Nucleotide polymorphisms and the 5'-UTR transcriptional analysis of the bovine growth hormone secretagogue receptor 1a (GHSR1a) gene.

Growth hormone secretagogue receptor 1a (GHSR1a) mediates the different actions of its endogenous ligand, ghrelin. Ghrelin-GHSR is involved in many important functions that include growth hormone secretion and food intake. We evaluated the haplotype variety and characterized the microsatellite ((TG)(n) , 5'-UTR) and nucleotide polymorphisms of the bovine GHSR1a gene. The nucleotide sequencing of this gene (∼6 kb) revealed 47 single nucleotide polymorphisms (SNPs), four indels and the microsatellite ((GTTT)(n) , Intron 1). The 19 haplotypes were constructed from all nucleotide viability patterns and were divided into three major groups. Four SNPs (L24V, nt456(G>A), D191N and nt667(C>T)) and DelR242 in Exon 1 and a haplotype block of approximately 2.2 kb (nt667(C>T) ∼ nt2884 (A>G)) were found in Bos taurus breeds. Breed differences in allele frequencies of the two microsatellites, nt-7(C>A), L24V, and DelR242 loci were found (P < 0.005). A DelR242 was found in the Japanese Shorthorn (frequency: ∼ 0.44), Japanese Brown, five European cattle breeds, the Philippine native cattle, but none detected in the Japanese Black or the Mishima island cattle. Additionally, 5'-rapid amplification of cDNA ends and RT-PCR analyses revealed that there were two different kinds of transcripts: spliced, without a microsatellite within 5'-UTR (GHSR1a); and non-spliced, with the microsatellite (GHSR1b).

The T allele at the g.1471620G>T in the EDG1 gene associated with high marbling in Japanese Black cattle is at a low frequency in breeds not selected for marbling.

Our previous study detected a single nucleotide polymorphism (SNP), g.1471620G>T, in the 5' flanking region of the endothelial differentiation sphingolipid G-protein-coupled receptor 1 (EDG1) gene, which has been considered as a positional functional candidate for the gene responsible for marbling, and showed association of the g.1471620G>T SNP with marbling in Japanese Black beef cattle. In the present study, we investigated the allele frequency distribution of the g.1471620G>T SNP among the 5 cattle breeds, Japanese Black, Japanese Brown, Japanese Short Horn, Holstein, and Brown Swiss breeds. The T allele at the g.1471620G>T SNP associated with high marbling was found at high frequency in Japanese Black breed that has been subjected to a strong selection for high marbling, while the allele was absent or at very low frequencies in the other breeds that have not been strongly selected for high marbling. Based on this finding, we hypothesized that the pressure of the strong selection for high marbling in Japanese Black breed has increased the frequency of the T allele at the g.1471620G>T SNP in the EDG1.

Cross-breed comparisons identified a critical 591-kb region for bovine carcass weight QTL (CW-2) on chromosome 6 and the Ile-442-Met substitution in NCAPG as a positional candidate.

BACKGROUND: Growth-related traits have been mapped on bovine chromosome 6 (BTA 6) in various bovine breed populations. We previously mapped a significant quantitative trait locus (QTL) for carcass and body weight (CW-2) between 38 and 55 cM on BTA 6 using a Japanese Black half-sib family. Additional QTL mapping studies detected four QTL for body or carcass weight that overlapped with CW-2 in Japanese Black and Japanese Brown half-sib families. To map the region in greater detail, we applied cross-breed comparisons of haplotypes that have been shown to be powerful in canine. RESULTS: We used 38 microsatellite markers to search for a shared Q (increasing carcass and/or body weight) haplotype within the 17-cM CW-2 region among five sires. Linkage disequilibrium mapping using maternal alleles of the offspring showed that an 815-kb shared Q haplotype was associated with body or carcass weight in both breeds. The addition of 43 single nucleotide polymorphism (SNP) markers narrowed the region to 591 kb containing 4 genes. The SNP changing Ile-442 to Met in NCAPG (chromosome condensation protein G) was significantly associated with carcass weight (p < 1.2 x 10-11) in a large Japanese Black population as well as in the five families. The Q allele of the SNP was also associated with a larger longissimus muscle area and thinner subcutaneous fat thickness in steers of all five families, indicating that the CW-2 locus is pleiotropic and favorable for marker-assisted selection of beef cattle. CONCLUSION: A 591-kb critical region for CW-2 was identified. The SNP changing Ile-442 to Met in NCAPG (chromosome condensation protein G) can be used as a positional candidate of CW-2 for marker-assisted selection.