Limits...
Overdominance effect of the bovine ghrelin receptor (GHSR1a)-DelR242 locus on growth in Japanese Shorthorn weaner bulls: heterozygote advantage in bull selection and molecular mechanisms.

Komatsu M, Sato Y, Negami T, Terada T, Sasaki O, Yasuda J, Arakawa A, Yoshida C, Takahashi H, Malau-Aduli AE, Suzuki K, Shimizu K - G3 (Bethesda) (2014)

Bottom Line: In this study, we found a significant sex difference in the frequency of the 3R allele.Statistical analysis revealed a significant overdominance effect of the DelR242 locus on growth in Japanese Shorthorn weaner bulls.However, additive/dominance/overdominance effects of the 3R allele on carcass traits in adult steers and dams were not significant.

View Article: PubMed Central - PubMed

Affiliation: Animal Breeding Research Group, NARO Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki 305-0901, Japan mkomatsu@affrc.go.jp.

Show MeSH

Related in: MedlinePlus

Summary of local LD and haplotype blocks in a 5.8-kb genomic region that surrounds the DelR242 locus of GHSR1a. (A) Thirty nucleotide variations (26 SNPs, 3 indels including Del242 and the intron 1 microsatellite) [(GTTT)5 or (GTTT)6: (GTTT)5 > 6] of 23 individuals (accession no. AB492155–AB492177). (B and C) Three nucleotide variations (nt-7(C > A), nt456(G > A), and DelR242) of 95 sires and 540 half sibs. LD plot generated in Haploview (Barrett et al. 2005) indicates r2 values between pairs of SNPs multiplied by 100; white, r2 = 0; shades of gray, 0 < r2 < 1; black, r2 = 1. The nt-7(C > A), nt456(G > A), and DelR242 loci are indicated with black squares. Transcription start regions are shown with black arrows. 5′UTR-(TG)n, 5′UTR microsatellite.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4321035&req=5

fig1: Summary of local LD and haplotype blocks in a 5.8-kb genomic region that surrounds the DelR242 locus of GHSR1a. (A) Thirty nucleotide variations (26 SNPs, 3 indels including Del242 and the intron 1 microsatellite) [(GTTT)5 or (GTTT)6: (GTTT)5 > 6] of 23 individuals (accession no. AB492155–AB492177). (B and C) Three nucleotide variations (nt-7(C > A), nt456(G > A), and DelR242) of 95 sires and 540 half sibs. LD plot generated in Haploview (Barrett et al. 2005) indicates r2 values between pairs of SNPs multiplied by 100; white, r2 = 0; shades of gray, 0 < r2 < 1; black, r2 = 1. The nt-7(C > A), nt456(G > A), and DelR242 loci are indicated with black squares. Transcription start regions are shown with black arrows. 5′UTR-(TG)n, 5′UTR microsatellite.

Mentions: We analyzed local LD and common haplotype patterns in a 5.8-kb genomic region around the DelR242 locus in GHSR1a. We found a haplotype block of approximately 2 kb from the nt667(C > T) in exon 1 to the nt2884 (A > G) in intron 1 (Figure 1A). In addition, local LD analysis clearly showed that the DelR242 locus is not in LD with nt-7(C > A), the 5′UTR-(TG)n, and the other 27 loci within GHSR1a, except for the nt456(G > A) locus. DelR242 is in LD with the nt456(G > A) locus (r2 = 1) (Figure 1 A). The strong LD between DelR242 and nt456(G > A) was confirmed in 95 sires and 540 half sibs (Figures 1, B and C). It was observed that nt70(C > G), nt580(G > A), nt667(C > T), and intron 1 microsatellite were fixed for the homozygous genotypes [C/C, G/G, C/C, and (GTTT)5/(GTTT)5, respectively] in the 540 half sibs. The 15 markers in intron 1 were considered as fixed for homozygotes on the basis of the result of local LD analysis in Japanese Shorthorn cattle (Figure 1). nt456(G > A) is a synonymous nucleotide substitution in exon 1.


Overdominance effect of the bovine ghrelin receptor (GHSR1a)-DelR242 locus on growth in Japanese Shorthorn weaner bulls: heterozygote advantage in bull selection and molecular mechanisms.

Komatsu M, Sato Y, Negami T, Terada T, Sasaki O, Yasuda J, Arakawa A, Yoshida C, Takahashi H, Malau-Aduli AE, Suzuki K, Shimizu K - G3 (Bethesda) (2014)

Summary of local LD and haplotype blocks in a 5.8-kb genomic region that surrounds the DelR242 locus of GHSR1a. (A) Thirty nucleotide variations (26 SNPs, 3 indels including Del242 and the intron 1 microsatellite) [(GTTT)5 or (GTTT)6: (GTTT)5 > 6] of 23 individuals (accession no. AB492155–AB492177). (B and C) Three nucleotide variations (nt-7(C > A), nt456(G > A), and DelR242) of 95 sires and 540 half sibs. LD plot generated in Haploview (Barrett et al. 2005) indicates r2 values between pairs of SNPs multiplied by 100; white, r2 = 0; shades of gray, 0 < r2 < 1; black, r2 = 1. The nt-7(C > A), nt456(G > A), and DelR242 loci are indicated with black squares. Transcription start regions are shown with black arrows. 5′UTR-(TG)n, 5′UTR microsatellite.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4321035&req=5

fig1: Summary of local LD and haplotype blocks in a 5.8-kb genomic region that surrounds the DelR242 locus of GHSR1a. (A) Thirty nucleotide variations (26 SNPs, 3 indels including Del242 and the intron 1 microsatellite) [(GTTT)5 or (GTTT)6: (GTTT)5 > 6] of 23 individuals (accession no. AB492155–AB492177). (B and C) Three nucleotide variations (nt-7(C > A), nt456(G > A), and DelR242) of 95 sires and 540 half sibs. LD plot generated in Haploview (Barrett et al. 2005) indicates r2 values between pairs of SNPs multiplied by 100; white, r2 = 0; shades of gray, 0 < r2 < 1; black, r2 = 1. The nt-7(C > A), nt456(G > A), and DelR242 loci are indicated with black squares. Transcription start regions are shown with black arrows. 5′UTR-(TG)n, 5′UTR microsatellite.
Mentions: We analyzed local LD and common haplotype patterns in a 5.8-kb genomic region around the DelR242 locus in GHSR1a. We found a haplotype block of approximately 2 kb from the nt667(C > T) in exon 1 to the nt2884 (A > G) in intron 1 (Figure 1A). In addition, local LD analysis clearly showed that the DelR242 locus is not in LD with nt-7(C > A), the 5′UTR-(TG)n, and the other 27 loci within GHSR1a, except for the nt456(G > A) locus. DelR242 is in LD with the nt456(G > A) locus (r2 = 1) (Figure 1 A). The strong LD between DelR242 and nt456(G > A) was confirmed in 95 sires and 540 half sibs (Figures 1, B and C). It was observed that nt70(C > G), nt580(G > A), nt667(C > T), and intron 1 microsatellite were fixed for the homozygous genotypes [C/C, G/G, C/C, and (GTTT)5/(GTTT)5, respectively] in the 540 half sibs. The 15 markers in intron 1 were considered as fixed for homozygotes on the basis of the result of local LD analysis in Japanese Shorthorn cattle (Figure 1). nt456(G > A) is a synonymous nucleotide substitution in exon 1.

Bottom Line: In this study, we found a significant sex difference in the frequency of the 3R allele.Statistical analysis revealed a significant overdominance effect of the DelR242 locus on growth in Japanese Shorthorn weaner bulls.However, additive/dominance/overdominance effects of the 3R allele on carcass traits in adult steers and dams were not significant.

View Article: PubMed Central - PubMed

Affiliation: Animal Breeding Research Group, NARO Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki 305-0901, Japan mkomatsu@affrc.go.jp.

Show MeSH
Related in: MedlinePlus