Mean Number Of Alleles Research Articles

Genetic Characterization of the "Chusca Lojana", a Creole Goat Reared in Ecuador, and Its Relationship with Other Goat Breeds.

Simple SummaryAn individual from a population presents a series of characteristics that differ from the rest and that increase as the kinship relationships are lower; this leads to the fact that two populations that stop exchanging genetic material through mating eventually come to present characters common to all members of each, but different between the two. This was what happened with the animal populations brought to America more than 500 years ago from the Iberian Peninsula in the colonization period, resulting in Creole populations that inhabit the harshest environments of our immense geography. The Creole goat “Chusca Lojana” has adapted to live in the dry forest region of Southern Ecuador, where environmental conditions are warm-dry, with sparse vegetation and a rather irregular topography. In the present study, the intra-breed genetic diversity of this goat is analyzed as well as its genetic relationships with other breeds. Significant FIS and intra-breed structure show that there is some heterogeneity and structure within the breed. However, inter-breed structure results underline that this breed is differentiated from other Creole breeds, because crossbreeding with other breeds was not detected; therefore, we must take advantage of this valuable genetic resource, and ensure its conservation and selection.The largest population of goats (62%) in Ecuador is in the dry forest region in the south of the country. A Creole goat, named “Chusca Lojana”, has adapted to the dry forest region where environmental conditions are warm-dry, with sparse vegetation. Knowledge of the genetic information of the Creole goat is important to determine intra-racial diversity, the degree of genetic distance among other breeds of goats, and the possible substructure of the population, which is valuable for the conservation of such a species’ genetic resources. A total of 145 samples of the Creole goat was taken from the four biotypes previously identified. Genetic analyses were performed using 38 microsatellites recommended for studies of goat genetic diversity (FAO-ISAG). The results of within-breed genetic diversity showed a mean number of alleles per locus (MNA) of 8, an effective number of alleles (Ae) of 4.3, an expected heterozygosity (He) of 0.71, an observed heterozygosity (Ho) of 0.63, polymorphic information content (PIC) of 0.67, and an FIS value of 0.11. Between-breed genetic diversity among 43 goat populations (native of Spain, American Creole, Europeans, and Africans) showed the following values: FIS = 0.087, FIT = 0.176, and FST = 0.098. Regarding the analysis of the population structure, the results showed that the Creole Chusca Lojana goat population is homogeneous and no genetic separation was observed between the different biotypes (FST = 0.0073). In conclusion, the Chusca Lojana goat has a high genetic diversity, without exhibiting a genetic substructure. Therefore, it should be considered as a distinct population because crossbreeding with other breeds was not detected.

Assessment of genetic diversity and differentiation among four indigenous Turkish sheep breeds using microsatellites.

Conservation and breeding programmes of livestock species depend on determination of genetic diversity. Today in livestock species, microsatellite markers are commonly used to reveal population structure and genetic diversity in both breeds and varieties. In this study, population structure, genetic diversity, and differentiation among four native Turkish sheep breeds including Güney Karaman, Kangal, Norduz, and Karakas were assessed by using 21 microsatellite loci. By genotyping 120 individuals belonging to four sheep breeds, a total of 275 different alleles, 37 of which were private alleles, were observed across all loci. The mean number of alleles per breed ranged from 7.28 (Güney Karaman) to 8.09 (Karakas), while allelic richness ranged from 7.22 (Güney Karaman) to 7.87 (Karakas). Mean observed heterozygosity varied from 0.60 (Kangal) to 0.66 (Norduz and Karakas). The lowest pairwise value (0.084) was between Kangal and Karakas populations, while the highest pairwise value (0.142) was between Norduz and Karakas populations. Polymorphic information content (PIC) values, ranging from 0.71 (ETH10) to 0.91 (OarFCB304), were highly polymorphic (PIC 0.5) and informative in studied populations. In the present study, the results of phylogenetic analysis were of importance, since all studied populations have been accepted as Akkaraman varieties till today. However, factorial correspondence and structure analysis, pairwise values, and an unweighted pair group method with arithmetic mean analysis (UPGMA) dendrogram revealed that Güney Karaman and Norduz populations have became genetically different from the Akkaraman breed due being raised in different parts of Turkey under different climatic conditions together with their breeding practices. Therefore, we recommend that more comprehensive molecular studies should be conducted to clarify genetic differentiation of Akkaraman sheep varieties.

Use of Microsatellites in Genetic Diversity Assessment, Parentage Testing and Individual Identification of the Kangal Shepherd Dog

Abstract The Kangal Shepherd Dog is considered the most common dog breed of Turkish origin. This study investigated variations in ten autosomal microsatellite markers (PEZ01, PEZ03, PEZ05, PEZ06, PEZ08, PEZ12, PEZ20, FHC2010, FHC2054 and FHC2079) for the purposes of genetic diversity assessment of the Kangal breed. In addition, the use of markers was assessed in parentage testing and individual identification within the Kangal breed. The microsatellite markers were typed in 51 Kangal dogs. The total number of alleles in the study population was 69. The mean number of alleles per locus was 6.9, and varied from four (FHC2079) to 12 (PEZ12). The polymorphic information content (PIC) ranged from 0.52 (FHC2079) to 0.87 (PEZ12), with the mean value for all loci of 0.717. Power of exclusion (PE) in 10 microsatellites investigated varied between 0.143 (FHC2054) and 0.472 (PEZ08) per locus. In order to determine the efficiency of using microsatellites for individual identification in the Kangal breed, power of discrimination (PD) and matching probability (MP) were calculated for each microsatellite marker. The panel achieved high combined MP (6.77 × 10-10) and high combined PD value of 99.99999%. The obtained results may contribute to further recognition of the Kangal breed, and confirm that the investigated microsatellites enable a reliable parentage testing and individual identification of the breed.

A genomic exploration of 15 autosomal STR loci for establishment of a DNA profile database of the population of Himachal Pradesh.

In order to create an autosomal STR loci population database for Himachal Pradesh, 259 blood samples were taken from people residing in various regions of the state and AmpFlSTR® Identifiler® Plus PCR amplification kit was used for evaluation of 15 autosomal STR markers. A total of 149 alleles were investigated in this study with a mean allele number of 9.933 per locus. The locus D2S1338 was most informative in our data, as it had the highest discrimination power (PD-0.967) and the highest polymorphic information content (PIC-0.86). The matching probability and typical paternity index for all the studied loci were observed as 2.9x10-18 and 4.7x105, respectively. Discrimination power (CPD) and exclusion power (CPE) for all the studied loci were observed as 1 and 0.999998.

Development and Characterization of EST-SSR Markers for the Endangered Tree Magnolia patungensis (Magnoliaceae)

Magnolia patungensis (Magnoliaceae) is an endangered tree species endemic to China. To facilitate analysis of its genetic variability, we developed novel polymorphic expressed sequence tag-simple sequence repeat (EST-SSR) markers using transcriptome data. In total, 37 774 SSRs amounting to 91.52 Mb were identified from 131 132 unigenes, with the frequency of 28.81% and the average density of 2.42 kb. Mononucleotide (50.81%) and dinucleotide (34.12%) were the most abundant repeat types. We randomly selected 102 putative loci to test the amplification efficiency and the degree of polymorphism using three populations from which 15 individuals per population were sampled. The successful amplification rate was 36.27% and the polymorphism rate 12.75%. The 13 polymorphic SSR marker primers selected were used to characterize the genetic diversity of M. patungensis. A total of 40 alleles were identified for the species, ranging from 2 to 5 per locus. At the population level, the mean number of alleles per locus ranged from 1.9 to 2.5, and the mean observed and expected heterozygosity values from 0.308 to 0.446 and 0.304 to 0.424, respectively. Significant genetic differentiation (FST = 0.286) and low gene flow (Nm = 0.627) among populations were discovered. Transferability of the markers was tested in five congeneric species. Nine loci were successfully amplified in M. dandyi, eight in M. insignis, M. fordiana and M. hookeri, and seven in M. conifera. These new EST-SSR markers will be an essential tool for the conservation of this endangered species as well as for investigating the evolutionary history for M. patungensis and its congenerics.

Genome-based development of 15 microsatellite markers in fluorescent multiplexes for parentage testing in captive tigers

As one of the most endangered species, tiger (Panthera tigris) inbreeding has become an urgent issue to address. Using a microsatellite (short tandem repeat, STR) identification system, paternity testing may be helpful to avoid inbreeding in captive breeding programs. In this study, we developed a genome-based identification system named tiger pedigree identification multiplex system (TPI-plex). By analyzing the entire tiger genome, 139,967 STR loci were identified and 12.76% of these displayed three to six alleles among three re-sequenced individual tiger genomes. A total of 204 candidate STRs were identified and screened with a reference population containing 31 unrelated captive tigers. Of these, 15 loci were chosen for inclusion in the multiplex panel. The mean allele number and mean expected heterozygosity (He) were 7.3333 and 0.7789, respectively. The cumulative probability of exclusion (CPE) and total probability of discrimination power (TDP) reached 0.999999472 and 0.999999999999995, respectively. The results showed that the TPI-plex system can be applied in routine pedigree identification for captive tigers. We also added a sex identification marker named TAMEL into the TPI-plex for sex determination.

Genetic integrity and individual identification-based population size estimate of the endangered long-tailed goral, Naemorhedus caudatus from Seoraksan National Park in South Korea, based on a non-invasive genetic approach

ABSTRACT The long-tailed goral (also called the Amur goral) Naemorhedus caudatus (subfamily Caprinae), a vulnerable and protected species designated by IUCN and CITES, has sharply been declining in the population size and is now becoming critically endangered in South Korea. This species has been conserved as a natural monument by the Korean Cultural Heritage Administration since 1968. In this study, using 78 fecal DNA samples with a non-invasive genetic approach, we assessed the genetic integrity and individual identification-based population size for the goral population from Seoraksan National Park representing the largest wild population in Korea. Using the successfully isolated 38 fecal DNA, phylogeographic and population genetic analyses were performed with mitochondrial DNA control region (CR) sequences and nine microsatellite loci. We found seven CR haplotypes, of which five were unique to the Seoraksan population, considering previously determined haplotypes in Korean populations. The Seoraksan population showed higher haplotype diversity (0.777 ± 0.062) and mean number of alleles (4.67 ± 1.563) relative to southern populations in Korea reported from previous studies, with no signal of a population bottleneck. Microsatellite-based individual identification estimate based on probability of identity (PID) indicated a population size of ≥30 in this population. Altogether, we suggest that for future management efforts of this species in the Seoraksan National Park, conserving its genetic integrity as an ‘endemic’ lineage, and curbing a decrease in its number through mitigating habitat destruction might be key to secure the population for the long term.

Identification of Genetic Variation in Introduced Reindeer Populations using DNA Markers

In order to improve the genetic diversity of the only reindeer population in China, the Genhe forestry bureau introduced 129 reindeer from Finland. In this study, we identified the genetic diversity and of genetic variation of introduced reindeer populations. The results showed that there was a heterozygous deletion in introduced population. A total of 9 haplotypes were found using individual mtDNA D-Loop sequences and the mean allele number of the 14 microsatellite loci was 9.1429. The genetic diversity of the introduced reindeer population was higher than Chinese reindeer population. They carry some new alleles in some individuals. Furthermore, the phylogenetic tree reveals that the evolutionary status of Chinese and introduced reindeer populations were both closed to Russian reindeer populations.

Genetic diversity in muskmelon based on SSR markers and morphological traits under well-watered and water-deficit condition

Abstract In the present study genetic diversity among 48 muskmelon accessions was analyzed employing various morphological traits under well-watered and water-deficit condition and SSR markers. Maximum values for horticultural traits were, 44 cm for fruit polar circumference, 33.2 cm for fruit equatorial circumference, 21 for number of fruits, 41.5 for days to first male flowering, 44 for days to 50% male flowering, 44 days to first female flowering, 45 days to 50% female flowering and 5.66 for number of shoot branching under well-watered condition. While under water-deficit condition maximum values of same parameters were 28.8 cm, 26 cm, 18, 37.2, 39, 47, 46.2 and 4.4, respectively. Based on morphological traits genotypes were clustered in three major clusters under well-watered condition, while grouped in five major clusters under water-deficit condition. Out of the 52 SSR markers, 35 produced polymorphic patterns, a total of 125 amplification products were obtained, the mean number of alleles per locus was 3.57, and the size of amplified products ranged from 120 bp to 605 bp. The average PIC value was estimated to be 0.492. Jaccard similarity coefficients calculated from SSR data varied from 0.03 to 0.89 with a mean value of 0.46. The clustering pattern of muskmelon accessions based on SSR markers was random but not in consonance with the groupings based on quantitative traits under well-watered and water-deficit condition. High genetic variability was observed based on various morphological traits, under both well-watered and water-deficit condition and SSR markers, indicating genetically diverse accessions.

Genetic characterization and molecular fingerprint of traditional Umbrian tomato (Solanum lycopersicum L.) landraces through SSR markers and application for varietal identification

Genetic erosion, mainly caused by the replacement of local landraces with high yielding or exotic varieties is causing loss of agrobiodiversity. Landraces of horticultural species, grown by small producers, represent today an important value in the preservation of agrobiodiversity. Umbria, a region of central Italy, is characterized by agricultural systems linked to tradition and cultivation of local landraces. In this study, the genetic profile of some traditional Umbrian tomato landraces was characterized for the first time, and the landraces uniqueness was evaluated by comparison with commercial varieties. One-hundred and twenty-one plants provided by local farmers and seed companies, represented by local and commercial varieties were analyzed using 19 SSRs markers. A total of 60 alleles were found with moderate levels of diversity. The mean number of alleles per locus was 3.158 and the average polymorphism information content was 0.38. Unweighted UPGMA clustered the accessions into four groups. The gene pool of Umbrian landraces seems to be highly differentiated compared to commercial varieties, with landraces showing a genetic distinctiveness. Furthermore, an identifying fingerprinting code of each tomato landrace was generated and an innovative method for varietal identification based on the ‘QR code’ was proposed. The results obtained in this study will be useful for a better management, conservation and propagation of tomato genetic resources in Umbria region.

Genomic diversity in the Goud population of Telangana, India inferred using twenty three autosomal marker PowerPlex® Fusion 6C System

Abstracts With the aim to investigate the genetic diversity of the Goud population of Telangana, India, 121 randomly selected healthy individuals were chosen for this study. The genetic diversity of the studied population was inferred using the PowerPlex® Fusion 6C system. A total of 257 alleles were observed in the studied population, along with the mean number of alleles 11.174 per locus. The locus SE33 showed the maximum number of observed allele i.e., 32, whereas locus TPOX showed the least number of observed allele i.e., 5. The studied population showed a wide range of allele frequencies ranged from 0.004 to 0.442. This wide range of allele frequency showed the diverse nature of the studied population, which is also supported by the broad range of observed Heterozygosity with the minimum value 0.628 to maximum 0.893, suggest the multidirectional gene flow in the studied population. The locus SE33 was also observed as the most polymorphic among all the studied loci. The combined value of the power of discrimination, power of exclusion, paternity index, and matching probability was found to be 1, 0.999999999178452, 9.86 × 108, and 4.5 × 10–28, respectively, for all the studied loci. Neighbor-Joining Tree and Principal Component Analysis (PCA) Plot showed the genetic affinity of the studied population with the Indian, central Indian, and populations of Uttar Pradesh and Jharkhand. This is the first global genetic report of genetic diversity in the Goud population of Telanagana using 23 markers PowerPlex® Fusion 6C system. The obtained genetic data of this study will be useful for forensic application, anthropological, and medical studies.

Multi-generational genetic consequences of reinforcement in a bird metapopulation

Translocation of conspecific individuals to reduce extinction risk of small, isolated populations and prevent genetic depletion is a powerful tool in conservation biology. An important question is how the translocated individuals influence the long-term genetic composition of the recipient population. Here, we experimentally reinforced a house sparrow (Passer domesticus) population, and examined the impact of this translocation on allele frequencies, levels of heterozygosity and genetic differentiation over six cohorts. We found no permanent increase in the mean number of alleles across loci or levels of observed heterozygosity, but a few alleles private to the translocated individuals remained in the population and we found a short-term increase in heterozygosity. Consequently, genetic differentiation of the recipient population compared to the genetic composition prior to reinforcement was small. The limited genetic impact was due to combined effects of a small probability of establishment and low mating success for the translocated individuals, together with increased genetic drift in the recipient population. Our findings emphasize the importance of selection and genetic drift as forces that may decrease the genetic contribution of reinforcement, especially in small populations. Conservation managers should aim to improve habitat quality in the recipient population to reduce genetic drift following translocation and thereby avoid the need for continued reinforcement. Furthermore, by facilitating establishment success and selecting individuals expected to have high mating success, possibly indicated by sexually selected traits, genetic contribution of released individuals is increased which in turn will decrease reproductive skew and genetic drift.

Design and development of a multiplex microsatellite panel for the genetic characterisation and diversity assessment of domestic turkey (Meleagris gallopavo gallopavo)

Domestic turkey production generally utilises only a few genetically improved lines, and local breeds are severely endangered as a result. Furthermore, the genetic resources of domestic turkeys have not been properly investigated, which could, ultimately, lead to the extinction of local breeds and negatively affect their corresponding genetic diversity and environmental adaptation. Although, several microsatellite markers have been designed for mapping and quantitative trait locus analysis, there is no standard panel of markers for genetic characterisation or genetic diversity assessment. Accordingly, the present study aimed to develop a set of polymorphic microsatellite markers that could be used for international turkey population studies. Thirty-nine microsatellites were selected based on polymorphism, DNA sequence and chromosome position, as well as on amplification efficiency, success rate and the absence of nonspecific amplification. The markers were screened using 105 DNA samples from local turkey breeds from Mexico, the United States, Italy, Brazil, Egypt and Spain. A total of 401 alleles were identified, with a mean number of alleles per marker of 10.28 ± 4.25. All microsatellites were polymorphic, with at least four alleles and no more than 19 alleles. Furthermore, allelic richness ranged from 3.810 to 17.985, mean heterozygosity ranged from 0.452 ± 0.229 to 0.667 ± 0.265, polymorphic information content values ranged from 0.213 (MNT264) to 0.850 (RHT0024) and the mean Fis value was 0.322. Overall, the panel was highly polymorphic and exhibited moderate Hardy–Weinberg disequilibrium, thereby indicating its value as a tool for biodiversity and population structure studies that could play an important role in promoting the conservation of local turkey breeds. Highlights Important genetic resources reside within indigenous turkey populations. These are linked to historic heritage production values and breeds. It is important to preserve this heritage and genetic diversity, which threatens to be lost as production systems focus on production characteristics. Microsatellite markers, even though, they are now replaced by single nucleotide polymorphism automatic genotyping platforms in many fields of genetics, remain a viable alternative thanks to their cheapness and simplicity of study which makes them particularly useful when the population to be studied lacks information of the prior genetic structure.

Molecular Identification of the "Facciuta Della Valnerina" Local Goat Population Reared in the Umbria Region, Italy.

Simple SummaryThe Facciuta goat originated from Valnerina, a geographic area in central Italy, including the adjacent parts of four regions: Umbria, Marche, Lazio, and Abruzzo. The aim of this study was to assess how useful microsatellite molecular markers are for the genetic discrimination of the local goat, Facciuta della Valnerina, compared with the two cosmopolitan breeds, Saanen and Camosciata delle Alpi, reared in the same geographic area. The results revealed a very clear separation between the local population (Facciuta della Valnerina) and the two reference goat breeds (Saanen and Camosciata delle Alpi). Furthermore, reducing the number of markers from 16 to 12 still allowed us to distinguish the local population, indicating that microsatellite markers are an inexpensive method to discriminate local livestock breeds. This could be a fast and inexpensive genomic tool to trace goat products and distinguish their origin.Italy holds important genetic resources of small ruminant breeds. By distinguishing goat breeds at the DNA level, certification of products from specific breeds can be valorized. The aim of this study was to establish the genetic identity of Facciuta della Valnerina, a local goat population of Italy, compared with the cosmopolitan breeds, Saanen and Camosciata delle Alpi, reared in the same geographic area. A total of 116 microsatellite alleles ranging from 4 to 13 were detected at 16 loci in the three goat populations/breeds. A total of 23 private alleles with frequencies lower than 0.3 were detected in the Facciuta della Valnerina population. The mean numbers of alleles were 6.67, 4.58, and 4.92 in Facciuta della Valnerina, Camosciata delle Alpi, and Saanen, respectively. The expected heterozygosity ranged from 0.20 to 0.86. Most loci were highly polymorphic and informative (polymorphic information content ≥0.50). Factorial correspondence analysis and principal components analysis revealed very clear separation between Facciuta della Valnerina and the two reference goat breeds. Reducing the number of markers from 16 to 12 (on the basis of polymorphic information content and the number of alleles) still allowed us to distinguish the local population, indicating that microsatellite markers are capable of discriminating local livestock breeds at a low cost.

Selection strategies in a segregating passion fruit population aided by classic and molecular techniques

ABSTRACT Combining the use of agronomic, disease-resistance, and molecular informationcan greatly contribute to genetic progress in breeding programs. This study was developed to estimate the genetic distance between genotypes derived from backcrosses and their parents using morphoagronomic and molecular information and information pertaining to resistance to the Cowpea aphid-borne mosaic virus (CABMV), and indicate genotypes with potential for generation advancement. The studied population consisted of 91 genotypes from the first backcross, oneinterspecific hybrid, and the species Passiflora setacea and P. edulis. For morphoagronomic characterization, the traits number of fruits, total fruit weight, average fruit weight, and area under the disease progress curve (AUDPC, related to resistance to CABMV) were evaluated. Fourteen microsatellite primers were used to estimate genetic diversity among the genotypes, estimatediversity parameters and quantify the proportion of parental genome in the evaluated genotypes. The use of morphoagronomic and molecular information revealed the existence of genetic variability among the genotypes. The mean number of alleles is close to that expected for the population. Observed heterozygosity (0.42) was higher than the expected heterozygosity (0.30), indicating an elevated number of heterozygous individuals in the population. Due to their good agronomic performance, resistance to the virus, and genotypic and phenotypic distinction, genotypes 484 and 312 are recommended to compose the future stages of the passion fruit breeding program aimed at resistance to CABMV

Estivasyon ve Hibernasyon Gösteren Doğal Bombus terrestris (L.) Populasyonlarında Genetik Yapıların Moleküler Markerler Kullanılarak Karşılaştırılması

Bu çalışmada estivasyon gösteren Faselis ve hibernasyon gösteren Termesos doğal B. terrestris popülasyonları arasındaki genetik farklılıkların 20 mikrosatellit lokus ve iki mtDNA gen bölgesi (COI ve cytb) temelinde incelenmesi amaçlanmıştır. Termesos ve Faselis popülasyonlarında sırasıyla; lokus başına ortalama allel sayısı 12,00 ve 11,00 olarak, gözlenen heterozigotluk değeri 0,68 ve 0,65 olarak, akrabalı yetiştirme katsayısı ise 0,22 ve 0,26 olarak tespit edilmiştir. İkişerli FST değeri 20 mikrosatellit lokus kullanılarak 0,023 olarak hesaplanmıştır. mtDNA COI gen bölgesine göre Termesos ve Faselis popülasyonlarındaki tüm örneklerin tek bir haplotipe dâhil olduğu (Haplotip B) belirlenmiştir. mtDNA cytb gen bölgesine göre 4 farklı haplotip (Haplotip 1-4) belirlenmiştir. mtDNA cytb bölgesine göre ikişerli FST değeri 0,0013 olarak hesaplanmıştır. Sonuç olarak, estivasyon ve hibernasyon gösteren bu iki doğal B. terrestris popülasyonu arasında incelenen 20 mikrosatellit ve iki mtDNA lokus bakımından önemli genetik farklılıklar bulunmamıştır. Araştırma sonuçlarına göre farklı B. terrestris doğal popülasyonlarının yaşam döngüsü bakımından farklılıklarının genetik etkilerden çok çevresel faktörler (fotoperiyod, sıcaklık, nem, yükseklik, bitki örtüsü vs.) ile şekillendiği anlaşılmaktadır.

Development and characterization of a duplex PCR assay in Chinese sturgeon (Acipenser sinensis) for genetic analysis

Chinese sturgeon (Acipenser sinensis) has been listed as a critically endangered species on the IUCN Red List and is an endemic fish of China. Five sets of duplex polymerase chain reactions (PCR) assays were developed with 10 tetranucleotide microsatellites for Chinese sturgeon. The size of CS57, ZHX43, ZHX69, AS105, ZHX51, AS074, ZHX2, AS078, AS026 and AS073 products in 184 Chinese sturgeon individuals ranged from 257–305, 191–241, 251–285, 172–244, 236–260, 169–209, 194–234, 92–176, 165–257 and 120–164, respectively. The observed allele number of the 10 microsatellites ranged from 7 to 16, and the total number of alleles was 106. The number of alleles per individual in CS57, ZHX43, AS105, AS074, AS078 and AS026 was 1–4. The number of alleles per individual in ZHX69, ZHX51, ZHX2 and AS073 was 2–4. The mean number of alleles per locus per individual ranged from 2.01–3.76. The expected heterozygosity (HE), observed heterozygosity (HO), polymorphic information content (PIC) and Shannon-Weiner diversity index (H′) ranged from 0.582 to 0.899, from 0.676 to 1, from 0.518 to 0.886 and from 1.034 to 2.34, respectively. Despite many advantages, the use of microsatellites as genetic analysis tools can be limited by the cost of the associated experiment. To solve this problem, this set of five duplex PCRs will provide tools that are more helpful, less expensive and less time consuming than others used for genetic analyses in Chinese sturgeon.

Assessment of genetic diversity in main local sheep breeds from Romania using microsatellite markers.

The state of the local breeds of farm animals is increasingly precarious worldwide because of the aggressive introduction of breeds with improved economical traits. The preference of the breeders for local breeds is due to their higher adaptability to the particular climate and relief conditions of the mountain areas, to the high rate of assimilation of the feeds from these regions and to their increased resistance to diseases. This study analyzes the genetic variation of the main four local Romanian sheep breeds (Tsurcana, Tsigai, Ratska and Teleorman Blackhead) in terms of stock and economic importance, using 18 microsatellite markers. The mean number of alleles per locus was of 9.764. The values of genetic diversity parameters exhibited a high degree of polymorphism for the analyzed breeds, although inbreeding was highlighted particularly in Tsurcana and Tsigai. These breeds also showed an intense gene flow among them and were less differentiated in comparison with Ratska and Teleorman Blackhead. The results of this study may be useful for breeding programs and conservation plans since the genetic resources of the local breeds must be preserved so as to maintain an adequate level of biodiversity in animal husbandry.

Development and Characterization of Simple Sequence Repeat Markers for, and Genetic Diversity Analysis of Liquidambar formosana

Liquidambar formosana (Hamamelidaceae) is a relatively fast-growing deciduous tree of high ornamental value that is indigenous to China. However, few molecular markers are available for the species or its close relatives; this has hindered genomic and genetic studies. Here, we develop a series of transferable expressed sequence tag-simple sequence repeats (EST-SSRs) for genomic analysis of L. formosana. We downloaded the sequence of the L. formosana transcriptome from the National Center of Biotechnology Information Database and identified SSR loci in the Unigene library. We found 3284 EST-SSRs by mining 34,491 assembled unigenes. We synthesized 100 random primer pairs for validation of eight L. formosana individuals; of the 100 pairs, 32 were polymorphic. We successfully transferred 12 EST-SSR markers across three related Liquidambar species; the markers exhibited excellent cross-species transferability and will facilitate genetic studies and breeding of Liquidambar. A total of 72 clones of three Liquidambar species were uniquely divided into three main clusters; principal coordinate analysis (PCoA) supported this division. Additionally, a set of 20 SSR markers that did not exhibit nonspecific amplification were used to genotype more than 53 L. formosana trees. The mean number of alleles (Na) was 5.75 and the average polymorphism information content (PIC) was 0.578, which was higher than that of the natural L. formosana population (0.390). In other words, the genetic diversity of the plus L. formosana population increased, but excellent phenotypic features were maintained. The primers will be valuable for genomic mapping, germplasm characterization, gene tagging, and further genetic studies. Analyses of genetic diversity in L. formosana will provide a basis for efficient application of genetic materials and rational management of L. formosana breeding programs.

Demographic and genetic structure of a severely fragmented population of the endangered hog deer (Axis porcinus) in the Indo-Burma biodiversity hotspot.

The population of the globally endangered hog deer (Axis porcinus) has declined severely across its geographic range. Intensive monitoring of its demographic and genetic status is necessary. We examined the demographic and genetic structure of a small hog deer population in Keibul Lamjao National Park (KLNP), located on the western fringe of the Indo-Burma biodiversity hotspot for conservation planning. The distribution pattern of hog deer in the Park was derived based on the presence/absence of faecal pellets in 1 km × 1 km grids. We used double-observer distance sampling method to derive the hog deer abundance and population structure and compared with previous data to derive the population trend. We determined the genetic diversity of the population through microsatellite screening and bottleneck detection. The overall pellet density was 0.34 ± 0.02 pellets km-2 restricted to only 22.34 ± 0.20 km2 area of the park. The estimated density of the deer in the park was 1.82–4.32 individuals km-2. The population showed a declining trend from 2006–08 (p < 0.05, R2 = 0.916) with 8% annum-1 and an increasing trend from 2003–2018 (p < 0.05, R2 = 0.9304) with 10% annum-1. The adult male-to-female ratio and fawn-to-doe ratio were 36.2 ± 1.9 males per 100 females and 16.5 ± 0.4 fawns per 100 females, respectively. The molecular examination suggested that the mean number of alleles at 23 loci was 2.70 ± 0.18, the observed heterozygosity (Ho) ranged from 0.26 to 0.63 (mean 0.42 ± 0.02), the expected heterozygosity (He) ranged from 0.23 to 0.73 (χ = 0.51 ± 0.03), and the polymorphic information content (PIC) ranged from 0.2 to 0.67 (χ = 0.43 ± 0.03) indicating a moderate level of genetic diversity. Although no bottleneck in the population was observed, the loss of genetic diversity may affect the evolutionary potential of the species at the site by limiting the selection flexibility. Conservation planning coupled with scientific management regime will help in the long term persistence of the population in the region.