Characterization of porcine autism susceptibility candidate 2 as a candidate gene for the number of corpora lutea in pigs

In a previous study, we mapped two quantitative trait loci (QTL) approximately 50cM apart, both influencing the number of corpora lutea in pigs on chromosome 3. One locus included functional candidate genes for proteins related to specific aspects of fertility, such as the follicle-stimulating hormone receptor and the luteinizing hormone/choriogonadotropin receptor. However, specific genes related to the second locus have not yet been identified. This study aims to identify another candidate gene influencing the number of corpora lutea in pigs. Using 12 polymorphic markers, we fine-mapped a narrow region of pig chromosome 3 that had been shown to contain a QTL for corpora lutea. In the critical region, only 1 gene, autism susceptibility candidate 2 (AUTS2), was identified as a positional candidate. Our results demonstrate that the porcine AUTS2 gene consists of 19 exons with a complete open reading frame of 3768bp encoding an AUTS2 protein of 1256 amino acids. We screened the whole coding sequence and parts of the untranslated region for polymorphisms in an F(2) population of Duroc×Meishan crosses. We found 1 ins/del and 7 single nucleotide polymorphisms (SNP), including 2 nonsynonymous variants, c.943C>T in exon 7 and c.2828C>T in exon 19, resulting in P315S and A943V, respectively. The SNP c.943C>T within a proline-rich domain was genotyped in several breeds; the C allele occurred in all breeds, whereas the T allele occurred only in Meishan pigs. Using in situ hybridization, the mRNA expression of the AUTS2 gene was observed on granulosa cells in the porcine ovary and thus may be associated with hormone sensitivity.     

The porcine gonadotropin-releasing hormone receptor gene (GNRHR): genomic organization, polymorphisms, and association with the number of corpora lutea.

The interaction of gonadotropin-releasing hormone (GNRH) and its receptor (GNRHR) is critical in the endocrine regulation of reproduction. The gene (GNRHR) encoding the receptor has been mapped to porcine chromosome 8. There is evidence for three quantitative trait loci (QTL) influencing ovulation rate on this chromosome. We obtained an almost complete sequence (3993 bp, excluding intron 1) of the porcine GNRHR gene using PCR-based comparative genomic walking and inverse genomic walking approaches. Twelve polymorphisms were detected by sequencing of pooled DNA of Chinese Taihu and European Large White pigs, including 7 base substitutions and 5 insertions-deletions (indels). A F2 population of Meishan x European Large White pigs was genotyped for a TG indel in the promoter region, and a C/G substitution in the 3' UTR (untranslated region). A significant association of the C/G substitution with number of corpora lutea at first parity was observed.     

Genomic sequence analysis of a potential QTL region for fat trait on pig chromosome 6

On pig chromosome 6, the SW71 microsatellite is located in the region corresponding to several quantitative trait loci (QTL), such as those for intramuscular fat content and for body weight at 4 weeks of age. The genomic sequence of approximately 909 kb was obtained from seven BAC clones encompassing the SW71 region corresponding to human 18q11.21-q11.22. By searching the NCBI GenBank using BLASTX and BLASTN, this 909-kb segment was found to contain eight genes, RAB31, TXNDC2, VAPA, APCDD1, NAPG, FAM38B, C18orf30, and C18orf58, and one putative gene (DN119777). The average G + C content in the sequence of this contig was 45.75% and 33 CpG islands were detected. CpG islands were scattered throughout the region in which most of the putative genes were located. Dense CpG islands of approximately 840 bp were observed, including within the 5' UTR and exon 1 of the orthologs of the RAB31, VAPA, APCDD1, and NAPG genes. Comparative analysis of conserved segments of six species showed that K(a)/K(s) ratios of the TXNDC2 gene in collinear and rearranged segments were significantly different at 4.1 and 1.3, respectively. In conclusion, we demonstrated the genomic organization of pig chromosome 6, including the gene order surrounding SW71, which provides important information for comparative mapping. Moreover, the genes revealed in this study may be positional candidate genes associated with QTL on chromosome 6 that affect fat deposition in pigs.     

Interrelationships of porcine X and Y chromosomes with pituitary gonadotropins and testicular size

Endocrine and testicular responses to unilateral castration on 1, 10, 56, or 112 days of age were characterized in 132 Chinese Meishan (MS) x White composite (WC) crossbred boars in which testicular size associates with a quantitative trait locus (QTL) on X chromosome. At 220 days of age, testicles of boars unilaterally castrated on Day 1 or 10 weighed more and had greater total daily sperm production (DSP) than one testicle of bilaterally intact boars (P < 0.05); compensation did not double these two responses. Boars with MS alleles at the X chromosome QTL had smaller testicles, darker colored parenchyma, and lower total DSP than boars with WC alleles (P < 0.05). The MS alleles engendered greater (P < 0.05) plasma FSH and LH during puberty than WC alleles. Plasma FSH increased (P < 0.05) within 48 h of unilateral castration on Days 1, 10, and 56. Subsequent increases occurred earlier during puberty (P < 0.05) after unilateral castration at younger ages than after unilateral castration at older ages. Pubertal increases in plasma FSH and LH were greater (P < 0.05) in boars with MS alleles than in those with WC alleles for the X chromosome QTL. Breed of Y chromosome had no effect on testicular traits, FSH, testosterone, or estrone. For LH, boars with an MS Y chromosome had greater (P < 0.01) plasma LH across all ages than boars with a WC Y chromosome. We conclude that a gene or groups of genes that reside on the porcine X chromosome regulate testicular development and pubertal gonadotropin concentrations.     

Isolation and molecular characterization of the porcineSLC6A14 gene excludes it as a candidate gene for fat deposition and growth

The gene encoding solute carrier family 6 member 14 (SLC6A14) has been considered as a candidate gene affecting human obesity. In this study, full-length cDNA (2237 bp) and DNA sequence (24 541 bp) of the porcineSLC6A14 gene were isolated. The porcineSLC6A14 cDNA contains a 5’-untranslated region of 57 bp, a 3’-untranslated region of 254 bp, and an open reading frame of 1926 bp, encoding a deduced protein of 642 amino acids with a molecular mass of 72. 475 kDa and an isoelectric point of 7.82. The genomic structure of the porcineSLC6A14 gene is similar to mammalian orthologs, particularly in terms of exon size and exon/intron boundaries. It comprises 14 exons and 13 introns. A semi-quantitative RT-PCR showed that the porcineSLC6A14 mRNA expression was tissue-specific. FourSLC6A14 single-nucleotide polymorphisms (SNPs) were identified, and 3 informative SNPs were chosen for genotyping in a White Duroc × Erhualian resource population with phenotype data of growth and fatness traits. The association analysis showed that the c.1438 G>A nonsynonymous polymorphism was associated with birth weight and 21-day body weight (P<0.05), while g.7944 A>T was associated with 46-day body weight. Linkage and radiation hybrid mapping assignedSLC6A14 to a region aroundSW1522 on SSCXp13, which did not fall in the confidence interval of the quantitative trait locus (QTL) for growth and fatness traits on SSCX in the resource population. These results indicate thatSLC6A14 is not a positional candidate gene for the QTL affecting fatness and growth traits in pigs.     

Organization of the mouse microfibril-associated glycoprotein-2 (MAGP-2) gene

A 1.4-kb EST clone encoding mouse microfibril-associated glycoprotein-2 (MAGP-2), identified by its similarity with the reported human cDNA, was used to screen a mouse 129 genomic bacterial artificial chromosome (BAC) library. The mouse gene contains 10 exons spanning 16 kb, located on the distal region of Chromosome (Chr) 6. The exons range in size from 24 to 963 bp, with the ATG located in exon 2. The tenth and largest exon contains 817 bp of 3′ untranslated sequence, including a B2 repetitive element. Northern analysis demonstrates abundant expression of MAGP-2 mRNA in skeletal muscle, lung, and heart. Sequence analysis of additional cDNA clones suggests that the two mRNA forms of MAGP-2 in the mouse arise from alternative polyadenylation site usage. The promoter does not contain an obvious TATA box, and the sequence surrounding the start site does not conform to the consensus for an initiator promoter element. Additionally, the mouse promoter contains 22 copies of a CT dinucleotide repeat sequence located ∼155 bp 5′ to exon 1. Received: 27 August 1999 / Accepted: 2 November 1999     

Identification and characterization of a new allele for the beta subunit of follicle-stimulating hormone in Chinese pig breeds

During evaluation of follicle-stimulating hormone-beta (FSHB) expression in anterior pituitary glands by an RNase protection assay (RPA), the expected fragment of 205 nucleotides at positions 759-963 was not detected in one boar that had moderate plasma and pituitary FSH concentrations. After subcloning and sequencing, mRNA from this boar lacked an 11-bp fragment (5'-CATTTGGAAAC-3') at nucleotide positions 807-817 of the 3'-untranslated region (3'-UTR, D allele). Wild-type FSHB (WT allele) was present in pituitary RNA and genomic DNA in both Meishan (MS) and White Composite (WC) pigs; whereas the D allele was present only in MS pigs (P < 0.01; 5/6 MS vs. 0/6 WC). Also, we found the D allele in five other Chinese breeds but absent in ten American Landrace, 11 Yorkshire and 17 Berkshire pigs. Additionally, the D allele had one silent nucleotide change in the coding region plus six, single nucleotide changes in the 3'-UTR.     

Localization of Period 1 mRNA in the ruminant oocyte and investigations of its role in ovarian function

The clock gene Period 1 (Per1) may be a prolificacy gene, because it localized to the mouse oocyte and Per1-null drosophila shed fewer eggs. Because Per1 mapped to a region of mouse chromosome 11 syntenic to bovine chromosome 19 where a quantitative trait loci (QTL) for ovulation rate existed, we hypothesized that Per1 influenced folliculogenesis and ovulation rate in ruminants. Ovarian cortex was collected at slaughter on days 5, 12, 15, 17, and 20 after estrus for real-time RT-PCR evaluation of Per1 mRNA expression in Dorset (n = 18), Romanov (n = 10), Romanov/Dorset (n = 21), and Composite (n = 22) ewes. Ovarian cortex was also collected from cows selected for increased ovulation rate (n=37) or unselected controls (n = 28) on days 4, 5, and 6 of the estrous cycle for in situ hybridization and real-time RT-PCR. To examine the role of Per1 in early follicular development, ovarian cortex from neonatal calves (n = 5) was cultured for 10 days and Per1 mRNA levels were measured on day 0 and on day 10 of culture. The primers generated a 483bp amplicon with 100% sequence homology to bovine RIGUI-like protein (Per1). In silico mapping of this sequence placed Per1 on bovine chromosome 19; however, it was 20cM from the QTL. Per1 mRNA expression was unaffected by prolificacy, day of the cycle, or pregnancy status in ewes or cows. The riboprobe hybridized to oocytes of bovine preantral and antral follicles. In bovine ovarian cortical cultures on day 0, the tissue contained mostly primordial follicles (5.6+/-0.6 follicles/section); however, after 10 days in culture, the number of primordial follicles per section decreased (0.5 follicles/section) and the number of primary follicles increased as follicles activated (day 0 = 0.5+/- 0.6 versus day 10 = 10.4 +/-0.6 primary follicles/section; P < 0.001). Per1 mRNA did not change over time in culture. We conclude that Per1 mRNA is expressed by ruminant oocytes in preantral and antral follicles; however, its physiological role in mammalian ovarian function remains to be elucidated.