Gene and haplotype polymorphisms of the Prion gene (PRNP) in Japanese Brown, Japanese native and Holstein cattle

Polymorphisms in the prion protein gene ( PRNP ) are known to be associated with transmissible spongiform encephalopathies in human, sheep and goats. There is tentative association between PRNP promoter polymorphism and bovine spongiform encephalopathy (BSE) susceptibility in cattle. In this study, we genotyped for six bovine PRNP polymorphic sites including a 23-bp indel in the promoter, a 12-bp indel in the intron 1, two nonsynonymous single nucleotide polymorphisms (SNPs), octapeptide repeats in the coding region and a 14-bp indel in the 3'-untranslated region in 178 animals representing Japanese Brown, Kuchinoshima feral, Mishima, Japanese Shorthorn and Holstein. In 64 Japanese Brown cattle, three indel sites were polymorphic. All of the six sites were monomorphic in Kuchinoshima. The 23-bp and 12-bp indel sites were polymorphic in Mishima cattle. The 23-bp and 14-bp indel sites were polymorphic in Japanese Shorthorn cattle. Both SNP sites were monomorphic in all cattle examined in this study. At the 23-bp indel site, the genotype frequencies of Japanese Brown and Holstein breeds were similar to that of BSE affected cattle. We estimated 12 different haplotypes from these genotypic data. A '23-12-K6S14+' haplotype was the major haplotype in all populations, whose frequencies ranged from 0.50 to 1.00.     

Evaluation of inbreeding and genetic diversity in Japanese Shorthorn cattle by pedigree analysis

The Japanese Shorthorn is a Japanese Wagyu breed maintained at a small population size. We assessed the degree of inbreeding and genetic diversity among Japanese Shorthorn cattle using pedigree analysis. We analyzed the pedigree records of registered Japanese Shorthorn born between 1980 and 2018, after evaluating the pedigree completeness. The average of the actual inbreeding coefficients increased at the same rates annually from approximately 1.5% in 1980 to 4.2% in 2018 and was higher than the expected inbreeding coefficients over time. The effective population size based on the individual coancestry rate largely decreased from 127.8 in 1980 to 82.6 in 1999, and then remained almost constant at approximately 90. Three effective numbers of ancestors decreased over time until 1995, then remained almost constant. In particular, the effective number of founder genomes (N_ge) decreased from 43.8 in 1980 to 11.9 in 2018. The index of genetic diversity based on N_ge decreased from 0.99 in 1980 to 0.96 in 2018 due to genetic drift in non-founder generations. Changes in inbreeding and genetic diversity parameters were similar between Japanese Shorthorn and other Japanese Wagyu breeds, but the magnitude of the changes was lower in the Japanese Shorthorn.     

The assessment of genetic diversity within and among the eight subpopulations of Japanese Black cattle using 52 microsatellite markers

Japanese Black cattle are at risk for genetic homogeneity due to intensive use of a few sires. Therefore, assessment of the actual genetic diversity of this breed is important for future breeding plans. In the present study, we investigated the genetic diversity within and among eight subpopulations of Japanese Black cattle using 52 microsatellite markers. The parameters for genetic diversity of Japanese Black cattle were comparable to those of other cattle breeds, suggesting that the relatively high genetic diversity of the breed. However, upon comparison among the eight subpopulations, the Hyogo subpopulation showed markedly low genetic diversity. The results of the pairwise F_ST values, phylogenetic network and structure analysis indicated that the Hyogo population has remarkably high level of genetic differentiation from other populations, while Yamagata, Niigata, Hiroshima and Kagawa populations have low levels of genetic differentiation. Furthermore, multidimensional scaling plots indicated that individuals in some subpopulations were separated from individuals in the other subpopulations. We conclude that while the overall genetic diversity of Japanese Black cattle is still maintained at a relatively high level, that of a particular subpopulation is significantly reduced, and therefore the effective population size of the breed needs to be controlled by correct mating strategies.     

陇东地方牛种遗传多样性研究

对陇东地方牛种及其与秦川牛和南德温牛杂交群体共计113个个体线粒体D-loop区461 bp序列进行多态性分析,结果表明,3个群体该区域A+T含量(64.2%)明显高于G+C含量(35.8%),表现出明显的碱基偏倚;3个群体核苷酸变异率介于0.42%和3.27%之间,陇东牛和南德温牛杂交群体核苷酸变异率最高;核苷酸变异类型以转换为主,转换占核苷酸多态位点的90.94%,其次为颠换,占4.59%,同样表现出明显的碱基替换偏倚;3个群体核苷酸岐异度介于0.008 95和0.029 06之间,遗传距离介于0.000 15和0.008 36之间,陇东地方牛及其与秦川牛的杂交群体核苷酸歧异度和遗传距离最小。     

甘孜藏牛mtDNA 基因组遗传多样性分析

［目的］探究甘孜藏牛的mtDNA基因组遗传多样性与母系起源。［方法］采用mtDNA全基因组序列比对及生物信息学方法。［结果］结果显示：在28头甘孜藏牛mtDNA 基因组中,共检测到1232个变异位点,确定了22种单倍型,其单倍型多样度（Hd）为0.98820±0.00010,核苷酸多样度（Pi）为0.02420±0.00003,表明甘孜藏牛具有丰富的母系遗传多样性。系统发育树和网络分布图表明,28头甘孜藏牛mtDNA基因组包括4种母系支系,分别为普通牛的T2、T3与T4支系,还有牦牛支系,其中T2支系占7.14%,T3支系占64.29%,T4支系占3.57%,牦牛支系占25 %。［结论］甘孜藏牛具有较丰富的母系遗传多样性,为普通牛母系起源,但与牦牛有杂交。     

秦川牛mtDNA全基因组遗传多样性与母系起源研究

[目的]从32头秦川牛全基因组中提取其mtDNA全基因组序列进行分析,以揭示秦川牛mtDNA基因组的遗传多样性与母系起源。[方法]采用mtDNA全基因组序列比对及生物信息学方法。[结果]在32头秦川牛mtDNA全基因组序列中,共检测到30种不同的单倍型,其平均单倍型多样度（Hd±SD）为0.996±0.009,其平均核苷酸多样度（π±SD）为0.0067±0.0010,表明秦川牛具有丰富的母系遗传多样性。构建的mtDNA全基因组系统发育树与单倍型网络图表明,32头秦川牛的mtDNA全基因组序列包括T2、T3、T4、I1共4个不同的支系,其中T2支系占21.88%,T3支系占40.625%,T4支系占9.375%,I1支系占28.125%。说明秦川牛具有普通牛和瘤牛两个支系,其中普通牛支系占71.88%,瘤牛支系占28.12%。[结论]秦川牛具有丰富的母系遗传多样性,有普通牛和瘤牛两个母系起源,但以普通牛起源为主。     

温岭高峰牛线粒体DNA全基因组遗传多样性分析

[目的]通过测定温岭高峰牛线粒体DNA全基因组序列以分析温岭高峰牛的母系起源及遗传多样性。[方法]采用DNA提取、测序及生物信息学方法。[结果]通过对19头温岭高峰牛线粒体DNA全基因组序列分析,共发现263个变异位点,定义9种单倍型,单倍型多样度(Hd±SD)为0.778±0.096,核苷酸多样度(Pi±SD)为0.0017±0.0014,表明温岭高峰牛的遗传多样性较低。构建的NJ系统发育树和单倍型进化网络图表明温岭高峰牛有普通牛和瘤牛2种母系起源。[结论]温岭高峰牛线粒体DNA基因组的遗传多样性较低,有瘤牛和普通牛两个母系起源,但主要受瘤牛的影响。     

Genetic diversity of Chinese domestic goat based on the mitochondrial DNA sequence variation

The aim of this study was to characterize the genetic diversity of domestic goat in China. For this purpose, we determined the sequence of the mitochondrial DNA (mtDNA) control region in 72 individuals of the Yangtze River delta white goat, and reanalysed 723 published samples from 31 breeds/populations across China. All goat haplotypes were classified into four haplogroups (A–D) previously described. The phylogenetic pattern that emerged from the mtDNA control region sequence was confirmed by the analysis of the entire cytochrome b sequence of eight goats representative of the four haplogroups. It appeared that in Chinese domestic goat, haplogroups A and B were dominant and distributed in nearly all breeds/populations, while haplogroups C and D were only found in seven breeds/populations. Four breeds/populations contained all four haplogroups. When grouping the breeds/populations into five geographic groups based on their geographic distributions and ecological conditions, the southern pasturing area had the highest diversity whereas the northern farming area had the lowest diversity. 84.29% and 11.37% of the genetic variation were distributed within breeds and among breeds within the ecologically geographical areas, respectively; only 4% of genetic variation was observed among the five geographic areas. We speculate that the traditional seasonal pastoralism, the annual long-distance migrations that occurred in the past, and the commercial trade would account for the observed pattern by having favoured gene flows.     

Genetic diversity of growth hormone receptor gene in cattle

Growth hormone receptor (GHR) belongs to a member of the cytokine receptor superfamily. Polymorphism of presence or absence of an approximately 1.2 kbp LINE-1 element is observed in bovine GHR gene. The present study was carried out for estimating the genetic diversity and the origin of the LINE-1 element in 10 European, Southeastern Asian and East Asian cattle breeds or populations. Genotyping of the LINE-1 revealed predominant LINE-1 presence in European breeds (0.917∼0.991), absence in the Bos taurus indicus populations (0.000∼0.017), and intermediate presence in Northeast Asian cattle (0.417∼0.522). From genetic features of LINE families, LINE-1 of GHR could be attributed to the same origin in both European and Asian cattle, and Asian LINE-1 may not be derived from recent introgression. This result suggested that LINE-1 in bovine GHR gene could have arisen in an ancestral population of Bos taurus taurus .     

Genetic diversity of Jiangsu native chicken breeds assessed with the mitochondrial DNA D-loop region

1. The objective of this study was to determine the origin and evolution of chickens from 5 native breeds that are traditionally raised in Jiangsu Province.

2. To address this question, the complete mitochondrial DNA D-loop sequence of 149 chickens from 5 native breeds of Jiangsu Province was analysed.

3. Sequence read lengths of the native breeds were 1231 to 1232 bp, with a single-base deletion from the 859 bp site in the 1231 bp haplotype. A total of 33 variable sites that defined 19 haplotypes were identified. The average haplotype diversity and nucleotide diversity were 0.862 ± 0.017 and 0.00591 ± 0.00135.

4. Phylogenetic analysis showed that genetic structure of the mtDNA haplotypes of Jiangsu chickens are distributed across 5 clades (haplogroups): Clades A, B, C, D, and E. However, most of the individuals characterised in this study belonged to clades A and B.

5. The results of this study indicate that Jiangsu chicken populations have relatively low nucleotide and haplotype diversity and likely share 5 common maternal lineages.     

贵州威宁黄牛线粒体DNA D-loop区全序列分析

为了解贵州威宁黄牛的遗传多样性及遗传背景，测定了19个个体的线粒体DNAD-loop区全序列。威宁黄牛D-loop区全序列中，A＋T平均含量为61．4％，G＋C含量为38．6％。经比对，共检测到威宁黄牛D-loop区8种单倍型，核苷酸多态位点45个，其中7种为普通牛血统的单倍型，1种为瘤牛血统的单倍型，表明威宁黄牛同时受到普通牛和瘤牛的影响。在威宁黄牛19个个体中，其单倍型多样度为0．715，核苷酸歧异度（π值）为2．415％，表明威宁黄牛品种的遗传多样性丰富。     

贵州黎平黄牛线粒体DNA D-loop区全序列初步分析

为了解贵州黎平黄牛的遗传多样性及遗传背景,我们测定了20头黄牛的线粒体DNA D-loop区序列。结果检测到8种单倍型,其中4种为普通牛血统的单倍型,4种为瘤牛血统的单倍型,表明黎平黄牛同时受普通牛和瘤牛的影响。该研究对于黎平黄牛的保种及持续利用有着重要的理论指导意义。     

隆林牛与郏县红牛线粒体DNA全基因组遗传多样性比较研究

摘　要：［目的］本研究旨在从基因组水平探究隆林牛和郏县红牛的线粒体DNA（mtDNA）全基因组遗传多样性与母系起源,并对2个黄牛品种的mtDNA全基因组遗传多样性进行比较分析。［方法］采用全基因组重测序及生物信息学方法。［结果］在15头隆林牛和28头郏县红牛mtDNA全基因组序列中,共检测到36种单倍型,其中郏县红牛有26种单倍型,隆林牛仅有8种单倍型,2个黄牛品种共享2种单倍型。郏县红牛和隆林牛的平均单倍型多样度（Hd）分别为1.000和0.943,平均核苷酸多样度（Pi）分别为0.0080和0.0053,表明其遗传多样性丰富。构建的系统发育树表明,隆林牛和郏县红牛具有瘤牛和普通牛两个母系支系。［结论］隆林牛以瘤牛起源为主,郏县红牛为普通牛与瘤牛的混合起源,这2个地方黄牛品种具有独特的母系遗传信息,表现出明显的母系遗传差异。     

Effects of genetic and environmental factors on muscle glycogen content in Japanese Black cattle

Monosaccharides such as glucose contribute to the development of meat flavor upon heating via the Maillard reaction; therefore, monosaccharide content is related to beef palatability. Here, we analyzed the effects of genetic and environmental factors on the content of glycogen, one of the precursors of monosaccharides, in the muscles of 958 fattened Japanese Black cattle from Yamagata Prefecture. Analysis of variance showed that muscle glycogen content was affected by the farm and postmortem periods, but not by sex, slaughter age, slaughter month or number of days detained at the slaughter yard. Additionally, consumption of digestible brown rice feed elevated muscle glycogen levels. Glycogen heritability was estimated to be 0.34, and genetic correlations between glycogen and carcass weight (CW) or beef marbling standard (BMS) were weak. The predicted breeding values varied among paternal lines. These results demonstrated that genetic factors might improve muscle glycogen content and therefore beef palatability, but do not influence CW or BMS.     

Genetic diversity decreases as population density declines: Implications of temporal variation in mitochondrial haplotype frequencies in a natural population of Tscherskia triton

Although the spatial genetic differentiation that occurs in animal populations has been extensively studied, information on temporal variations in genetic structure and diversity is still lacking, especially for animals with oscillating populations. In the present study, we used the mtDNA D‐loop sequence to assess the temporal genetic variation in samples from six successive years for the greater long‐tailed hamster, Tscherskia triton. Sampling was carried out between 1998 and 2003 in cropland on the North China Plain, China. A total of 108 individuals were analyzed. The temporal samples showed a high level of genetic diversity. Substantial genetic changes in haplotype frequencies over time were detected for the hamster population. Random genetic drift and migration are likely to be the major factors responsible for the observed temporal pattern. The genetic diversity of the hamster population was higher in years with higher population density, and lower in years with lower population density. The result supports our hypothesis that genetic diversity decreases when population density declines in animals whose population oscillates greatly between years. The combined effects of inbreeding and genetic drift caused by reproduction, dispersal and population size might play important roles in the observed changes in genetic structure and diversity between years.     

Genetic relationships between temperament of calves at auction and carcass traits in Japanese Black cattle

Correlations of calves’ temperament with carcass traits were estimated to clarify the genetic relationships between them in Japanese Black cattle. The temperament records for 3128 calves during auction at a calf market were scored on a scale of 1 (calm) to 5 (nervous) as temperament score (TS ), and the TS were divided into two groups (TSG ): TS 1 and 2 comprised TSG 1, and 3 to 5 constituted TSG 2. Carcass data were obtained from 33 552 fattened cattle. A threshold animal model was used for analyzing the underlying liability for TSG , whereas a linear one was used for TS and carcass traits. The heritability estimates for TS and TSG were 0.12 and 0.11, respectively. On the other hand, moderate to high heritability estimates were obtained for carcass traits (0.40 to 0.68). The temperament scores were negatively correlated with carcass weight, rib thickness and subcutaneous fat thickness (?0.13 to ?0.59). In contrast, weak to moderate positive correlations were found between the temperament scores and rib eye area or yield estimate (0.16 to 0.45). The temperament scores and beef marbling score had no correlation. These results showed that it is possible to improve temperament and carcass traits simultaneously.     

Mitochondrial DNA diversity of Anatolian indigenous domestic goats

Anatolia has been an important region for civilizations and agricultural revolution as a major domestication centre for livestock species. Goats (Capra hircus) were among the earliest domesticated animals in this region. In this study, genetic diversity of Anatolian goat breeds was characterized by comparison of mitochondrial DNA hypervariable region 1. A total of 295 individuals, including 99 Anatolian Black goats, 96 Angora goats and 100 Kilis goats, were used. Haplogroup A was found to be the dominant haplogroup in all three breeds. The highest haplogroup diversity, including haplogroups A, B2, C and G, was observed in the Anatolian Black breed. Haplogroup D was only observed in Kilis and Angora goats. Haplogroup G was found in Angora and Anatolian Black breeds. The Anatolian goat breeds had high genetic diversity values and a weak phylogeographical structure. The nucleotide diversity values were found to be higher than those in previously studied goat breeds. The fact that Anatolia is a domestication centre and its geographical position as a junction of trade routes may have caused the higher genetic diversity of Anatolian goat breeds.     

Genetic diversity and origin of Gayal and cattle in Yunnan revealed by mtDNA control region and SRY gene sequence variation

There are hump, humpless cattle and gayal distributed in Yunnan province, south‐west China, but their genetic background remains unclear. To determine the origin and genetic diversity of Yunnan gayal and cattle (Diqing, Nujiang and Wenshan cattle), we analysed mtDNA control region sequences of 71 samples and SRY gene sequences of 39 samples, together with the available sequences in GenBank. The neighbour‐joining phylogeny and the reduced median network analysis showed that Yunnan gayal originated from the hybridization between male Bos frontalis and female Bos taurus or Bos indicus, and that Yunnan cattle mostly originated from B. indicus, also containing some hybrids of male B. indicus and female B. taurus. The phylogenetic pattern of Yunnan cattle was consistent with the recently described cattle matrilineal pool from China and indicated more contribution to the Yunnan cattle from B. indicus than from B. taurus.     

Genetic diversity of Bangladeshi native chickens based on complete sequence of mitochondrial DNA D-loop region

ABSTRACT

1. The aim of this study was to explore genetic diversity and possible origin of Bangladeshi (BD) native chickens. The complete mtDNA D-loop region was sequenced in 60 chickens representing five populations; naked neck, full feathered, Aseel, Hilly and autosomal dwarf. The 61 reference sequences representing different domestic chicken clades in China, India, Laos, Indonesia, Myanmar, and other Eurasian regions were included. The mtDNA D-loop sequence polymorphism and maternal origin of five BD populations were analysed.

2. A total of 35 polymorphic sites, and 21 haplotypes were detected in 60 mtDNA D-loop sequences. The haplotype and nucleotide diversity of the five populations were 0.921 ± 0.018 and 0.0061 ± 0.0019, respectively. Both mtDNA network and phylogenetic analysis indicated four clades (four haplogroups) in BD populations (21 haplotypes) along with 61 reference haplotypes. Clade E contained the most individuals (20) and haplotypes (11) of BD chickens, followed by clade D (17, 6), clade C (12, 2) and clade F (11, 2), respectively.

3. The higher number of unique haplotypes found in Yunnan, China, suggested that the origin of BD chickens was in this region. The haplotypes from different haplogroups were introduced in Bangladeshi chickens from India, China and Myanmar. The phylogenetic tree showed a close relationship of BD chickens with the clusters from India, China, Myanmar and Laos, and indicated the dispersion of BD chickens from these sources. The phylogenetic information revealed high genetic diversity of BD chickens because of their origin from different lineages with high genetic variation and distance, which was determined from four cluster and neighbour-joining trees.

4. In conclusion, BD populations had high genetic diversity. The mtDNA network profiles and phylogenetic trees showed multiple maternal origins of BD chickens from India, China, Myanmar and Laos.     

Estimation of genetic parameters for carcass defects of Japanese Black cattle in Kagoshima

Cattle exhibit a range of carcass defects, including blood splash (BLS), intramuscular edema (INE), muscle steatosis (MUS), bruising (BR), trim loss (TRL) and others (OTH). These defects lower the carcass value and can result in significant economic loss to producers. We estimated the incidence, relationship with inbreeding coefficients and genetic parameters of carcass defects in Japanese Black cattle using 561 619 carcass records from Kagoshima, Japan during April 1988 through March 2011. The defect incidence ranged from 0.22% for TRL to 5.73% for BR. The incidence of MUS and BR increased from 1.21% to 6.57% and from 1.06% to 9.31%, respectively. The incidence of INE peaked at 7.44% in 1999 and decreased thereafter. We observed a positive linear relationship between the defect incidence and the inbreeding coefficients in MUS, BR and TRL (P < 0.01). The heritabilities estimated by univariate animal model with Gibbs sampling for BLS, INE, MUS, BR and TRL were 0.24, 0.06, 0.18, 0.05 and 0.02, respectively. The contribution of farm variance to phenotypic variance was negligible (0.01 to 0.04). Significant genetic correlations of TRL were estimated with MUS (0.63) and BR (0.63). Our results suggest that genetic factors contribute to the incidence of BLS and MUS.