The Noma horse breed is the smallest among the eight native Japanese horse breeds. The population of Noma horses has been decreasing consistently, and they are listed as a critical breed; thus, conservation measures are urgently required. In this study, we estimated the pedigree-based inbreeding (FPED) and genomic inbreeding coefficients (FIS and FROH) of 24 Noma horses bred in Imabari City, Ehime Prefecture. We used 65 K equine SNP chip (GeneSeek/Neogen) data, and identified a total of 31,133 autosomal SNP genotypes after quality control steps. They were used to estimate the genomic inbreeding coefficient. We found that two full siblings had identical FPED (0.303) and different FIS (-0.157 and 0.077). When the mean FIS value was compared between this study (-0.098) and the previous study (Kakoi et al. 2007) (-0.130), this study had higher inbreeding values. A total of 815 ROH segments larger than 1 Mb were identified in 24 horses, and 78.7% of them were longer than 4 Mb, confirming recent inbreeding in this population. FROH (FROH–All, FROH1–2Mb, FROH2–4Mb, FROH4–8Mb, FROH8–16Mb, FROH> 16Mb) was calculated for different ROH lengths (all segments, 1–2, 2–4, 4–8, 8–16, and > 16 Mb, respectively). These estimates increased with increasing ROH length suggesting higher inbreeding in recent generations.
In Laos, water buffaloes are traditionally used as draft animals, but their role as movable property for wealth accumulation has increased in recent years. However, little is known about the genetic makeup of these water buffaloes. This study aimed to clarify the gene composition and genetic diversity of four native water buffalo populations in Laos using the mtDNA D-loop region as maternal information and the ZFY gene on the Y chromosome as paternal information. A total of 82 D-loop sequences from four populations were compared, and 18 haplotypes with 36 substitution sites were identified. From the neighbor-joining phylogenetic tree and the median-joining network, it was confirmed that the Laos native water buffaloes belong to the swamp buffalo, and two lineages were clarified. It was also found that the nucleotide sequence of the ZFY gene was identical to that of the swamp buffalo and that there were two haplotypes. Both the neutrality test and the analysis of molecular variance suggested that the population size of Houaphan and Attapeu had decreased in the past. These results indicate that the native water buffaloes of Laos are a genetically diverse population with at least two maternal and paternal ancestors each.
We previously reported that 4,237 of 33,063 single nucleotide polymorphism (SNP) markers genotyped by commercial SNP chips were monomorphic in Japanese Black fattened steers slaughtered at carcass market in Hyogo prefecture. Here we investigated their distribution and extracted their neighboring genes. Genomic regions were detected as candidate homozygous regions where ≥ 2 of these SNPs were consecutively located, and the genes located within the regions were extracted. The 672 homozygous regions detected were widely distributed throughout the genome. The 608 extracted genes included ones previously studied as candidate genes for the degree of marbling in Japanese Black cattle. Gene ontology enrichment analysis (GO analysis) of the extracted genes found many significant GO terms related to lipids and lipid metabolism (P <0.05). Network analysis of the genes belonging to the significant term" nucleotide binding (GO: 000166)" in the STRING database suggested several connections (edges) among the genes. The results could be useful to characterize the Japanese Black cattle, especially the Hyogo subpopulation.
The Japanese wild boar (Sus scrofa leucomystax) is an indigenous subspecies of the wild boar, which is distributed in Honshu, Shikoku, Kyushu, and other smaller islands of Japan. The distribution area of the Japanese wild boar has in the last 40 years expanded by 1.9-fold due to improved suitable survival conditions, such as global warming which has decreased snowfall, increased abandoned farmland, and decreased hunting pressure. As a result, the negative impacts of this population increase on humans continue to spread. In this study, 1,251 Japanese wild boars were sampled from 32 prefectures which nearly cover the entire expanded distribution area in Japan, and phylogeographical analysis was performed using 30 Measurement of Domestic Animal Diversity recommended microsatellite markers. Both neighbor-joining (NJ) phylogenetic trees constructed using Nei's DA genetic distance matrix and population genetic structure analysis classified Japanese wild boar into six phylogeographical subpopulations, including northern Honshu, eastern Honshu, central Honshu, western Honshu, Shikoku, and Kyushu. The six identified genetic subpopulations were speculated to form as a result of several factors, including human activity between the northern and eastern Honshu, occurrence of three mountain ranges of 3,000-meter height between the eastern and central Honshu, the inland sea between western Honshu and Shikoku, and the presence of strait between western Honshu and Kyushu. Interestingly, some individual wild boars from Gunma, Tochigi, and Miyazaki areas formed distinct and separate subpopulations, with animals within these subgroups exhibiting traits such as low genetic differentiation and high diversity, which likely suggested gene influx from domestic pigs or other sources.
Heat stress is one of the adverse effects on productivity in the livestock. In pig, it is shown that the growth rate decreases under heat stress conditions. Moreover, it is reported that genetic variation is associated with heat stress tolerance. However, much less study has been done on identification of candidate genes and pathways associated with heat stress tolerance in pig. Here, this study aimed to identify the candidate genes and pathways associated with heat stress tolerance for growth rate in pig using microarray and RNA-seq. These methods were used to investigate differences in small intestine gene expression profiles among two finishing pig groups (high-tolerant and low-tolerant) with divergent heat stress tolerance for growth rate under heat stress conditions and control finishing pig group under non-heat stress conditions. The results of microarray and RNA-seq, respectively, showed that a total of 1277 genes for microarray and 2970 genes for RNA-seq were regarded as the genes showing heat stress responsive differential expression profiles associated with heat stress tolerance, and also 825 genes for microarray and 1233 genes for RNA-seq were upregulated and 452 genes for microarray and 1737 genes for RNA-seq were downregulated in hightolerant group as compared to low-tolerant group. Among these genes, we found overrepresentation of a set of genes involved in TGFβ signaling pathway. The gene set exhibited differential expression profiles between hightolerant and low-tolerant groups which are reported to lead to activation of TGFβ signaling pathway, resulting in cell differentiation and regeneration of intestinal cell in hightolerant group. These results suggested that the TGFβ signaling pathway was identified as the intriguing pathway showing heat stress-responsive activation associated with heat stress tolerance for growth rate in small intestine of finishing pig.
特定の形質の改良に制限を課したいような改良(制限 付き選抜や改良目標に基づく改良)における選抜方法 についての推定育種価の利活用に関する研究は非常に 限られているといえる。 そこで本研究では、アニマルモデル BLUP 法に基づ いて得られた推定育種価の利活用に関する応用研究を 様々な視点から検討することを目的とする。また、推 定育種価に基づく遺伝分散共分散行列を算出する方法 を提案し、その方法の妥当性と応用例についても検討 することにした
The six Bubalus species include the two species of anoa, the tamaraw, the Asian wild water buffaloes, and the domesticated riverine and swamp buffaloes. However, the phylogenetic relationships and taxonomic positions of the Bubalus species have few published data and are still unresolved. Thus, this paper aimed to elucidate the relationship among these species of the genus Bubalus using the variation of the control region of mtDNA D-loop. This study generated D-loop sequences from 17 riverine buffaloes from India and Brazil that Philippine government imported. The analysis also included 836 D-loop sequences of Bubalus species from the Asia region that were retrieved from NCBI Genbank. Results revealed the highest genetic distance between tamaraw and lowland anoa, while the lowest was between the tamaraw and swamp buffalo, which confirmed their taxonomic assignment to belong to the same genus but different species. Moreover, a total of 853 sequences of 368 nucleotide sites from Bubalus species included 61 haplotypes with 214 nucleotide sites. The branch supported two major groups, the first group from the sub-species of anoa and the second group from tamaraw and domesticated water buffaloes. The genetic distance, phylogenetic, and Median-Joining structure analyses highlighted that domesticated riverine and swamp buffaloes have distinct maternal ancestry and showed the tamaraw's close affinity to the swamp lineage B. In addition, these results showed the shared common ancestry between the tamaraw and swamp buffaloes, suggesting that the evolution of tamaraw occurred prior to the domestication of swamp buffaloes.
This study attempted to infer the population structure of Japanese Black cattle by using genotype data on 33,063 genomewide single nucleotide polymorphism (SNP) markers of totally 4,348 fattened steers slaughtered at carcass markets in Tokyo, Osaka, Hyogo, Tottori, and Hiroshima prefectures. We evaluated allele frequency, heterozygosity, linkage disequilibrium, correlation of linkage phase, and genotype concordance among the steers. The distribution of allele frequencies in the steers sampled in Hyogo differed from the others, showing >10% of the SNPs as monomorphic. Observed heterozygosity was lowest and degree of linkage disequilibrium was highest in Hyogo. Genotypes were more similar among Hyogo steers than between other steer pairs. These results show the genetic characteristics of the Japanese Black cattle populations inferred from genotype data on genome-wide SNPs obtained using a commercial chip.
We performed Bayesian clustering analysis using STRUCTURE software with genotype data on 33,063 commercial single nucleotide polymorphism (SNP) markers in 4,348 Japanese Black fattened steers slaughtered at carcass markets in Tokyo, Osaka, Hyogo, Tottori, and Hiroshima prefectures. When the number of the assumed clusters in STRUCTURE was 2, the steers from Hyogo prefecture were clearly separated from the others. This indicates the usefulness of the STRUCTURE analysis with commercial SNP markers for the clarifications of the difference of the genetic constitutions of each prefecture. Next, genomic predictions for carcass traits were conducted using a statistical model including the proportions of the clusters as partial linear regressions. Genomic breeding values predicted by the model without the STRUCTURE covariates were likely to be divided into the part of explaining the STRUCTURE analysis and the remaining part. This result shows the possibility that the accuracy of genomic prediction depends on the degree of information of the genomic population structure.
This study was conducted to perform phenotypic characterization of four meat-type and two game-type populations of Myanmar indigenous chickens. A total of 114 adult chickens (52 males and 62 females) were measured to evaluate seven body measurement traits. The measurements were subjected to analysis of variance (ANOVA) and correlation coefficient matrix. The ANOVA revealed that sex and population factors were highly significant (p < 0.05) for all body measurement traits. For all traits, males were larger than females. Among the six populations, the indigenous chickens from the Yangon region had the largest body size, but the shortest shank length. There were some differences between the two types of fighting cock collected from different areas. The correlation coefficients of all body measurement traits were positive and significant (p < 0.01) ranging from 0.24 to 0.80. The highest correlations of body weight to other traits were seen in height and toe to back length. The findings of this study could contribute to the better understanding of Myanmar indigenous chickens. In the future, these populations should be kept under the same management and further experiments should be conducted for unbiased results.
al . 2012; Kadri et al . 2016; Kong et. al . 2008), and Kong et al . (2004) also reported that the genome-wide recombination rate correlate positively with reproductive success of females in human. RNF212 (ring finger protein 212) acts as a putative regulator of crossover (Reynolds et al . 2013; Qiao et al . 2014). The studies on mice and human showed that mutations of Rnf212/RNF212 caused the diminishing of crossover and sterility in both sexes (Reynolds et al . 2013; Fujiwara et al . 2015; Riera-Escamilla et al . 2019). Sandor et al . (2012) and Kong et al . (2008) reported that genetic varianst of RNF212 showed significant association with genome-wide recombination rate in cattle and human, respectively. These lines of evidences suggested that the variants of RNF212 could associate with female fertility via
The Journal of Animal Genetics (2021) 49, 67–75 INTRODUCTION In Japanese Black cattle, beef quality, especially beef marbling, has been improved to add value to the beef for more than sixty years (Gotoh et al. 2014). As the results, its beef is appreciated worldwide for the high marbling (Whreeler et al. 2004). Breeders for Japanese Black cattle have, recently, focused on fat quality as one of factors for beef quality in addition to beef marbling. In particular, fatty acid composition is regarded as an important indicator for beef quality because a ratio of various fatty acids affects tenderness and flavor of beef (Yang et al. 1999; Smith et al. 2006). For instance, beef representing high oleic acid (C18:1) percentage would be evaluated as high quality because the beef is tender and has a good flavor. In addition, unsaturated fatty acids including C18:1 have a favorable effect on human health by reducing LDL-cholesterol (Rudel et al. 1995). For these reasons, beef representing higher percentage of unsaturated fatty acids is recognized as high quality. Fatty acid composition is regulated by various genes related to fatty acid metabolism such as synthesis, oxidation, transport, and desaturation for fatty acids. In fact, some studies suggested that fatty acid composition would be able to be genetically improved since its heritability ranged moderate to high in Japanese Black cattle (Inoue et al. 2011; Nogi et al. 2011; Sakuma et al. 2017). Meanwhile, DNA markers for fatty acid composition have been developed. Taniguchi et al. (2004) reported that an amino acid substitution A293V in stearoyl-CoA desaturase (SCD) gene was significantly associated with the percentage of monounsaturated fatty acid (MUFA) and melting point of beef fat. In fatty acid synthase (FASN) gene, two amino acid substitutions (T1950A and W1955R), which were in almost complete linkage disequilibrium (LD), and a SNP in promoter region (g.841G>C) were significantly associated with fatty acid composition (Abe et al. 2009; Hayakawa et al. 2015). Since the SCD and FASN genes are involved in fatty acid desaturation and synthesis, respectively, these polymorphisms would be the promising candidates as responsible polymorphisms for fatty acid composition. However, the proportion of genetic variance explained by the SCD and FASN polymorphisms was reported to range from 3.29 to 24.71 in a Japanese Black population (Matsuhashi et al. 2011). In addition, promising candidate polymorphisms for fatty acid composition had never been identified except for SCD and FASN polymorphisms. These previous reports suggested that there would be some other genes which have effects on fatty acid composition. Then, we have tried to identify novel responsible genes and polymorphisms for fatty acid composition in Japanese Black cattle in the past few years.
