Verification of Candidate SNP Effects Reveals Two QTLs on BTA7 for Beef Marbling in Two Japanese Black Cattle Populations.

In our previous study, we used genome resequencing to detect all candidate polymorphisms within a quantitative trait loci (QTL) region for beef marbling reported previously at 10-30 Mbp on bovine chromosome 7, and we selected 6044 polymorphisms as candidate quantitative trait nucleotides (QTNs). In the present study, we aimed to identify quantitative trait genes (QTGs) and QTNs in this QTL region by verifying the effect of SNPs on beef marbling in two Japanese Black cattle populations using a Dynamic Array integrated fluidic circuit. In total, 96 selected SNPs were genotyped in 441 and 529 animals in Hyogo and Miyazaki cattle populations, respectively. The most significant p-values were detected in a SNP in a splice region of ALDH7A1 (SNP93_ALDH7A1; p = 3.46 × 10-5) in Hyogo cattle and a missense polymorphism of intercellular adhesion molecule-1 (ICAM1) (SNP37_ICAM1; p = 3.33 × 10-4) in Miyazaki cattle. Interestingly, SNP93_ALDH7A1 was not significant (p = 0.459) in Miyazaki cattle, and SNP37_ICAM1 showed a weakly significant association (p = 0.043) in Hyogo cattle. Thus, each population would likely have different QTGs and QTNs for beef marbling in the QTL region. In the Hyogo population, it was not possible to determine the accurate range of the linkage disequilibrium (LD) block in LD block analysis because of a strong LD structure throughout the assessed region. In Miyazaki cattle, however, an LD block containing SNP37_ICAM1 had a range of 15.8-16.1 Mbp, suggesting that QTNs would be located within this region. The functions of 19 genes in the LD block were investigated. ICAM1 is known to play an important role in adipocyte differentiation; given this function and the effect of amino acid substitution, SNP37_ICAM1 was identified as a promising candidate QTN for beef marbling. Further research on the effect of SNP37_ICAM1 on adipocyte differentiation is expected to provide insights into the mechanism underlying beef marbling formation.

Estimation of genetic parameters for carcass grading traits, image analysis traits, and monounsaturated fatty acids in Japanese Black cattle from Hyogo Prefecture.

Genetic parameters for carcass grading traits, image analysis traits, and monounsaturated fatty acid (MUFA) percentages were estimated in 29,942 Japanese Black cattle from Hyogo Prefecture. The analyzed traits included five carcass grading traits, two image analysis traits, fat area ratio and fineness index, and two MUFA traits, one measured in intermuscular fat using near-infrared spectroscopy (NIRS) and the other in intramuscular fat using gas chromatography (GC). The heritability estimates of image analysis traits and MUFA were moderate to high, ranging from 0.395 to 0.740, and it was considered that they could be improved simultaneously with carcass grading traits because no severe genetic antagonism was observed. Although the heritability of the NIRS-based intermuscular MUFA was slightly lower than that of the GC-based intramuscular MUFA, the genetic correlation between the two methods was as high as 0.804. These results indicate that the NIRS method can be used as an alternative evaluation procedure to predict MUFA in intramuscular fat in the longissimus muscle.

Detection of candidate polymorphisms around the QTL for fat area ratio to rib eye area on BTA7 using whole-genome resequencing in Japanese Black cattle.

In our previous study, we performed genome-wide association study (GWAS) to identify the genomic region associated with Fat area ratio to rib eye area (FAR) and detected a candidate in BTA7 at 10-30 Mbp. The present study aims to comprehensively detect all polymorphisms in the candidate region using whole-genome resequencing data. Based on whole-genome resequencing of eight animals, we detected 127,090 polymorphisms within the region. Of these, 31,945 were located within the genes. We further narrowed the polymorphisms to 6,044 with more than five allele differences between the high and low FAR groups that were located within 179 genes. We subsequently investigated the functions of these genes and selected 170 polymorphisms in eight genes as possible candidate polymorphisms. We focused on SLC27A6 K81M as a putative candidate polymorphism. We genotyped the SNP in a Japanese Black population (n = 904) to investigate the effect on FAR. Analysis of variance revealed that SLC27A6 K81M had a lower p-value (p = .0009) than the most significant SNP in GWAS (p = .0049). Although only SLC27A6 K81M was verified in the present study, subsequent verification of the remaining candidate genes and polymorphisms could lead to the identification of genes and polymorphisms responsible for FAR.

LH and testosterone secretions in response to GnRH challenge in pubertal Japanese Black beef bulls with normal and abnormal semen.

Plasma luteinizing hormone (LH) and testosterone concentrations were examined in Japanese Black beef bulls with normal and abnormal semen in response to gonadotropin releasing hormone (GnRH) challenge at the start (10 months) and completion (20 months) of puberty. Bulls with normal semen had higher testosterone concentrations after GnRH treatment at 20 months than they did at 10 months, while LH concentrations did not differ between the two age groups. LH and testosterone concentrations were not different between bulls with normal and abnormal semen at 20 months. Thus, testosterone secretions in response to the GnRH challenge were higher for bulls with normal semen at pubertal completion compared to bulls at the start of puberty, but responsiveness of LH to GnRH and of testosterone to the LH increment was not altered in bulls with abnormal semen.

Relationships of plasma insulin-like peptide 3, testosterone, inhibin, and insulin-like growth factor-I concentrations with scrotal circumference and testicular weight in Japanese Black beef bull calves.

This study was conducted to clarify the relationships of plasma concentrations of insulin-like peptide 3 (INSL3), testosterone, inhibin, and insulin-like growth factor-I (IGF-I) with scrotal circumference and testicular weight in Japanese Black beef bull calves (n = 20), from birth to pre-puberty. Monthly blood sampling (0 to 7 months) and scrotal circumference measurements (0 to 7 months) were performed. Testicular weight was recorded immediately after castration at 7 months. Plasma INSL3, testosterone, inhibin, and IGF-I concentrations were measured either by enzyme immunoassay or time-resolved fluorescence immunoassay. The correlation coefficients of these hormonal concentrations with scrotal circumference were significant (P < 0.0001) and it was higher for INSL3 (r = 0.647) than for testosterone (r = 0.597), IGF-I (r = 0.400), and inhibin (r = -0.453). Calves with heavier testes (> 60 g) at castration (7 months) had higher (P < 0.05) plasma INSL3 (from 3 to 7 months) and inhibin (from 1 to 4 months) concentrations than those with lighter testes (< 60 g). The calves with heavier testes at castration had larger (P < 0.05) scrotal circumference than those with lighter testes from 3 to 7 months. In conclusion, blood INSL3 concentrations may be the best functional indicator among the hormones analyzed for determining total testicular volume during pre-puberty in bull calves. In addition, inhibin and INSL3 concentrations in early calfhood may be functional predictors for testicular weight at pre-puberty.

Pool-based genome-wide association study identified novel candidate regions on BTA9 and 14 for oleic acid percentage in Japanese Black cattle.

Fatty acid composition is an important indicator of beef quality. The objective of this study was to search the potential candidate region for fatty acid composition. We performed pool-based genome-wide association studies (GWAS) for oleic acid percentage (C18:1) in a Japanese Black cattle population from the Hyogo prefecture. GWAS analysis revealed two novel candidate regions on BTA9 and BTA14. The most significant single nucleotide polymorphisms (SNPs) in each region were genotyped in a population (n = 899) to verify their effect on C18:1. Statistical analysis revealed that both SNPs were significantly associated with C18:1 (p = .0080 and .0003), validating the quantitative trait loci (QTLs) detected in GWAS. We subsequently selected VNN1 and LYPLA1 genes as candidate genes from each region on BTA9 and BTA14, respectively. We sequenced full-length coding sequence (CDS) of these genes in eight individuals and identified a nonsynonymous SNP T66M on VNN1 gene as a putative candidate polymorphism. The polymorphism was also significantly associated with C18:1, but the p value (p = .0162) was higher than the most significant SNP on BTA9, suggesting that it would not be responsible for the QTL. Although further investigation will be needed to determine the responsible gene and polymorphism, our findings would contribute to development of selective markers for fatty acid composition in the Japanese Black cattle of Hyogo.

A genome-wide association study for fat-related traits computed by image analysis in Japanese Black cattle.

The objective of this study was to identify genomic regions associated with fat-related traits using a Japanese Black cattle population in Hyogo. From 1836 animals, those with high or low values were selected on the basis of corrected phenotype and then pooled into high and low groups (n = 100 each), respectively. DNA pool-based genome-wide association study (GWAS) was performed using Illumina BovineSNP50 BeadChip v2 with three replicate assays for each pooled sample. GWAS detected that two single nucleotide polymorphisms (SNPs) on BTA7 (ARS-BFGL-NGS-35463 and Hapmap23838-BTA-163815) and one SNP on BTA12 (ARS-BFGL-NGS-2915) significantly affected fat percentage (FAR). The significance of ARS-BFGL-NGS-35463 on BTA7 was confirmed by individual genotyping in all pooled samples. Moreover, association analysis between SNP and FAR in 803 Japanese Black cattle revealed a significant effect of SNP on FAR. Thus, further investigation of these regions is required to identify FAR-associated genes and mutations, which can lead to the development of DNA markers for marker-assisted selection for the genetic improvement of beef quality.

Effects of acrosomal conditions of frozen-thawed spermatozoa on the results of artificial insemination in Japanese Black cattle.

The purposes of this study were to examine the relationship between male artificial insemination (AI) fertility and sperm acrosomal conditions assessed by new and conventional staining techniques and to identify possible reproductive dysfunctions causing low conception rates in AI using frozen-thawed spermatozoa with poor acrosomal conditions in Japanese Black bulls. We investigated individual differences among bulls in the results concerning (1) acrosomal conditions of frozen-thawed spermatozoa as assessed by not merely peanut agglutinin-lectin staining (a conventional staining technique) but also immunostaining of acrosomal tyrosine-phosphorylated proteins (a new staining technique), (2) routine AI using frozen-thawed spermatozoa as assessed by pregnancy diagnosis, (3) in vivo fertilization of frozen-thawed spermatozoa and early development of fertilized eggs as assessed by superovulation/AI-embryo collection tests and (4) in vitro fertilization of frozen-thawed spermatozoa with oocytes. The percentages of frozen-thawed spermatozoa with normal acrosomal conditions assessed by the abovementioned staining techniques were significantly correlated with the conception rates of routine AI, rates of transferable embryos in superovulation/AI-embryo collection tests and in vitro fertilization rates. These results are consistent with new suggestions that the distribution of acrosomal tyrosine-phosphorylated proteins as well as the acrosomal morphology of frozen-thawed spermatozoa are AI fertility-associated markers that are valid for the prediction of AI results and that low conception rates in AI using frozen-thawed spermatozoa with poor acrosomal conditions result from reproductive dysfunctions in the processes between sperm insemination into females and early embryo development, probably failed fertilization of frozen-thawed spermatozoa with oocytes.

A novel mutation of the bovine EDA gene associated with anhidrotic ectodermal dysplasia in Holstein cattle.

Anhidrotic ectodermal dysplasia (EDA) is a genetic disease characterized by the absence or hypoplasia of hair, teeth and eccrine sweat glands that has been reported in humans, the tabby mouse mutants, cattle and dogs. The EDA gene on the X chromosome encodes a protein, ectodysplasin-A (EDA), which is responsible for EDA. Here we describe a novel mutation of the EDA gene in which a 19 bp deletion in exon 1 in male Holstein calves demonstrated the phenotypic features of EDA. The dam and the grand-dam of the affected calves were heterozygous for this deletion. It is assumed that this deletion close to the start codon confuses all transcripts, and leads to the complete loss of pleiotropic functions of the bovine EDA gene. These results suggest that this mutation might be useful as animal models for the investigation of the pathogenic mechanisms of the anhidrotic ectodermal dysplasia.