Phylogeographic Analysis of Madagascan Goats Using mtDNA Control Region and SRY Gene Sequences.

In the present study, we estimated the genetic diversity and relationships, as well as the propagation routes, of Madagascan goats using mtDNA control region and SRY gene sequences. The mtDNA sequences of 40 Madagascan goats revealed 10 haplotypes and a quite low nucleotide diversity (0.0014), suggesting a founder and/or bottleneck effect resulting from goat migration to Madagascar island. The analysis of sequences identical to Madagascan haplotypes indicated close genetic relationships between goats from Madagascar and Africa. Sequence analysis of the SRY gene in 40 male Madagascan goats revealed two haplotypes: Y1A (45%) and Y2A (55%). The paternal result indicated genetic influences from Africa, South Asia, and the Near East proximal to Madagascar. The analyses of the mtDNA control region and SRY gene sequences suggested a genetic relationship between Africa and Madagascar. Moreover, SRY sequences indicated influences from South Asia and the Near East. These phylogenetic results provide important genetic information for elucidating the propagation routes of Madagascan goats.

Comprehensive genotyping analysis of single nucleotide polymorphisms responsible for beef marbling in Japanese Black cattle.

BACKGROUND: Beef marbling is considered a desirable trait in the meat industry. Therefore, understanding the genetic factors that cause marbling is important. Previously, we performed a genome-wide association study to examine genetic factors associated with beef marbling in Japanese Black cattle and identified a candidate region between 10-30 Mbp on chromosome 7. We verified the effect of the SNPs in this region on beef marbling using linkage disequilibrium block analysis. We narrowed down the candidate region to a range of 15.8-16.1 Mbp. In this study, we comprehensively detected all of the SNPs in this region and verified their effects on beef marbling. RESULTS: Genome resequencing using four animals exhibiting high beef marbling standard (BMS) and four with low BMS revealed a total of 1,846 polymorphisms within the candidate region. Based on the annotation, we selected 13 SNPs exhibiting a moderate impact, as no high-impact SNPs were detected. All of the SNPs represented missense polymorphisms and were located in the following seven genes: RDH8, ANGPTL6, DNMT1, MRPL4, ICAM1, ICAM3, and ICAM5. Finally, we determined the effects of these SNPs on the BMS of a Japanese Black cattle population (n = 529). Analysis of variance revealed that the five SNPs were located in genes encoding the intercellular adhesion molecules (ICAM1, ICAM3, and ICAM5), and showed a highly significant association compared with the remainder (p < 0.01). The lowest p-value was observed for ICAM3_c.739G > A (p = 1.18E-04). Previous studies have suggested that intercellular adhesion molecules (ICAM) may be an upstream factor that regulates adipocyte differentiation. Therefore, considering the polymorphism and putative gene function, we suggest that ICAM1 is potentially responsible for beef marbling. c.470C > G and/or c.994G > A on ICAM1 may be responsible for this quantitative trait locus. CONCLUSIONS: Promising SNP candidates responsible for beef marbling were identified using extensive polymorphism verification in a previously reported QTL region. We aim to elucidate the mechanism of beef marbling in future studies by investigating how these polymorphisms alter protein structure and function.

The SNP in the promoter region of the bovine ELOVL5 gene influences economic traits including subcutaneous fat thickness.

Genetic analyses have contributed to improvements of economically important traits derived from adipose tissue such as fatty acid composition in beef. Elongation of very long chain fatty acids (ELOVL) genes encode for the enzymes that play an important role in elongation of long-chain fatty acids. In this study, we aimed to discover genetic polymorphisms of ELOVL gene family in cattle populations to develop genetic markers. As a result, five synonymous mutations were detected in the coding regions of the ELOVL1, ELOVL2, ELOVL3 and ELOVL5 genes. In addition, six mutations were identified in promoter region of the ELOVL5. Two of five mutations in the promoter region of ELOVL5 were expected to alter the ELOVL5 expression and influence the economic traits, because of the high synteny of the region which was essential for activation of Elovl5 in mouse. Therefore, we performed association analysis between the genotypes and traits and our result revealed that T allele of g.-110T>C in ELOVL5 gene promoter indicated significantly thinner subcutaneous fat thickness (TT, 2.39 cm; CT, 2.35 cm) than that of C allele (CC, 2.68 cm) in a Japanese Black population. Our results suggest that the g.-110T>C is a useful genetic marker for the breeding in beef cattle.

The SNPs in the ACACA gene are effective on fatty acid composition in Holstein milk.

Fatty acid composition is an important economic trait for both dairy and beef cattle and controlled by genetic factors. Candidate genes controlling fatty acid composition may be found in fat synthesis and metabolism pathways. Acetyl-CoA carboxylase is the flux-determining enzyme in the regulation of fatty acid synthesis in animal tissues. One of two isozymes of this enzyme, acetyl-CoA carboxylase-α (ACACA), catalyses the first committed step of fatty acid synthesis in mammalian cytosol, leading to the biosynthesis of long-chain fatty acids. In the current study, the sequence comparison of the coding sequence (CDS) and two promoter regions (PIA and PIII) in bovine ACACA gene was performed between Japanese Black and Holstein cattle to detect nucleotide polymorphisms influencing fatty acid composition in milk and beef. Five single nucleotide polymorphisms (SNPs) were identified in the CDS region, 28 SNPs in the PIA region and three SNPs in the PIII region. Association study revealed that CCT/CCT type of PIII_#1, #2/PIA_#26 indicated a higher percentage of C14:0 in the milk of the Holstein cattle than CCT/GTC type (p = 0.050) and that a difference of the percentage of C16:0 was observed between CCT/CCT and GTC/GTC type (p = 0.023). CDS_#2 T/T type indicated a higher percentage of C18:0 than T/C type (p = 0.008). In addition, the Japanese Black cattle with CC/GT type of PIII_#1, #2 showed a higher percentage of C18:2 in the meat than those with GT/GT type (p = 0.025). Since PIII is the promoter specific to mammary gland during lactation, the altered expression of the ACACA gene owing to the SNPs in the PIII region may influence the fatty acid composition in the milk.

Sampling method for estimating neutral allele frequency in a pedigreed population.

The estimated allele frequency at neutral DNA marker loci is a fundamental parameter for establishing a conservation scheme for a set of livestock breeds. In this study, we propose a novel 'minimum distance (MD) method' for estimating neutral allele frequencies, which minimizes the error by the use of pedigree information. Using computer simulation and actual microsatellite data for a pedigreed cattle population, the performance of the proposed method was compared with that of conventional random sampling (RND). MD manifests a promising superiority to RND, irrespective of the sample size and the depth of pedigree. It is theoretically demonstrated that the error of the estimates depends on both the sample size and the distance of founder allele frequencies between the sampled and the non-sampled individuals. MD samples individuals so as to minimize the latter source of estimation error.

Comprehensive assessment of genetic diversity, structure, and relationship in four Japanese cattle breeds by Illumina 50 K SNP array analysis.

There are four unique cattle breeds in Japan: Japanese Black, Japanese Brown, Japanese Polled, and Japanese Shorthorn. The objective of this study was to comprehensively assess the genetic diversity, structure, relationship, and the degree of influence from foreign breeds (Angus, Simmental, Hanwoo, Shorthorn, Ayrshire, Brown Swiss, and Devon) in the Japanese cattle breeds using Illumina 50 K SNP array. In principal component analysis, each Japanese breed was separately clustered except for Japanese Shorthorn and Shorthorn. Japanese cattle breeds also showed different genetic components from each other at K ≥ 5 in population structure analysis. Japanese Shorthorn, on the other hand, had a very similar structure to Shorthorn at K ≤ 9, and Japanese Polled had a partially similar component with Angus at K = 3-7. Such close relationships were also observed in the phylogenetic tree. These findings imply that Japanese cattle breeds share genetic components with European cattle breeds to some extent while they have been almost differentiated. In population structure analysis, Japanese Black cattle shared little genetic component (3.5%) with European breeds. This is the first study to determine the extent to which European breeds impact Japanese breeds.

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.

Phylogenomics and Spatiotemporal Dynamics of Bovine Leukemia Virus Focusing on Asian Native Cattle: Insights Into the Early Origin and Global Dissemination.

Bovine leukemia virus (BLV), the causative agent of enzootic bovine leukosis, is currently one of the most important pathogens affecting the cattle industry worldwide. Determining where and in which host it originated, and how it dispersed across continents will provide valuable insights into its historical emergence as the cattle pathogen. Various species in the Bos genus were domesticated in Asia, where they also diversified. As native cattle (taurine cattle, zebu cattle, yak, and water buffalo) are indigenous and adapted to local environments, we hypothesized that Asian native cattle could have harbored BLV and, therefore, that they were important for virus emergence, maintenance, and spread. In this study, phylogeographic and ancestral trait analyses-including sequences obtained from Asian native cattle-were used to reconstruct the evolutionary history of BLV. It was shown that, since its probable emergence in Asia, the virus spread to South America and Europe via international trade of live cattle. It was inferred that zebu cattle were the hosts for the early origin of BLV, while taurine cattle played the significant role in the transmission worldwide. In addition, the results of positive selection analysis indicate that yak had a substantially minor role in the transmission of this virus. In this study, endogenous deltaretrovirus sequences in bats, collected in Asian countries, were also analyzed on whether these sequences were present in the bat genome. Endogenous deltaretrovirus sequences were detected from bat species endemic to specific regions and geographically isolated for a long time. Endogenous deltaretrovirus sequences from these geographically isolated species represent ancient exogenous deltaretroviruses distributions. The phylogenetic analysis revealed that these newly obtained endogenous deltaretrovirus sequences were closely related to those of BLV from Asian native cattle, indicating that BLV-related ancient deltaretroviruses circulated in Asia long before the emergence of BLV. Together, our analyses provide evidence for origin and spatiotemporal dynamics of BLV.

Application of Mass Spectrometry for Determining the Geographic Production Area of Wagyu Beef.

Japanese Black cattle (Japanese Wagyu) beef is attracting attention for its aroma and marbling, and its handling is increasing worldwide. Here, we focused on the origin discrimination of Wagyu beef and analyzed the nutritional components of Japanese Wagyu (produced in multiple prefectures of Japan), Hybrid Wagyu (a cross between Angus and Wagyu cattle born in Australia and transported to Japan), and Australian Wagyu beef using mass spectrometry (MS). Triple-quadrupole liquid chromatography-MS was used to clarify the molecular species of lipids in Wagyu beef. Fourteen classes of lipids were separated, and 128 different triacylglycerides (TGs) were detected. A simple comparative analysis of these TGs using high-performance liquid chromatography revealed significantly higher levels of triolein (C18:1/C18:1/C18:1; abbreviated OOO) and C18:1/C18:1/C16:1 (OOPo) in Japanese Wagyu. Wagyu elements beef were comprehensively analyzed using inductively coupled plasma (ICP)-MS and ICP-optical emission spectrometry. We found significant differences in the rubidium, cesium, and lithium levels of Japanese and Australian Wagyu beef. On comparing metabolites using gas chromatography-MS, we identified significant differences in the levels of amino acids and other components of the Japanese and Australian Wagyu beef. These results suggest the possibility of determining the origin of Wagyu cattle breeds using MS and genetic discrimination.

Zebu cattle are an exclusive legacy of the South Asia neolithic.

Animal domestication was a major step forward in human prehistory, contributing to the emergence of more complex societies. At the time of the Neolithic transition, zebu cattle (Bos indicus) were probably the most abundant and important domestic livestock species in Southern Asia. Although archaeological evidence points toward the domestication of zebu cattle within the Indian subcontinent, the exact geographic origins and phylogenetic history of zebu cattle remains uncertain. Here, we report evidence from 844 zebu mitochondrial DNA (mtDNA) sequences surveyed from 19 Asiatic countries comprising 8 regional groups, which identify 2 distinct mitochondrial haplogroups, termed I1 and I2. The marked increase in nucleotide diversity (P < 0.001) for both the I1 and I2 haplogroups within the northern part of the Indian subcontinent is consistent with an origin for all domestic zebu in this area. For haplogroup I1, genetic diversity was highest within the Indus Valley among the three hypothesized domestication centers (Indus Valley, Ganges, and South India). These data support the Indus Valley as the most likely center of origin for the I1 haplogroup and a primary center of zebu domestication. However, for the I2 haplogroup, a complex pattern of diversity is detected, preventing the unambiguous pinpointing of the exact place of origin for this zebu maternal lineage. Our findings are discussed with respect to the archaeological record for zebu domestication within the Indian subcontinent.

Development of DNA markers for improvement of meat quality in a Japanese Black cattle population in Hyogo Prefecture.

The polymorphisms associated with economic traits in livestock animals provide useful information as genetic indicators for breeding improvement. Over the last two decades, several DNA markers have been developed in Japanese Black cattle; however, the effect of these markers differs across populations due to differences in their genetic structures and backgrounds. As such, there is a need to verify the effectiveness of these markers in each population. This review summarizes the effectiveness of previously reported markers on carcass traits and the development of novel DNA markers in a Japanese Black cattle population in Hyogo Prefecture. As result of genome wide association studies and resequencing analyses, two novel significant markers associated with meat quality-related traits (beef marbling and fatty acid composition) were developed. These findings will lead to the identification of responsible genes and polymorphisms and contribute to the development of novel DNA markers for numerous traits in various cattle populations.

Effect of Five Polymorphisms on Percentage of Oleic Acid in Beef and Investigation of Linkage Disequilibrium to Confirm the Locations of Quantitative Trait Loci on BTA19 in Japanese Black Cattle.

Five polymorphisms associated with the percentage of oleic acid (C18:1) in beef fat were previously reported on bovine chromosome 19 in different Japanese Black cattle populations. This study aimed to verify the effects of these five polymorphisms on C18:1 using the same Japanese Black cattle population and conduct linkage disequilibrium (LD) analysis in order to determine the locations of the quantitative trait loci (QTLs). We genotyped the five polymorphisms (SREBP1 c.1065 + 83 (84bp indel), STARD3 c.1187 C > T, GH c.379 C > G, FASN g.841 G > C, and FASN g.16024 A > G) in two populations, which were bred in Hyogo and Gifu Prefectures, Japan (n = 441 and 443, respectively) in order to analyze their effects on C18:1 using analysis of variance (ANOVA). In the Hyogo population, SREBP1 c.1065 + 83 and STARD3 c.1187 C > T were significantly associated with C18:1 (p < 0.001). Meanwhile, FASN g.841 G > C, FASN g.16024 A > G, and GH c.379 C > G were significantly associated with C18:1 (p < 0.01) in the Gifu population. LD analysis was subsequently conducted to detect the range of the QTLs, which ranged from 32.2 to 46.4 Mbp and from 47.8 to 52.1 Mbp in the Hyogo and Gifu populations, respectively. In conclusion, this study confirmed the existence of QTLs on BTA19 and divided the candidate region for each QTL based on LD coefficients. These results could contribute to efficient searches for responsible genes and polymorphisms for fatty acid composition.

FGF5 and EPAS1 gene polymorphisms are associated with high-altitude adaptation in Nepalese goat breeds.

Several studies have reported the gene polymorphisms associated with high-altitude adaptation in goats. The FGF5 gene is a regulator in the hair-growth and a SNP c.-253G>A located within 5'UTR has been reported to cause long-haired phenotype. The EPAS1 gene is a transcription factor for various genes that have hypoxia-adaptive functions and a nonsynonymous SNP (Q579L) located in exon 5 has been reported to be associated with the mean corpuscular hemoglobin concentration. Nepal has large difference in altitudes in the north-south direction and four indigenous goat breeds are bred depending on the altitude. We used a total of 130 animals in Nepal, Chyangra (n = 37), Sinhal (n = 24), Khari (n = 33), and Terai (n = 36), and genotyped these two gene polymorphisms to compare the gene frequencies among the breeds and investigate the associations between breeding altitudes and allele frequencies. The genotyping results revealed that the mutant allele frequency in both polymorphisms tended to increase, as the breeding altitude of each population increased. In addition, correlation coefficients showed a relatively strong positive correlation between the breeding altitude and the mutant allele frequencies (r = 0.87 in FGF5 and r = 0.68 in EPAS1). These results suggested that both polymorphisms would significantly contribute to the high-altitude adaptation in Nepalese goat breeds.

Genetic characteristics of Korean Jeju Black cattle with high density single nucleotide polymorphisms.

OBJECTIVE: Conservation and genetic improvement of cattle breeds require information about genetic diversity and population structure of the cattle. In this study, we investigated the genetic diversity and population structure of the three cattle breeds in the Korean peninsula. METHODS: Jeju Black, Hanwoo, Holstein cattle in Korea, together with six foreign breeds were examined. Genetic diversity within the cattle breeds was analyzed with minor allele frequency (MAF), observed and expected heterozygosity (HO and HE), inbreeding coefficient (FIS) and past effective population size. Molecular variance and population structure between the nine breeds were analyzed using a model-based clustering method. Genetic distances between breeds were evaluated with Nei's genetic distance and Weir and Cockerham's FST. RESULTS: Our results revealed that Jeju Black cattle had lowest level of heterozygosity (HE = 0.21) among the studied taurine breeds, and an average MAF of 0.16. The level of inbreeding was -0.076 for Jeju Black, while -0.018 to -0.118 for the other breeds. Principle component analysis and neighbor-joining tree showed a clear separation of Jeju Black cattle from other local (Hanwoo and Japanese cattle) and taurine/indicine cattle breeds in evolutionary process, and a distinct pattern of admixture of Jeju Black cattle having no clustering with other studied populations. The FST value between Jeju Black cattle and Hanwoo was 0.106, which was lowest across the pair of breeds ranging from 0.161 to 0.274, indicating some degree of genetic closeness of Jeju Black cattle with Hanwoo. The past effective population size of Jeju Black cattle was very small, i.e. 38 in 13 generation ago, whereas 209 for Hanwoo. CONCLUSION: This study indicates genetic uniqueness of Jeju Black cattle. However, a small effective population size of Jeju Black cattle indicates the requirement for an implementation of a sustainable breeding policy to increase the population for genetic improvement and future conservation.

Accumulation of caveolin-3 protein is limited in damaged muscle in chicken muscular dystrophy.

Members of the caveolin family are the main component of caveolae, and caveolin-3 is a muscle-specific protein. Caveolin-3 deficiency induces a muscular dystrophic phenotype, while its overexpression is also harmful to muscle cells. Increased caveolae were observed in chicken muscular dystrophy; however, the underlying mechanism causing the onset remains unclear. Therefore, the current study analyzes the expression of caveolin-3 and other caveola-related proteins in dystrophic chickens. Western blotting and semi-quantitative RT-PCR analysis revealed that (1) caveolin-3 is highly expressed in the damaged muscle of dystrophic chickens (7.12-fold); (2) the amount of caveolin-3 protein is regulated in posttranslational modification, since no significant increase is observed at the mRNA level (1.09-fold); and (3) the expression pattern of other caveola-related proteins is similar to that of caveolin-3. These results suggest that the accumulation of caveolin-3 protein may be associated with the causative process of chicken muscular dystrophy.

Effect of DNA markers on the fertility traits of Japanese Black cattle for improving beef quantity and quality.

Carcass traits have been efficiently improved by recent selection using DNA markers in beef cattle. Additionally, DNA markers might have an effect on other traits such as fertility traits; therefore attention should also be paid to such pleiotropic effects. However, the effects of the markers on both carcass and fertility traits have never been evaluated in the same population, since they are generally measured in different populations. The objective in the current study was to discuss effectiveness of DNA markers developed for carcass traits through investigation of their effects on carcass and fertility traits in a population. We genotyped six markers SCD V293A, FASN g.841G>C, PLAG1 g.49066C>G, NCAPG I442M, DGAT1 K232A, and EDG1 g.1471620G>T in a Japanese Black cattle population ( n = 515 ). To investigate their effects on carcass and fertility traits, we performed statistical analysis (ANOVA and the Tukey-Kramer honestly significant difference (HSD) test). In the results, three of six markers, SCD V293A, NCAPG I442M, and EGD1 g.1471620G>T, were significantly associated with both carcass and fertility traits. Remarkably, the same allele for each marker had positive effects on both traits, suggesting that we would be able to simultaneously improve them using these markers in this population. However, previous studies reported that the effects of DNA markers could differ among populations. Therefore, it is necessary to confirm the effect of the marker in each population before it is used for improvement.

Cattle mitogenome variation reveals a post-glacial expansion of haplogroup P and an early incorporation into northeast Asian domestic herds.

Surveys of mitochondrial DNA (mtDNA) variation have shown that worldwide domestic cattle are characterized by just a few major haplogroups. Two, T and I, are common and characterize Bos taurus and Bos indicus, respectively, while the other three, P, Q and R, are rare and are found only in taurine breeds. Haplogroup P is typical of extinct European aurochs, while intriguingly modern P mtDNAs have only been found in northeast Asian cattle. These Asian P mtDNAs are extremely rare with the exception of the Japanese Shorthorn breed, where they reach a frequency of 45.9%. To shed light on the origin of this haplogroup in northeast Asian cattle, we completely sequenced 14 Japanese Shorthorn mitogenomes belonging to haplogroup P. Phylogenetic and Bayesian analyses revealed: (1) a post-glacial expansion of aurochs carrying haplogroup P from Europe to Asia; (2) that all Asian P mtDNAs belong to a single sub-haplogroup (P1a), so far never detected in either European or Asian aurochs remains, which was incorporated into domestic cattle of continental northeastern Asia possibly ~ 3700 years ago; and (3) that haplogroup P1a mtDNAs found in the Japanese Shorthorn breed probably reached Japan about 650 years ago from Mongolia/Russia, in agreement with historical evidence.

Indonesian native goats (Capra hircus) reveal highest genetic frequency of mitochondrial DNA haplogroup B in the world.

The objective of this study was to determine mtDNA sequences of the 481 bp HV1 region from two Indonesian native goat breeds, Kacang and Marica, to confirm the phylogeographic distribution of caprine haplogroup B in Southeast Asia. Based on these sequences, 12 haplotypes were observed and categorized into the predominant haplogroup B and minority haplogroup A, indicating that Indonesian native goats present the highest frequency (0.950) of the haplogroup B in the world. These results strongly emphasize previous observations of the haplogroup B frequencies tending to increase southeastward in Southeast Asia. Additionally, this suggests that goats primary bred into Southeast Asia might predominantly carry haplogroup B. This could essentially contribute to the understanding of the origin, propagation route and/or introgression history of Southeast Asian goats.

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.

The non-synonymous mutation in bovine SPP1 gene influences carcass weight.

Meat quality in beef cattle is controlled by genetic factors. SPP1 (secreted phosphoprotein 1) gene, coding a multifunctional cytokine with diverse biological functions, is the candidate gene influencing carcass traits. In this study, we tried to discover DNA polymorphisms associated with beef quality in bovine SPP1 gene, so that two SNPs (single nucleotide polymorphisms) in the promoter region and one SNP in the CDS (coding sequence) region were identified. Although the formers were predicted to alter SPP1 expression, they did not show any effects on the traits. On the contrary, statistical analysis revealed that g.58675C > T, a non-synonymous mutation from threonine to methionine in the conservative region, had a significant effect on carcass weight. Carcass weight of the animals with C/T allele (473.9 ± 6.0 kg) was significantly heavier than that of the C/C homozygotes (459.2 ± 2.8 kg). Because SPP1 gene functions in skeletal muscle cells as a positive regulator, the non-synonymous mutation might influence muscle development and remodeling, resulting in increased carcass weight of the C/T animals. Our results indicate that the SNP can be applied as a DNA marker for the improvement of beef cattle.