa/Illumina’s Genome Analyzer platform to investigate the differences in prenatal and postnatal skeletal muscle between the two breeds.ResultsMuscle morphological changes indicate the importance of primary fiber formation from 30 to 40 dpc (days post coitus), and secondary fiber formation from 55 to 70 dpc. We screened 4,331 differentially expressed genes in TC and 2,259 in YK (log2 ratio >1 and probability >0.7). Cluster analysis showed different gene expression patterns between TC and YK pigs. The transcripts were annotated in terms of Gene Ontology related to muscle development. We found that the genes CXCL10, EIF2B5, PSMA6, FBXO32, and LOC100622249 played vital roles in the muscle regulatory networks in the TC breed, whereas the genes SGCD, ENG, THBD, AQP4, and BTG2 played dominant roles in the YK breed. These genes showed breed-specific and development-dependent differential expression patterns. Furthermore, 984 genes were identified in myogenesis. A heat map showed that significantly enriched pathways (FDR <0.05) had stage-specific functional regulatory mechanisms. Finally, the differentially expressed genes from our sequencing results were confirmed by real-time quantitative polymerase chain reaction.ConclusionsThis study detected many functional genes and showed differences in the molecular mechanisms of skeletal muscle development between TC and YK pigs. TC pigs showed slower muscle growth and more complicated genetic regulation than YK pigs. Many differentially expressed genes showed breed-specific expression patterns. Our data provide a better understanding of skeletal muscle developmental differences and valuable information for improving pork quality.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1580-7) contains supplementary material, which is available to authorized users.

Relationship between polymorphisms in exon 10 of FSHR gene and litter size in swine.

Follicle-stimulating hormone (FSH), a glycoprotein secreted by the anterior pituitary, can regulate ovarian function through the FSH receptor (FSHR). To evaluate the effects of the FSHR gene on reproductive traits in pigs, polymorphisms in exon 10 of the FSHR gene were observed by polymerase chain reaction-single-strand conformation polymorphism, and 3 single nucleotide polymorphisms (C1491T, G1885A, and C1977T) in exon 10 of the porcine FSHR gene, and 3 genotypes (AA, AB, and BB) for C1491T and 2 haplotypes (D and E) for G1885A and C1977T were identified. Further analysis of single nucleotide polymorphism genotypes associated with reproductive traits including total number born (TNB) and number born alive (NBA) was carried out in 3 pig populations including Berkshire, Wannan Black (a Chinese indigenous pig breed), and BW pigs (two-way crossbred pigs produced from Berkshire ♂ and Wannan Black pig ♀). The results showed that the TNB and NBA of Wannan Black pigs with the AB genotype were significantly higher than in AA genotype sows (P < 0.01) in multiparity sows and all parities. The TNB and NBA of Berkshire pigs with the DE genotype were significantly higher than the DD and EE genotype sows (P < 0.01) in gilts, sows and all parities. Overall, TNB and NBA from the 3 identified genotypes was DE > DD > EE. The results showed that polymorphisms in exon 10 of the FSHR gene had a significant effect on litter size traits of Wannan Black and Berkshire pigs. These results can be applied for marker-assisted selection in the 2 swine breeds.

A genome-wide association study of limb bone length using a Large White × Minzhu intercross population.

BackgroundIn pig, limb bone length influences ham yield and body height to a great extent and has important economic implications for pig industry. In this study, an intercross population was constructed between the indigenous Chinese Minzhu pig breed and the western commercial Large White pig breed to examine the genetic basis for variation in limb bone length. The aim of this study was to detect potential genetic variants associated with porcine limb bone length.MethodsA total of 571 F2 individuals from a Large White and Minzhu intercross population were genotyped using the Illumina PorcineSNP60K Beadchip, and phenotyped for femur length (FL), humerus length (HL), hipbone length (HIPL), scapula length (SL), tibia length (TL), and ulna length (UL). A genome-wide association study was performed by applying the previously reported approach of genome-wide rapid association using mixed model and regression. Statistical significance of the associations was based on Bonferroni-corrected P-values.ResultsA total of 39 significant SNPs were mapped to a 11.93 Mb long region on pig chromosome 7 (SSC7). Linkage analysis of these significant SNPs revealed three haplotype blocks of 495 kb, 376 kb and 492 kb, respectively, in the 11.93 Mb region. Annotation based on the pig reference genome identified 15 genes that were located near or contained the significant SNPs in these linkage disequilibrium intervals. Conditioned analysis revealed that four SNPs, one on SSC2 and three on SSC4, showed significant associations with SL and HL, respectively.ConclusionsAnalysis of the 15 annotated genes that were identified in these three haplotype blocks indicated that HMGA1 and PPARD, which are expressed in limbs and influence chondrocyte cell growth and differentiation, could be considered as relevant biological candidates for limb bone length in pig, with potential applications in breeding programs. Our results may also be useful for the study of the mechanisms that underlie human limb length and body height.Electronic supplementary materialThe online version of this article (doi:10.1186/s12711-014-0056-6) contains supplementary material, which is available to authorized users.

Analysis of genome-wide copy number variations in Chinese indigenous and western pig breeds by 60 K SNP genotyping arrays.

Copy number variations (CNVs) represent a substantial source of structural variants in mammals and contribute to both normal phenotypic variability and disease susceptibility. Although low-resolution CNV maps are produced in many domestic animals, and several reports have been published about the CNVs of porcine genome, the differences between Chinese and western pigs still remain to be elucidated. In this study, we used Porcine SNP60 BeadChip and PennCNV algorithm to perform a genome-wide CNV detection in 302 individuals from six Chinese indigenous breeds (Tongcheng, Laiwu, Luchuan, Bama, Wuzhishan and Ningxiang pigs), three western breeds (Yorkshire, Landrace and Duroc) and one hybrid (Tongcheng×Duroc). A total of 348 CNV Regions (CNVRs) across genome were identified, covering 150.49 Mb of the pig genome or 6.14% of the autosomal genome sequence. In these CNVRs, 213 CNVRs were found to exist only in the six Chinese indigenous breeds, and 60 CNVRs only in the three western breeds. The characters of CNVs in four Chinese normal size breeds (Luchuan, Tongcheng and Laiwu pigs) and two minipig breeds (Bama and Wuzhishan pigs) were also analyzed in this study. Functional annotation suggested that these CNVRs possess a great variety of molecular function and may play important roles in phenotypic and production traits between Chinese and western breeds. Our results are important complementary to the CNV map in pig genome, which provide new information about the diversity of Chinese and western pig breeds, and facilitate further research on porcine genome CNVs.