Genetic structure in Atlantic brown trout (Salmo trutta L.) populations in the Iberian peninsula: evidence from mitochondrial and nuclear DNA analysis

Brown trout (Salmo trutta L.) was sampled in rivers belonging to three different Spanish basins in order to analyse the distribution of genetic variability. The genetic analysis was performed by using two systems and techniques: nuclear DNA was screened through random amplified polymorphic DNAs (screening 2 × 10⁵ bp of the whole genome), and mitochondrial DNA (mtDNA) through sequencing of the hypervariable control region. Genetic distances between the populations were similar using either analysis although some differences arise. For example, some populations of the Tajo basin were very close through nuclear analysis but more distant using mtDNA. Differences between the two DNA sources could be the result of a different evolutionary rate, and the fact that mtDNA is maternally transmitted and differences in sex migration rates will influence the patterns of genetic variation between the transmitted DNAs. Total variation was partitioned using amova showing a clear subdivision among basins although intrapopulation variation remained as high as 62%. A correspondence analysis defined the differences in a three‐dimensional way, clustering the populations according to their common basin. When mtDNA was sequenced, higher variability was noted in the segment between 400 and 600 bp of the whole D‐loop sequence, suggesting that these 200 bp improved the analysis of the variability more than sequencing the t‐RNA ends of the control region. A comparison was made between the t‐RNA^Pro ends of the 10 populations screened here and the rest of the published sequences found in the literature, leading to a concentration of these populations in group IV which includes all trouts which originate in the Atlantic. The analyses performed suggest that a high genetic variability is present in all populations and that although there has been a probable interference from stocked strains introduced to increase population density, this was only detectable through the variance between rivers which reflect different policies according to the region where the basin is located. However, the genetic analysis using the two approaches allows the control of the natural populations avoiding a loss of their genetic potential.     

Mitochondrial D‐loop analysis reveals low diversity in Mangalica pigs and their relationship to historical specimens

The genetic relationship between 195 Mangalica and 79 non‐Mangalica pigs was studied using mitochondrial D‐loop SNP genotyping. Altogether, 35 polymorphic sites and 27 haplotypes were identified. Of the haplotypes, eight and 16 are Mangalica and non‐Mangalica specific, respectively, while three contain both Mangalica and non‐Mangalica individuals. Genetic distance values and phylogenetic analysis indicate that Mangalica individuals are very closely related, and five haplotypes represent approximately 92% of the Mangalica pigs involved in the study, thus determining the major maternal lineages. In contrast to previous microsatellite studies, individuals of Mangalica could not be distinguished as three separate breeds using mtDNA genotyping. Comparing modern and archaeological mtDNA sequences revealed that present day Mangalica is related to pigs that lived in the Carpathian basin where postulated ancestors of Mangalica also lived. This is the first DNA‐based genetic evidence to support the described breeding history of Mangalica.     

Mitochondrial DNA sequence variation in Hippopotamus amphibius from Kruger National Park,Republic of South Africa

Populations of Hippopotamus amphibius have declined throughout Africa in recent years, and are expected to decline further. An understanding of the population genetics of individual populations of hippos is necessary for effective management. To that end, we sequenced a portion of the mitochondrial DNA (mtDNA) control region or D-loop from 37 H. amphibius, from six herds in the central region of Kruger National Park (KNP), Republic of South Africa. We amplified a 453 bp segment by PCR, and identified 21 polymorphic sites and seven haplotypes. All of these haplotypes are private alleles, not found in other populations of hippos from southern Africa. Overall nucleotide diversity (π) was 0.01739, and haplotype diversity (hd) was 0.8273, within the range observed in other parts of Africa. Mismatch analysis conformed more closely to a model of constant population size than either rapid demographic or spatial expansion. An analysis of molecular variance demonstrated no significant differentiation among herds, and Mantel tests showed no significant relationship between geographic and genetic distance among herds separated by up to 47 km (measured as Euclidean [x,y] distance) or 77 km (measured along rivers). Over this range, the population appears to be a single panmictic unit. A test of the hypothesis that calves are more likely to share a mtDNA haplotype with an adult female in the same herd than an adult female from a different herd was not significant.     

Polymorphism and evolutionary profile of mitochondrial DNA control region inferred from the sequences of Pakistani goats

Complete mitochondrial DNA (mtDNA) control region of 30 Pakistani domestic goats was sequenced to investigate the genetic diversity and organization. Twenty‐two new haplotypes were observed and all were classified into mt‐lineage A. Phylogenetic analysis revealed two distinct clusters in mt‐lineage A, A1 and A2. A 17 bp deletion and a 76 bp insertion were detected in the L‐domain and observed 10 and one animals, respectively, in 232 Pakistani domestic goats. These remarkable deletion/insertion events would be useful to investigate mtDNA diversity within the highly divergent mt‐lineage A. In analysis of the control region feature, the caprine mtDNA was A/T rich as observed for other artiodactyls. Four conserved regions, Block A in the L domain, the C‐domain, Block B and CSB1 in the R domain, were defined as well as in the other species.     

Mitochondrial DNA variation of indigenous goats in Narok and Isiolo counties of Kenya

Phylogenetic relationships among and genetic variability within 60 goats from two different indigenous breeds in Narok and Isiolo counties in Kenya and 22 published goat samples were analysed using mitochondrial control region sequences. The results showed that there were 54 polymorphic sites in a 481‐bp sequence and 29 haplotypes were determined. The mean haplotype diversity and nucleotide diversity were 0.981 ± 0.006 and 0.019 ± 0.001, respectively. The phylogenetic analysis in combination with goat haplogroup reference sequences from GenBank showed that all goat sequences were clustered into two haplogroups (A and G), of which haplogroup A was the commonest in the two populations. A very high percentage (99.90%) of the genetic variation was distributed within the regions, and a smaller percentage (0.10%) distributed among regions as revealed by the analysis of molecular variance (amova ). This amova results showed that the divergence between regions was not statistically significant. We concluded that the high levels of intrapopulation diversity in Isiolo and Narok goats and the weak phylogeographic structuring suggested that there existed strong gene flow among goat populations probably caused by extensive transportation of goats in history.     

Genetic diversity and matrilineal genetic origin of fat-rumped sheep in Ethiopia

Ethiopia is home to a diverse gene pool of indigenous sheep populations. Therefore, a better understanding of genetic variation holds the key to future utilization through conservation. Three of these breeds, Afar, Blackhead Somali, and Hararghe Highland, are found in eastern Ethiopia where they contribute significantly to the livelihood of most pastoralist, agro-pastoralist, and smallholder farmers. These indigenous sheep are recognized on the basis of morphotype and their genetic distinction remains unknown. Here, to assess genetic variation, and matrilineal genetic origin and relationship of fat-rumed sheep found in eastern Ethiopia, 300 individuals from the three breeds were genotyped for 22 microsatellite markers and sequenced for the mitochondrial DNA displacement loop (mtDNA d-loop) region. The overall H_O and H_E were 0.57 and 0.75, respectively. Differentiation statistics revealed that a high proportion (97%) of the total genetic variation was explained by differences between individuals within populations. Genotype assignment independent of the population of origin showed K?=?2 to be the optimum number of genetic backgrounds present in the dataset. This result was further confirmed by mtDNA D-loop sequences comparison in which the matrilineal genetic origin of eastern Ethiopia sheep is from two haplotype groups (types A and B) among the five haplotypes globally observed. Taken together, our findings suggest that the sheep populations from three breeds originated from two ancestral genetic backgrounds that may have diverged prior to their introduction to Ethiopia. However, to obtain a complete picture of the evolutionary dynamics of Ethiopian indigenous sheep, more samples and populations from within and outside of the country will need to be analyzed.

     

Genetic diversity and structure of the West Balkan Pramenka sheep types as revealed by microsatellite and mitochondrial DNA analysis

Several different phenotypes of the native Pramenka sheep have been developed in the Balkan region for different environmental and socio‐cultural conditions. Animals from seven West Balkan Pramenka sheep types were analysed for 15 microsatellite markers and for mitochondrial DNA (mtDNA) and the results were used to assess genetic variation within and among the types and to infer the genetic population structure of the Pramenka sheep. Mean expected heterozygosity and allelic richness over the microsatellite loci and sheep types were 0.78 and 7.9, respectively. A Bayesian statistical method for estimating hidden genetic structure suggested that a core of the largest panmictic population was formed by Serbian, Kosovan, Bosnian, Montenegrin and Albanian types, while Croatian and Macedonian types comprised two other main populations, respectively. Mitochondrial DNA analysis revealed two mtDNA haplogroups in the Pramenka sheep, B and A, with a frequency of 93.7% and 6.3%, respectively. A total of 60 mtDNA haplotypes were found in 64 animals sequenced, and the mean nucleotide and haplotypic diversities over the types were 0.013 and 0.945, respectively. Molecular analysis suggests that the West Balkan Pramenka sheep types have their origins in two distinct maternal lineages of domestic sheep and different Pramenka phenotypes tend to form few panmictic populations. The Pramenka sheep represents a valuable resource of genetic diversity in sheep.     

Genetic structure of the oriental white stork (Ciconia boyciana): implications for a breeding colony in a non‐breeding area

The oriental white stork (Ciconia boyciana) is a threatened species, and their numbers are still in decline due to habitat loss and poaching. China is a breeding and main wintering area for this animal and in recent years some individuals have been found breeding in wintering areas and at some stopover sites. These new breeding colonies are an exciting sign, however, little is understood of the genetic structure of this species. Based on the analysis of a 463‐bp mitochondrial DNA (mtDNA) control region, we investigated the genetic structure and genetic diversity of 66 wild oriental white storks from a Chinese population. We analyzed the sequences of 66 storks obtained in this study and the data of 17 storks from a Japanese population. Thirty‐seven different haplotypes were detected among the 83 samples. An analysis of molecular variance showed a significant population subdivision between the two populations (F_ST= 0.316, P < 0.05). However, the phylogenetic analysis revealed that the samples from the different populations did not form separate clusters and that there were genetic exchanges between the two populations. Compared with the Japanese population, the Chinese population had a relatively higher genetic diversity with a haplotype diversity (hπ SD) of 0.953 ± 0.013 and a nucleotide diversity (π± SD) of 0.013 ± 0.007. The high haplotype diversity and low nucleotide diversity indicate that this population might be in a rapidly increasing period from a small effective population. A neighbor‐joining tree analysis indicated that genetic exchange had occurred between the newly arisen southern breeding colony and the northern breeding colony wintering in the middle and lower Yangtze River floodplain. These results have important implications for the conservation of the oriental white stork population in China.     

Genetic analysis of river,swamp and hybrid buffaloes of north‐east India throw new light on phylogeography of water buffalo (Bubalus bubalis)

This study analysed buffaloes from north‐east India and compared their nuclear and mitochondrial DNA variations with buffaloes of mainland India, China, Mediterranean and South‐East Asia. Microsatellite genotypes of 338 buffaloes including 210 from six north‐east Indian buffalo populations and three mainland Indian breeds were analysed to evaluate their genetic structure and evolutionary relationships. Phylogenetic analysis and multidimensional scaling plot of pairwise F_ST revealed the clustering of all swamp‐type buffaloes of north‐east India with Lower Assamese (significantly hybrid type) buffaloes in one plane and all the mainland river buffaloes in another plane while the upper Assamese buffaloes being distinct from both these clusters. Analysis of mtDNA D‐loop region of 530‐bp length was performed on 345 sequences belonging to 23 buffalo populations from various geographical regions to establish the phylogeography of Indian water buffalo. The swamp buffaloes of north‐east India clustered with both the lineages of Chinese swamp buffalo. Multidimensional scaling display of pairwise F_ST derived from mitochondrial DNA data showed clustering of upper Assamese, Chilika and Mediterranean buffaloes distinctly from all the other Indian buffalo populations. Median‐joining network analysis further confirmed the distinctness and ancestral nature of these buffaloes. The study revealed north‐east region of India forming part of the wider hybrid zone of water buffalo that may probably extend from north‐east India to South‐East Asia.     

Past climate change and recent anthropogenic activities affect genetic structure and population demography of the greater long‐tailed hamster in northern China

The genetic diversity and the spatial structure of a species are likely consequences of both past and recent evolutionary processes, but relevant studies are still rare in East Asia where the Pleistocene climate has unique influences. In this study, we examined the impact of past climate change and recent anthropogenic activities on the genetic structure and population size of the greater long‐tailed hamster (Tscherskia triton), an agricultural rodent pest species in northern China. DNA sequence data of 2 mitochondrial genes and genotypic data of 11 microsatellite DNA loci from 41 populations (545 individuals) were gathered. Phylogenetic and population genetic analyses, as well as species distribution modeling and coalescent simulations, were conducted to infer its historical and demographic patterns and processes. Two deeply diverged mitochondrial clades were recovered. A small one was restricted to the Shandong Peninsula while the main clade was further divided into 3 geographic clusters by their microsatellite DNA genotypes: Northwest, North‐center and Northeast. Divergence dating indicated a Middle‐to‐Late Pleistocene divergence between the 2 clades. Demographic analysis indicated that all 3 and pooled populations showed consistent long‐period expansions during last glacial period; but not during the Holocene, probably due to the impact of climate warming and human disturbances. Conflicting patterns between mtDNA and microsatellite markers imply an anthropogenic impact on North‐center populations due to intensified agricultural cultivation in this region. Our study demonstrated that the impact of past glaciation on organisms in East Asia significantly differs from that of Europe and North America, and human activity is an important factor in determining the genetic diversity of a species, as well as its spatial structure.     

泰国红色原鸡和中国红色原鸡mtDNA控制区遗传多态性和分类关系研究

对泰国红色原鸡Gallus gallus gallus亚种和中国红色原鸡Gallus gallus spadiceus亚种各16个个体mtDNAD-loop序列进行系统分析,测定线粒体D-loop部分序列大小约为560bp,A、C、G、T这4种核苷酸的平均比例分别为13.6%、43.2%、4.3%和38.9%,A+T含量高于G+C含量。结果共发现27个变异位点,颠换和转换之比为0.13,没有观测到插入/缺失情况。测定的6种单倍型中,2个红色原鸡亚种没有共享单倍型,单倍型多样度分别为0.250和0.695,平均核苷酸差异数分别为3.750和10.833,核苷酸多样度分别为0.954%和2.757%。泰国红色原鸡中性检验的Tajima'sD值为-1.800(P<0.05),不符合中性突变。2个红色原鸡亚种间核苷酸分歧度(Dxy)为2.847%,核苷酸净遗传距离(Da)为0.991%。序列群体间的方差组分(Va)占总变异的47.31%,Fst=0.473,差异极显著(P<0.01);群体间mtDNAD-loopFst值也差异显著(P=0.035)。红色原鸡2个亚种具有不同的群体遗传结构,群体之间存在明显的遗传分化,本研究支持这2个亚种并非是同一个亚种的观点。     

Mitochondrial DNA variation and genetic relationships in Spanish donkey breeds (Equus asinus)

In this study, the mitochondrial DNA diversity of six Spanish donkey breeds and two African donkey populations (one from Morocco and the other from Zimbabwe) was analysed. A total of 79 animals were sequenced for 313 bp of the cytochrome b gene, and 91 individuals for 383 bp of the D‐loop region or control‐region. Sequence comparisons and phylogenetic analyses of both Spanish and African populations revealed low diversity. Only six and seven haplotypes respectively were found in cytochrome b and the D‐loop region. Relatively low nucleotide diversity (π) values were detected in these populations. The π values, from the D‐loop region, ranged from 0.0006 to 0.0169 for the Catalana and Andaluza breeds, respectively. The obtained results seem to confirm the existence of two divergent maternal lineages of African origin (Equus asinus africanus and E. a. somaliensis). In this paper the genetic relationships between these breeds are analysed and compared with those obtained in other European populations. Also, the data on the genetic relationships between the populations, obtained from nuclear DNA (microsatellites) and mitochondrial DNA (cytochrome b and D‐loop region) is argued and interpreted.     

The origin of Chinese domestic horses revealed with novel mtDNA variants

The origin of domestic horses in China was a controversial issue and several hypotheses including autochthonous domestication, introduction from other areas, and multiple‐origins from both introduction and local wild horse introgression have been proposed, but none of them have been fully supported by DNA data. In the present study, mitochondrial DNA (mtDNA) sequences of 714 Chinese indigenous horses were analyzed. The results showed that Chinese domestic horses harbor some novel mtDNA haplogroups and suggested that local domestication events may have occurred, but they are not the dominant haplogroups and the geographical distributions of the novel mtDNA haplogroups were rather restricted. Conclusively, our results support the hypothesis that the domestic horses in China originated from both the introduced horses from outside of China and the local wild horses' introgression into the domestic populations. Results of genetic diversity analysis suggested a possibility that the introduced horses entered China through northern regions from the Eurasian steppe.     

Development of the Lipizzan Horse Breed

The development and a brief history of the Lipizzan horse breed are reviewed. The contribution of several breeds, some of them already extinct, to the development of the Lipizzan horse, gives it a special status representing an important gene pool. This well‐documented breed is a part of the common European natural and cultural heritage. Breeding practices establishing stallion and mare family lines as well as availability of pedigrees are described. Molecular analysis of mitochondrial DNA (mtDNA) and microsatellite data allowed us to analyse the structure of the Lipizzan population, to estimate genetic variability within the population and to test the reliability of the pedigree data. DNA sequence analysis of the mtDNA control region confirmed relative high variability of the gene pool, containing majority of mtDNA haplotypes found in horse populations worldwide. Microsatellite analysis showed that the level of heterozygosity in the Lipizzan population is comparable with the heterozygosity in other populations. The fact that majority of the Lipizzan population is bred on eight state studs in the Central and Eastern Europe contributes to the structuring of the population which results in three clusters: classical cluster, represented by studs Lipica, Piber and Monterotondo, transition cluster, represented by studs Szilvasvarad, Djakovo and Topol?ianky and eastern cluster represented by studs Beclean and Fagaras. The molecular markers also allowed verification of pedigree data, and the rough estimation of pedigree errors was about 10%.     

建昌马mtDNA D-loop区遗传多样性及系统进化分析

试验旨在以线粒体DNA(mitochondrial DNA,mtDNA)为切入点,研究建昌马的母系遗传多样性与系统进化。从建昌马(n=39)血液中提取基因组DNA,用PCR方法扩增mtDNA D-loop区并直接测序,分析其高变区247 bp序列信息,统计mtDNA D-loop区的单倍型及变异位点,计算单倍型多样性(haplotype diversity,Hd)、核苷酸多样性(nucleotide diversity,Pi)和平均核苷酸变异数(average number of nucleotide differences,K)。构建包括建昌马在内的19个品种马的NJ系统进化树,计算各品种间的遗传距离。结果显示,试验获得了清晰的PCR扩增产物,并通过直接测序方法获得了约1200 bp的序列。39匹建昌马mtDNA D-loop区247 bp序列(其中1个样品缺失1 bp)的AT碱基含量为61.45%,属AT碱基对富集区,检测到33个多态性位点,共显示26种单倍型,其中4种为共享单倍型,且Hap7和Hap1为优势单倍型,单倍型多样性为0.947,核苷酸多样性为0.02399,平均核苷酸变异数为5.901,显示丰富的母系遗传多样性;NJ系统进化树显示,建昌马分布在A、C、D、E、F、G共6个支系中,约50%的样品分布在A支系,显示出复杂的母系起源;建昌马与关中马的遗传距离最小(0.021),其次是三河马、文山马、韩国车巨马(0.024),与韩国济州岛马遗传距离最大(0.032)。本研究结果表明,建昌马的mtDNA D-loop高变区遗传多样性丰富,具有多个母系起源,且A支系占有明显优势,与关中马、文山马可能有共同的母系起源。     

Genetic Diversity of Mitochondrial DNA D-loop Sequences in Huili Black Goat

To explore the genetic diversity and origin for genetic resource protection of Huili Black goat, the mitochondrial DNA (mtDNA) D-loop was investigated. mtDNA D-loop sequences of 41 goats were analyzed by PCR, sequencing techniques, and biological information and the phylogenetic trees were constructed. The mtDNA sequences of the Huili Black goat ranged from 1211 to 1213 bp, and 2 sequences were 1211 bp, 29 sequences 1212 bp, and 10 sequences 1213 bp. The content of A+T (60.1%) was higher than one of G+C (39.9%). There were 9 haplotypes, and the haplotype diversity was 0.842+0.00368. The nucleotide diversity was 0.01542+0.00034. The phylogenetic analysis showed that Huili Black goat was distributed in a branch, and were closed to Jianchang Black goat, Chengdu Ma goat, Jintang Black goat, Guizhou White goat, Guizhou Black goat, but they were less related to Capra falconeri. Huili Black goats had rather abundant genetic diversity, and were greatly affected by other goat breeds in history.     

The Mitochondrial Genome in Embryo Technologies

The mammalian mitochondrial genome encodes for 37 genes which are involved in a broad range of cellular functions. The mitochondrial DNA (mtDNA) molecule is commonly assumed to be inherited through oocyte cytoplasm in a clonal manner, and apparently species‐specific mechanisms have evolved to eliminate the contribution of sperm mitochondria after natural fertilization. However, recent evidence for paternal mtDNA inheritance in embryos and offspring questions the general validity of this model, particularly in the context of assisted reproduction and embryo biotechnology. In addition to normal mt DNA haplotype variation, oocytes and spermatozoa show remarkable differences in mtDNA content and may be affected by inherited or acquired mtDNA aberrations. All these parameters have been correlated with gamete quality and reproductive success rates. Nuclear transfer (NT) technology provides experimental models for studying interactions between nuclear and mitochondrial genomes. Recent studies demonstrated (i) a significant effect of mtDNA haplotype or other maternal cytoplasmic factors on the efficiency of NT; (ii) phenotypic differences between transmitochondrial clones pointing to functionally relevant nuclear–cytoplasmic interactions; and (iii) neutral or non‐neutral selection of mtDNA haplotypes in heteroplasmic conditions. Mitochondria form a dynamic reticulum, enabling complementation of mitochondrial components and possibly mixing of different mtDNA populations in heteroplasmic individuals. Future directions of research on mtDNA in the context of reproductive biotechnology range from the elimination of adverse effects of artificial heteroplasmy, e.g. created by ooplasm transfer, to engineering of optimized constellations of nuclear and cytoplasmic genes for the production of superior livestock.     

Phylogenetic relationship and variation of alarm call traits of populations of red‐cheeked ground squirrels (Spermophilus erythrogenys sensu lato) suggest taxonomic delineation

Distribution area and taxonomic borders within the species complex Spermophilus erythrogenys sensu lato remain questionable. Early evidence suggests that red‐cheeked ground squirrels of Southeast Kazakhstan are remarkably different in terms of the acoustic structure of their alarm calls from the red‐cheeked ground squirrels of the Kurgan region in Russia. In this study, we analyzed the differences in the acoustic structure of the alarm call and mitochondrial DNA (complete control region, 1005–1006 bp and complete cytochrome b gene, 1140 bp) in 3 populations of red‐cheeked ground squirrels (Tara, Altyn‐Emel and Balkhash), all located within areas isolated by geographical barriers in Southeast Kazakhstan. We found that the alarm call variables were similar between the 3 study populations and differed by the maximum fundamental frequency (8.46 ± 0.75 kHz) from the values (5.62 ± 0.06 kHz) reported for the red‐cheeked ground squirrels from the Kurgan region of Russia. Variation in mtDNA control region was only 3% and variation in cytochrome b gene was only 2.5%. Phylogenetic trees based on cytochrome b gene polymorphism of 44 individuals from the study area and adjacent territories indicated 3 clades with high (98–100%) bootstrap support: “intermedius,” “brevicauda” and “iliensis”). We conclude that the 3 study populations in Southeast Kazakhstan belong to the clade intermedius and suggest a taxonomical revision of the species complex Spermophilus erythrogenys sensu lato, including analyses of nuclear DNA and alarm calls for populations of the brevicauda and iliensis clades.     

鸳鸯mtDNA D-loop序列分析

采用PCR和直接测序方法测定鸳鸯线粒体DNA(mtDNA)控制区全序列,与GenBank上已知序列相比较分析mtDNA D-loop 3个区的序列变异。结果发现,鸳鸯mtDNA控制区序列长1035 bp;与欧洲鸳鸯相比,鸳鸯(样品采集来自贵州省石阡县)mtDNA控制区共存在25处转换、12处颠换、2处插入和12处缺失;两种鸳鸯之间mtDNA控制区Ⅰ、Ⅱ和Ⅲ区的序列变异率分别为14.5%、0.64%和0.8%,Ⅰ区的变异速率最快;mtDNA控制区的A、C、T、G碱基含量分别是26.6%、16.0%、26.6%和30.8%,A+T含量稍高于C+G含量,G含量最高,符合序列组成的碱基偏倚性。与其他鸭科物种进行了mtDNA控制区序列一致性的比较,结果均高于80%。     

Genetic diversity analysis of two buffalo populations of northern India using microsatellite markers

The genetic diversity in two buffalo populations of northern India, the Bhadawari and the Tarai was assessed using a set of 22 heterologous (bovine) microsatellite markers. The average number of alleles across all loci in both populations was found to be 4.7, indicating that this set of 22 bovine microsatellite markers could be used to study genetic variation in buffalo species also. The overall polymorphic information content (PIC) value for these markers was 0.54. The average observed and expected heterozygosities for both populations were 0.59 and 0.64, respectively. Common alleles with varying allele frequencies in both populations also represented the genetic variability existing between Bhadawari and Tarai buffaloes. However the θ estimates for population differentiation indicated low levels of differentiation between the two populations. This was further supported by the low genetic distance (0.155) between Bhadawari and Tarai, which was calculated using Nei's standard genetic distance method. The present study on Bhadawari and Tarai populations represents a much‐needed preliminary effort that could be extended to other local buffalo populations of India as well.