A variant of porcine thyroxine-binding globulin has reduced affinity for thyroxine and is associated with testis size

Functional genomics of reproduction in pigs: Are we there yet?

Reproductive failure is the main reason for culling females in swine herds and is both a financial and sustainability issue. Because reproductive traits are complex and lowly to moderately heritable, genomic selection within populations can achieve substantial genetic gain in reproductive efficiency. A better understanding of the physiological components affecting the expression of these traits will facilitate greater understanding of the genes affecting reproductive traits and is necessary to improve and optimize management strategies to maximize reproductive success of gilts and sows. Large-scale genotyping with single-nucleotide polymorphism (SNP) arrays are used for genome-wide association studies (GWAS) and have facilitated identification of positional candidate genes. Transcriptomic data can be used to weight SNP for GWAS and could lead to previously unidentified candidate genes. Resequencing and fine mapping of candidate genes are necessary to identify putative functional variants and some of these have been incorporated into new genotyping arrays. Sequence imputation and genotype by sequence are newer strategies that could reveal novel functional mutations. In this study, these approaches are discussed. Advantages and limitations are highlighted where additional research is needed.

Extensive Variation in Gene Expression is Revealed in 13 Fertility-Related Genes Using RNA-Seq, ISO-Seq, and CAGE-Seq From Brahman Cattle

Fertility is a key driver of economic profitability in cattle production. A number of studies have identified genes associated with fertility using genome wide association studies and differential gene expression analysis; however, the genes themselves are poorly characterized in cattle. Here, we selected 13 genes from the literature which have previously been shown to have strong evidence for an association with fertility in Brahman cattle (Bos taurus indicus) or closely related breeds. We examine the expression variation of the 13 genes that are associated with cattle fertility using RNA-seq, CAGE-seq, and ISO-seq data from 11 different tissue samples from an adult Brahman cow and a Brahman fetus. Tissues examined include blood, liver, lung, kidney, muscle, spleen, ovary, and uterus from the cow and liver and lung from the fetus. The analysis revealed several novel isoforms, including seven from SERPINA7. The use of three expression characterization methodologies (5′ cap selected ISO-seq, CAGE-seq, and RNA-seq) allowed the identification of isoforms that varied in their length of 5′ and 3′ untranslated regions, variation otherwise undetectable (collapsed as degraded RNA) in generic isoform identification pipelines. The combinations of different sequencing technologies allowed us to overcome the limitations of relatively low sequence depth in the ISO-seq data. The lower sequence depth of the ISO-seq data was also reflected in the lack of observed expression of some genes that were observed in the CAGE-seq and RNA-seq data from the same tissue. We identified allele specific expression that was tissue-specific in AR, IGF1, SOX9, STAT3, and TAF9B. Finally, we characterized an exon of TAF9B as partially nested within the neighboring gene phosphoglycerate kinase 1. As this study only examined two animals, even more transcriptional variation may be present in a genetically diverse population. This analysis reveals the large amount of transcriptional variation within mammalian fertility genes and illuminates the fact that the transcriptional landscape cannot be fully characterized using a single technology alone.

Assessing the association of single nucleotide polymorphisms in thyroglobulin gene with age of puberty in bulls

Puberty is a stage of sexual development determined by the interaction of many loci and environmental factors. Identification of genes contributing to genetic variation in this character can assist with selection for early pubertal bulls, improving genetic progress in livestock breeding. Thyroid hormones play an important role in sexual development and spermatogenic function. The objective of this study was to evaluate the association between single nucleotide polymorphisms (SNPs) located in thyroglobulin(TG) gene with age of puberty in Angus bulls. Four SNPs were genotyped in 273 animals using SEQUENOM technology and the association between markers and puberty age was analyzed. Results showed a significant association (P < 0.05) between these markers and puberty age estimated at a sperm concentration of 50 million and a progressive motility of 10%. This is the first report of an association of TG polymorphisms with age of puberty in bulls, and results suggest the importance of thyroidal regulation in bovine sexual development and arrival to puberty.

Genome-wide association study for inhibin, luteinizing hormone, insulin-like growth factor 1, testicular size and semen traits in bovine species

The fertility of young bulls impacts on reproduction rates, farm profit and the rate of genetic progress in beef herds. Cattle researchers and industry therefore routinely collect data on the reproductive performance of bulls. Genome-wide association studies were carried out to identify genomic regions and genes associated with reproductive traits measured during the pubertal development of Tropical Composite bulls, from 4 to 24 months of age. Data from 1 085 bulls were collected for seven traits: blood hormone levels of inhibin at 4 months (IN), luteinizing hormone following a gonadotropin releasing hormone challenge at 4 months (LH), insulin-like growth factor 1 at 6 months (IGF1), scrotal circumference at 12 months (SC), sperm motility at 18 months (MOT), percentage of normal spermatozoa at 24 months (PNS) and age at a scrotal circumference of 26 cm (AGE26, or pubertal age). Data from 729 068 single-nucleotide polymorphisms were used in the association analysis. Significant polymorphism associations were discovered for IN, IGF1, SC, AGE26 and PNS. Based on these associations, INHBE, INHBC and HELB are proposed as candidate genes for IN regulation. Polymorphisms associated with IGF1 mapped to the PLAG1 gene region, validating a reported quantitative trait locus on chromosome 14 for IGF1. The X chromosome contained most of the significant associations found for SC, AGE26 and PNS. These findings will contribute to the identification of diagnostic genetic markers and informed genomic selection strategies to assist breeding of cattle with improved fertility. Furthermore, this work provides evidence contributing to gene function annotation in the context of male fertility.

Fine mapping of fatness QTL on porcine chromosome X and analyses of three positional candidate genes

BACKGROUND

Porcine chromosome X harbors four QTL strongly affecting backfat thickness (BFT), ham weight (HW), intramuscular fat content (IMF) and loin eye area (LEA). The confidence intervals (CI) of these QTL overlap and span more than 30 cM, or approximately 80 Mb. This study therefore attempts to fine map these QTL by joint analysis of two large-scale F₂ populations (Large White × Meishan and White Duroc × Erhualian constructed by INRA and JXAU respectively) and furthermore, to determine whether these QTL are caused by mutations in three positional candidate genes (ACSL4, SERPINA7 and IRS4) involved in lipid biosynthesis.

RESULTS

A female-specific linkage map with an average distance of 2 cM between markers in the initial QTL interval (SW2456-SW1943) was created and used here. The CI of QTL for BFT, HW and LEA were narrowed down to 6-7 cM, resulting from the joint analysis. For IMF, two linked QTL were revealed in the INRA population but not in the JXAU population, causing a wider CI (13 cM) for IMF QTL. Linkage analyses using two subsets of INRA F₁ dam families demonstrate that the BFT and HW QTL were segregating in the Meishan pigs. Moreover, haplotype comparisons between these dams suggest that within the refined QTL region, the recombination coldspot (~34 Mb) flanked by markers MCSE3F14 and UMNP1218 is unlikely to contain QTL genes. Two SNPs in the ACSL4 gene were identified and showed significant association with BFT and HW, but they and the known polymorphisms in the other two genes are unlikely to be causal mutations.

CONCLUSION

The candidate QTL regions have been greatly reduced and the QTL are most likely located downstream of the recombination coldspot. The segregation of SSCX QTL for BFT and HW within Meishan breed provides an opportunity for us to make effective use of Meishan chromosome X in crossbreeding. Further studies should attempt to identify the impact of additional DNA sequence (e.g. CNV) and expression variation in the three genes or their surrounding genes on these traits.

[Detecting selection signatures on X chromosome in pig through high density SNPs]

In the process of domestic pig breeding, many important economic traits were subject to strong artificial se-lection pressure. With the availability of high density single nucleotide polymorphism (SNP) markers in farm animals, selection occurring in those traits could be traced by detecting selection signatures on genome, and the genes experiencing selection can also be further mined based on selection signatures. Due to the special characteristic of X chromosome, many approaches of genetic analysis fitted for autosome are not plausible for X chromosome. Fortunately, detecting selection signature provides an effective tool to settle such situation. In this study, the Cross Population Extend Haplotype Homozygosity Test (XP-EHH) was implemented to identify selection signatures on chromosome X in three pig breeds (Landrace, Songliao, and Yorkshire) using high density SNPs, and the genes located within selection signature regions were revealed through bioinformatic analysis. In total, 29, 13, and 15 selection signature regions, with 3.59, 4.92, and 4.07 SNPs on average in each region, were identified in Landrace, Songliao, and Yorkshire, respectively. Some overlaps of selection signature regions were observed between Songliao and Landrace, and between Landrace and Yorkshire, while no overlaps between Yorkshire and Songliao were found. Bioinformatic analysis revealed that many genes in the selection signature regions were related to reproduction and immune traits, and some of them have not been reported in pigs, which might serve as important candidate genes in future study.

Porcine insulin receptor substrate 4 (IRS4) gene: cloning, polymorphism and association study

Using PCR and inverse PCR techniques we obtained a 4,498 bp nucleotide sequence FN424076 encompassing the complete coding sequence of the porcine insulin receptor substrate 4 (IRS4) gene and its proximal promoter. The 1,269 amino acid porcine protein deduced from the nucleotide sequence shares 92% identity with the human IRS4 and possesses the same domains and the same number of tyrosine phosphorylation motifs as the human protein. We detected substitution FN424076:g.96C<G in the promoter region that segregates in Meishan and a synonymous substitution FN424076:g.1829T<C in the coding sequence with allele C present only in Meishan. Linkage mapping placed the IRS4 gene at position 82 cM on the current USDA-USMARC linkage map of porcine chromosome X. Association analyses were performed on 555 animals of 12th-15th generation of the Meishan × Large White cross and showed that both SNPs were highly significantly associated with backfat depth (P=0.0005) and that the SNP FN424076:g1829T<C was also associated with loin depth (P=0.017). The Meishan alleles increased back fat depth and decreased loin depth. IRS4 can be considered a positional candidate gene for at least some of the QTL located at the centromeric region of porcine chromosome X.

Evaluations of boar gonad development, spermatogenesis with regard to semen characteristics, libido and serum testosterone levels based on large White Duroc x Chinese Erhualian crossbred boars

Chinese Erhualian pigs are known for prolificacy with distinct reproductive traits compared with Western commercial breeds. In this study, a four-generation intercross resource population was constructed using White Duroc boars and Chinese Erhualian sows as founder animals, and a total of 14 male reproductive traits were recorded in 411 F2/F3 boars including the testis and epididymis weights, the seminiferous tubular diameter and spermatogenesis at 60, 90 and 300 days of age, semen characteristics, serum testosterone concentration and libido level at 300 days of age. The White Duroc-Erhualian boars showed remarkable segregations in the traits measured except for the seminiferous tubular diameter and had high ratio (13.9%) of the abnormality of spermatogenesis, providing a good experimental population for detecting quantitative trait loci affecting these male reproductive traits. Furthermore, the correlations among nine male reproductive traits at 300 days of age indicated that the testis weight and the body weight were strongly correlated with the sperm production, supporting the two traits as important parameters for boar selection to increase sperm production and ultimately improve boar fertility. The libido level in the White Duroc-Erhualian boars that was evaluated by a new and easily recorded scoring system showed a significant correlation with serum testosterone concentration. Yet, both libido and serum testosterone concentration were not correlated with the sperm production. Results of this study provided new information on the male reproductive physiology and genetics in Chinese Erhualian and White Duroc boars.

Recombinational landscape of porcine X chromosome and individual variation in female meiotic recombination associated with haplotypes of Chinese pigs

BACKGROUND

Variations in recombination fraction (theta) among chromosomal regions, individuals and families have been observed and have an important impact on quantitative trait loci (QTL) mapping studies. Such variations on porcine chromosome X (SSC-X) and on other mammalian chromosome X are rarely explored. The emerging assembly of pig sequence provides exact physical location of many markers, facilitating the study of a fine-scale recombination landscape of the pig genome by comparing a clone-based physical map to a genetic map. Using large offspring of F1 females from two large-scale resource populations (Large White male symbol x Chinese Meishan female symbol, and White Duroc male symbol x Chinese Erhualian female symbol), we were able to evaluate the heterogeneity in theta for a specific interval among individual F1 females.

RESULTS

Alignments between the cytogenetic map, radiation hybrid (RH) map, genetic maps and clone map of SSC-X with the physical map of human chromosome X (HSA-X) are presented. The most likely order of 60 markers on SSC-X is inferred. The average recombination rate across SSC-X is of approximately 1.27 cM/Mb. However, almost no recombination occurred in a large region of approximately 31 Mb extending from the centromere to Xq21, whereas in the surrounding regions and in the Xq telomeric region a recombination rate of 2.8-3.3 cM/Mb was observed, more than twice the chromosome-wide average rate. Significant differences in theta among F1 females within each population were observed for several chromosomal intervals. The largest variation was observed in both populations in the interval UMNP71-SW1943, or more precisely in the subinterval UMNP891-UMNP93. The individual variation in theta over this subinterval was found associated with F1 females' maternal haplotypes (Chinese pig haplotypes) and independent of paternal haplotype (European pig haplotypes). The theta between UMNP891 and UMNP93 for haplotype 1122 and 4311 differed by more than fourteen-fold (10.3% vs. 0.7%).

CONCLUSIONS

This study reveals marked regional, individual and haplotype-specific differences in recombination rate on SSC-X. Lack of recombination in such a large region makes it impossible to narrow QTL interval using traditional fine-mapping approaches. The relationship between recombination variation and haplotype polymorphism is shown for the first time in pigs.

Endocrine regulation of the establishment of spermatogenesis in pigs

Somatic and germ cell maturation precedes the start of spermatogenesis and is coordinated, so efficient spermatogenesis will occur in the adults. The present study was conducted to evaluate endocrine regulation of germ and somatic cell homeostasis in the neonatal boar testis associated with the establishment of spermatogenesis. Testis tissue obtained from 3-, 5-, 7- and 14-day-old piglets were ectopically xenografted onto castrated, immunodeficient nude mice. Grafts were removed 22 weeks later and evaluated for growth and the establishment of spermatogenesis. Recipient mouse testosterone biosynthesis and follicle-stimulating hormone (FSH) concentrations were also assayed. Testis tissue graft growth was significantly greater in testis grafts from 3-day donor tissue when compared to all other ages; 5-, 7- and 14-day-old donor tissue weights were not significantly different at removal. Follicle-stimulating hormone concentrations in recipient mice supporting testis grafts from 5-, 7- and 14-day-old donor tissues did not differ and were similar to normal physiological levels in age-matched, intact nude mice. Serum FSH levels were significantly lower in recipient mice supporting testis grafts from 3-day-old donor tissue. Radioimmunoassay and biological assay indicated no differences in testosterone production by testis tissue grafts of varying donor age. Porcine testis tissue obtained from 3-, 5-, 7- and 14-day-old neonatal boars were all capable of producing round and elongate spermatids after 22 weeks of grafting, but testis grafts from 14-day-old donors had a significantly greater (eightfold) percentage of seminiferous tubules with spermatids compared to all other donor ages (p < 0.05). Cryopreservation did not affect the ability of testis tissue grafts to grow, produce testosterone or establish spermatogenesis when compared to controls (p < 0.05). Collectively, these data demonstrate intrinsic differences in the biological activity of germ and somatic cell populations during neonatal boar testis development associated with the establishment of spermatogenesis.

Studies on 5alpha-androst-16-en-3-one binding to porcine serum, plasma and testicular cytosolic fraction and to human serum

The present study evaluated whether a specific androstenone-binding protein is present in porcine and human serum, and in the cytosolic fraction of porcine testis. The binding of [(3)H]-androstenone to serum and testicular cytosol was measured in the absence (total binding) and presence (non-specific binding) of unlabelled androstenone. The optimization of the assay is described. As a part of the assay validation, the binding of [(3)H]-dihydrotestosterone ([(3)H]-DHT) to porcine and human serum was also examined. As expected, specific binding of [(3)H]-DHT was detected in human serum, but not in porcine serum. No specific androstenone-binding protein was detected, either in porcine or human serum, or in the cytosolic fraction of porcine testis. The amount of non-specific binding of [(3)H]-androstenone was slightly lower in porcine serum compared to human serum. Between-animal variations in [(3)H]-androstenone binding were studied in plasma samples from 15 animals with androstenone concentrations ranging from 1.1 to 23.1 ng/mL. Mean values+/-standard deviations of binding in these samples were 15.2+/-0.9% for total binding and 15.9+/-0.8% for non-specific bindings. Low between-animal variations indicate that androstenone binding does not affect androstenone accumulation in fat.

Mapping of QTL on chromosome X for fat deposition, muscling and growth traits in a wild boar x Meishan F2 family using a high-density gene map

Quantitative trait loci (QTL) for fat deposition, growth and muscling traits have been previously mapped on the basis of low-density linkage maps in a wild boar x Meishan F2family to the chromosome X region flanked by SW2456 and SW1943. Improved QTL resolution was possible using data for F2 animals with a marker density of 2.7 cM distance in the SW2456 to SW1943 region, including AR, SERPINA7 and ACSL4 as candidate genes. The resolution of the QTL scan was increased substantially, as evidenced by the higher F-ratio values for all QTL. Maxima of F-ratio values for fat deposition, muscling and growth traits were 28.6, 18.2 and 16.5 respectively, and those QTL positions accounted for 7.9%, 5.0% and 4.5% of the F2 phenotypic variance (VF2) respectively. QTL for fatness and growth and for most muscling traits mapped near ACSL4, with the exception of the QTL for ham traits that mapped proximally, in the vicinity of AR. An analysis performed separately for F2 male animals showed the predominant QTL affecting fat deposition traits (up to 13.6% VF2) near AR and two QTL for muscling traits (up to 9.9% VF2) mapped close to ACSL4. In the F2 female animals, QTL affecting muscling (up to 12.1% VF2) mapped at ACSL4 and SW2456, and QTL for fat deposition (10% VF2) and growth (up to 10.5% VF2) mapped at ACSL4.

Breed differences in clearance of porcine FSH in hypophysectomized rats

Extracts of anterior pituitary (AP) glands were infused i.v. into hypophysectomized male rats followed by sequential sampling of blood for 120 min. Determination of follicle-stimulating hormone (FSH) concentrations established that FSH from Chinese Meishan males decreased in the circulation of rats more slowly than FSH in extracts of AP from crossbred occidental pigs (P<0.003). Additionally, FSH from AP extracts of castrated males disappeared somewhat more slowly (P<0.06) than FSH from extracts of boars. Evaluation of FSH by bioassay and radioimmunoassay yielded similar concentrations in AP from Meishan and crossbred boars. Serum testosterone concentrations increased with time through 90 min after infusion of AP, but the rate of increase of testosterone was not related to amount of luteinizing hormone (LH) that was administered indicating LH receptor saturation. Unexpectedly, the rate of increase in testosterone was more rapid with AP extracts from boars than with extracts from castrated males. Observations from the current study imply structural alterations of FSH in the AP of Meishan males relative to crossbred males allowing sustained concentrations in the circulation, and this FSH possesses similar activation of the FSH receptor. The amount of LH in the AP extracts saturated the LH receptors of the hypophysectomized male rats, but some factor in extracts of boars differed from those of castrated males.

Detection of single nucleotide polymorphisms associated with ultrasonic backfat depth in a segregating Meishan x White Composite population

Multiple genomic scans have identified QTL for backfat deposition across the porcine genome. The objective of this study was to detect SNP and genomic regions associated with ultrasonic backfat. A total of 74 SNP across 5 chromosomes (SSC 1, 3, 7, 8, and 10) were selected based on their proximity to backfat QTL or to QTL for other traits of interest in the experimental population. Gilts were also genotyped for a SNP thought to influence backfat in the thyroxine-binding globulin gene (TBG) on SSC X. Genotypic data were collected on 298 gilts, divided between the F8 and F10 generations of the US Meat Animal Research Center Meishan resource population (composition, one-quarter Meishan). Backfat depths were recorded by ultrasound from 3 locations along the back at approximately 210 and 235 d of age in the F8 and F10 generations, respectively. Ultrasound measures were averaged for association analyses. Regressors for additive, dominant, and parent-of-origin effects of each SNP were calculated using genotypic probabilities computed by allelic peeling algorithms in GenoProb. The association model included the fixed effects of scan date and TBG genotype, the covariates of weight and SNP regressors, and random additive polygenic effects to account for genetic similarities between animals not explained by known genotypes. Variance components for polygenic effects and error were estimated using MTDFREML. Initially, each SNP was fitted (once with and once without parent-of-origin effects) separately due to potential multi-collinearity between regressions of closely linked markers. To form a final model, all significant SNP across chromosomes were included in a common model and were individually removed in successive iterations based on their significance. Across all analyses, TBG was significant, with an additive effect of approximately 1.2 to 1.6 mm of backfat. Three SNP on SSC3 remained in the final model even though few studies have identified QTL for backfat on this chromosome. Two of these SNP exhibited irregular parent-of-origin effects and may not have been detected in other genome scans. One significant SNP on SSC7 remained in the final, backward-selected model; the estimated effect of this marker was similar in magnitude and direction to previously identified QTL. This SNP can potentially be used to introgress the leaner Meishan allele into commercial swine populations.

Identification of functional candidate genes for body composition by expression analyses and evidencing impact by association analysis and mapping

This study aims to identify hepatic genes affecting traits related to muscularity and obesity by combining expression analyses, association studies, and gene mapping. Functional candidate genes with trait-associated expression were obtained by hybridising custom made application-specific cDNA microarrays with targets of discordant sib pairs of a porcine experimental population. Out of 238 genes addressed, nine genes were regulated by the factor>or=2 between the sib pairs. Differential gene expression was independently confirmed for selected genes by real time RT-PCR. Transcript levels of four genes (APOH, PEDF, SLCO1B3, TBG) were significantly different between the phenotype groups. Screening for trait associated markers within TBG and APOH by comparative sequencing of discordant sib pairs revealed a SNP at position nt 778 (A>C) (N229H) of TBG. No polymorphism in APOH was detected. Association analysis confirmed effects of TBG on carcass traits statistically. Allocating TBG to a QTL region on chromosome X revealed genetic evidence for the effect. Moreover, our results indicate that there are probably two polymorphisms segregating-one (N229H) altering binding capability of TBG and another still to be detected altering the transcription rate of TBG.