Nonlethal Tissue Sampling Techniques and Microsatellite Markers Used for First Report of Genetic Diversity in Two Populations of the Endangered Somatochlora hineana (Odonata: Corduliidae)

Abstract Rhesus monkeyss (Macaca mulatta) are extensively used in the field of medical and psychological research as valuable experimental animals. 15 polymorphic chromosome-specific microsatellite markers were used to analyze the genetic diversity and population structure in two captive individuals. A total of 155 alleles were identified, with the number of alleles per locus ranging from 7 to 15, giving an average number of 10.3 alleles per locus. The mean number of effective alleles (Ne), observed heterozygosity (Ho), expected heterozygosity (He), and the polymorphism information content (PIC) were 5.602, 0.7297, 0.8016, and 0.7716, respectively. The populations HS and XJ shared partial common alleles, however, the remaining in XJ were not detected. Structure analysis indicated that two populations belong to three genetic lineages. AMOVA showed that the genetic variance was 91% among individuals, while it was 9% among populations, respectively. The bottleneck effect analysis revealed that the two captive populations were in accordance with mutation-drift equilibrium. In the comparison of the genetic parameters and structure between the HS and XJ, we speculated that the genetic diversity was higher, which may be attributed to the exchange of germplasm resources and the input of new individuals from wild populations.

Download Full-text

Assessment of genetic diversity and phylogenetic relationships in Black Pied cattle in the Novosibirsk Region using microsatellite markers

Vavilov Journal of Genetics and Breeding ◽

10.18699/vj21.096 ◽

2022 ◽

Vol 25 (8) ◽

pp. 831-838

Author(s):

R. B. Aitnazarov ◽

T. M. Mishakova ◽

N. S. Yudin

Keyword(s):

Genetic Diversity ◽

Microsatellite Markers ◽

Population Distribution ◽

Cattle Breed ◽

Principal Component ◽

Indigenous Cattle ◽

Cattle Breeds ◽

Novosibirsk Region ◽

Breed Improvement ◽

Two Populations

There are currently over a thousand indigenous cattle breeds well adapted to local habitat conditions thanks to their long history of evolution and breeding. Identification of the genetic variations controlling the adaptation of local cattle breeds for their further introduction into the genome of highly productive global breeds is a matter of great relevance. Studying individual populations of the same breed with the use of microsatellite markers makes it possible to assess their genetic diversity, relationships, and breed improvement potential. Although the Black Pied breed is the most common dairy cattle breed in Russia, there are only a few studies on genetic diversity in local Black Pied populations in some Russian regions. The goal of the present study was to analyze the genetic diversity in Black Pied cattle populations in the Novosibirsk Region and compare them with other Russian populations; to identify significantly divergent populations with a view to preserving them under the programs aimed at maintaining the genetic diversity of the domestic Black Pied breed. DNA samples from 4788 animals of the Black Pied breed from six breeding enterprises in the Novosibirsk Region have been studied using 11 microsatellite markers. No significant differences in genetic variability parameters were found between individual populations. Private alleles have been identified in five out of six populations. Five populations have shown inbreeding coefficient values (FIS) below zero, which indicates heterozygosity excess. The population distribution test, principal component analysis, FST and DEST values, cluster analysis, and phylogenetic analysis have revealed two populations genetically distinct from the others. Essentially, the genetic diversity parameters of the six studied Black Pied cattle populations from the Novosibirsk Region show no significant differences from other Russian populations of the breed. Excess heterozygosity is observed in most breeding enterprises, which is a sign of a low inbreeding rate. To maintain the genetic diversity of the Russian Black Pied cattle, we recommend focusing on the two populations with significant genetic distinctions from the others.

Download Full-text

Genetic diversity between and within populations of Handroanthus heptaphyllus (Vell.) Mattos using microsatellite markers

CERNE ◽

10.1590/s0104-77602012000100002 ◽

2012 ◽

Vol 18 (1) ◽

pp. 9-15 ◽

Cited By ~ 2

Author(s):

Neide Tomita Mori ◽

Mario Luiz Teixeira de Moraes ◽

Caroline Midori Morita ◽

Edson Seizo Mori

Keyword(s):

Genetic Diversity ◽

Microsatellite Markers ◽

Germplasm Collection ◽

Fixation Index ◽

Allelic Polymorphism ◽

Forest Fragments ◽

Germplasm Preservation ◽

The Family ◽

The Mean ◽

Two Populations

Handroanthus heptaphyllus (Vell.) Mattos, popularly known as ipê-roxo, is a species of the family Bignoneaceae much appreciated for its beauty, excellent quality wood which is used for making medicinal products and also in reforestation programs of degraded areas, as well as landscaping and restoration. The aim of this study was to investigate the genetic diversity between and within populations of H. heptaphyllus using microsatellite markers. The 192 seedlings were produced from seeds collected on 30 trees into the two populations of natural forest fragments in Botucatu region, São Paulo, Brazil. Eight microsatellite loci were analyzed, with allelic polymorphism varying from six alleles for locus TAU22 to 14 alleles for loci TAU12, TAU30, and TAU31, with an expected mean number of alleles per locus (Âe) of 4.9. The mean expected heterozygosity(Ĥe) for the two populations was 0.785, the mean observed heterozygosity(Ĥo) was 0.609, and the fixation index (^F) was low between populations, with a mean of 0.222. The gene differentiation between the two populations (Ĝst') was 0.100. We concluded that the higher genetic diversity is within populations; therefore, as far as germplasm collection programs in Botucatu region are concerned, it is recommended that a larger sampling of individuals should be considered within populations, thereby providing good genetic representativeness. The populations have enough genetic diversity to support genetic improvement and germplasm preservation programs.

Download Full-text

Genetic diversity and structure of Chinese grass shrimp, Palaemonetes sinensis, inferred from transcriptome-derived microsatellite markers

BMC Genetics ◽

10.1186/s12863-019-0779-z ◽

2019 ◽

Vol 20 (1) ◽

Cited By ~ 4

Author(s):

Yingying Zhao ◽

Xiaochen Zhu ◽

Zhi Li ◽

Weibin Xu ◽

Jing Dong ◽

...

Keyword(s):

Genetic Diversity ◽

Microsatellite Markers ◽

In Situ Conservation ◽

Grass Shrimp ◽

The Other ◽

Fixation Index ◽

High Genetic Diversity ◽

Genetic Diversity And Structure ◽

Polymorphic Microsatellite ◽

Two Populations

Abstract Background The Chinese grass shrimp, Palaemonetes sinensis, is an economically important freshwater shrimp in China, and the study of genetic diversity and structure can positively contribute to the exploration of germplasm resources and assist in the understanding of P. sinensis aquaculture. Microsatellite markers are widely used in research of genetic backgrounds since it is considered an important molecular marker for the analyses of genetic diversity and structure. Hence, the aim of this study was to evaluate the genetic diversity and structure of wild P. sinensis populations in China using the polymorphic microsatellite makers from the transcriptome. Results Sixteen polymorphic microsatellite markers were developed for P. sinensis from transcriptome, and analyzed for differences in genetic diversity and structure in multiple wild P. sinensis populations in China. Totally of 319 individual shrimps from seven different populations were genotyped to find that allelic polymorphisms varied in two to thirteen alleles seen in the entire loci. Compared to other populations analyzed, the two populations including LD and SJ showed lower genetic diversity. Both the genetic distance (D) and Wrights fixation index (FST) comparing any two populations also indicated that LD and SJ populations differed from the other five populations. An UPGMA tree analysis showed three main clusters containing SJ, LD and other populations which were also confirmed using STRUCTURE analysis. Conclusion This is the first study where polymorphic microsatellite markers from the transcriptome were used to analyze genetic diversity and structures of different wild P. sinensis populations. All the polymorphic microsatellite makers are believed useful for evaluating the extent of the genetic diversity and population structure of P. sinensis. Compared to the other five populations, the LD and SJ populations exhibited lower genetic diversity, and the genetic structure was differed from the other five populations. Therefore, they needed to be protected against further declines in genetic diversity. The other five populations, LP, LA, LSL, LSY and LSH, are all belonging to Liaohe River Drainage with a relatively high genetic diversity, and hence can be considered as hot spots for in-situ conservation of P. sinensis as well as sources of desirable alleles for breeding values.

Download Full-text

Primer Note: Microsatellite-AFLP development for Araucaria araucana (Mol.) K. Koch, an endangered conifer of Chilean and Argentinean native forests

Silvae Genetica ◽

10.1515/sg-2011-0037 ◽

2011 ◽

Vol 60 (1-6) ◽

pp. 285-288 ◽

Cited By ~ 4

Author(s):

G. Marconi ◽

M. A. Martín ◽

M. Cherubini ◽

L. Raggi ◽

F. Drake ◽

...

Keyword(s):

Genetic Diversity ◽

Microsatellite Markers ◽

Native Species ◽

Conservation Strategy ◽

Native Forests ◽

Araucaria Araucana ◽

The Mean ◽

Two Populations ◽

Aflp Technique

Abstract Araucaria araucana (Mol.) K. Koch is one of the most important native species of Chile and Argentina, and also one of the most endangered. In this study, we report the development and characterization of a set of microsatellite markers in the species by means of the microsatellite-AFLP (M-AFLP) technique. A total of 25 M-AFLP derived bands, showing a typical microsatellite pattern, were selected and sequenced. Of these, 12 that contained microsatellite sequences, were used for primer extension. Six of the resulting SSR markers provided easily interpretable patterns and were used to investigate the level of genetic diversity in two populations of A. araucana. A total of 43 alleles were amplified. The mean overall loci of observed and expected heterozygosities for the Conguillio and Villa Araucaria populations were 0.322 and 0.443, respectively. The primers presented in this study may provide useful information for the establishment of a conservation strategy in the species.

Download Full-text

Genetic Markers for Species Conservation and Timber Tracking: Development of Microsatellite Primers for the Tropical African Tree Species Prioria balsamifera and Prioria oxyphylla

Forests ◽

10.3390/f10111037 ◽

2019 ◽

Vol 10 (11) ◽

pp. 1037 ◽

Cited By ~ 1

Author(s):

Vanden Abeele ◽

Hardy ◽

Beeckman ◽

Ilondea ◽

Janssens

Keyword(s):

Genetic Diversity ◽

Microsatellite Markers ◽

Tree Species ◽

Spatial Genetic Structure ◽

Species Conservation ◽

Population Level ◽

Timber Tracking ◽

Polymorphic Microsatellite ◽

Set Up ◽

Two Populations

Research Highlights: Two novel sets of polymorphic microsatellite markers were developed for Prioria balsamifera and Prioria oxyphylla through high-throughput sequencing. Validation in two populations of each species proved the utility of the developed primers to estimate genetic diversity at population level. Background and Objectives: Prioria balsamifera and Prioria oxyphylla are tropical tree species from Central Africa. They produce a high-quality, multi-purpose timber that is of great interest to the international market. Prioria balsamifera has been included as ‘endangered’ on the IUCN Red List of Threatened Species. In order to set up adequate management plans and facilitate timber tracking, knowledge on the genetic diversity at population level is needed. Therefore, we aim to develop microsatellite markers that can be used for species conservation, forensics, plant breeding and population genetics studies. Materials and Methods: Genomic DNA of P. balsamifera and P. oxyphylla was sequenced on an Illumina NextSeq platform (Illumina Inc., San Diego, CA, USA), generating 829,421 and 772,018 paired-end reads that contained 7148 and 7004 microsatellite sequences, respectively. The QDD-pipeline was used to design primers, which were tested for amplification in two populations of each species. Cross-species amplification was tested in all seven African Prioria species. Results: For P. balsamifera, 16 polymorphic microsatellite markers were developed and combined in three multiplexes. Inbreeding appeared to be absent but genetic diversity was low in both populations. For P. oxyphylla, 15 polymorphic microsatellite markers were developed and combined in three multiplexes. Genetic diversity was low in both populations and estimated null allele frequencies were high for multiple loci. Cross-species amplification tests demonstrated the occurrence of conserved loci that amplified for most of the African Prioria species. Conclusions: The microsatellite markers prove to be useful for estimating genetic diversity at population level. These novel markers can be used to study gene flow and spatial genetic structure in Prioria species, which is needed to set up proper conservation guidelines and to prevent genetic erosion.

Download Full-text

Allozyme Variation and Population Substructuring in the Caucasian Ground Lizards Lacerta derjugini and Lacerta praticola

Russian Journal of Herpetology ◽

10.30906/1026-2296-1997-4-2-115-119 ◽

2011 ◽

Vol 4 (2) ◽

pp. 115-119 ◽

Cited By ~ 1

Author(s):

Ross D. MacCulloch ◽

Ilya S. Darevsky ◽

Robert W. Murphy ◽

Jinzhong Fu

Keyword(s):

Genetic Diversity ◽

Allozyme Variation ◽

Close Proximity ◽

Geographic Separation ◽

Population Substructuring ◽

Allozyme Loci ◽

Two Populations

Genetic diversity at 35 allozyme loci was surveyed in Lacerta derjugini (3 populations) and L. praticola (2 populations). Indices of variability were consistent with those found in other Caucasian Lacerta. There was little genetic substructuring between two populations of L. praticola despite considerable geographic separation. Conversely, populations of L. derjugini in close proximity to one another exhibited considerable substructuring.

Download Full-text