FSHβ subunit gene is associated with major gene controlling litter size in commercial pig breeds

An insertion fragment in porcine FSHβ subunit gene was cloned by PCR. Sequencing data show that the insertion is a retroposon of 292 bp siting in intronⅠ at the site between +809 and +810 base. Based on these results, a PCR programme was created to genotype animal individuals in different pig breeds at FSHβ locus and polymorphism of FSHβ gene was analyzed. With the combination of genotype and litter size of sows, it was demonstrated that FSHβ locus is closely associated with major gene controlling litter size in commercial pig breeds, such as Yorkshire, Landrace, Durco. Averagely the AA sows give more 1.5 piglets than BB sows do per litter.     

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.     

Allelic variation in the erythropoietin receptor gene is associated with uterine capacity and litter size in swine

A single nucleotide polymorphism (SNP; C vs. T) that creates an extra GATA-1 site (T allele) in intron 4 of the swine erythropoietin receptor (EPOR) gene was discovered and a genotyping assay for this SNP was developed. A total of 402 gilts from lines selected either at random (control), for ovulation rate (OR) or for uterine capacity (UC) for 11 generations were unilaterally hysterectomized-ovariectomized (UHO) at 160 days of age, mated at approximately 250 days of age and slaughtered at 105 days of pregnancy. Blood samples and spleens were collected from each foetus and the numbers of corpora lutea (CL) and live foetuses, the weights of each foetus and placenta, and each foetal haematocrit were recorded. In addition, intact gilts from the OR line or from a Yorkshire, Landrace, Duroc, crossbred line (BX) were mated and farrowed. At farrowing, the numbers of fully formed and live piglets were recorded for each litter. Genomic DNA was isolated for both the UHO and intact gilts, from foetuses from the UHO gilts that were heterozygous for the EPOR SNP, and from the boars from the BX line and were then used to determine EPOR SNP genotypes. Only CC and CT gilts were observed in the control, OR and UC selected lines. Presence of the EPOR T allele was associated (P < 0.05) with increased UC in these gilts. The number of heterozygous and homozygous foetuses did not differ within UHO litters, or did EPOR genotype influence foetal haematocrit. In intact gilts from the OR line, litter size was significantly associated (P < 0.05) with EPOR SNP genotype. Finally, results from intact gilts of the BX line, in which both the gilt and the boar genotypes were known, allowed an analysis to determine the effect of the gilt and/or the foetal genotype on litter size. This analysis indicated that the predicted foetal genotype (with gilt genotype as covariate) was associated with litter size (an increase of 2.6 +/- 1.0 piglets born alive predicted for homozygous T litters compared with homozygous C litters, P < 0.01) whereas the effect of the gilt genotype (adjusted for foetal genotype) on litter size was not significant. These results indicate that the EPOR SNP is associated with UC and litter size in two distinct populations and could be useful in increasing litter size in swine that are not limited in OR.     

Microparasite species richness in rodents is higher at lower latitudes and is associated with reduced litter size

Parasite species loads are expected to be higher in the tropics and higher parasite species richness to have cumulative effects on host physiology or demography. Despite being regularly assumed or predicted, empirical evidence on species–latitude patterns is scarce or contradictory and studies on the impacts of concomitant infections have mainly been done at host intra‐specific level. Broad generalizations are then very hard, if not spurious. By focusing on rodent species and their non‐eukaryotic microparasites (i.e. viruses and bacteria), we investigated, using a comparative approach, microparasite species richness across rodent species according to the latitude where they occur. We also explored the links between rodents’ reproductive traits, latitude and microparasite species richness. We find for the first time in rodents that virus species richness increases towards tropical latitudes, and that rodent litter size seems to decrease when microparasite species richness increases independently from the latitude. These results support the hypotheses that rodent species in the tropics effectively harbour higher parasite species loads, at least in terms of species richness for viruses, and that parasite species richness influences rodent life‐history traits. Although some other factors, such as seasonality, were not taken into account due the lack of data, our study stresses the idea that chronic microparasite infections may have detrimental effects on their rodent host reservoirs, notably by affecting litter size.     

Two missense mutations in exon 9 of caprine PRLR gene were associated with litter size

Guanzhong (n = 321) and Boer (n = 191) goat breeds were used to detect single nucleotide polymorphisms (SNPs) in the coding regions of the prolactin receptor (PRLR) gene by DNA sequencing and PCR‐RFLP. Two SNPs (c.1457G>A and c.1645G>A) were identified that caused amino acid variations p.Ser485Asn and p.Val548Met respectively. Statistical results indicated that the c.1457G>A and c.1645G>A SNPs were significantly associated with litter size in Boer and Guanzhong goat breeds. Further analysis revealed that combined genotype C4 (GGGG) and haplotype G‐G were better than the others for litter size in both goat breeds. These results might contribute to goat genetic resources and breeding.     

The imprinted gene DIO3 is a candidate gene for litter size in pigs

Genomic imprinting is an important epigenetic phenomenon, which on the phenotypic level can be detected by the difference between the two heterozygote classes of a gene. Imprinted genes are important in both the development of the placenta and the embryo, and we hypothesized that imprinted genes might be involved in female fertility traits. We therefore performed an association study for imprinted genes related to female fertility traits in two commercial pig populations. For this purpose, 309 SNPs in fifteen evolutionary conserved imprinted regions were genotyped on 689 and 1050 pigs from the two pig populations. A single SNP association study was used to detect additive, dominant and imprinting effects related to four reproduction traits; total number of piglets born, the number of piglets born alive, the total weight of the piglets born and the total weight of the piglets born alive. Several SNPs showed significant (q-value < 0.10) additive and dominant effects and one SNP showed a significant imprinting effect. The SNP with a significant imprinting effect is closely linked to DIO3, a gene involved in thyroid metabolism. The imprinting effect of this SNP explained approximately 1.6% of the phenotypic variance, which corresponded to approximately 15.5% of the additive genetic variance. In the other population, the imprinting effect of this QTL was not significant (q-value > 0.10), but had a similar effect as in the first population. The results of this study indicate a possible association between the imprinted gene DIO3 and female fertility traits in pigs.     

Hypermethylation in the ZBTB20 gene is associated with major depressive disorder

Background

Although genetic variation is believed to contribute to an individual’s susceptibility to major depressive disorder, genome-wide association studies have not yet identified associations that could explain the full etiology of the disease. Epigenetics is increasingly believed to play a major role in the development of common clinical phenotypes, including major depressive disorder.

Results

Genome-wide MeDIP-Sequencing was carried out on a total of 50 monozygotic twin pairs from the UK and Australia that are discordant for depression. We show that major depressive disorder is associated with significant hypermethylation within the coding region of ZBTB20, and is replicated in an independent cohort of 356 unrelated case-control individuals. The twins with major depressive disorder also show increased global variation in methylation in comparison with their unaffected co-twins. ZBTB20 plays an essential role in the specification of the Cornu Ammonis-1 field identity in the developing hippocampus, a region previously implicated in the development of major depressive disorder.

Conclusions

Our results suggest that aberrant methylation profiles affecting the hippocampus are associated with major depressive disorder and show the potential of the epigenetic twin model in neuro-psychiatric disease.     

Polymorphism of the pig acetyl-coenzyme A carboxylase α gene is associated with fatty acid composition in a Duroc commercial line

Acetyl-coenzyme A carboxylase α (ACACA) catalyses the first committed step in the biosynthesis of long-chain fatty acids (FA) by converting acetyl-CoA into malonyl-CoA. In pigs, the ACACA gene maps to a chromosome 12 QTL with important effects on FA composition. In the present study, we have sequenced the coding region of the pig ACACA gene in 15 pigs, identifying 21 polymorphic sites that were either synonymous or non-coding. Ten of these SNPs segregated in a Duroc commercial population ( n  = 350) for which lipid metabolism and meat and carcass quality trait records were available. Significant associations were found between two linked single nucleotide polymorphisms (c.4899G>A and c.5196T>C) and percentages of carcass lean, intramuscular fat, monounsaturated, saturated (myristic, palmitic and stearic) and polyunsaturated (linoleic) FAs in the longissimus thoracis et lumborum muscle, along with serum HDL-cholesterol concentration. The most important allele substitution effects were observed for the polyunsaturated/saturated FA ratio (13–21% of the phenotypic mean) as well as for the percentages of ω-6 and polyunsaturated FAs, especially linoleic acid (7–16% of the phenotypic mean). These results suggest the existence of a causal mutation, mapping to the chromosomal region containing the pig ACACA gene, with marked effects on FA composition of meat.     

Known mutation (A3072G) in intron 3 of theIGF2 gene is associated with growth and carcass composition in Polish pig breeds

IGF2 is one of the genes that control muscle development. Moreover,IGF2 is imprinted, as only the paternal allele is expressed in the offspring. Using real-time PCR forIGF2 genotyping (Carrodegous et al. 2005), we evaluated the frequency of theIGF2 A3072G mutation (Van Laere et al. 2003) in pigs: Polish Landrace (PL,N = 271) and Large White (LW,N = 267). Our results are consistent with previous reports, showing that theA allele is common in breeds subjected to strong selection for lean meat content (A allele frequency was 0.79 in LW and 0.69 in PL). Moreover, we compared body composition, growth performance and meat quality traits in pigs carrying opposite genotypes (A/A andG/G) inthe IGF2 gene. The association study revealed that theA allele increases the weight of loin (WL) (additive gene effect = 450±50 g in LW and 213±64g in PL), weight of ham (WH) (544±48 g in LW and 302±72 g in PL), loin eye area (LEA) (4.9±0.46 cm² in LW and 2.1 ±0.95 cm² in PL), carcass meat percentage (CP) (3.12±0.27% in LW and 1.89±0.47% in PL), and decreases average backfat thickness (ABF) (−0.2±0.036 cm in LW and −0.2±0.048 cm in PL). Additionally, in PL, theA allele increases the weight of tenderloin (WT) (11±0.01 g), average daily gain (ADG) (30.7±17.29 g), and decreases feed intake (F) (−121±45 g) and days of feeding (DF) (−3.5±2.08 days). No significant effects were observed for meat quality traits. Our results suggest that selection based on theIGF2 mutation in Poland may be very useful in PL and LW pigs, where theG allele is still relatively frequent.     

A novel polymorphism of the myogenin gene is associated with body measurement traits in native Chinese breeds

Using PCR-SSCP and DNA sequencing technology, we examined the association of single nucleotide polymorphisms (SNPs) in the bovine MyoG gene with body measurement traits in 779 individuals of six native Chinese cattle breeds, namely Luxi, Luxi × Simmental crossbred, Nanyang, Xia'nan, Jiaxian red, and Qinchuan. A novel SNP, T314C, was detected. Allelic frequencies of MyoG-T/C in the six breeds were 0.8308/0.1692, 0.8774/0.1226, 0.8021/0.1979, 0.8209/0.1791, 0.8630/0.1370, 0.8044/0.1956, respectively. Least squares analysis revealed a significant (P < 0.05) association of the MyoG SNP with rump length in four breeds (Luxi, Xia'nan, Jiaxian red, and Qinchuan), with hucklebone width in three breeds (Luxi × Simmental crossbred, Nanyang and Xia'nan), with waist height in two breeds (Luxi × Simmental crossbred and Nanyang) and with body length in the Luxi breed. We conclude that the MyoG SNP has potential as a genetic marker for economically relevant body measurement traits in native Chinese cattle breeds.     

Polymorphism of FecB gene in nine sheep breeds or strains and its effects on litter size, lamb growth and development

Nine sheep breeds or strains, including 615 individuals were screened with forced PCR RFLP method for the FecB gene to study the polymorphism and its effects on litter sizes, body weights and body sizes. Results show that the polymorphism frequencies of FecB gene are significantly imbalanced in these breeds or strains. The Hu sheep were all homozygous carriers (BB). In the Chinese Merino prolific meat strain, the genotype frequencies of BB, B+ and ++ are 51%, 30% and 19%, respectively, whereas all the other flocks had only the wild-type (++) genotype. Results within Chinese Merino prolific meat strain showed that mean litter sizes of ewes with genotype BB and B+ are 2.8 (+/-0.74) and 2.3 (+/-0.63) (P > 0.05), whereas ++ ewes had a litter size of only 1.2 (+/-0.68) (P < 0.01). At 90 days after birth, the body weights of BB/B+ lambs were higher than that of ++ lambs (18.6 +/- 3.70 kg, 18.0 +/- 3.71 kg versus 15.6 +/- 2.22 kg, P < 0.05). In addition, the heart girth and chest width of BB/B+ lambs were significantly longer than ++ lambs (P < 0.05). No significant differences were observed in either body weight or body size at day 120. Litter size at first lambing from Hu at Natural Source Conservative Region was found to be significantly higher than that from the other two regions sampled (P < 0.05). In addition to the additive effect on litter size, these findings show for the first time that the FecB gene had a positive effect on early postnatal body growth.     

Association analysis of the INHA gene with litter size in Boer goats

This study investigated the association between differences in litter size in Boer does, with genetic polymorphisms in the inhibin alpha gene. Our preliminary (n = 209) results found 12 SNPs, including the non-synonymous polymorphisms 911T/C and 946A/C, resulting in corresponding 299V/A and 311T/P amino acid polymorphisms. Of the SNPs, 651A/G was preliminarily suggested as a useful marker for litter size of the second parity in the population studied, showing an overdominance effect. Polymorphisms, sequence, and genotype distributions were also characterized.     

Polymorphisms of BMPR-IB gene and their relationship with litter size in goats

The bone morphogenetic protein receptor IB (BMPR-IB) gene was studied as a candidate gene for the prolificacy of goats. According to mRNA sequence of ovine BMPR-IB gene, ten pairs of primers were designed to detect single nucleotide polymorphisms (SNPs) of exon 1, exon 2, exon 6 to exon 10 and 3′ untranslated region (UTR) of the BMPR-IB gene in both high prolificacy breed (Jining Grey goat) and low prolificacy breeds (Wendeng Dairy and Inner Mongolia Cashmere goats) by polymerase chain reaction (PCR)-single strand conformation polymorphism (SSCP) method. Only the products amplified by primers P8 and P10 of the 3′UTR displayed polymorphisms. For primer P8, three genotypes (AA, AB and BB) were detected in Jining Grey and Wendeng Dairy goats, two genotypes (AA and AB) were in Inner Mongolia Cashmere goats. Sequencing revealed one mutation (71C→T) of the BMPR-IB gene in genotype BB compared with AA. The differences of least squares mean (LSM) for litter size between genotypes AA, AB and BB were non-significant (P > 0.05) in Jining Grey goats. For primer P10, three genotypes (CC, CD and DD) were detected in Jining Grey and Wendeng Dairy goats and one genotype (CC) in Inner Mongolia Cashmere goats. Sequencing revealed one mutation (130T→C) of the BMPR-IB gene in genotype DD compared with CC. The differences of LSM for litter size between genotypes CC, CD and DD were non-significant (P > 0.05) in Jining Grey goats. These results preliminarily showed that the detected loci of the BMPR-IB gene had no significant effect on prolificacy of Jining Grey goats.     

FUT1基因多态性及其与产仔性状的关联性研究

采用PCR-RFLP技术6个中外品种共245头猪的FUT1基因进行了研究, 结果表明, Hin 6Ⅰ位点上, 大白猪、长白猪和杜洛克猪3个外来猪种均存在多态, 且以敏感型(GG型和AG型)居多; 山西黑猪、太原花猪和马身猪3个本地猪种的所有检测样品都表现为GG型。用方差分析方法分析FUT1基因型、品种和胎次与产仔性状之间的关系, 基因型和品种对猪的总产仔数的影响显著, 胎次对总产仔数影响不显著。而基因型、品种和胎次对产活仔数影响均不显著。     

A genome-wide detection of selection signatures in conserved and commercial pig breeds maintained in Poland

Background

Identification of selection signatures can provide a direct insight into the mechanism of artificial selection and allow further disclosure of the candidate genes related to the animals’ phenotypic variation. Domestication and subsequent long-time selection have resulted in extensive phenotypic changes in domestic pigs, involving a number of traits, like behavior, body composition, disease resistance, reproduction and coat color. In this study, based on genotypes obtained from PorcineSNP60 Illumina assay we attempt to detect both diversifying and within-breed selection signatures in 530 pigs belonging to four breeds: Polish Landrace, Pu?awska, Z?otnicka White and Z?otnicka Spotted, of which the last three are a subject of conservative breeding and substantially represent the native populations.

Results

A two largely complementary statistical methods were used for signatures detection, including: pairwise F_ST and relative extended haplotype homozygosity (REHH) test. Breed-specific diversifying selection signals included several genes involved in processes connected with fertility, growth and metabolism which are potentially responsible for different phenotypes of the studied breeds. The diversifying selection signals also comprised PPARD gene that was previously found to have a large effect on the shape of the external ear in pigs or two genes encoding neuropeptide Y receptors (Y2 and Y5) involved in fat deposition and stress response which are important features differentiating the studied breeds. REHH statistics allowed detecting several within-breed selection signatures overlapping with genes connected with a range of functions including, among others: metabolic pathways, immune system response or implantation and development of the embryo.

Conclusions

The study provides many potential candidate genes with implication for traits selected in the individual breeds and gives strong basis for further studies aiming at identification of sources of variation among the studied pig breeds.