Genetic Diversity and Population Structure of Polish Konik Horse Based on Individuals from All the Male Founder Lines and Microsatellite Markers

The Polish Konik horse is a primitive native breed included in the genetic resource conservation program in Poland. After World War II, intensive breeding work began, aimed at rebuilding this breed. Now, the whole Polish Konik population is represented by six male founder lines (Wicek, Myszak, Glejt I, Goraj, Chochlik and Liliput). Individuals representing all six paternal lineages were selected based on their breeding documentation. We performed a fragment analysis with 17 microsatellite markers (STRs) recommended by the International Society for Animal Genetics (ISAG). The genetic diversity and structure within the paternal lineages and the whole of the studied group were investigated. The average allelic richness was 6.497 for the whole studied group. The fixation index (FST; measure of population differentiation) was low (about 3%), the mean inbreeding coefficient (FIT) was low and close to 0, and the mean inbreeding index value (FIS) was negative. The mean expected heterozygosity was established at 0.7046 and was lower than the observed heterozygosity. The power of discrimination and power of exclusion were 99.9999%. The cumulative parentage exclusion probability equaled 99.9269% when one parental genotype was known and 99.9996% with both parents’ genotypic information was available. About 3% of the genetic variation was caused by differences in the breed origin and about 97% was attributed to differences among individuals. Our analysis revealed that there has been no inbreeding in the Polish Konik breed for the studied population. The genetic diversity was high, and its parameters were similar to those calculated for native breeds from other countries reported in the literature. However, due to the small number of breed founders and paternal lineages with unknown representation, the population’s genetic diversity and structure should be monitored regularly.

Download Full-text

Evaluation of Genetic Diversity and Structure of Turkish Water Buffalo Population by Using 20 Microsatellite Markers

Animals ◽

10.3390/ani11041067 ◽

2021 ◽

Vol 11 (4) ◽

pp. 1067

Author(s):

Emel Özkan Ünal ◽

Raziye Işık ◽

Ayşe Şen ◽

Elif Geyik Kuş ◽

Mehmet İhsan Soysal

Keyword(s):

Genetic Diversity ◽

Microsatellite Markers ◽

Water Buffalo ◽

Polymorphic Information Content ◽

Breeding Strategy ◽

Weinberg Equilibrium ◽

Expected Heterozygosity ◽

Genetic Diversity And Structure ◽

Hardy Weinberg Equilibrium ◽

The Mean

The present study was aimed to investigate the genetic diversity among 17 Turkish water buffalo populations. A total of 837 individuals from 17 provincial populations were genotyped, using 20 microsatellites markers. The microsatellite markers analyzed were highly polymorphic with a mean number of alleles of (7.28) ranging from 6 (ILSTS005) to 17 (ETH003). The mean observed and expected heterozygosity values across all polymorphic loci in all studied buffalo populations were 0.61 and 0.70, respectively. Observed heterozygosity varied from 0.55 (Bursa (BUR)) to 0.70 (Muş (MUS)). It was lower than expected heterozygosity in most of the populations indicating a deviation from Hardy–Weinberg equilibrium. The overall value for the polymorphic information content of noted microsatellite loci was 0.655, indicating their suitability for genetic diversity analysis in buffalo. The mean FIS value was 0.091 and all loci were observed significantly deviated from Hardy–Weinberg Equilibrium (HWE), most likely based on non-random breeding. The 17 buffalo populations were genetically less diverse as indicated by a small mean FST value (0.032 ± 0.018). The analysis of molecular variance (AMOVA) analysis indicated that about 2% of the total genetic diversity was clarified by population distinctions and 88 percent corresponded to differences among individuals. The information produced by this study can be used to establish a base of national conservation and breeding strategy of water buffalo population in Turkey.

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

Genetic Diversity and Structure in a Collection of Ancient Spanish Pear Cultivars Assessed by Microsatellite Markers

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.135.5.428 ◽

2010 ◽

Vol 135 (5) ◽

pp. 428-437 ◽

Cited By ~ 32

Author(s):

Carlos Miranda ◽

Jorge Urrestarazu ◽

Luis G. Santesteban ◽

José B. Royo ◽

Valero Urbina

Keyword(s):

Genetic Diversity ◽

Microsatellite Markers ◽

Core Collection ◽

Heterogeneous Material ◽

Fixation Index ◽

Factorial Correspondence Analysis ◽

Model Based Clustering ◽

Genetic Diversity And Structure ◽

Ssr Loci ◽

Different Origins

A collection of 141 old and local Spanish accessions of pear (Pyrus communis) from the Escuela Técnica Superior de Ingeniería Agraria-Universidad de Lleida (ETSIA-UdL) Pear Germplasm Bank in Lleida, Spain, were studied using a set of eight microsatellite markers to estimate the genetic diversity of the collection, to identify the genetic structure and relationships among its accessions, and to establish a representative core collection. An additional set of 13 well-known pear cultivars, currently grown in Spain and which represent a wide genetic diversity, were added as reference. The eight simple sequence repeat (SSR) loci amplified 97 alleles, with nine to 15 alleles per locus, and with the expected heterozygosity ranging from 0.65 to 0.89. All of the accessions except for 16 had at least one of the 48 rare alleles (frequency < 0.05) identified, and seven unique alleles were found in six accessions. Fifteen accessions were identified as synonyms and were excluded from the analysis. Genetic analyses performed by hierarchical clustering, Bayesian model-based clustering, and factorial correspondence analysis supported the existence of three groups among the accessions with moderate [fixation index (FST) = 0.074], but significant, differentiation. As a whole, most of the germplasm (about 75%) curated at the collection showed its genetic distinctness with respect to the main pear cultivars used in European orchards. In fact, most reference cultivars were included in one single cluster that, moreover, had the lowest genetic diversity and allelic richness, in spite of having been chosen as heterogeneous material from different origins. The obtained results were also used to create a core collection with 35 accessions constituting an efficient and accessible entry point in the ETSIA-UdL pear collection for breeding and research communities.

Download Full-text

Development of microsatellite markers at the National Agrobiodiversity Center in Korea for the genetic assessment of underutilized crops

Plant Genetic Resources ◽

10.1017/s1479262114000525 ◽

2014 ◽

Vol 12 (S1) ◽

pp. S125-S129

Author(s):

Gi-An Lee ◽

Sok-Young Lee ◽

Ho-Sun Lee ◽

Kyung-Ho Ma ◽

Jae-Gyun Gwag ◽

...

Keyword(s):

Genetic Diversity ◽

Microsatellite Markers ◽

Germplasm Management ◽

Underutilized Crops ◽

Crop Species ◽

Closely Related Species ◽

Polymorphic Loci ◽

Allele Number ◽

The Mean ◽

Genetic Assessment

The RDA Genebank at the National Agrobiodiversity Center (NAAS, RDA, Republic of Korea) has conserved about 182,000 accessions in 1777 species and is working at preserving agricultural genetic resources for the conservation and sustainable utilization of genetic diversity. The detection of genetic variability in conserved resources is important for germplasm management, but the molecular evaluation tools providing genetic information are insufficient for underutilized crops, unlike those for major crops. In this regard, the Korean National Agrobiodiversity Center has been developing microsatellite markers for several underutilized crops. We designed 3640 primer pairs flanking simple sequence repeat (SSR) motifs for 6310 SSR clones in 21 crop species. Polymorphic loci were revealed in each species (7–36), and the mean ratio of polymorphic loci to all the loci tested was 12%. The average allele number was 5.1 (2.8–10.3) and the expected heterozygosity 0.51 (0.31–0.74). Some SSRs were transferable to closely related species, such as within the genera Fagopyrum and Allium. These SSR markers might be used for studying the genetic diversity of conserved underutilized crops.

Download Full-text

Review: Genetic diversity studies using microsatellite markers and their contribution in supporting sustainable sheep breeding programs

Asian Journal of Agriculture ◽

10.13057/asianjagric/g010109 ◽

2017 ◽

Vol 1 (01) ◽

pp. 46-51

Author(s):

OUMER SHERIFF ◽

KEFYALEW ALEMAYEHU

Keyword(s):

Genetic Diversity ◽

Microsatellite Markers ◽

Polymorphic Information Content ◽

Domestic Sheep ◽

Breeding Programs ◽

Sheep Breeding ◽

Population Structures ◽

The Mean ◽

Tree Building ◽

Diversity Studies

Sheriff O, Alemayehu K. 2017. Review: Genetic diversity studies using microsatellite markers and their contribution in supporting sustainable sheep breeding programs. Asian J Agric 1: 46-51. Microsatellites have been widely accepted and employed as useful molecular markers for measuring genetic diversity and divergence within and among populations. The various parameters developed so far to measure genetic diversity within and among populations are observed and expected heterozygosities (Ho and He), the mean number of alleles per locus (MNA),polymorphic information content (PIC), genetic distance and phylogenetic or tree building approach.The objective of thisreview was therefore to quantifythe genetic diversity studies of domestic sheep populations using microsatellite markersand their contribution in supporting sustainable sheep breeding programs. From the review, it is possible to see that there was high within population genetic variations in all the studied sheep populations, poor level of population differentiations and high levels of inbreeding. On the other hand, low estimates of hetrozygosities and mean number of alleles and employing only few and weak markers were observed in some of the studies. The gaps observed in the previous genetic diversity studies of the sheep populations may demand further works to reveal more information on the population structures andto start appropriate and sustainable breeding programs.

Download Full-text

Genetic diversity in Brazilian tall coconut populations by microsatellite markers

Cropp Breeding and Applied Biotechnology ◽

10.1590/s1984-70332013000400006 ◽

2013 ◽

Vol 13 (4) ◽

pp. 356-362 ◽

Cited By ~ 4

Author(s):

Francisco Elias Ribeiro ◽

Luc Baudouin ◽

Patricia Lebrun ◽

Lázaro José Chaves ◽

Claudio Brondani ◽

...

Keyword(s):

Genetic Diversity ◽

Microsatellite Markers ◽

Cape Verde ◽

Coconut Palm ◽

Different Populations ◽

The Mean ◽

High Level ◽

Brazilian Populations

The tall coconut palm was introduced in Brazil in 1553, originating from the island of Cape Verde. The aim of the present study was to evaluate the genetic diversity of ten populations of Brazilian tall coconut by 13 microsatellite markers. Samples were collected from 195 individuals of 10 different populations. A total of 68 alleles were detected, with an average of 5.23 alleles per locus. The mean expected and observed heterozygosity value was 0.459 and 0.443, respectively. The number of alleles per population ranged from 36 to 48, with a mean of 40.9 alleles. We observed the formation of two groups, the first formed by the populations of Baía Formosa, Georgino Avelino and São José do Mipibu, and the second by the populations of Japoatã, Pacatuba and Praia do Forte. These results reveal a high level of genetic diversity in the Brazilian populations.

Download Full-text

Genetic Diversity and Structure of Latvian Tilia cordata Populations

Proceedings of the Latvian Academy of Sciences. Section B. Natural, Exact, and Applied Sciences. ◽

10.2478/prolas-2021-0039 ◽

2021 ◽

Vol 75 (4) ◽

pp. 261-267

Author(s):

Dainis Edgars Ruņģis ◽

Baiba Krivmane

Keyword(s):

Genetic Diversity ◽

Microsatellite Markers ◽

Vegetative Reproduction ◽

Growth Conditions ◽

Climatic Conditions ◽

Tilia Cordata ◽

High Genetic Diversity ◽

Genetic Diversity And Structure ◽

Broadleaf Tree ◽

Broadleaf Species

Abstract Changing climatic conditions are transforming the ecological and silvicultural roles of broadleaf tree species in northern Europe. Small-leaved lime (Tilia cordata Mill.) is distributed throughout most of Europe, and is a common broadleaf species in Latvia. This species can tolerate a broad range of environmental and ecological conditions, including temperature, water availability, and soil types. The aim of this study was to assess the genetic diversity and differentiation of Latvian T. cordata populations using nuclear microsatellite markers developed for Tilia platyphyllos. After testing of 15 microsatellite markers, Latvian T. cordata samples were genotyped at 14 micro-satellite loci. Latvian T. cordata populations had high genetic diversity, and were not overly isolated from each other, with moderate gene flow between populations. No highly differentiated populations were identified. Vegetative reproduction was identified in most analysed populations, and almost one-third of analysed individuals are of clonal origin. T. cordata has high timber production potential under the current climatic and growth conditions in Latvia, and therefore this species has potential for use in forestry, as well as playing a significant role in maintaining biodiversity and other ecosystem services.

Download Full-text

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

Small Ruminant Research ◽

10.1016/j.smallrumres.2016.12.029 ◽

2017 ◽

Vol 148 ◽

pp. 43-50 ◽

Cited By ~ 2

Author(s):

Le Thi Thuy ◽

Dinh Van Binh ◽

Nguyen Trong Binh ◽

Luu Quang Minh ◽

Tran Thi Thu Thuy ◽

...

Keyword(s):

Genetic Diversity ◽

Microsatellite Markers ◽

Genetic Diversity And Structure

Download Full-text

Genotyping-by-Sequencing Reveals Molecular Genetic Diversity in Italian Common Bean Landraces

Diversity ◽

10.3390/d11090154 ◽

2019 ◽

Vol 11 (9) ◽

pp. 154 ◽

Cited By ~ 2

Author(s):

Lucia Lioi ◽

Diana L. Zuluaga ◽

Stefano Pavan ◽

Gabriella Sonnante

Keyword(s):

Genetic Diversity ◽

Common Bean ◽

Genotyping By Sequencing ◽

Fixation Index ◽

Most Probable Number ◽

Probable Number ◽

Individual Snps ◽

Starting Point ◽

Genetic Diversity And Structure ◽

The Common

The common bean (Phaseolus vulgaris L.) is one of the main legumes worldwide and represents a valuable source of nutrients. Independent domestication events in the Americas led to the formation of two cultivated genepools, namely Mesoamerican and Andean, to which European material has been brought back. In this study, Italian common bean landraces were analyzed for their genetic diversity and structure, using single nucleotide polymorphism (SNP) markers derived from genotyping-by-sequencing (GBS) technology. After filtering, 11,866 SNPs were obtained and 798 markers, pruned for linkage disequilibrium, were used for structure analysis. The most probable number of subpopulations (K) was two, consistent with the presence of the two genepools, identified through the phaseolin diagnostic marker. Some landraces were admixed, suggesting probable hybridization events between Mesoamerican and Andean material. When increasing the number of possible Ks, the Andean germplasm appeared to be structured in two or three subgroups. The subdivision within the Andean material was also observed in a principal coordinate analysis (PCoA) plot and a dendrogram based on genetic distances. The Mesoamerican landraces showed a higher level of genetic diversity compared to the Andean landraces. Calculation of the fixation index (FST) at individual SNPs between the Mesoamerican and Andean genepools and within the Andean genepool evidenced clusters of highly divergent loci in specific chromosomal regions. This work may help to preserve landraces of the common bean from genetic erosion, and could represent a starting point for the identification of interesting traits that determine plant adaptation.

Download Full-text