Mean FIS Research Articles

Evaluation of genetic diversity and structure of Vietnamese goat populations using multi locus microsatellite markers

Goats are an important component of the Vietnamese livestock industry but little is known about their genetic diversity, differentiation and population structure. We evaluated genetic diversity of seven indigenous goat populations located in different provinces (CoVBV (Co goats from Ba Vi), (CoVSL) Co goats from Son La, CoVTH (Co goats from Thanh Hoa), CoVNT (Co goats from Ninh Thuan), CoVHg (Co goats from Ha Giang), BTVBV (Bach Thoa goat from Ba Vi) and BTVNT (Bach Thoa goats from Ninh Thuan)) and used microsatellite markers to assess the gene flow and population structure among them. The basic diversity measures viz. allelic diversity and heterozygosity were low in Vietnam goats as compared to West Asian and European goats. The overall mean FIS was significantly positive in Co goats (0.203) whereas it was only 0.003 in Bach Thao goats. Considerable genetic differentiation existed among goat populations from different provinces with the mean global FST, FIT and FIS estimated to be 0.083, 0.178 and 0.104 respectively. The phylogenetic tree constructed on pair-wise allele sharing distances revealed clustering of the two Bach Thao goat populations together. Among the Co goat populations, Son La (CoVSL) and Ha Giang (CovHG) clustered together distinctly while Thanh Hoa (CoVTH), Ba Vi (CoVBV) and Ninh Thuan (CoVNT) populations clustered intermediately. The results of multi-dimensional scaling plot of pairwise FST showed a similar picture except that Co-Ninh Thuan (CoVNT) was differentiated from other Co goat populations. When genotype assignment was performed at breed level, the percent correct assignment of Bach Thao goats (93.7%–96.2%) was consistently higher than Co goats (86.8%–88.1%) across the three evaluated methods. When genotype assignment at sub-population level was done, both Co (CoVNT) and Bach Thao (BTHNT) goat populations in Ninh Thuan province were assigned correctly while the percent correct assignment differed among goat populations from other provinces. AMOVA and Bayesian clustering analysis revealed the existence of significant sub-population structure and varying levels of admixture within Co goats among different provinces. The present study is the first report on genetic diversity and structure of indigenous goat populations raised in different provinces of Vietnam.

The effect of general anesthesia for ambulatory dental treatment on children in Chongqing, Southwest China.

The incidence of early childhood caries shows a significant increasing trend. Often, children younger than 6years need additional help to finish the dental treatment. Therefore, general anesthesia (GA) could help to provide a successful environment for pediatric dental treatment. The aim of this study was to assess the effect of dental treatment under general anesthesia (DGA) on the patients' oral health in Chongqing, Southwest China using the P-CPQ and the FIS questionnaires. We collected the hospital's records of the children who received DGA from 2013 to 2014 and the questionnaires answered by their parents or caregivers before and after the treatment. Then the data were integrated and analyzed to assess the effect of DGA on the children and their family, the incidence of the complications during or after DGA, and the satisfaction of their parents. We collected 659 patients' records including 55.4% boys and 44.6% girls. There were 443 children younger than 4years, and 216 children older than 4years. The main reason why they chose DGA was the patients' fear for the treatment (95.1%). The mean cost of DGA almost reached a half (61.5%) or a third (15.3%) of the family's monthly earning. The mean P-CPQ score and FIS score significantly decreased after DGA. The highest incidence of complications was emergence agitation, headache, and nausea/vomiting. The incidence of emergence agitation and headache was related to the operation time. The majority of families reported a high degree of satisfaction. Children's oral health-related quality of life after DGA improved significantly. Meanwhile DGA showed a positive effect on the whole family and majority of families reported a high degree of satisfaction to it.

Morphological and genetic diversity of shea tree (Vitellaria paradoxa) in the savannah regions of Ghana

Vitellaria paradoxa C. F. Gaertn., commonly known as shea tree or Vitellaria, is ranked the most important tree species of the savannah regions in the most African countries due to its ecological and economic importance for livelihoods and national economies. However, the savannah regions are the most vulnerable areas to the global climate change. Moreover, the Vitellaria populations on farmlands are threatened by the dominance of old trees with low or lack of regeneration. In this study both morphological and genetic diversity were assessed using several phenotypic traits and 10 microsatellite markers, respectively, to assess the impact of land use and agro-ecozone types on Vitellaria in Ghana. The land use types were forests and farmlands, and the agro-ecozone types included the Transitional, Guinea, and Sudan savannah zones. The mean values of morphological traits, such as diameter at breast height (DBH) and canopy diameter (CD), were statistically different between forest (DBH = 22.20, CD = 5.37) and farmland (DBH = 39.85 CD = 7.49) populations (P < 0.00001). The Sudan savannah zone with mean petiole length of 4.96 cm showed significant difference from the other zones, likely as a result of adaptation to drier climate conditions. Genetic data analysis was based on 10 microsatellite markers and revealed high genetic diversity of Vitellaria in Ghana: mean expected heterozygosity, H e was 0.667, and allelic richness, measured as number of effective alleles A e , was 4.066. Both farmlands and forests were very diverse indicating lack of negative influence of farmer’s selection on genetic diversity. Fixation index was positive for all populations (mean F IS = 0.136) with farmlands recording relatively higher values than forests in all ecological zone types studied, probably indicating less gene flow in the farmlands. Moderate differentiation (F′ ST = 0.113) was comparable to other similar tree species. Both land use and ecological zone types influenced genetic differentiation of Vitellaria at varying levels. The species was spatially structured across three ecozones and following climatic gradient. The forest reserves are used in situ conservation for Vitellaria in Ghana. High diversity observed in the most arid zones provides opportunity to find and use appropriate plant materials for breeding climate change resilient trees.

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.

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.

Estimating microsatellite based genetic diversity in Rhode Island Red chicken.

This study aimed to estimate microsatellite based genetic diversity in two lines (the selected RIR(S) and control line RIR(C)) of Rhode Island Red (RIR) chicken. Genomic DNA of 24 randomly selected birds maintained at Central Avian Research Institute (India) and 24 microsatellite markers were used. Microsatellite alleles were determined on 6% urea-PAGE, recorded using GelDoc system and the samples were genotyped. Nei's heterozygosity and Botstein's polymorphic information content (PIC) at each microsatellite locus were estimated. Wright's fixation indices and gene flow were estimated using POPGENE software. All the microsatellite loci were polymorphic and the estimated PIC ranged from 0.3648 (MCW0059) to 0.7819 (ADL0267) in RIR(S) and from 0.2392 (MCW0059) to 0.8620 (ADL0136) in RIR(C). Most of the loci were highly informative (PIC>0.50) in the both lines, except for five loci in RIR(S) and six loci in RIR(C) line. Nei's heterozygosity per locus ranged from 0.4800 (MCW0059) to 0.8056 (ADL0267) in RIR(S) and from 0.2778 (MCW0059) to 0.875 (ADL0136) in RIR(C). Out of 24 loci, 15 (62.5%) in RIR(S) and 14 loci (58.33%) in RIR(C) revealed moderate to high negative FIS index indicating heterozygote excess for these loci in corresponding lines, but the rest revealed positive FIS indicating heterozygosity deficiency. A mean FIS across the both lines indicated overall 10.77% heterozygosity deficit and a mean FIT indicated 17.19% inbreeding co-efficient favoring homozygosity over the two lines. The mean FST indicated that 10.18% of the microsatellite variation between the two lines was due to their genetic difference.

Balance between inbreeding and outcrossing in a nannandrous species, the moss Homalothecium lutescens.

Epiphytic dwarf males on the females present a possible solution to the problem of short fertilization distances in mosses. However, leptokurtic spore dispersal makes dwarf males likely to be closely related to their host shoot, with an accompanying risk of inbreeding. The capacity of a female to harbour a high number of different dwarf males suggests that there may be mechanisms in place that counteract inbreeding, such as polyandry and post-fertilization selection. We have genotyped sporophytes, female host shoots and dwarf males in four populations of the moss Homalothecium lutescens. We found no evidence of selective sporophyte abortion based on level of heterozygosity. The occurrence of entirely homozygous sporophytes together with significantly positive inbreeding coefficients in three of the populations (mean FIS between 0.48 and 0.64) suggest frequent mother-son mating events. However, 23% of all sampled sporophytes had a higher level of heterozygosity compared with the mean expected heterozygosity at the population level. Polyandry was frequent, on average 59% of the sporophytes on a female shoot were sired by distinct fathers. In conclusion, sporadic fertilizations by dwarf males originating from nonhost female shoots appear to counteract strong inbreeding.

Genetic variability of ten Chinese indigenous goats using MHC-linked microsatellite markers

In this study, the genetic variability of Chinese indigenous goat breeds (Capra hircus) was analyzed using the MHC-associated microsatellite markers BF1, BM1818, BM1258, and DYMS1. To examine genetic variability, the levels of heterozigosity, degrees of inbreeding, and genetic differences among the breeds were analyzed. The mean number of alleles ranged from 5.50±3.70 in Enshi black goats (EB) to 11.50±3.70 in the Jianyang big ear (JE) breed. The mean observed heterozygosity and mean expected heterozygosity varied from 0.25±0.04 in Jining Qing goats (JQ) to 0.54±0.05 in Chuannan black goats (CN) and from 0.49±0.18 in Hechuan white goats (HW) to 0.78±0.05 in JE, respectively. The mean FIS values ranged from 0.23 in HW to 0.51 in JQ. In addition, the genetic variation among populations and geographic location did indicate a correlation of genetic differences with geographic distance, which was revealed by the phylogenetic network. In conclusion, the high variability and population structure among Chinese native goats in the Major Histocompatibility Complex would be caused by co-evolution between MHC alleles and the epidemic history or pathogens in different agro-ecological zones.

Population genetics of the invasive giant hogweed (Heracleum sp.) in a northern European region

Heracleum mantegazzianum is a successful invader in many European countries. Besides its impact on biodiversity, it represents a health hazard because of its phototoxic sap. Population genetic studies may help to predict which species are most likely to become invasive. In this study, we investigated the population genetic variation and structure of Heracleum sp., identified as H. mantegazzianum in Finland, i.e., within its northern range of distribution, using microsatellite markers. Our aims were to reveal the genetic characteristics and evolutionary processes that have resulted in observed patterns. The amount of genetic variation measured as expected heterozygosity was modest (mean H E = 0.406), which may be due to relatively small founder populations and/or inbreeding (mean F IS = 0.268). Mean allele numbers per population ranged from 2.0 to 4.7. The pairwise F ST values were generally high, and the mean F ST among all populations equalled 0.498. Based on F ST values, populations were significantly differentiated from each other, indicating restricted gene flow among the populations. The Bayesian structure analysis provided additional information on population genetic structure. The analysis divided the eight populations into two main clusters. Genetic analyses indicate that H. mantegazzianum has been introduced to Finland multiple times. Distinct population genetic patterns indicate that human-mediated dispersal is important.

Diversidad genética y estructura de población de cabras autóctonas nigerianas usando marcadores microsatélites DNA

Se analizaron 29 microsatélites para evaluar la diversidad genética de tres razas caprinas Nigerianas y establecer las relaciones genéticas entre ellas utilizando las razas Saanen y Kalahari como poblaciones outgroup. Se analizaron 244 distribuidas de la siguiente manera: en Sahel (47), Maradi (47) y WestAfrican Dwarf (67), Kalahari (47) y Saanen (36). El ADN se extrajo a partir de sangre conservada en tarjetas FTA Classic siguiendo las instrucciones del fabricante y se amplificaron los microsatélites mediante PCR. Se calcularon el número medio de alelos (MNA), las heterocigocidades observada (Ho) y esperada (He) y las distancias genéticas entre pares de poblaciones. Se hizo una prueba de equilibrio Hardy-Weinberg (HWE) y un análisis de la estructura genética de las poblaciones mediante el programa STRUCTURE. La diversidad genética encontrada fue alta con valores de MNA entre 6,69 y 8,79 para Kalahari y West African Dwarf, respectivamente. Los valores de Ho oscilaron entre un 59 % para West African Dwarf y un 64,9 % para Saanen. La He más alta se encontró en la raza West African Dwarf (70 %), mientras que el valor más bajo se observó en la raza Saanen (He= 66,5 %). Los valores medios de Fis para las poblaciones estudiadas variaron entre 0,055 en Kalahari y 0,148 en West African Dwarf. La distancia genética más elevada fué la encontrada entre Saanen y Maradi (0,386) y la menor entre Maradi y Sahel (0,025). La prueba de equilibrio de HWE reveló que dieciocho, diecisiete, trece, veintitrés y veintiún loci estaban en equilibrio HWE (p&gt;0,05) en las razas Maradi, West African Dwarf, Sahel, Saanen y Kalahari, respectivamente. Una representación gráfica del análisis de estructura genética reveló que las cabras de Nigeria descienden de un ancestro común diferente de las razas sudafricanas y europeas que fueron utilizadas como grupos externos.

High molecular diversity in the true service tree (Sorbus domestica) despite rareness: data from Europe with special reference to the Austrian occurrence.

Sorbus domestica (Rosaceae) is one of the rarest deciduous tree species in Europe and is characterized by a scattered distribution. To date, no large-scale geographic studies on population genetics have been carried out. Therefore, the aims of this study were to infer levels of molecular diversity across the major part of the European distribution of S. domestica and to determine its population differentiation and structure. In addition, spatial genetic structure was examined together with the patterns of historic and recent gene flow between two adjacent populations. Leaf or cambium samples were collected from 17 populations covering major parts of the European native range from north-west France to south-east Bulgaria. Seven nuclear microsatellites and one chloroplast minisatellite were examined and analysed using a variety of methods. Allelic richness was unexpectedly high for both markers within populations (mean per locus: 3·868 for nSSR and 1·647 for chloroplast minisatellite). Moreover, there was no evidence of inbreeding (mean Fis = -0·047). The Italian Peninsula was characterized as a geographic region with comparatively high genetic diversity for both genomes. Overall population differentiation was moderate (FST = 0·138) and it was clear that populations formed three groups in Europe, namely France, Mediterranean/Balkan and Austria. Historic gene flow between two local Austrian populations was high and asymmetric, while recent gene flow seemed to be disrupted. It is concluded that molecular mechanisms such as self-incompatibility and high gene flow distances are responsible for the observed level of allelic richness as well as for population differentiation. However, human influence could have contributed to the present genetic pattern, especially in the Mediterranean region. Comparison of historic and recent gene flow may mirror the progress of habitat fragmentation in eastern Austria.

Genetic variation among different morphotypes of the male freshwater prawn Macrobrachium rosenbergii (De Man)

The genetic differences between the blue claw male (BC), orange claw male (OC) and small male (SM) morphotypes of male freshwater prawns were assessed using microsatellite DNA markers. Thirty individuals from each of the three groups of male prawns were collected from a hatchery rearing system in Port Dickson, Negeri Sembilan, Malaysia. Significant differences in growth were observed between the three groups. The total numbers of alleles per locus in the BC, OC and SM groups were found to be 23, 27 and 21, respectively from all loci. The average observed heterozygosities (Ho) ranged from 0.48 to 0.56 across all loci in the three groups. The mean FIS of −0.018 indicated an excess of heterozygosity. The pair-wise comparisons and the FST values revealed significant genetic differentiation across the groups. The greatest genetic distance was observed between the BC and SM groups and lowest one was between the BC and the OC groups.

Population Genetic Structure of Asclepias Tuberosa In Northwest Iowa: A Comparison Within and Between Remnant Prairies and Commercially Available Seed

Isolated in scattered remnants, less than 0.1% of Iowa's original tallgrass prairie remains. The small populations remaining are at risk for reduced genetic diversity, inbreeding depression, and outbreeding depression. In light of these concerns, we used microsatellite analysis to assess the genetic structure of butterfly milkweed (Asclepias tuberosa) populations on prairie remnants in northwest Iowa. We compared remnant populations with a restoration population at Dordt College in Sioux Center, Iowa, and with an Oklahoma seed source. Microsatellites identified for use in common milkweed (Asclepias syriaca) had sufficient polymorphism information content (PIC) across the butterfly milkweed (A. tuberosa) populations sampled (mean PIC = 0.624). The FIS values indicated a lack of inbreeding (mean FIS = −0.1455) even in the commercially expanded seed. The pairwise FST values showed a low degree of differentiation among the remnants (mean FST = 0.0453) but a moderate degree (mean FST = 0.105) of differentiation when comparing the remnants to the Dordt restoration or to seed from Oklahoma. Despite massive loss and fragmentation of the tallgrass prairie, our microsatellite analysis revealed no evidence of inbreeding in A. tuberosa. However, evidence of genetic differentiation suggests that effort should be made to preserve the diversity still present. Seed expansion efforts appear to have had minimal impact on overall genetic diversity, although the diversity in particular selectable traits may be reduced. The differences between the genetics of the propagated seed at the Dordt restoration and the Oklahoma seed when compared to native remnants support the usefulness of source-identified seed.

Genetic Differentiation Between Segugio Dell’Appeinnino and Segugio Maremmano Dog Breeds Assessed by Microsatellite Markers

The domestic dog (Canis Familiaris) was the first species to be tamed and bred to occupy a variety of functions. The Segugio dell’Appennino and Segugio Maremmano are two Italian breeds used extensively as hunting dogs. Microsatellites and other genetic markers are useful tools in evaluating the within and between breed genetic variation. The aim of this study was to investigate genetic differentiation among the two breeds through the analysis of 21 microsatellite markers. The two populations share the same geographical regions but have been over time selected on different parameters to achieve specific functions. All the analysed microsatellite markers were polymorphic and the average number of alleles per locus was 8.19. The mean FIT index (0.051; P<0.05) highlights that at some point in time, the normal gene flow among the animals was disrupted, giving rise to a heterozygote deficiency in both breeds, and this is confirmed by the mean FST fixation index (0.010; P<0.05) clearly indicating an absence of a significant genetic differentiation between the two breeds. The mean FIS value was significantly different from zero (0.042) (P<0.05) reconfirming the presence of a lack of heterozygosity in the studied samples. The values of observed and expected heterozygosity were similar in the two breeds. AMOVA, PCA and STRUCTURE analysis, all emphasise the lack of significant differences among the two breeds in terms of genetic differentiation. The presence of a population substructure is probably due to a genetic introgression from different Segugio breeds, that can be confirmed with further studies.

Micro-satellite based diversity estimation of Local hill fowl (Uttara fowl): A unique poultry strain of Uttarakhand

Nainital and Pithoragarh districts of Uttarakhand in Himalayan region have 2 types of poultry populations. Uttara fowl is reared under backyard system. But no information is available in the literature of Uttara fowl. The aim of the study was to analyze the genetic diversity in Local hill fowl of Uttarakhand (Uttara Fowl) using panel of micro-satellite markers recommended by FAO. The 50 blood samples were collected from randomly selected Uttara fowl. A total of 25 micro-satellite loci were used for this study. All the analyzed 25 loci were polymorphic and a total of 158 alleles were observed in the present study of Uttara Fowl. The observed and expected heterozygosity ranged from 0.292 (LEI-155) to 0.729 (LEI-90) and from 0.414 (MCW–250) to 0.838 (MCW-228) in Uttara fowl, respectively. Wright’s fixation index (Fis) values among loci ranged from –0.085 (for LEI-90) to 0.747(MCW-84). The mean Fis for 25 microsatellite loci was estimated 0.168. Deviation from Hardy-Weinberg equilibrium was observed in Uttara fowl in the commercial cross. The overall population heterozygote deficiency was 0.168. The existence of sufficient genetic diversity within Local hill fowls, estimated through molecular markers analysis would further aid in a conservation scheme, enabling the planning of new strategies for the improvement of in situ conservation schemes.

Genetic structure of fragmented southern populations of African Cape buffalo (Syncerus caffer caffer).

BackgroundAfrican wildlife experienced a reduction in population size and geographical distribution over the last millennium, particularly since the 19th century as a result of human demographic expansion, wildlife overexploitation, habitat degradation and cattle-borne diseases. In many areas, ungulate populations are now largely confined within a network of loosely connected protected areas. These metapopulations face gene flow restriction and run the risk of genetic diversity erosion. In this context, we assessed the “genetic health” of free ranging southern African Cape buffalo populations (S.c. caffer) and investigated the origins of their current genetic structure. The analyses were based on 264 samples from 6 southern African countries that were genotyped for 14 autosomal and 3 Y-chromosomal microsatellites.ResultsThe analyses differentiated three significant genetic clusters, hereafter referred to as Northern (N), Central (C) and Southern (S) clusters. The results suggest that splitting of the N and C clusters occurred around 6000 to 8400 years ago. Both N and C clusters displayed high genetic diversity (mean allelic richness (Ar) of 7.217, average genetic diversity over loci of 0.594, mean private alleles (Pa) of 11), low differentiation, and an absence of an inbreeding depression signal (mean FIS = 0.037). The third (S) cluster, a tiny population enclosed within a small isolated protected area, likely originated from a more recent isolation and experienced genetic drift (FIS = 0.062, mean Ar = 6.160, Pa = 2). This study also highlighted the impact of translocations between clusters on the genetic structure of several African buffalo populations. Lower differentiation estimates were observed between C and N sampling localities that experienced translocation over the last century.ConclusionsWe showed that the current genetic structure of southern African Cape buffalo populations results from both ancient and recent processes. The splitting time of N and C clusters suggests that the current pattern results from human-induced factors and/or from the aridification process that occurred during the Holocene period. The more recent S cluster genetic drift probably results of processes that occurred over the last centuries (habitat fragmentation, diseases). Management practices of African buffalo populations should consider the micro-evolutionary changes highlighted in the present study.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-014-0203-2) contains supplementary material, which is available to authorized users.

New polymorphic microsatellite markers for the Korean manila clam (Ruditapes philippinarum) and their application to wild populations.

Manila clam (Ruditapes philippinarum) is a valuable and intensively exploited shellfish species in Korea. Despite its importance, information on its genetic background is scarce. For the genetic characterization of R. philippinarum, expressed sequence tag-derived microsatellite markers were developed using next-generation sequencing. A total of 5879 tandem repeats containing di- to hexanucleotide repeat motifs were obtained from 236,746 reads (mean = 413 bp). Of the 62 loci screened, 24 (38.7%) were successfully amplified, and 10 were polymorphic in 144 individuals from 2 manila clam populations (Incheon and Geoje, Korea). The number of alleles ranged from 2 to 17 in the Incheon population and from 3 to 13 in the Geoje population (overall AR = 7.21). The mean observed and expected heterozygosities were estimated to be 0.402 and 0.555, respectively. Hence, there is less genetic variability in the Geoje population than in the Incheon population, although no significant reductions of genetic diversity were found between the populations (P > 0.05). However, significant genetic differentiation was detected between the populations (FST = 0.064, P < 0.001). Significant deviations from Hardy-Weinberg equilibrium and high inbreeding coefficients (mean FIS = 0.22-0.26) were detected in both populations. The 10 novel polymorphic microsatellite loci used in this study will be useful for future genetic mapping studies and for characterizing population structures, monitoring genetic diversity for successful aquaculture management, and developing conservation strategies for manila clam populations in Korea.

Genetic characterization of hatchery populations of Korean spotted sea bass (Lateolabrax maculatus) using multiplex polymerase chain reaction assays.

The spotted sea bass, Lateolabrax maculatus, is an important commercial and recreational fishery resource in Korea. Aquacultural production of this species has increased because of recent resource declines, growing consumption, and ongoing government-operated stock release programs. Therefore, the genetic characterization of hatchery populations is necessary to maintain the genetic diversity of this species and to develop more effective aquaculture practices. In this study, the genetic diversity and structure of three cultured populations in Korea were assessed using multiplex assays with 12 highly polymorphic microsatellite loci; 144 alleles were identified. The number of alleles per locus ranged from 6 to 28, with an average of 13.1. The mean observed and expected heterozygosities were 0.724 and 0.753, respectively. Low levels of inbreeding were detected according to the inbreeding coefficient (mean FIS = 0.003-0.073). All hatchery populations were significantly differentiated from each other (overall fixation index (FST) = 0.027, P < 0.01), and no population formed a separate cluster. Pairwise multilocus FST tests, estimates of genetic distance, mantel test, and principal component analyses did not show a consistent relationship between geographic and genetic distances. These results could reflect the exchange of breeds and eggs between hatcheries and/or genetic drift due to intensive breeding practices. For optimal resource management, the genetic variation of hatchery stocks should be monitored and inbreeding controlled within the spotted sea bass stocks that are being released every year. This genetic information will be useful for the management of both L. maculatus fisheries and the aquaculture industry.

Y chromosome analysis of native Turkish cattle breeds by microsatellite markers

The aim of this study was to determine phylogenetic relationships of 6 native cattle breeds of Turkey using 7 Y chromosome-specific microsatellite DNA markers. DNA samples were isolated from Anatolian Black, Anatolian Grey, South Anatolian Red, Native Southern Anatolian Yellow, East Anatolian Red, and Zavot cattle using a standard phenol/chloroform method. PCR products were separated by capillary electrophoresis and marker genotypes were determined. A total of 41 different alleles were observed. The mean allele number was 5.86 and mean FIS value was 0.427 for all populations. The INRA189 locus was monomorphic for all populations except for South Anatolian Red. UMN0307 and INRA124 loci were monomorphic in the East Anatolian Red and Anatolian Black populations, respectively. The Anatolian Black population was assigned to its own population at a maximum level (78.26%). In this study, a taurine-specific allele was identified in the INRA124 locus. Zebu- and taurine-specific alleles were observed in BM861, INRA189, and UMN0103 loci. Allele 134 in INRA124 seems to be a specific allele of taurine or zebu. The alleles of the UMN0307 and UMN0504 loci need to be investigated for zebu- or taurine-specific alleles. The resulting neighbor-joining tree and structure analysis suggested that the breeds analyzed are consistent with their modern geographical locations.

Genetic characterization of Curraleiro Pé-Duro bovine breed from a conservation herd of Brazilian semiarid.

Curraleiro Pé-Duro is a rustic bovine taurine breed found in Northeast of Brazil; this breed has decreased its production potentially in order to adapt to the region environment conditions. Consequently, it is under risk of extinction and is maintained at a preservation center in Piauí State, Brazil, as a source of genetic material adapted to local conditions. We analyzed genetic variability of this breed using microsatellite markers. Sixty animals were genotyped using 11 microsatellite loci normally used for paternity tests in bovines. The observed number of alleles ranged from 5 to 9, and the effective number of alleles ranged from 2.01 to 4.64. The Shannon index ranged from 0.949 to 1.669. The expected heterozygosity ranged from 0.510 to 0.798. Polymorphism information content values ranged from 0.453 to 0.751. Divergence from Hardy-Weinberg equilibrium was significant and the mean FIS value was 0.010. We conclude that this breed still has some genetic diversity, but with evident risk due to genetic drift caused by current breeding management. It will be necessary to insert animals from other herds to obtain the desired level of genetic variability in this breed remnant.