Genetic diversity present within the near-complete mtDNA genome of 17 breeds of indigenous Chinese pigs

The genetic diversity present within the near-complete mitochondrial genome (15,982 bp) was determined from 17 indigenous Chinese pig breeds and 3 European breeds. Animals were selected from 17 Chinese breeds that reflect the large phenotypic diversity of Chinese pigs and represent each of the six breed types, which are grouped based on morphological characteristics. Analysis of nucleotide diversity confirmed a high level of divergence between animals of European versus Asian origin; however, much more limited variation was observed between the 17 indigenous Chinese breeds. Each had a unique haplotype, but the lowest pairwise sequence divergence was only 0.01 +/- 0.01%, observed between the Tongcheng and Yushan Black. Comparison of control region sequence diversity revealed the 17 Chinese breeds contain a lower average pairwise distance (0.61 +/- 0.19%) than a group of European commercial breeds (0.91 +/- 0.21%). The dendrogram constructed from the near-complete mtDNA sequences showed the Chinese sequences loosely clustering into two groups. Although some correspondence with geographic origin was present, notable differences between the dendrogram and the traditional pig breed grouping system were observed.     

Genetic diversity and population structure of six Chinese indigenous pig breeds in the Taihu Lake region revealed by sequencing data

The Chinese indigenous pig breeds in the Taihu Lake region are the most prolific pig breeds in the world. In this study, we investigated the genetic diversity and population structure of six breeds, including Meishan, Erhualian, Mi, Fengjing, Shawutou and Jiaxing Black, in this region using whole‐genome SNP data. A high SNP with proportions of polymorphic markers ranging from 0.925 to 0.995 was exhibited by the Chinese indigenous pigs in the Taihu Lake region. The allelic richness and expected heterozygosity also were calculated and indicated that the genetic diversity of the Meishan breed was the greatest, whereas that of the Fengjing breed was the lowest. The genetic differentiation, as indicated by the fixation index, exhibited an overall mean of 0.149. Both neighbor‐joining tree and principal components analysis were able to distinguish the breeds from each other, but structure analysis indicated that the Mi and Erhualian breeds exhibited similar major signals of admixture. With this genome‐wide comprehensive survey of the genetic diversity and population structure of the indigenous Chinese pigs in the Taihu Lake region, we confirmed the rationality of the current breed classification of the pigs in this region.     

Population genetic analyses of seven Chinese indigenous chicken breeds in a context of global breeds

Jiangxi province in China is rich in indigenous chicken breeds, which have diverse phenotypes and represent a valuable genetic resource for further genetic improvement of modern breeds. Here, we conducted a series of analyses to reveal genetic diversity, phylogenetic relationships and population structure of seven chicken breeds in Jiangxi province in the context of nine non‐local chicken breeds, using 600K SNP data. We show that Jiangxi indigenous breeds have more abundant nucleotide diversity than do European local and commercial breeds. Among Jiangxi breeds, Dongxiang Blue‐eggshell (DX) and Chongren Partride (CR) display remarkably reduced genetic diversity, as the two breeds exhibit increased inbreeding coefficients, runs of homozygosity, extent of linkage disequilibrium and reduced expected heterozygosity. DX, CR and Taihe Silkie (TH) represent three ancestral lineages of the Jiangxi chicken and display genetic differentiation from the other four Jiangxi breeds, which show a signature of admixture with European commercial breeds. These findings provide insight for the establishment of an efficient conservation program for Jiangxi chicken breeds. Considering the current status of genetic diversity and ancestral representativeness, particular attention should be paid to DX, CR and TH chickens.     

The genetic diversity and population structures of indigenous pig breeds in Zhejiang Province revealed by GGRS sequencing

Chinese indigenous pigs in Zhejiang Province are well known for their high fecundity. In order to verify breed subdivision at the genomic level, we investigated genetic diversity and population structure of seven breeds and made comparisons with three Western pig breeds using next‐generation sequencing data. Parameters obtained from allelic richness and proportion of polymorphic markers indicated that the genetic diversity of the Chinese indigenous pigs was higher than that of the Western pigs, with the highest and lowest values found in the Chaluand and the Landrace pigs respectively. Both neighbor‐joining tree and principal components analysis could distinguish breeds from one another and structure analysis showed less differentiation among Western pigs than among the Chinese pigs. The average linkage disequilibrium decay over distance was significantly less in the Chinese pigs compared with the Western pigs, ranging from 188.2 to 280.6 kb for the Chinese pigs and 680.3 to 752.8 kb for the Western breeds and showing an average r² threshold value of 0.3. Results obtained from high‐density SNP comparison over the whole genome on genetic diversity and population structure were in agreement with the current breed classification of the pigs in Zhejiang Province. More importantly, the results presented here advances our current understanding of the genomic biology of Chinese indigenous pigs in Zhejiang Province and allows for implementation of conservation strategies in additional breeds.     

Population structure and genetic diversity of four Henan pig populations

To investigate the population structure and genetic diversity of Henan indigenous pig breeds, samples from a total of 78 pigs of 11 breeds were collected, including four pig populations from Henan Province, three Western commercial breeds, three Chinese native pig breeds from other provinces and one Asian wild boar. The genotyping datasets were obtained by genotyping‐by‐sequencing technology. We found a high degree of polymorphism and rapid linkage disequilibrium decay in Henan pigs. A neighbor‐joining tree, principal component analysis and structure analysis revealed that the Huainan and Erhualian pigs were clustered together and that the Queshan black pigs were clearly grouped together but that the Nanyang and Yuxi pigs were extensively admixed with Western pigs. In addition, heterozygosity values might indicate that Henan indigenous pigs, especially the Queshan black and Huainan pigs, were subjected to little selection during domestication. The results presented here indicate that Henan pig breeds were admixed from Western breeds, especially Nanyang and Yuxi pigs. Therefore, establishment of purification and rejuvenation systems to implement conservation strategies is urgent. In addition, it is also necessary to accelerate genetic resources improvement and utilization using modern breeding technologies, such as genomic selection and genome‐wide association studies.     

Genetic evidence for the introgression of Western NR6A1 haplotype into Chinese Licha breed associated with increased vertebral number

There is evidence that NR6A1 is a strong candidate for being a causal gene underlying vertebral number in pigs. The Licha Black is one of the leanest Chinese indigenous pig breeds, having an average vertebral number of 21.5. The introgression of Western germplasm into Licha Black, resulting in increased vertebral number, has been assumed but is not confirmed. This study detected allele frequencies of the NR6A1 causative mutation (c.575T>C) in 519 pigs from three Western and seven Chinese breeds including Licha Black, and evaluated the genetic variation in a 650-kb region containing NR6A1 in the 10 breeds. Allele T for increased vertebral number was fixed in Western breeds. In contrast, this allele was very rare in most of the Chinese native breeds. Notably, the T allele was present in the Licha Black at a rather higher frequency (0.585) and in the Laiwu at lower frequency (0.250). As expected, selection pressure has wiped out the genetic variability in the 650 kb region in Western breeds. Conversely, Chinese indigenous breeds showed a high degree of genetic variability in this region. However, the Licha Black displayed dramatically reduced heterozygosity at the loci proximal to the causative mutation. Moreover, a high proportion (45.9%) of Licha Black pigs and a small number (21%) of Laiwu pigs had the Western NR6A1 haplotype, and the two breeds showed closer relationships with Western commercial breeds than other Chinese breeds in the phylogenic tree. When the results are taken together, this study supports the assumption that the Western NR6A1 haplotypes were introduced into Licha Black and possibly Laiwu and are associated with increased vertebral number.     

中国主要地方品种猪血液蛋白遗传多样性研究

实验采用水平板淀粉凝胶电泳技术,对中国地方猪五大类型９个品种,１个引入品种共２０１个个体进行了遗传多样性分析。共分析遗传座痊３０个,其中只有ＭＤＨ、ＰＥＰＢ、Ａ从位具有多在记民生。中国主要地方猪品种的多态座位百分比Ｐ＝０．２００,平均杂２合度Ｈ＝０．０６５,平均等位基因数Ａ＝１．３００。根据基因频率采用ＰＨＹＬＩＰ３．５ｃ民计算Ｎｅｉ氏遗传距离,然后用“ＮＥＩＧＨＢＯＲ”程序分别构建Ｎｅｉｇｈｂｏ     

24个中外猪种(群)的AFLP多态性及其群体遗传关系

利用12对AFLP引物组合检测了19个中国地方猪种（群）,1个培育猪种和4个欧美引进猪种混合基因组DNA的遗传变异,根据AFLP分析结果计算了24个猪种（群）间的遗传相似系数,据此构建了UPGMA聚类关系图,结果表明,AFLP标记有着很高的多态检测效率（Ai),平均每个引物组合检测到17.3个多态标记,非常适合于猪种（群）遗传多样性分析和品种鉴定;中国地方猪种与欧美引进猪种间的遗传分化十分明显,两类猪群间的亲缘关系较远;南昌白猪与大白猪,铅山黑猪与玉山黑猪有着极近的亲缘关系,分别与其育成历史,地理分布和RAPD分析结果相一致。另外还对部分猪种（群）的聚类分析结果与其形态学,地理分布和现行分类情况不相一致的原因进行了探讨。     

TYR基因外显子1的序列变异

为了分析家猪与野猪的遗传多样性及起源,测定了来自１２个中国地方家猪品种、３个欧洲引进猪品种以及8个中国野猪和2个越南野猪共36个个体的酪氨酸酶基因（TYR）外显子1的序列,共检出６个单核苷酸多态性位点（SNPs）,且这6个位点的变异均为同义突变,根据这些变异可将酪氨酸酶基因DNA序列归结为４种单倍型。结合已发表的数据,构建了简约中介网络图。 在网络图中,单倍型TYR*2主要为欧洲家猪与欧洲野猪和三条亚洲家猪染色体。大部分亚洲家猪和野猪共享单倍型TYR*1,表明这是一个亚洲类型的单倍型;同时也有部分欧洲家猪与野猪携带这一单倍型。 而单倍型TYR*3和TYR*4为本研究检测到的稀有单倍型,这两种单倍型主要由中国家猪与亚洲野猪组成。这种网络图结构支持家猪的欧洲和亚洲独立起源学说,同时也表明相当部分的欧洲家猪品种受到亚洲猪的基因渗透,而少量中国家猪和日本野猪也受到了欧洲猪的基因渗透。     

Genome‐wide genetic variation discovery in Chinese Taihu pig breeds using next generation sequencing

The Chinese Taihu pig breeds are an invaluable component of the world's pig genetic resources, and they are the most prolific breeds of swine in the world. In this study, the genomes of 252 pigs of the six indigenous breeds in the Taihu Lake region were sequenced using the genotyping by genome reducing and sequencing approach. A total of 950 million good reads were obtained using an Illumina Hiseq2000 at an average depth of 13× (for SNP calling) and an average coverage of 2.3%. In total, 122 632 indels, 31 444 insertions, 44 056 deletions and 455 CNVs (copy number variants) were identified in the genomes of the pigs. Approximately 2.3% of these genetic markers were mapped to gene exon regions, and 25% were in QTL regions related to economically important traits. The KEGG pathway or GO enrichment analyses revealed that genetic variants assumed to be large‐effect mutations were significantly overrepresented in 22 SNP, 56 indel, 26 insertion, 28 deletion and three CNV gene sets. A total of 343 breed‐specific SNPs were also identified in the six Chinese indigenous pigs. The findings from this study can contribute to future investigations of the genetic diversity, population structure, positive selection signals and molecular evolutionary history of these pigs at the genome level and can serve as a valuable reference for improving the breeding and cultivation of these pigs.     

Uncontrolled admixture and loss of genetic diversity in a local Vietnamese pig breed

The expansion of intensive livestock production systems in developing countries has increased the introduction of highly productive exotic breeds facilitating indiscriminate crossbreeding with local breeds. In this study, we set out to investigate the genetic status of the Vietnamese Black H'mong pig breed by evaluating (1) genetic diversity and (2) introgression from exotic breeds. Two exotic breeds, namely Landrace and Yorkshire used for crossbreeding, and the H'mong pig population from Ha Giang (HG) province were investigated using microsatellite markers. Within the province, three phenotypes were observed: a White, a Spotted and a Black phenotype. Genetic differentiation between phenotypes was low (0.5-6.1%). The White phenotypes showed intermediate admixture values between exotic breeds and the Black HG population (0.53), indicating a crossbreed status. Management practices were used to predict the rate of private diversity loss due to exotic gene introgressions. After 60 generations, 100% of Black private alleles will be lost. This loss is accelerated if the admixture rate is increased but can be slowed down if the mortality rate (e.g., recruitment rate) is decreased. Our study showed that a large number of markers are needed for accurately identifying hybrid classes for closely related populations. While our estimate of admixture still seems underestimated, genetic erosion can occur very fast even through indiscriminate crossbreeding.     

Genetic diversity of autochthonous pig breeds analyzed by microsatellite markers and mitochondrial DNA D-loop sequence polymorphism

The evaluation of the genetic structure of autochthonous pig breeds is very important for conservation of local pig breeds and preservation of diversity. In this study, 18 microsatellite loci were used to detect genetic relationship between autochthonous pig breeds [Black Slavonian (BS), Turopolje pig (TP), and Croatian wild boar] and to determine phylogenetic relationship among Croatian autochthonous pig breeds and certain Asian and European pigs using the mitochondrial DNA (mtDNA) D-loop sequence polymorphism. Relatively high degree of genetic variation was found between the observed populations. The analysis of mtDNA showed that haplotypes of the studied pig populations are different from the other European and Chinese haplotypes. BS pigs showed some similarities with Mangalitsa and Duroc breeds. The genetic distances of TP can be explained by high degree of inbreeding during the past century. Despite the European origin of Croatian pig breeds with some impact of Chinese breeds in the past, the results of present study show that genetic diversity is still pronounced within investigated breeds. Furthermore, the genetic diversity is even more pronounced between Croatian breeds and other European and Chinese pig breeds. Thus, conservation of Croatian pig breeds will contribute to overall genetic diversity preservation of pig breeds.     

我国6个地方绵羊品种微卫星DNA多态性研究

利用聚丙烯酰胺凝胶电泳技术研究了我国蒙古羊、乌珠穆沁羊、哈萨克羊、阿勒泰羊、滩羊和藏绵羊 6个地方绵羊品种 17个微卫星标记的多态性 ,以探讨其遗传多样性、起源分化及群体间的遗传亲缘关系。结果表明微卫星标记不同位点间遗传多样性差异极显著 (P <0 0 1) ,群体间多态信息含量 (PIC)、近交程度 (Fis)和观察杂合度 (Obs .Het)差异不显著 ,但基因多样性 (genediversity)和期望杂合度 (Exp .Het)差异显著 (P <0 0 5 )。所研究的我国 6个地方绵羊品种与欧洲品种具有相似的遗传多样性 ,但具有较高的近交系数。个体和群体的聚类分析结果提示我国地方绵羊品种可能起源于两类祖先。群体间的聚类分析结果还表明 ,蒙古羊与乌珠穆沁羊分化不明显且具有较近的遗传亲缘关系 ,蒙古羊与藏绵羊间分化明显且具有较远的遗传亲缘关系。滩羊、阿勒泰羊以及藏绵羊间也具有较近的遗传亲缘关系。所研究的我国 6个地方绵羊品种的遗传分化 (Fst)与西班牙绵羊品种接近 ,但明显小于欧洲其他绵羊品种     

Genetic diversity of Chinese indigenous sheep breeds inferred from microsatellite markers

To determine the genetic diversity and phylogenetic relationships among Chinese sheep, 10 indigenous breeds and one introduced breed were genotyped for 19 microsatellite loci. The mean number of alleles per breed ranged from 5.44 (Guide Black Fur sheep) to 9.13 (Ujumqin sheep and Hulunbeier sheep), the expected heterozygosity varied from 0.623 (Guide Black Fur sheep) to 0.737 (Zhaotong sheep), and the allelic richness ranged from 5.169 (Guide Black Fur sheep) to 7.610 (Zhaotong sheep). The deviation from Hardy–Weinberg equilibrium (HWE) was statistically significant (P < 0.05) at three loci (SRCRSP5, OarAE129 and DYMS1) in most of the breeds. Chinese sheep breeds had maintained a high level of within-population genetic differentiation (95.23%), with the remainder explained by differentiation among populations (4.77%). The genetic differentiation pattern and genetic relationships among Chinese sheep breeds displayed a high consistency with the traditional classification. Both the Bayesian cluster and principal component analyses showed a reliable clustering pattern, which revealed three major clusters in Chinese indigenous sheep (Mongolian sheep, Kazakh sheep and Tibetan sheep), except Zhaotong and Guide Black Fur sheep. There were probably caused by different breeding history, geography isolation and different levels of inbreeding. This study will help to interpret the genetic characters of Chinese indigenous sheep and benefit to the future conservation programs.     

The phylogeny of Chinese indigenous pig breeds inferred from microsatellite markers

A genetic study of 32 local Chinese, three foreign pig breeds [Duroc (DU), Landrace and Yorkshire], and two types of wild boar (Hainan and Dongbei wild boar) based on 34 microsatellite loci was carried out to clarify the phylogeny of Chinese indigenous pig breeds. The allele frequencies, effective numbers of alleles, and the average heterozygosity within populations were calculated. The results showed that the genetic variability of the Lingao pig was the largest, while the Jiaxing pig was the lowest. The greatest distance between domestic pigs was found between Shanggao and DU pig and the shortest was found between Wuzhishan and Lingao pig, respectively. A neighbour-joining tree constructed from Modified Cavalli-Sforza genetic distances divided Chinese pigs into two clusters; four subclusters were also identified. Our results only partly agree with the traditional types of classification and also provide a new relationship among Chinese local pig breeds. Our data also confirmed that Chinese pig breeds have a different origin from European/American breeds and can be utilized in programmes that aim to maintain Chinese indigenous pig breeds.     

Microsatellite and Mitochondrial DNA Study of Native Eastern European Cattle Populations: The Case of the Romanian Grey

The Eastern European Grey cattle are regarded as the direct descendants of the aurochs (Bos taurus primigenius). Nowadays in Romania, less than 100 Grey animals are being reared and included in the national gene reserve. We examined the genetic diversity among Romanian Grey, Brown, Spotted and Black and White cattle breeds, with a particular focus on Romanian Grey through the use of (i) 11 bovine specific microsatellite markers on 83 animals and (ii) 638 bp length of mitochondrial DNA (mtDNA) D-loop region sequence data from a total of 81 animals. Both microsatellite and mtDNA analysis revealed a high level of genetic variation in the studied breeds. In Romanian Grey a total of 100 alleles were found, the mean number of observed alleles per locus was 9.091; the average observed heterozygosity was 0.940; the Wright’s fixation index (F_IS) was negative (-0.189) and indicates that there is no inbreeding and no selection pressure. MtDNA analysis revealed 52 haplotypes with 67 variable sites among the Romanian cattle breeds without any insertion or deletion. Haplotype diversity was 0.980 ± 0.007 and ranged from 0.883 ± 0.056 (Brown) to 0.990 ± 0.028 (Spotted and Black and White). The highest genetic variability of the mtDNA was recorded in the Grey breed, where 18 haplotypes were identified. The most frequent mtDNA D-loop region belonged to T3 haplogroup (80.247%), which was found across all studied breeds, while T2 haplotypes (16.049%) was only found in Grey, Spotted and Black and White genotypes. The T1 haplotypes (3.704%) were found in the Grey and Spotted. The current results contribute to the general knowledge on genetic diversity found in Eastern European cattle breeds and could prove a valuable tool for the conservation efforts of animal genetic resources (FAnGR).     

绵羊线粒体DNA D-loop区串联重复序列变异研究

对来自69个我国地方绵羊品种和8个国外引入品种共计77个个体线粒体DNA控制区长度为75bp的串联重复序列进行了测序分析。在309个重复序列中检测到28个变异位点,其中7个为具有2个变异体的单现突变,1个为具有3个变异体的单现突变,20个为具有2个变异体的简约位点。由28个变异位点中归纳出63个单倍型,其中单倍型Ⅰ和单倍型Ⅲ具有较高的比例,分别为12．94％和30.42％。研究结果揭示我国地方绵羊可能起源于两个母系祖先。哈萨克羊和阿勒泰羊间以及蒙古羊和乌珠穆沁羊间分别具有较近的亲缘关系且没有明显的遗传分化。藏绵羊、蒙古羊和乌珠穆沁羊相对哈萨克羊和阿勒泰羊而言具有较低的遗传多样性。     

Study on Tandem Repeat Sequence Variation in Sheep mtDNA D-loop Region

The 75-nt-long tandem repeat sequence in the control region of mtDNA of 77 individuals, of which 69 were from different indigenous sheep breeds in China and 8 were from imported breeds, was sequenced and analyzed to investigate the origin and differentiation of Chinese indigenous sheep breeds and also the genetic diversities and relationships among them. A total of 28 variable sites were detected within 309 repeated sequences, among which 7 sites were singleton variable sites with two variants, 1 site was a singleton variable site with three variants, and 20 sites were parsimony informative sites with two variants. A total of 63 haplotypes were sorted from 28 polymorphic sites, among which two main and basic haplotypes, namely, Hap 1 and Hap 3 were present at a much higher proportion, at 12.94% and 30.42%, respectively. It could be inferred that Chinese indigenous sheep breeds originated from two maternal ancestors because of the maternal inheritance characteristics of the mtDNA. Altay sheep and Kazakstan sheep are closely related and do not differentiate significantly. Mongolian sheep and Ujumuqin sheep also share a close relationship. Tibetan sheep, Mongolian sheep, and Ujumuqin sheep have lower genetic diversity than Altay sheep and Kazakstan sheep.     

应用Weitzman方法分析华中型猪品种的遗传多样性

本文根据华中型20个猪品种27个微卫星DNA标记的研究数据, 应用Weitzman方法, 即通过估计总体遗传多样性、期望多样性、品种对总体遗传多样性的贡献、边际遗传多样性、保种潜力等指标, 评估华中型20个猪品种的遗传多样性, 并通过构建品种间遗传多样性的最大似然树, 图示化展示20个品种间遗传多样性的相互关系。20个华中型猪品种的总体遗传多样性是11,707, 期望多样性占总的遗传多样性的66.96%, 金华猪、皖南花猪、嵊县花猪和乐平猪是对总体遗传多样性贡献最大的4个品种, 其贡献率分别是8.90%、7.46%、7.40%和7.04%, 保种潜力最大的4个品种分别是金华猪、嵊县花猪、杭猪和大花白猪。根据遗传多样性进行聚类分析, 大致可将华中型猪分为3类: 大围子猪、沙子岭猪、宁乡猪等分布于湖南、湖北的品种为一类; 南城猪、嵊县花猪与杭猪聚成另一类; 金华猪与皖南花猪单独聚成一类。研究结果可为我国华中型地方猪种遗传多样性的最大化保护和利用提供科学决策依据, 本文也对Weitzman方法在应用中的关键性问题进行了探讨。     

Biodiversity of pig breeds from China and Europe estimated from pooled DNA samples: differences in microsatellite variation between two areas of domestication

Microsatellite diversity in European and Chinese pigs was assessed using a pooled sampling method on 52 European and 46 Chinese pig populations. A Neighbor Joining analysis on genetic distances revealed that European breeds were grouped together and showed little evidence for geographic structure, although a southern European and English group could tentatively be assigned. Populations from international breeds formed breed specific clusters. The Chinese breeds formed a second major group, with the Sino-European synthetic Tia Meslan in-between the two large clusters. Within Chinese breeds, in contrast to the European pigs, a large degree of geographic structure was noted, in line with previous classification schemes for Chinese pigs that were based on morphology and geography. The Northern Chinese breeds were most similar to the European breeds. Although some overlap exists, Chinese breeds showed a higher average degree of heterozygosity and genetic distance compared to European ones. Between breed diversity was even more pronounced and was the highest in the Central Chinese pigs, reflecting the geographically central position in China. Comparing correlations between genetic distance and heterozygosity revealed that China and Europe represent different domestication or breed formation processes. A likely cause is a more diverse wild boar population in Asia, but various other possible contributing factors are discussed.