scholarly journals Microsatellite variability reveals high genetic diversity and low genetic differentiation in a critical giant panda population

2011 ◽  
Vol 57 (6) ◽  
pp. 717-724 ◽  
Author(s):  
Jiandong Yang ◽  
Zhihe Zhang ◽  
Fujun Shen ◽  
Xuyu Yang ◽  
Liang Zhang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Differentiation ◽  
Giant Panda ◽  
Population Decline ◽  
Management Strategies ◽  
Ailuropoda Melanoleuca ◽  
High Genetic Diversity ◽  
Giant Pandas ◽  
Allele Number ◽  
High Level

Abstract Understanding present patterns of genetic diversity is critical in order to design effective conservation and management strategies for endangered species. Tangjiahe Nature Reserve (NR) is one of the most important national reserves for giant pandas Ailuropoda melanoleuca in China. Previous studies have shown that giant pandas in Tangjiahe NR may be threatened by population decline and fragmentation. Here we used 10 microsatellite DNA markers to assess the genetic variability in the Tangjiahe population. The results indicate a low level of genetic differentiation between the Hongshihe and Motianling subpopulations in the reserve. Assignment tests using the Bayesian clustering method in STRUCTURE identified one genetic cluster from 42 individuals of the two subpopulations. All individuals from the same subpopulation were assigned to one cluster. This indicates high gene flow between subpopulations. F statistic analyses revealed a low FIS-value of 0.024 in the total population and implies a randomly mating population in Tangjiahe NR. Additionally, our data show a high level of genetic diversity for the Tangjiahe population. Mean allele number (A), Allelic richness (AR) and mean expected heterozygosity (HE) for the Tangjiahe population was 5.9, 5.173 and 0.703, respectively. This wild giant panda population can be restored through concerted effort.

scholarly journals Microsatellite genotyping from faeces of Lontra longicaudis from southern Brazil

2009 ◽  
Vol 99 (1) ◽  
pp. 5-11 ◽  
Author(s):  
Laura I. Weber ◽  
Cintia G. Hildebrand ◽  
Anderson Ferreira ◽  
Gustavo Pedarassi ◽  
José A. Levy ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Conservation Status ◽  
Significant Degree ◽  
Southern Brazil ◽  
High Genetic Diversity ◽  
Low Degree ◽  
Faecal Samples ◽  
High Level ◽  
Degree Of Differentiation ◽  
Lontra Longicaudis

A genetic study of the neotropical river otter Lontra longicaudis (Olfers, 1818), which has an unknown conservation status, was carried out at the Taim Ecological Station and the margins of the Vargas stream, Rio Grande do Sul, southern Brazil. Faecal samples were collected, and DNA was extracted using a silica-guanidine method. Five microsatellite loci were amplified using PCR with heterologous primers previously described for Lutra lutra (Linnaeus, 1758). Sixteen faecal samples out of 29 from Taim and 11 out of 14 from Vargas stream margins contained enough DNA for genetic analysis. A total of 49 different alleles were found at both localities, from which 18 were exclusively found in individuals from Taim and 17 were exclusives from Vargas individuals. The most common allele was the same at both locations for three loci (Lut715, Lut733, and Lut818). A high level of genetic diversity was found at both sites (NeTaim=4.1, HoTaim=0.299, HeTaim=0.681; NeVargas=4.9, HoVargas=0.355, HeVargas=0.724), being higher at the Vargas stream site. A high and significant level of heterozygote deficiency was observed at most loci according to the χ2 test. The homogeneity χ2 test (P<0.001) showed that there were significant differences in the allele frequencies between the two locations. Genotyping for more than one locus was possible in 81.5% of samples, from which only 37% were possible to genotype for more than three loci. A low degree of relatedness was found among individuals from Taim (R=0.055±0.310), but an even lower value of relatedness was found at the Vargas site (R= -0.285±0.440). The significant degree of differentiation (I=0.890; F ST=0.059) found between Taim and Vargas individuals suggests that there is more than one population of otters in the southern extreme of Brazil, which probably are associated with the water body systems found in this region, the Mirim and the Caiuvá/Flores/Mangueira Lagoons. The high genetic diversity and low relatedness found at the Vargas stream, lead us to believe that the Vargas stream may be acting as a corridor between these water bodies for otter dispersion.

scholarly journals Genetic Dissimilarity in Conyza sumatrensis Revealed by Simple Sequence Repeat (SSR) Markers

2020 ◽  
Vol 38 ◽  
Author(s):  
T. SCHNEIDER ◽  
M.A. RIZZARDI ◽  
S.P. BRAMMER ◽  
S.M. SCHEFFER-BASSO ◽  
A.L. NUNES
Keyword(s):  
Genetic Diversity ◽  
Management Strategies ◽  
Rapid Evolution ◽  
Jaccard Coefficient ◽  
Mechanisms Of Resistance ◽  
High Genetic Diversity ◽  
Resistance To Herbicides ◽  
Geographic Regions ◽  
Genetic Dissimilarity ◽  
Simple Sequence

ABSTRACT: In view of the rapid evolution of Conyza sumatrensis populations resistant to glyphosate, it is necessary to understand the genetic diversity aimed to improve strategies for managing this weed. We investigated the genetic dissimilarity among 15 biotypes of C. sumatrensis from different geographic regions using microsatellite loci. The biotypes, were cultivated in a greenhouse to obtain vegetal material for DNA extraction. Nineteen microsatellite markers (SSR), were developed for C. sumatrensis biotypes. The genetic dissimilarity was estimated by the Jaccard coefficient (JC) and the biotypes grouped by the UPGMA method. The results demonstrated a high dissimilarity (JC = 7.14 to 82.62) of the analyzed material, with the biotypes forming five groups, being one group formed just by the susceptible biotype and in the others grouped by biotypes from distinct locations in the same group The high genetic diversity of C. sumatrensis indicates that the biotypes may show different responses to different management strategies, and that the mechanisms of resistance to herbicides and characteristics of evolution of populations due to adaptability may be some of the factors involved in the genetic variability of the species.

scholarly journals Immune profiles of male giant panda (Ailuropoda melanoleuca) during breeding season

2021 ◽  
Author(s):  
haibo shen ◽  
Caiwu Li ◽  
Ming He ◽  
Yan Huang ◽  
Jing Wang ◽  
...  
Keyword(s):  
Pattern Recognition ◽  
Breeding Season ◽  
Giant Panda ◽  
Expression Profiles ◽  
Killer Cell ◽  
Pattern Recognition Receptors ◽  
Ailuropoda Melanoleuca ◽  
Giant Pandas ◽  
Altered Expression ◽  
Immune Related Genes

Abstract Background: The giant panda (Ailuropoda melanoleuca) is a threatened endemic Chinese species and a flagship species of national and global conservation concern. Life history theory proposes that reproduction and immunity can be mutually constraining and interrelated. Knowledge of immunity changes of male giant pandas during the breeding season is limited.Results: Here, we researched peripheral blood gene expression profiles associated with immunity. Thirteen captive giant pandas, ranging from 9 to 11 years old, were divided into two groups based on their reproductive status. We identified 318 up-regulated DEGs and 43 down-regulated DEGs, which were enriched in 87 GO terms and 6 KEGG pathways. Additionally, we obtained 45 immune-related genes with altered expression, mostly up-regulated, and identified four hub genes HSPA4, SUGT1, SOD1, and IL1B in PPI analysis. These 45 genes were related to pattern recognition receptors, autophagy, peroxisome, proteasome, natural killer cell, antigen processing and presentation. SUGT1 and IL1B were related to pattern recognition receptors. HSP90AA1 was the most up-regulated gene and is a member of heat shock protein 90 family. HSP90 contributes to the translocation of extracellular antigen. KLRD1 encodes CD94, whose complex is an inhibitor of the cytotoxic activity of NK cells, was down-regulated. IGIP, which has the capability of inducing IgA production by B cells, was down-regulated, suggesting low concentration of IgA in male giant pandas. Our results suggest that most immune-related genes were up-regulated and more related to innate immune than adaptive immune. Conclusions: Our results indicated that breeding male giant pandas presented an immunoenhancement in innate immunity, enhanced antigen presentation and processing in cellular immunity compared to non-breeding males. The humoral immunity of male giant pandas may show a tendency to decrease during the breeding season. This study will provide a foundation for further studies of immunity and reproduction in male giant pandas.

Anogenital gland secretions code for sex and age in the giant panda, Ailuropoda melanoleuca

2004 ◽  
Vol 82 (10) ◽  
pp. 1596-1604 ◽  
Author(s):  
Hong Yuan ◽  
Dingzhen Liu ◽  
Lixing Sun ◽  
Rongping Wei ◽  
Guiquan Zhang ◽  
...  
Keyword(s):  
Giant Panda ◽  
Fatty Acid Esters ◽  
Ailuropoda Melanoleuca ◽  
Giant Pandas ◽  
Analog Form ◽  
Males And Females ◽  
Relative Abundances ◽  
Anogenital Gland Secretions ◽  
Acid Esters ◽  
Form Information

Anogenital gland secretions play a major role in chemical communication by giant pandas, Ailuropoda melanoleuca (David, 1869). We analyzed 45 samples of anogenital gland secretions collected from 24 captive pandas (5 male adults, 6 female adults, 6 male subadults, and 7 female subadults) by gas chromatography and mass spectrometry. The secretions contained over 95 compounds. Based on 56 common compounds (relative abundances >0.1%) shared by more than three individuals, we identified steroids, long-chain fatty acids, fatty-acid esters, aldehydes, alkanes, alkenes, amines, terpenes, and furans. The chemical composition of each secretion was individual-specific. Although none of these individual compounds was age- or sex-specific, the relative abundances of several compounds differed between males and females and between adults and subadults. This result shows that information about sex and age could be coded in analog form. Information about age but not gender could also be digitally coded by the presence or absence of some of the 56 compounds, in addition to the analog coding.

scholarly journals Genetic diversity and population structure of black cottonwood (Populus deltoides) revealed using simple sequence repeat markers

BMC Genetics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Cun Chen ◽  
Yanguang Chu ◽  
Changjun Ding ◽  
Xiaohua Su ◽  
Qinjun Huang
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Differentiation ◽  
River Basin ◽  
Simple Sequence Repeat ◽  
Populus Deltoides ◽  
Sequence Repeat ◽  
Black Cottonwood ◽  
High Genetic Diversity ◽  
Simple Sequence

Abstract Background Black cottonwood (Populus deltoides) is one of the keystone forest tree species, and has become the main breeding parents in poplar hybrid breeding. However, the genetic diversity and population structure of the introduced resources are not fully understood. Results In the present study, five loci containing null alleles were excluded and 15 pairs of SSR (simple sequence repeat) primers were used to analyze the genetic diversity and population structure of 384 individuals from six provenances (Missouri, Iowa, Washington, Louisiana, and Tennessee (USA), and Quebec in Canada) of P. deltoides. Ultimately, 108 alleles (Na) were detected; the expected heterozygosity (He) per locus ranged from 0.070 to 0.905, and the average polymorphic information content (PIC) was 0.535. The provenance ‘Was’ had a relatively low genetic diversity, while ‘Que’, ‘Lou’, and ‘Ten’ provenances had high genetic diversity, with Shannon’s information index (I) above 1.0. The mean coefficient of genetic differentiation (Fst) and gene flow (Nm) were 0.129 and 1.931, respectively. Analysis of molecular variance (AMOVA) showed that 84.88% of the genetic variation originated from individuals. Based on principal coordinate analysis (PCoA) and STRUCTURE cluster analysis, individuals distributed in the Mississippi River Basin were roughly classified as one group, while those distributed in the St. Lawrence River Basin and Columbia River Basin were classified as another group. The cluster analysis based on the population level showed that provenance ‘Iow’ had a small gene flow and high degree of genetic differentiation compared with the other provenances, and was classified into one group. There was a significant relationship between genetic distance and geographical distance. Conclusions P. deltoides resources have high genetic diversity and there is a moderate level of genetic differentiation among provenances. Geographical isolation and natural conditions may be the main factors causing genetic differences among individuals. Individuals reflecting population genetic information can be selected to build a core germplasm bank. Meanwhile, the results could provide theoretical support for the scientific management and efficient utilization of P. deltoides genetic resources, and promote the development of molecular marker-assisted breeding of poplar.

Giant panda (Ailuropoda melanoleuca) spermatozoon decondensation in vitro is not compromised by cryopreservation

2006 ◽  
Vol 18 (7) ◽  
pp. 767 ◽  
Author(s):  
Rebecca E. Spindler ◽  
Huang Yan ◽  
JoGayle Howard ◽  
Wang PengYan ◽  
Zhang Hemin ◽  
...  
Keyword(s):  
Giant Panda ◽  
Acrosome Reaction ◽  
Ailuropoda Melanoleuca ◽  
Genetic Management ◽  
Giant Pandas ◽  
Before And After ◽  
In Captivity ◽  
Oocyte Cytoplasm ◽  
Natural Breeding

Natural breeding of giant pandas in captivity is compromised, making artificial insemination and spermatozoa cryopreservation essential for genetic management. This study examined the influence of freeze–thawing on traditional parameters such as motility and spermatozoon functionality, specifically decondensation in vitro. Giant panda spermatozoa were assessed before and after rapid cryopreservation (4°C to –130°C over 2 min) in liquid nitrogen vapour. Spermatozoa pre-incubated in medium for 6 h were co-incubated with cat zonae (2 zonae μL–1) for 30 min to effect capacitation and an acrosome reaction. Spermatozoa were then mixed with mature cat oocyte cytoplasm (2 cytoplasm μL–1) for 4 h and evaluated for decondensation. Frozen spermatozoa were less motile (P < 0.05) than fresh counterparts immediately post-thawing, but not after 6 h incubation. There were more (P < 0.05) spermatozoa with completely diffused chromatin post-thaw (10.4 ± 1.3%; mean ± s.e.m.) compared to fresh counterparts (5.1 ± 1.0%). However, there was no overall difference (P > 0.05) in the incidence of decondensation between fresh (4 h, 69.8 ± 5.9%) and thawed (4 h, 71.5 ± 4.9%) spermatozoa after exposure to cat oocyte cytoplasm. It is concluded that the ‘rapid’ method now used to cryopreserve giant panda spermatozoa has little impact on spermatozoon decondensation.

Genetic Diversity of Rice vampireweed (Rhamphicarpa fistulosa) Populations in Rainfed Lowland Rice in West Africa

Weed Science ◽  
2016 ◽  
Vol 64 (3) ◽  
pp. 430-440
Author(s):  
Norliette Zossou ◽  
Hubert Adoukonèou-Sagbadja ◽  
Daniel Fonceka ◽  
Lamine Baba-Moussa ◽  
Mbaye Sall ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Differentiation ◽  
Lowland Rice ◽  
Rice Grain ◽  
High Genetic Diversity ◽  
Genetic Groups ◽  
Rainfed Lowland ◽  
Rice Genotypes ◽  
The Relationship ◽  
Aflp Technique

Rice vampireweed belongs to the Orobanchaceae and is found in Africa and Australia. It is a hemiparasitic weed of lowland rice genotypes and causes losses of 40 to 100% of rice grain yield. Our study addressed the genetic diversity of rice vampireweed in Benin and Senegal. The specific objectives of this research were to study the genetic diversity of rice vampireweed accessions in Benin and Senegal and the relationship between the different genotypes of rice vampireweed through agroecological areas. To achieve these objectives, the genetic diversity of rice vampireweed accessions using the AFLP technique was studied. Based on our results, dendrogram classification has distinguished four different genetic groups. The populations of Benin and Senegal are genetically diverse. Substantial genetic differentiation (GST) exists among agroecological areas within Benin and Senegal (GST = 0.17). The high genetic diversity of rice vampireweed in Benin and Senegal presents a challenge for the development of resistant rice germplasm.

SSR cross-amplification and variation within coffee trees (Coffea spp.)

Genome ◽  
2004 ◽  
Vol 47 (6) ◽  
pp. 1071-1081 ◽  
Author(s):  
V Poncet ◽  
P Hamon ◽  
J Minier ◽  
C Carasco ◽  
S Hamon ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Null Allele ◽  
Polymorphic Locus ◽  
Coffea Canephora ◽  
Fixation Index ◽  
High Genetic Diversity ◽  
Allele Number ◽  
Primer Sets ◽  
Polymorphism Level ◽  
Potential Use

Primer sets were developed from 85 Coffea arabica sequences in addition to 25 already published primer sets. They were subsequently used for amplification in six African Coffea species: Coffea canephora (CAN), Coffea eugenioides (EUG), Coffea heterocalyx (HET), Coffea liberica (LIB), Coffea sp. Moloundou (MOL) and Coffea pseudozanguebariae (PSE). The amplification percentages for these 110 primer pairs ranged from 72.7% for LIB to 86.4% for PSE. Good transferability was thus obtained within the Coffea genus. When focusing on the two species CAN and PSE, high genetic diversity, high polymorphic locus rates (above 80%) and a mean allele number per polymorphic locus of more than 3 were noted. The estimated null allele percentage was –11% for PSE and –9% for CAN. Sixty three percent (CAN) and 79.5% (PSE) of the fixation index (Fis) values were positive. The within-species polymorphism information content (PIC) distribution showed two modes for both species. Although the two species shared 30 polymorphic loci, no correlation between CAN and PSE PIC values was obtained. All of these data are discussed in relation to the polymorphism level and the potential use of these SSRs for subsequent analysis of genetic diversity or genetic mapping.Key words: microsatellite, Coffea, transferability, genetic diversity.

scholarly journals Topographic habitat features preferred by the Endangered giant panda Ailuropoda melanoleuca: implications for reserve design and management

Oryx ◽  
2011 ◽  
Vol 45 (2) ◽  
pp. 252-257 ◽  
Author(s):  
Ming-Hao Gong ◽  
Yan-Ling Song
Keyword(s):  
Geographical Information Systems ◽  
Giant Panda ◽  
Decisive Role ◽  
Reserve Design ◽  
Geographical Information ◽  
Limiting Factors ◽  
Ailuropoda Melanoleuca ◽  
High Quality ◽  
Giant Pandas ◽  
Habitat Features

AbstractThe effect of landscape on populations is of great importance, especially given the number of species inhabiting patchy landscapes. Developments in geographical information systems are facilitating a greater application of spatial analyses to threatened species, such as the Endangered giant panda Ailuropoda melanoleuca, for which habitat patchiness and quality are key limiting factors. Of all factors that influence the suitability of habitat for the giant panda, topography is not subject to change. Here, we report a spatial and statistical analysis of the high quality topographic habitat preferred by the giant panda across its stronghold in the Qinling Mountains, China. High quality topographic habitat, as indicated by a combination of elevation, slope and aspect, covers 92,788 ha, accounting for 15% of the current range of the species. The distribution of the giant panda closely follows patterns of topography and areas with patches of high quality topographic habitat are strongly associated with areas supporting greater numbers of giant pandas. However, comparisons between our model and the existing reserve system reveals a number of inadequacies. Some of the reserves contain little high quality topographic habitat and many patches of high quality topographic habitat are unprotected. Given the importance of topography and the decisive role it plays in shaping habitat, landscapes containing high quality topographic features must be a critical consideration in the design of reserves for the giant panda. The existing system of nature reserves is heavily weighted towards judicial and administrative boundaries, to the detriment of other factors such as topography.

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