Mean Effective Number Of Alleles Research Articles

Genetic variability and phylogenetic relationship establishes distinctness of Kaunayen chicken of Manipur

Conservation of locally adapted indigenous livestock has become an important objective in sustainable animal breeding.The current study is first detailed analysis of the genetic diversity harboured by Kaunayen chicken of Manipur.The genotype data generated on 24 microsatellite markers was analysed to establish distinctness of Kaunayen from other registered poultry breeds of India. Large number of observed alleles (212) and heterozygosity (0.66) indicated high genetic diversity. Mean number of alleles observed in Kaunayen chicken were 8.83±0.31 and ranged between 4 (MCW250 and LEI174) and 15 (LEI120). Mean effective number of alleles was significantly less (4.11±0.38) than the observed number of alleles. The maximum observed heterozygosity (1.0) was observed in MCW262 locus and the minimum (0.368) in LEI166. The expected heterozygosity (0.706) was more than the observed heterozygosity (0.664±0.036) which points to heterozygote deficiency and was also reflected in positive FIS estimate (0.06) for the population. Non-significant heterozygote excess on the basis of Infinite allele model and Two-phase model in conjunction with mode-shift analysis test, indicated an absence of bottleneck. Phylogenetic reconstruction on the basis of genetic distance places Kaunayen chicken as a distinct population with respect to other poultry breeds of India. All analysis showed that a significant amount of genetic variation is maintained in Kaunayen chicken population and has appropriately been registered as the 17th chicken breed of India.

Analysis of genetic diversity of Chinese dairy goats via microsatellite markers.

In this study, 15 polymorphic microsatellite markers were used to analyze the genetic structure and phylogenetic relationships of 6 dairy goat breeds in China, including 4 native developed breeds and 2 introduced breeds. The results showed that a total of 172 alleles were detected in 347 samples of the dairy goat breeds included in this study. The mean number of effective alleles per locus was 4.92. Except for BMS0812, all of the remaining microsatellite loci were highly polymorphic (polymorphism information content [PIC] > 0.5). The analysis of genetic diversity parameters, including the number of effective alleles, PIC, and heterozygosity, revealed that the native developed dairy goat breeds in China harbored a rich genetic diversity. However, these breeds showed a low breeding degree and a high population intermix degree, with a certain degree of inbreeding and within-subpopulation inbreeding coefficient ( > 0). The analysis of population genetic differentiation and phylogenetic tree topologies showed a moderate state of genetic differentiation among subpopulations of native developed breed dairy goats in China (0.05 < gene fixation coefficient [] < 0.15). The native developed breeds shared a common ancestor, namely, the Saanen dairy goat, originating from Europe. The results showed that there was a close genetic relationship between Wendeng and Laoshan dairy goats while the Guanzhong dairy goat and the Xinong Saanen dairy goat were also found to have a close genetic relationship, which were both in agreement with the formation history and geographical distribution of the breeds. This study revealed that adopting genetic management strategies, such as expanding pedigree source and strengthening multi-trait selection, is useful in maintaining the genetic diversity of native developed breeds and improving the population uniformity of dairy goats.

Genetic Diversity of Populations of Akhal-Teke Horses from the Czech Republic, Russia, Estonia and Switzerland

Our research objective was to evaluate the genetic parameters in the populations of Akhal-Teke horses in 4 countries: Czech Republic, Russia, Estonia and Switzerland. The experiment involved a total of 325 Akhal-Teke horses; 121 horses came from the Czech Republic, 152 were from Russia, 28 were from Estonia and 24 horses came from Switzerland. For the divided database of micro satellites we evaluated the following parameters: effective number of alleles, frequency of alleles for the groups of horses; the observed heterozygosity (HO); the expected heterozygosity (HE); the inbreeding coefficient (Fis); and the genetic distance. The researched population is polymorphous. The population in the Czech Republic differs from the other three countries in the numbers of alleles per locus. The Czech population also includes Akhal-Teke horses which are not purebred Akhal-Teke horses. A confirmation of this fact is the effective number of alleles. The population in the Czech Republic exhibits the highest mean number of effective alleles. The Akhal-Teke population in Estonia exhibits the highest mean observed heterozygosity. By contrast, the population in the Czech Republic exhibits the lowest mean observed heterozygosity. In the Czech Republic the mean Fis value is a positive number indicating a reduced number of heterozygotes in the Czech Akhal-Teke population. The genetic distance is the highest between populations of horses bred in Russia and Estonia. The genetic distance is the lowest between populations of Akhal-Teke horses bred in Russia and in the Czech Republic.

Population genetic analysis of Theileria parva isolated in cattle and buffaloes in Tanzania using minisatellite and microsatellite markers

A population genetic study of Theileria parva was conducted on 103 cattle and 30 buffalo isolates from Kibaha, Lushoto, Njombe Districts and selected National parks in Tanzania. Bovine blood samples were collected from these study areas and categorized into 5 populations; Buffalo, Cattle which graze close to buffalo, Kibaha, Lushoto and Njombe. Samples were tested by nested PCR for T. parva DNA and positives were compared for genetic diversity to the T. parva Muguga vaccine reference strain, using 3micro and 11 minisatellite markers selected from all 4 chromosomes of the parasite genome. The diversity across populations was determined by the mean number of different alleles, mean number of effective alleles, mean number of private allele and expected heterozygosity. The mean number of allele unique to populations for Cattle close to buffalo, Muguga, Njombe, Kibaha, Lushoto and Buffalo populations were 0.18, 0.24, 0.63, 0.71, 1.63 and 3.37, respectively. The mean number of different alleles ranged from 6.97 (Buffalo) to 0.07 (Muguga). Mean number of effective alleles ranged from 4.49 (Buffalo) to 0.29 (Muguga). The mean expected heterozygosity were 0.07 0.29, 0.45, 0.48, 0.59 and 0.64 for Muguga, cattle close to buffalo, Kibaha, Njombe, Lushoto and Buffalo populations, respectively. The Buffalo and Lushoto isolates possessed a close degree of diversity in terms of mean number of different alleles, effective alleles, private alleles and expected heterozygosity. The study revealed more diversity in buffalo isolates and further studies are recommended to establish if there is sharing of parasites between cattle and buffaloes which may affect the effectiveness of the control methods currently in use.

Insights into the Introduction History and Population Genetic Dynamics of the Nile Monitor (Varanus niloticus) in Florida.

Invasive species are widely recognized as important drivers of the ongoing biodiversity crisis. The US state of Florida is especially susceptible to the proliferation of invasive reptiles, and nonnative lizards currently outnumber native lizard species. At present, there are 3 documented breeding populations of the Nile monitor (Varanus niloticus) in different regions of Southern Florida, and these populations are considered potential dangers to threatened, fossorial endemics, such as burrowing owls, American crocodiles, and gopher tortoises. Nevertheless, at present, both the introduction histories of these populations and the degree to which they are connected by gene flow are not known. To address these issues, we genotyped V. niloticus from Cape Coral, Homestead Air Reserve Base, and West Palm Beach at 17 microsatellite loci and conducted a variety of analyses to assess both intrapopulation genetic diversity, the degree of gene flow between populations, and the most likely introduction scenario. The results of our analyses demonstrate that all 3 populations have limited genetic diversity (mean number of effective alleles across loci in all 3 populations ~ 2.00) and are highly differentiated from one another (G ST = 0.268; G″ST = 0.628). Our results also suggest that these populations resulted from independent introduction events that occurred within the past few decades. Consequently, we advise that wildlife managers focus management efforts on containment of existing populations and intensification of monitoring efforts on potential migration corridors.

Molecular Characterization of New Zealand White and APAU Black Rabbits using Microsatellite Markers

Genetic diversity among two genetic groups (New Zealand White and APAU Black) was investigated with a set of 20 microsatellite markers in the present study. The results showed that out of 20 microsatellites, 12 rabbit specific markers were successfully amplified by PCR which were highly polymorphic. A total of 257 alleles were observed across the 12 loci amplified. Number of alleles ranged from 5 to 14 and 5 to 16 in New Zealand White and APAU Black populations, respectively. The overall mean values of observed heterozygosity (0.554 in New Zealand White and 0.556 in APAU Black), expected heterozygosity (0.870 in New Zealand White and 0.875 in APAU Black), Polymorphic Information Content (0.856 in New Zealand White and 0.862 in APAU Black) and the mean effective number of alleles (8.629 in New Zealand White and 8.876 in APAU Black) of these two genetic groups were high. Out of the 12 amplified loci 7 loci deviated significantly from Hardy-Weinberg equilibrium in New Zealand White and 5 loci deviated in case of APAU Black which may be due to selection followed. The mean FIS, FIT and FST values over all the population were found to be 0.377, 0.402 and 0.040, respectively. The results suggested that the 12 amplified rabbit specific microsatellite loci were effective markers for analysis of genetic relationships among rabbit populations.

Sampling strategies for natural Toona ciliata populations.

The genetic diversity and spatial autocorrelation of Toona ciliata populations were analyzed with eight microsatellite markers to determine an appropriate sampling strategy for the effective conservation of natural T. ciliata populations. The average number of alleles and effective number of alleles were 6.1 and 2.7, respectively. The mean expected heterozygosity was 0.6006. Overall, 96.6% of the genetic variation existed in two natural populations, which was concluded from the coefficient of genetic differentiation (FST = 0.1854). Therefore, two natural populations were selected for conservation and sampling. The mean effective number of alleles and expected heterozygosity increased with increasing sample number. The mean expected heterozygosity tended to be stable when the sampling number exceeded 30. The maximum value of expected heterozygosity was 0.4770 when the sampling number was 45. Therefore, 45 sampled individuals were sufficient for conservation and sampling. Similarity relationships existed between individuals within 240 m. There were marked differences among individuals over 240 m away. The distance between individuals exceeded 240 m when natural populations were sampled.

High polymorphism at microsatellite loci in the Chinese donkey.

To reveal the genetic diversity and phylogenetic relationships between Chinese donkey breeds, 415 individuals representing ten breeds were investigated using ten microsatellite markers. The observed number of alleles, mean effective number of alleles (NE), mean expected heterozygosity (HE), and polymorphic information content (PIC) of each breed and polymorphic locus were analyzed. The results showed that seven (HTG7, HTG10, AHT4, HTG6, HMS6, HMS3, and HMS7) of ten microsatellite loci were polymorphic. The mean PIC, HE, and NE of seven polymorphic loci for the ten donkey breeds were 0.7679, 0.8072, and 6.0275, respectively. These results suggest that domestic Chinese donkey breeds possess higher levels of genetic diversity and heterozygosity than foreign donkeys. A neighbor-joining tree based on Nei's standard genetic distance showed that there was close genetic distance among Xinjiang, Qingyang, Xiji, and Guanzhong donkey breeds. In addition, Mongolia and Dezhou donkey breeds were placed in the same category. The phylogenetic tree revealed that the genetic relationships between Chinese donkey breeds are consistent with their geographic distribution and breeding history.

Genetic variation of silver fir (Abies alba Mill.) preserved in the Katowice Forest District

Abstract Environmental pollution greatly decreases a tree’s health and results in dieback of forest stands. Owing to increasing industrial activity in the 20th century, silver fir became almost totally extinct in the Katowice Forest District. Only 19 individuals have survived to this day. The aim of the present study is to analyse growth characteristics and polymorphisms of 25 inter-simple sequence repeats (ISSR) of the preserved trees. The mean height of the inventoried silver firs was 19 m with a diameter at breast height (DBH) of 29 cm. Flowers were observed on few trees only. However, all trees were of high vitality without signs of fungal pathogen infections or insect outbreaks. Parameters of genetic variability, including mean effective number of alleles per locus and expected heterozygosity, were higher than that described in the literature so far and they amounted to 1.659 and 0.396, respectively.

Molecular characterization of camel breeds of Gujarat using microsatellite markers

Camels are the economic backbone of many nomadic tribes of the world including India. Camel population in India is restricted to western part of the country and is represented by eight breeds. The western most state of the country, Gujarat, possesses two camel breeds, Kachchhi and Kharai inhabiting in the same area. Populations of both are facing severe decline which calls for their immediate conservation. In the present study we examined genetic variability and structure in Kachchhi and two populations of Kharai (n=193) using 27 microsatellite markers. A total of 138, 112 and 95 alleles were observed in Kachchhi, Kharai (K) and Kharai (A) respectively with the mean effective number of alleles per locus 2.818±0.303; 2.373±0.245 and 2.313±0.224. The mean observed heterozygosity was 0.446±0.039 for Kachchhi, 0.272±0.040 for Kharai (K) and 0.423±0.044 for Kharai (A), which was lower than expected heterozygosity 0.535±0.045, 0.461±0.051 and 0.474±0.043 respectively. The average inbreeding coefficient (FIS) 0.233±0.037 was substantially high in both the breeds. The test for Hardy–Weinberg equilibrium showed significant deviations at most of loci. The mean multilocus FST value (0.237) suggested significant population differentiation. This was also supported by AMOVA (Analysis of Molecular Variance), Principal component analysis and Bayesian cluster analysis. The genetic distinctness of these camel breeds as revealed by microsatellite analysis may have significant impact on issues concerning conservation and biodiversity.

Assessing genetic diversity among six populations of Gossypium arboreum L. using microsatellites markers.

Among the four cultivated cotton species, G. hirsutum (allotetraploid) presently holds a primary place in cultivation. Efforts to further improve this primary cotton face the constraints of its narrow genetic base due to repeated selective breeding and hence demands enrichment of diversity in the gene pool. G. arboreum (diploid species) is an invaluable genetic resource with great potential in this direction. Based on the dispersal and domestication in different directions from Indus valley, different races of G. arboreum have evolved, each having certain traits like drought and disease resistance, which the tetraploid cotton lack. Due to lack of systematic, race wise characterization of G. arboreum germplasm, it has not been explored fully. During the present study, 100 polymorphic SSR loci were used to genotype 95 accessions belonging to 6 races of G. arboreum producing246 polymorphic alleles; mean number of effective alleles was 1.505. AMOVA showed 14% of molecular variance among population groups, 34% among individuals and remaining 52% within individuals. UPGMA dendrogram, based on Nei's genetic distance, distributed the six populations in two major clusters of 3 populations each; race 'bengalense' was found more close to 'cernuum' than the others. The clustering of 95 genotypes by UPGMA tree generation as well as PCoA analysis clustered 'bengalense' genotypes into one group along with some genotypes of 'cernuum', while rest of the genotypes made separate clusters. Outcomes of this research should be helpful in identifying the genotypes for their further utilization in hybridization program to obtain high level of germplasm diversity.

Genetic diversity status of Pacific white shrimp (Litopenaeus vannamei) using SSR markers in Iran

Genetic diversity is vital for the maintenance of genetic pool in cultured shrimps. In order to estimate the current status of genetic diversity in Litopenaeus vannamei shrimp in Iran, as an exotic species, a total of 45 individuals from Amiri and Gorgeaj farms in Jask port of Hormozgan province and one hatchery in Gomishan city of Golestan province, were detected using four microsatellite loci. The number of alleles per locus was 5–10, and the mean effective number of alleles (N e) across populations and loci ranged from 4.834 to 5.148. The overall mean observed heterozygosity (H o) ranged from 0.450 to 0.479, which was lower than the expected one (0.789–0.794). There was nothing remarkable about any of the allele frequencies across populations or loci. The mean inbreeding coefficient (F IS) and pairwise genetic differentiation (F ST) among populations were 41.6 % and 0.133, respectively. The three studied populations departed from Hardy–Weinberg equilibrium (HWE). Analysis of molecular variance revealed 14 % variability among and 86 % within populations. However, considering departing from HWE and the high F IS and F, the moderate pairwise F ST values, importance of introducing genetically diverse broodstock and monitoring to control inbreeding is discussed.

The Molecular Diversity-based ISSR of Durio tanjungpurensis Originating from West Kalimantan, Indonesia

The Durian Tengkurak ( Durio tanjungpurensis Navia) is one of the endangered exotic species in the Malvaceae family. The species is important for conservation of the germplasm and is considered a potential genetic resource for the development of durian in the future. The objective of this research project was to assess the molecular diversity of D. tanjungpurensis in West Kalimantan, based on Inter Simple Sequence Repeat (ISSR) markers. We applied ten ISSR primers to reveal the genetic diversity of 60 individuals from six natural endemic D. tanjungpurensis populations. The genetic diversity parameters were estimated based on binary data about PCR products (present or absent bands). The results showed that the mean number of observed alleles, the mean number of effective alleles, the genetic diversity, the Shannon’s Information Index score, the number of polymorphic loci, and the percentage of polymorphic loci were 1.53, 1.29, 0.17, 0.26, 77.83, and 52.59, respectively. An analysis of molecular variance (AMOVA) showed that the genetic diversity within a population (65%) was higher than that found between the populations (35%). UPGMA clustering and principal coordinate analysis, based on the DICE similarity matrix, were used to classify the populations into three groups: 1) Hutan Rejunak and Tembaga, 2) Bukit Merindang, and 3) Hutan Rawak, Bukit Sagu 1, and Bukit Sagu 2. Further analysis of the population structure using STRUCTURE software was used to classify all the individuals into two major categories, thus uniting Groups 2 and 3 as one major category. In conclusion, a high level of genetic diversity in the Durian Tengkurak was revealed utilizing the ISSR markers employed in the study.

SSR Analysis on Genetic Diversity of Different Generations in Castanopsis eyrei from Wuyishan,Fujian Province

The populations of Castanopsis eyrei collected from Daanyuan plots in Wuyishan city,Fujian province were divided into 3 generations according to the size class,i. e. adults,juveniles,seedlings. A total of92 alleles were detected with 14 pairs of SSR primers,and a mean of 6. 571 4 alleles were detected with per pair primer. The mean effective number of alleles( Ae) and expected heterozygosity(He) at population level were3. 905 4 and 0. 722 9,respectively. These data suggested that the genetic diversity of C. eyrei was quite high.SSR analyses showed that the highest effective number of alleles( Ae),expected heterozygosity(He),Nei index,Shannon information index were detected in seedlings,juveniles took the second place and the lowest were detected in adults. The most rare alleles was found in seedlings. It suggested that the trend of genetic diversity of the population of C. eyrei was in ascension. Analysis of molecular variance(AMOVA) showed that the genetic diversity might exist within and among different generations of C. eyrei populations,but mainly exist within generations. SSR analyses showed that gene differentiation coefficient(Fst) among generations of C. eyrei populations was 0. 074 3 while the gene flow( Nm) was 3. 115 4. The genetic identity between adults and seedlings was the lowest. The genetic distance between adults and seedlings was the highest. Based on the analysis of SSR,establishment of nature reserve and conservation of the rare alleles in seedlings and adults is of great importance.

Polymorphism in seed endosperm proteins (gliadins and glutenins) of Turkish cultivated einkorn wheat [Triticum monococcumssp.monococcum] landraces

The objective of this study is the analysis of polymorphism in seed endosperm proteins (gliadins and glutenins) of Turkish cultivated einkorn wheat [Triticum monococcum ssp. monococcum] landraces. The genetic diversity of high-molecular-weight (HMW) glutenin subunits and the gliadin proteins in 10 landrace populations of cultivated einkorn wheat, originating from Turkey, was investigated using sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and ammonium lactic acid polyacrylamide gel electrophoresis (A-PAGE), respectively. For glutenins, the mean number of alleles, the mean number of effective alleles, the mean value of genetic diversity and the mean value of average genetic diversity were detected as 3.50, 2.98, 0.65 and 0.28, respectively. The genetic differentiation was 0.57, while gene flow was 0.19 between populations. For gliadins, the mean number of alleles, the mean number of effective alleles, the mean value of total genetic diversity and the genetic diversity within population were detected as 2.00, 1.21, 0.17 and 0.15, respectively. The genetic differentiation was 0.08, whereas gene flow was 6.15 between populations. STRUCTURE is a software package program for population genetic analysis, was used to infer population structures of landraces populations. The optimum value for K was obtained as 10. Considering the high number of proteins and genetic variation, and increased interest in organic products, the farming of einkorn wheat should be supported and conservation of germplasm in landraces should be maintained as important genetic resources. The landraces germplasm should be conserved for future crop improvement processes.

Molecular characterization of madras red sheep using microsatellite markers

Genetic diversity of Madras Red sheep was investigated by microsatellite markers recommended by FAO. All the loci studied were highly informative and polymorphic. The number of observed alleles (Na) detected ranged from 3 to14, with an overall mean of 7.00±2.81. The mean effective number of alleles was (Ne) 4.42±2.12. The overall means for observed (Ho) and expected (He) heterozygosity were 0.65±0.25 and 0.73±0.16, respectively. The mean polymorphism information content (PIC) value was 0.6704 which ranged from 0.2170 to 0.8215. The within breed estimate (FIS) indicated heterozygosity shortage of 0.07. The Hardy-Weinberg equilibrium (HWE) test revealed that 76% (19/25)) loci deviated from equilibrium. Shannon's information index (I) was sufficiently high with a mean of 1.5578. The study revealed that even a breed with significant level of genetic variation needs proper genetic management for improvement and conservation.

Assessment of genetic diversity of cucumber cultivars in China based on simple sequence repeats and fruit traits.

The cucumber (Cucumis sativus L.) is an important crop grown worldwide. In this study, the genetic diversity of 42 cucumber cultivars in China was analyzed using 51 pairs of simple sequence repeat (SSR) primers. These primers identified 129 polymorphic loci, 95.6% of which were polymorphic. The mean effective number of alleles, mean Nei's gene diversity, and mean Shannon's information index were 0.36, 0.16, and 0.21, respectively. A cluster analysis demonstrated that the 42 cultivars could be divided into three groups, a result that was largely consistent with those of a principal component analysis (PCA). The PCA indicated that the three groups displayed significant variation in fruit traits. The cultivars of group 1 tended to have longer fruits (>30 cm), longer fruit ends (>4 cm), larger fruit diameters (>5 cm), a sharp strigose fruit spine, and the same fruit end shape. The basal color of the fruit in group 2 was dark green. Group 3 cultivars have no wax or mottling on the fruit surface. Our study demonstrates the value of our SSR primers for assessing genetic diversity in cucumber.

Mating system patterns of natural populations of Pinus koraiensis along its post-glacial colonization route in northeastern China.

To understand the genetic mechanisms underlying the endangerment of Pinus koraiensis, we studied the mating system of 49 families of this species in 3 natural populations along its post-glacial colonization route across ~1500 km in northeastern China using the chloroplast simple sequence repeat technique. We analyzed 11 polymorphic loci with clear and repeating bands, and we calculated the multi-locus outcrossing rate (tm), single-locus outcrossing rate, inbreeding index, and fixation index (F). Intra-population variation was not observed, but a large inter-population variation was observed in the outcrossing rate, and the tm increased from 0.767 (the south population) to 0.962 (the north population) along the post-glacial colonization route. The tm values within a population did not change with time over 2 consecutive years. The F values for the 3 populations were <0, which indicates an excess of heterozygotes. The mean effective number of alleles, Shannon diversity index, and Nei's genetic diversity index did not show a south-north pattern. The north population had the highest outcrossing rate but the lowest genetic diversity. The average genetic differentiation of P. koraiensis populations was 0.1251, which was within the average range of woody plants with outcrossing and wind pollination. This study suggests that the current endangerment of P. koraiensis is not related to its genetic structure; perhaps it is mainly caused by man-made and natural disturbances such as deforestation and fire. Therefore, reducing disturbances and enhancing habitats, rather than the genetic aspects, play more important roles in the long-term protection of P. koraiensis.

Genetic characterisation of Tiruchy Black sheep of Tamil Nadu using microsatellite markers

A total of 203 alleles were observed in the sampled population for the 25 marker loci under investigation. The number of alleles observed at each locus varied from 4 (OarHH41) to 13 (OarHH35) with a mean of 8.12±0.45 across all loci. The effective number of alleles ranged from 1.59 (OarHH41) to 7.51 (OarHH35). The mean number of effective alleles was 4.48±0.27 across all loci. The polymorphic information content values ranged from 0.7029 (OarHH41) to 0.9164 (OarHH35) with a mean of 0.8441±0.012, which showed high level of genetic variability. The x2 test revealed that among the 25 microsatellites studied only ten were in Hardy-Weinberg Equilibrium proportions. The observed heterozygosity ranged from 0.2609 (OarHH41) to 0.9600 (OarCP49) with a mean of 0.6995 and the expected heterozygosity ranged from 0.3734 (OarHH41) to 0.8756 (OarHH35) with a mean of 0.7575. The within population inbreeding estimates or heterozygotes deficiency within population (FIS) was observed in 13 loci and the positive FIS value ranged from 0.0796 (CSSM31) to 0.5895 (OarJMP8). Only twelve loci revealed negative FIS values (FIS

Assessment of Genetic Variability and Structuring of Riverine Buffalo Population (Bubalus bubalis) of Indo-Gangetic Basin

The buffalo population of Uttar Pradesh (UP) constitutes 26.1% of the total buffalo population of India, yet this population has not been classified into distinct breeds or subpopulations due to lack of systematic study. Genetic variation at 30 microsatellite loci was examined and statistical analysis was carried out to reveal genetic diversity, demographic parameters of these buffaloes and to investigate the existence of population substructures underlying geographical distribution. The mean number of alleles per locus was 13.26 and mean effective number of alleles was 3.74, whereas mean observed and expected heterozygosities were found to be 0.57 and 0.67 in UP buffaloes. Principal component analysis (PCA) based on allele frequency data revealed subclustering of UP buffalo population. Bayesian analysis result also revealed clear membership of individuals into five clusters indicating a genetic subdivision within the UP buffalo population. The buffaloes of Western and Central regions of UP were subtly separated while buffaloes of Tarai area and Bhadawari buffaloes revealed distinctive population structure. The buffaloes of Mau, Ballia and Ghazipur districts of Eastern region also had a distinctive genetic structure. The analysis of data on buffaloes of Indo-Gangetic plains revealed that population was in mutation drift equilibrium. The observed mean M ratio in the population was above the critical significance value (Mc) suggesting that it has not suffered any severe reduction in effective population size. The statistical tests revealed a historical constancy of size of buffalo in this geographical area. The high level of genetic variability indicates UP buffalo population is a vast reservoir of genetic diversity and this shall help in taking informed conservation decisions and sustainable utilization.