Molecular characterization and SNPs analysis of the porcine Deleted in AZoospermia Like (pDAZL) gene

Effect of NLR family pyrin domain containing 9 gene polymorphism on litter size in large white pigs

NLR family pyrin domain containing 9 (NLRP9) is a mammalian reproduction-related gene. In this study, we researched the associations between polymorphisms located in the coding sequence (CDS) of the NLRP9 gene, and both the total number of piglets born per litter (TNB) and the number of piglets born alive per litter (NBA) in Canada Large White pigs (CLW). We detected a single nucleotide polymorphism (SNP) within exon 3 (g.10910C > T). The allele frequencies at the NLRP9 locus were 0.474 for the C allele and 0.526 for the T allele. Three genotypes, CC, CT, and TT, occurred with frequencies of 0.216, 0.515, and 0.269, respectively. Sows with the CC genotype had the largest TNB and NBA, sows with TT had the smallest, and those with CT were in-between. This difference was statistically significant (p < 0.05). Furthermore, CC females grew faster than CT or TT females, and there was a significant relationship between NLRP9 polymorphism and the average daily gain (p < 0.05). Here, we provide the first evidence for a novel SNP in NLRP9 associated with litter size in CLW sows, which could be used as a genetic marker to improve litter size in pig breeding and production.

Allelic to genome wide perspectives of swine genetic variation to litter size and its component traits

Litter size is a complex and sex limited trait that depends on various biological, managemental and environmental factors. Owing to its low heritability it is inefficaciously selected by traditional methods. However, due to higher heritability of ovulation rate and embryo survival, selection based on component traits of litter size is advocated. QTL analysis and candidate gene approach are among the various supplementary/alternate strategies for selection of litter size. QTL analysis is aimed at identifying genomic regions affecting trait of interest significantly. Candidate gene approach necessitates identification of genes potentially affecting the trait. There are various genes that significantly affect litter size and its component traits viz. ESR, LEP, BF, IGFBP, RBP4, PRLR, CTNNAL1, WNT10B, TCF12, DAZ, and RNF4. These genes affect litter size in a complex interacting manner. Lately, genome wide association study (GWAS) have been utilized to unveil the genetic and biological background of litter traits, and elucidate the genes governing litter size. Favorable SNPs in these genes have been identified and offers a scope for inclusion in selection programs thereby increasing breeding efficiency and profit in pigs. The review provides a comprehensive coverage of investigations carried out globally to unravel the genetic variation in litter size and its component traits in pigs, both at allelic and genome wide level. It offers a current perspective on different strategies including the profiling of candidate genes, QTLs, and genome wide association studies as an aid to efficient selection for litter size and its component traits.

Porcine LIF gene polymorphisms and their association with litter size traits in four pig breeds

Leukemia inhibitory factor (LIF) is an important productivity-related gene in pigs. We found two polymorphisms — g.6646C>T and g.6988C>T — in exon 3 of LIF in pigs by using DNA sequencing and polymerase chain reaction-restriction fragment length polymorphism. Three genotypes were obtained and associated with litter size traits in Anqing Six-end-white (AQ), Wei (W), Wannan Black (WNB), and Large White (LW) pigs. At locus g.6646C>T, the g.6646C allele frequency variation was 0.6869 (AQ), 0.7473 (W), 1 (WNB), and 0.6852 (LW). In AQ pigs, sows with the TT genotype had higher total number of piglets born (TNB) and number of piglets born alive (NBA) in the first parity and multiparities (P < 0.01). In W and LW pigs, sows with the CC genotype had higher TNB and NBA in multiparities (P < 0.01). At locus g.6988C>T, the g.6988C allele frequency variation was 1 (AQ), 0.6154 (W), 1 (WNB), and 0.6667 (LW). The CC genotype significantly differed from CT or TT genotypes (P < 0.01) for TNB and NBA in W and LW pigs. Thus, LIF was shown to have a significant influence on litter size. Therefore, g.6646C>T and g.6988C>T loci of LIF could be potential marker-assisted selection tools for improving litter size in pig production.

Molecular characteristics and association analysis with litter size trait for porcine KLK7 gene

Kallikrein-related peptidase 7(KLK7) is a tumor-related gene. In this study, the full-length coding sequence of porcine KLK7 gene was cloned through RT-PCR. Sequence analysis revealed that the pig KLK7 gene encodes a protein of 257 amino acids which has high homology with the KLK7 protein of six species: polar bear (95%), Weddell seal(94%), dog (92%), Pacific walrus (95%), domestic cat (92%), and Amur tiger (91%). This gene is structured in five exons and four introns as revealed by computer-assisted analysis. Phylogenetic analysis showed that the pig KLK7 gene has a closer genetic relationship with the KLK7 gene of a domestic cat. PCR-Alu I-RFLP was established to detect the GU373714:c.390 C > T substitution of porcine KLK7 gene and eight pig breeds displayed obvious genotype and allele frequency differences at this mutation locus. Association of this SNP with litter size trait was assessed in Large White (n = 200) and Landrace (n = 200) pig populations and results demonstrated that this polymorphic locus was significantly associated with the litter size of all parities in Large White and Landrace sows (p < 0.05). Therefore, KLK7 is also an important reproduction related gene.

Genetic effect and combined genotype effect of ESR, FSHβ, CTNNAL1 and miR-27a loci on litter size in a Large White population

To select new Large White line with high number of piglets born, genotypes of estrogen receptor (ESR), the follicle stimulating hormone β subunit (FSHβ), catenin alpha like 1 (CTNNAL1) and miR-27a were tested in 472 Large White sows. The associations of different genotypes with litter size traits were also studied. The results showed ESR^BB and FSHβ^BB sows produced 0.41-1.49 more pigs per litter (p < .05) for total number born (TNB) and number born alive (NBA) than did other corresponding genotypes. TNB of CTNNAL1^CG sows is 0.50 more pigs per litter (p < .05) than that of CTNNAL1^GG sows with the dominance effect of 0.25 pigs per litter (p < .05). miR-27a^BB sows had a less estimated breeding value (EBV) to TNB and had a more number of mummified pigs (NM) than did miR-27a^AA or miR-27a^AB sows (p < .05). Therefore, ESR^B, FSHβ^B, CTNNAL1^G, miR-27a^A allele was favorable for litter size traits. Furthermore, combined genetic effect analysis showed ESR^AAFSHβ^BB, ESR^AACTNNAL1^CG, ESR^AAmiR-27a^AA, FSHβ^BBCTNNAL1^CC, FSHβ^BBmiR-27a^AA and CTNNAL1^CG miR-27a^AB was the favorable combined genotype for litter size traits. These results identified favorable alleles and genotypes for litter size traits and suggested a potential selection scheme for litter size in Large White pigs.

SLA-11 mutations are associated with litter size traits in Large White and Chinese DIV pigs

Litter size is an important economic traits in pigs. SLA-11 gene is a member of SLA (swine leukocyte antigen) complex. In our previous study, the SLA-11 gene was differentially expressed in PMSG-hCG stimulated preovulatory ovarian follicles of Chinese Taihu and Large White sows. Here, we identified two mutations (c.754-132 T > C and c.1421 + 38 T > C) in SLA-11 gene and analyzed the associations of two SNPs with litter size traits in Large White (n = 263) and DIV (n = 117) sows. The results showed that in Large White pigs, SLA-11 c.754-132 CC sows produced 0.74 and 0.87 more pigs per litter for TNB and NBA of all parities than did TT sows (p < .05); In DIV pigs, SLA-11 c.754-132 CC sows produced 1.17 more pigs per litter for TNB of all parities than did TC sows (p < .05). In Large White pigs, SLA-11 c.1421 + 38 CC sows produced 0.9 more pigs per litter for TNB of all parities than did TT sows (p < .05), while in DIV pigs SLA-11 c.1421 + 38 CC sows produced 0.84 and 0.7 less pigs per litter for TNB and NBA of all parities than did TT sows (p < .05). Our research indicated that SLA-11 mutations were potential molecular markers for improving the litter size traits in pigs.

Molecular Cloning of Porcine SUN5 Gene and Association between a SNP with Litter Size Trait

SUN domain-containing protein 5 (SUN5) is an important reproduction related gene. In this study, we cloned the full-length coding sequence of porcine SUN5 gene through RT-PCR. Sequence analysis of this gene revealed that the pig SUN5 gene encodes a protein of 383 amino acids that has high homology with the SUN5 protein of eight species: wild Bactrian camel (95%), alpaca (95%), Yangtze River dolphin (94%), sperm whale (94%), sheep (93%), black flying fox (93%), goat (92%), and horse (91%). This gene is structured into 13 exons and 12 introns as revealed by computer-assisted analysis. The prediction of transmembrane helices showed that pig SUN5 protein might be a transmembrane protein. PCR-Taq I-RFLP was established to detect the GU475008:c.138 G>A substitution of porcine SUN5 gene coding sequence and eight pig breeds displayed obvious genotype and allele frequency differences at this mutation locus. Association of this SNP with litter size traits was assessed in Large White (n = 200) and Landrace (n = 200) pig populations, and the results demonstrated that this polymorphic locus was significantly associated with the litter size of all parities in Large White and Landrace sows (P < 0.05). Therefore, the SUN5 gene could be a useful candidate gene for increasing the litter size in pigs.

A novel synonymous SNP (A47A) of the <i>TMEM95</i> gene is significantly associated with the reproductive traits related to testis in male piglets

Abstract. Transmembrane protein 95 (TMEM95) is located on the acrosomal membrane of the sperm head involved in the acrosome reaction; thus, it is regarded as affecting spermatogenesis and reproduction traits. The aim of this study was to explore the novel single nucleotide polymorphisms (SNPs) within the pig TMEM95 gene as well as to evaluate their associations with the testicular sizes in male Landrace (LD) and Large White (LW) breeds. After pool sequencing and bioinformatics analysis, only one novel coding SNP was found in exon 1, namely NC_010454.3: g.341T > C, resulting in a synonymous mutation (A47A). This SNP could be genotyped using the StuI polymerase chain reaction–restriction fragment length polymorphism (PCR-RFLP) assay. The minor allelic frequencies (MAFs) were 0.259 and 0.480 in the LD and LW breeds. Their polymorphism information content (PIC) values were 0.310 and 0.375. The LW population was at the Hardy–Weinberg equilibrium (HWE) (p > 0.05), whereas the LD population was not (p < 0.05). Association analyses demonstrated that a significant relationship was found between this A47A polymorphism and testis weight at 40 days of age in the LW population (p  =  0.047), and the heterozygote individuals showed lower testis weight than those with other genotypes. Moreover, this SNP was significantly associated with three testis measurement traits at 15 days of age in the LW population (p < 0.05); the individuals with genotypes TT and TC showed consistently superior testis measurement traits than those with genotype CC. These findings demonstrate that the A47A polymorphism had a significant effect on testis measurement traits, suggesting that the TMEM95 gene could be a candidate gene associated with reproductive traits. These results could contribute to breeding and genetics programs in the pig industry via DNA marker-assisted selection (MAS).

Molecular cloning, sequence identification, polymorphism and association of the porcine <i>SPATS2L</i> gene

Abstract. Spermatogenesis-associated, serine-rich 2-like (SPATS2L) is an important reproduction-related gene. In this study, the full-length cDNA sequence of the porcine SPATS2L gene was cloned through the RACE (rapid amplification of cDNA ends) method. The porcine SPATS2L gene encodes a protein of 559 amino acids which shares high homology with the SPATS2L proteins of seven species: dog (94 %), white-tufted-ear marmoset (91 %), human (92 %), rhesus monkey (92 %), horse (92 %), rat (88 %) and mouse (88 %). This novel porcine gene was assigned to GeneID: 100415809. The phylogenetic analysis revealed that the porcine SPATS2L gene has a close genetic relationship with the canine SPATS2L gene. PCR-Pst I-RFLP was established to detect GU474997:c.1687 C > T substitution of porcine SPATS2L gene mRNA, and eight pig breeds displayed obvious genotype and allele frequency differences at this mutation locus. Association of this single-nucleotide polymorphism (SNP) with litter size traits was assessed in Large White (n = 100) and Landrace (n = 100) pig populations, and results demonstrated that this polymorphic locus was significantly associated with the litter size of all parities in Large White sows and Landrace sows (P < 0.01). Therefore, SPATS2L gene could be an useful candidate gene in selection for increasing litter size in pigs.

Molecular Characterization, Polymorphism, and Association of Porcine GADD45G Gene

Growth arrest and DNA-damage-inducible gamma (GADD45G) is a reproduction related gene. In this study, the full-length cDNA sequence of porcine GADD45G gene was cloned through rapid amplification of cDNA ends (RACE) method. The porcine GADD45G gene encodes a protein of 159 amino acids that shares high homology with the GADD45G of nine species: chimpanzee (97%), sumatran orangutan (97%), white-tufted-ear marmoset (97%), northern white-cheeked gibbon (97%), cattle (97%), human (97%), rhesus monkey (97%), rat (96%), and mouse (95%). This novel porcine gene was assigned to GeneID: 100152997. Phylogenetic analysis revealed that the porcine GADD45G gene has a closer genetic relationship with the GADD45G gene of cattle. Computer-assisted analysis indicated that porcine GADD45G gene is structured in four exons and three introns. PCR-Rsa I-RFLP was established to detect an A/G mutation on the position of 294-bp of coding sequence and eight pig breeds display obvious genotype and allele frequency differences at this mutation locus. Association of this SNP with litter size traits was assessed in Large White (n = 100) and Landrace (n = 100) pig populations, and result demonstrated that this polymorphic locus was significantly associated with the litter size of all parities in Large White and Landrace sows (P < 0.01). Therefore, porcine GADD45G gene could be a useful candidate gene in selection for increasing the litter size. These data serve as a foundation for further insight into this novel porcine gene.

Associations of TCF12, CTNNAL1 and WNT10B gene polymorphisms with litter size in pigs

In previous research, several WNT signaling pathway genes including transcription factor 12 (TCF12), catenin alpha-like protein 1 (CTNNAL1) and wingless-type MMTV integration site family, member 10B (WNT10B) were differentially expressed in PMSG-hCG stimulated preovulatory ovarian follicles of Large White and Chinese Taihu sows. In the present research, these three genes were selected as the candidate genes for litter size traits in pigs. Four mutations (TCF12 c.-201+65 G>A, TCF12 c.-200-300 G>A, CTNNAL1 c.1878 G>C and WNT10B c.*12 C>T) were detected in eleven pig populations, and results indicated CTNNAL1 c.1878 G and WNT10B c.*12 C were the major alleles in all tested pig populations, while TCF12 c.-201+65 A and TCF12 c.-200-300 A were the major alleles in several Chinese native pig breeds. Association analysis of four mutations with litter size in Large White and DIV pigs showed that both the signficant differences of total number born (TNB) and number born alive (NBA) among three genotypes and the significance of additive effects appeared at TCF12 c.-200-300 G>A and CTNNAL1 c.1878 G>C loci, suggesting these two mutations might be reliable markers for pig selection and breeding.

Identification of the promoter region and genetic mutations of the porcine GALP gene

Galanin-like peptide (GALP) gene, encoding a member of the galanin family of neuropeptides involved in reproduction, was differentially expressed in PMSG-hCG stimulated pre-ovulatory ovarian follicles of Chinese Taihu and Large White sows in our previous study. In the present study, promoter region and genetic mutations of the porcine GALP gene were determined. A 1,322 bp contig in 5'-flanking region was predicted to contain 5 potential transcription promoters by Neural Network Promoter Prediction version 2.2. 5'-deletion expression in both CHO and hela cells showed that there were a negative regulatory element at -852 to -803 bp and a positive regulatory element at -1,318 to -1,269 bp. Comparative sequence analyses of Chinese Taihu and Large White GALP gene sequence revealed the c.*27C>G mutation in the 3'-UTR and the c.88-1225C>G mutation in intron 1, which can be detected by HhaI and AluI PCR-RFLP, respectively. The association analysis with litter size traits showed that at both loci CC and GG genotypes were different for NBA for all parities in DIV pigs (P < 0.05). However, two SNPs were not in significant linkage disequilibrium analyzed using SHEsis online software, and could be used in pig breeding individually.

Cloning, sequence, and association analysis of porcine OSAP gene

Ovary-specific acidic protein (OSAP) is an important reproduction-related gene. In this study, we cloned the full-length cDNA sequence of porcine OSAP gene through the rapid amplification of cDNA ends method. The porcine OSAP gene encodes a protein of 238 amino acids which shares high homology with the OSAP of five species: rhesus monkey (72 %), human (70 %), cattle (68 %), horse (68 %), and dog (61 %). This gene is structured in four exons and three introns as revealed by computer-assisted analysis. PCR-RFLP was established to detect the GU373669:c.854A>T substitution of porcine OSAP gene mRNA and association of this mutation with litter size traits was assessed in Large White (n=100) and Landrace (n=100) pig populations. Results demonstrated that this polymorphic locus was significantly associated with the litter size of all parities in Large White sows and Landrace sows (P<0.05). Therefore, OSAP gene could be a useful candidate gene in selection for increasing litter size in pigs. These data serve as a foundation for further insight into this novel porcine gene.

Data mining in networks of differentially expressed genes during sow pregnancy

Small to moderate gains in Pig fertility can mean large returns in overall efficiency, and developing methods to improve it is highly desirable. High fertility rates depend on completion of successful pregnancies. To understand the molecular signals associated with pregnancy in sows, expression profiling experiments were conducted to identify differentially expressed genes in ovary and myometrium at different pregnancy periods using the Affymetrix Porcine GeneChip^TM. A total of 974, 1800, 335 and 710 differentially expressed transcripts were identified in the myometrium during early pregnancy (EP) and late pregnancy (LP), and in the ovary during EP and LP, respectively. Self-Organizing Map (SOM) clusters indicated the differentially expressed genes belonged to 7 different functional groups. Based on BLASTX searches and Gene Ontology (GO) classifications, 129 unique genes closely related to pregnancy showed differential expression patterns. GO analysis also indicated that there were 21 different molecular function categories, 20 different biological process categories, and 8 different cellular component categories of genes differentially expressed during sow pregnancy. Gene regulatory network reconstruction provided us with an interaction model of known genes such as insulin-like growth factor 2 (IGF2) gene, estrogen receptor (ESR) gene, retinol-binding protein-4 (RBP4) gene, and several unknown candidate genes related to reproduction. Several pitch point genes were selected for association study with reproduction traits. For instance, DPPA5 g.363 T>C was found to associate with litter born weight at later parities in Beijing Black pigs significantly (p < 0.05). Overall, this study contributes to elucidating the mechanism underlying pregnancy processes, which maybe provide valuable information for pig reproduction improvement.

Molecular characterization, polymorphism and association of porcine MYST2 gene

MYST histone acetyltransferase 2 (MYST2) is an important reproduction related gene. In this study, we cloned the full-length cDNA sequence of porcine MYST2 gene through the rapid amplification of cDNA ends method. The porcine MYST2 gene encodes a protein of 611 amino acids which shares high homology with the MYST2 of six species: cattle (99%), rabbit (99%), human (99%), rat (99%), mouse (99%) and chicken (98%).The open reading frame of this gene is structured in 15 exons and 14 introns as revealed by computer-assisted analysis. The phylogenetic analysis revealed that the porcine MYST2 gene has a closer genetic distance with the MYST2 gene of cattle. PCR-RFLP was established to detect the GU373686:c.2872G > A substitution of porcine MYST2 gene mRNA and association of this mutation with litter size traits was assessed in Large White (n = 200) and Landrace (n = 200) pig populations. Results demonstrated that this polymorphic locus was significantly associated with the litter size of all parities in Large White sows and Landrace sows. These data serve as a foundation for further insight into this porcine gene.

Molecular characterization, tissue expression, polymorphism and association of porcine LCK gene

Lymphocyte-specific protein tyrosine kinase (LCK) is an important reproduction related gene. In this study, the full-length cDNA sequence of porcine LCK gene was cloned through the rapid amplification of cDNA ends (RACE) method. The porcine LCK gene encodes a protein of 509 amino acids which shares high homology with the LCK of nine species: giant panda (97%), dog (97%), cattle (96%), sheep (95%), rabbit (95%), human (96%), rat (94%), mouse (94%) and horse (94%). This novel porcine gene was assigned to GeneID: 100233188. The phylogenetic analysis revealed that the porcine LCK gene has a closer genetic relationship with the LCK gene of dog. This gene is structured in twelve exons and eleven introns as revealed by computer-assisted analysis. The tissue transcription profile analysis indicated that the porcine LCK gene is generally but differentially expressed in the detected tissues including large intestine, spleen, lung, muscle, fat, liver, heart, kidney and ovary. PCR-Alu I-RFLP was established to detect an A/G substitution at the position of 1127-bp of mRNA and eight pig breeds displayed obvious genotype and allele frequency differences at this mutation locus. Association of this single-nucleotide polymorphism with litter size traits was assessed in Large White (n = 100) and Landrace (n = 100) pig populations, and results demonstrated that this polymorphic locus was significantly associated with the litter size of all parities in Large White sows and Landrace sows (P < 0.01). Therefore, LCK gene could be an useful candidate gene in selection for increasing litter size in pigs. These data serve as a foundation for further insight into this novel porcine gene.

Characterization, expression profile, polymorphism and association of porcine NAT9 gene

The N-acetyltransferase 9 (NAT9) is an important reproduction related gene. In this study, we cloned the full-length cDNA sequence of porcine NAT9 gene through the rapid amplification of cDNA ends method. The porcine NAT9 gene encodes a protein of 206 amino acids which shares high homology with the NAT9 of seven species: rhesus monkey (87%), chimpanzee (87%), human (87%), horse (86%), rat (80%), mouse (79%) and gray short-tailed opossum (79%). This gene is structured in six exons and five introns as revealed by computer-assisted analysis. Tissue transcription profile analysis indicated that the porcine NAT9 gene is generally but differentially expressed in the detected tissues including spleen, large intestine, lung, fat, muscle, heart, liver, kidney and ovary. PCR-Alu I-RFLP was established to detect an A/G mutation on the position of 699-bp of mRNA and eight pig breeds display obvious genotype and allele frequency differences at this mutation locus. Association of this SNP with litter size traits was assessed in Large White (n = 100) and Landrace (n = 100) pig populations, and results demonstrated that this polymorphic locus is significantly associated with the litter size of first parity (P < 0.05). This suggests that the NAT9 gene can be an useful candidate gene in selection for increasing litter size in pigs.

Molecular cloning, sequence characterization, polymorphism and association analysis of porcine ROPN1 gene

The full-length cDNA sequence of one porcine gene, ROPN1, was isolated using the rapid amplification of cDNA ends (RACE) method based on one pig EST sequence which was highly homologous to the coding sequence of human ROPN1 gene. The porcine ROPN1 gene encodes a protein of 212 amino acids which shares high homology with the rhophilin associated protein 1 (ROPN1) of eight species: gray short-tailed opossum (96%), horse (95%), cattle (94%), mouse (93%), rat (92%), chimpanzee (85%), human (85%) and rhesus monkey (85%). Phylogenetic analysis revealed that the porcine ROPN1 gene has a closer genetic relationship with the ROPN1 gene of gray short-tailed opossum. Polymorphism analysis showed that there was a T/C mutation at the position of 536 bp of mRNA and this leaded to the amino acid alteration from the Arg residue to the Cys residue. PCR-Hae III-RFLP was established to detect this T/C mutation and eight pig breeds display obvious genotype and allele frequency differences at this mutation locus. Association of this SNP with litter size traits was assessed in Large White (n = 100) and Landrace (n = 100) pig populations, and results demonstrated that this polymorphic locus was significantly associated with the litter size of first parity (P < 0.01) and all parities (P < 0.05) in Large White sows, and also significantly associated with the litter size of all parities in Landrace sows (P < 0.01). Therefore, ROPN1 gene could be a useful candidate gene in selection for increasing litter size in pigs. These data serve as a foundation for further insight into this novel porcine gene.

Microarray profiling for differential gene expression in PMSG-hCG stimulated preovulatory ovarian follicles of Chinese Taihu and Large White sows

Background

The Chinese Taihu is one of the most prolific pig breeds in the world, which farrows at least five more piglets per litter than Western pig breeds partly due to a greater ovulation rate. Variation of ovulation rate maybe associated with the differences in the transcriptome of Chinese Taihu and Large White ovaries. In order to understand the molecular basis of the greater ovulation rate of Chinese Taihu sows, expression profiling experiments were conducted to identify differentially expressed genes in ovarian follicles at the preovulatory stage of a PMSG-hCG stimulated estrous cycle from 3 Chinese Taihu and 3 Large White cycling sows by using the Affymetrix Porcine Genechip™.

Results

One hundred and thirty-three differentially expressed genes were identified between Chinese Taihu and Large White sows by using Affymetrix porcine GeneChip (p ≤ 0.05, Fold change ≥ 2 or ≤ 0.5). Gene Ontology (GO) analysis revealed that these genes belonged to the class of genes that participated in regulation of cellular process, regulation of biological process, biological regulation, developmental process, cell communication and signal transduction and so on. Significant differential expression of 6 genes including WNT10B and DKK2 in the WNT signaling pathway was detected. Real-time RT-PCR confirmed the expression pattern in seven of eight selected genes. A search of chromosomal location revealed that 92 differentially expressed transcripts located to the intervals of quantitative trait loci (QTLs) for reproduction traits. Furthermore, SNPs of two differentially expressed genes- BAX and BMPR1B were showed to be associated with litter size traits in Large White pigs and Chinese DIV line pigs (p ≤ 0.1 or p ≤ 0.05).

Conclusions

Our study detected many genes that showed differential expression between ovary follicles of two divergent breeds of pigs. Genes involved with regulation of cellular process, regulation of biological process, in addition to several genes not previously associated with ovarian physiology or with unknown function, were differentially expressed between two breeds. The suggestive or significant associations of BAX and BMPR1B gene with litter size indicated these genetic markers had the potentials to be used in pig industry after further validation of their genetic effects. Taken together, this study reveals many potential avenues of investigation for seeking new insights into ovarian physiology and the genetic control of reproduction.

A SNP in the miR-27a gene is associated with litter size in pigs

MicroRNAs (miRNAs) are 20-25 nt, endogenous non-coding RNA molecules that act by binding to the complementary sequence of target messenger RNAs. Many evidences showed that miRNAs were involved in the process of germ proliferation and differentiation. In the present study, miR-27a gene was selected as a candidate gene for litter size due to its biological function, its location near a mummified pigs QTL, and its differentially expressed profile in Large White and Chinese Erhualian PMSG-hCG stimulated preovulatory ovaries. By comparative sequencing of miR-27a gene in Large White and Chinese Meishan pigs, one SNP (T/C) which created an additional HpaII site was detected. Then associations of this SNP with litter size traits were assessed in Large White (n=142) and DIV (n=140) pig populations. The statistical analysis demonstrated that AA differed from AB (P<0.01) and BB (P<0.05) for total number of piglets born in the first parities, and also differed from AB (P<0.01) for the number of piglets born alive in all parities (P<0.05) in DIV pigs. No significant difference was observed between different genotypes in Large White pigs.

Microarray-based approach identifies differentially expressed microRNAs in porcine sexually immature and mature testes

Background

MicroRNAs (miRNAs) are short non-coding RNA molecules which are proved to be involved in mammalian spermatogenesis. Their expression and function in the porcine germ cells are not fully understood.

Methodology

We employed a miRNA microarray containing 1260 unique miRNA probes to evaluate the miRNA expression patterns between sexually immature (60-day) and mature (180-day) pig testes. One hundred and twenty nine miRNAs representing 164 reporter miRNAs were expressed differently (p<0.1). Fifty one miRNAs were significantly up-regulated and 78 miRNAs were down-regulated in mature testes. Nine of these differentially expressed miRNAs were validated using quantitative RT-PCR assay. Totally 15919 putative miRNA-target sites were detected by using RNA22 method to align 445 NCBI pig cDNA sequences with these 129 differentially expressed miRNAs, and seven putative target genes involved in spermatogenesis including DAZL, RNF4 gene were simply confirmed by quantitative RT-PCR.

Conclusions

Overall, the results of this study indicated specific miRNAs expression in porcine testes and suggested that miRNAs had a role in regulating spermatogenesis.