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

CERNE ◽  
2012 ◽  
Vol 18 (1) ◽  
pp. 9-15 ◽  
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.

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

BMC Genetics ◽  
2019 ◽  
Vol 20 (1) ◽  
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.

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

2011 ◽  
Vol 60 (1-6) ◽  
pp. 285-288 ◽  
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.

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

Animals ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 1569
Author(s):  
Agnieszka Fornal ◽  
Katarzyna Kowalska ◽  
Tomasz Zabek ◽  
Agata Piestrzynska-Kajtoch ◽  
Adrianna Musiał ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
World War Ii ◽  
Microsatellite Markers ◽  
Fixation Index ◽  
Parental Genotype ◽  
Native Breed ◽  
Genetic Diversity And Structure ◽  
Genetic Resource Conservation ◽  
The Mean ◽  
Index Value

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.

scholarly journals Analysis of Genetic Diversity and Population Structure of Pigeonpea [Cajanus cajan (L.) Millsp] Accessions Using SSR Markers

Plants ◽  
2020 ◽  
Vol 9 (12) ◽  
pp. 1643
Author(s):  
Didas Kimaro ◽  
Rob Melis ◽  
Julia Sibiya ◽  
Hussein Shimelis ◽  
Admire Shayanowako
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Ssr Markers ◽  
Genetic Improvement ◽  
Polymorphic Information Content ◽  
Geographic Origin ◽  
Germplasm Collection ◽  
Fixation Index ◽  
Population Structure Analysis ◽  
The Mean

Understanding the genetic diversity present amongst crop genotypes is an efficient utilization of germplasm for genetic improvement. The present study was aimed at evaluating genetic diversity and population structure of 48 pigeonpea genotypes from four populations collected from diverse sources. The 48 pigeonpea entries were genotyped using 33 simple sequence repeat (SSR) markers that are polymorphic to assess molecular genetic diversity and genetic relatedness. The informative marker combinations revealed a total of 155 alleles at 33 loci, with an average of 4.78 alleles detected per marker with the mean polymorphic information content (PIC) value of 0.46. Population structure analysis using model based revealed that the germplasm was grouped into two subpopulations. The analysis of molecular variance (AMOVA) revealed that 53.3% of genetic variation existed within individuals. Relatively low population differentiation was recorded amongst the test populations indicated by the mean fixation index (Fst) value of 0.032. The Tanzanian pigeonpea germplasm collection was grouped into three major clusters. The clustering pattern revealed a lack of relationship between geographic origin and genetic diversity. This study provides a foundation for the selection of parental material for genetic improvement.

scholarly journals Genetic diversity and population structure of ridge gourd (Luffa acutangula) accessions in a Thailand collection using SNP markers

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Grimar Abdiel Perez ◽  
Pumipat Tongyoo ◽  
Julapark Chunwongse ◽  
Hans de Jong ◽  
Anucha Wongpraneekul ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Germplasm Collection ◽  
Snp Markers ◽  
Fixation Index ◽  
Breeding Programs ◽  
Total Fixation ◽  
Unrooted Phylogenetic Tree ◽  
Luffa Acutangula ◽  
Selection Of

AbstractThis study explored a germplasm collection consisting of 112 Luffa acutangula (ridge gourd) accessions, mainly from Thailand. A total of 2834 SNPs were used to establish population structure and underlying genetic diversity while exploring the fruit characteristics together with genetic information which would help in the selection of parental lines for a breeding program. The study found that the average polymorphism information content value of 0.288 which indicates a moderate genetic diversity for this L. acutangula germplasm. STRUCTURE analysis (ΔK at K = 6) allowed us to group the accessions into six subpopulations that corresponded well with the unrooted phylogenetic tree and principal coordinate analyses. When plotted, the STRUCTURE bars to the area of collection, we observed an admixed genotype from surrounding accessions and a geneflow confirmed by the value of FST = 0.137. AMOVA based on STRUCTURE clustering showed a low 12.83% variation between subpopulations that correspond well with the negative inbreeding coefficient value (FIS =  − 0.092) and low total fixation index (FIT = 0.057). There were distinguishing fruit shapes and length characteristics in specific accessions for each subpopulation. The genetic diversity and different fruit shapes in the L. acutangula germplasm could benefit the ridge gourd breeding programs to meet the demands and needs of consumers, farmers, and vegetable exporters such as increasing the yield of fruit by the fruit width but not by the fruit length to solve the problem of fruit breakage during exportation.

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

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.

Genetic Diversity among Calamus brandisii Becc. (Arecaceae) Populations in Kerala Part of Western Ghats

2021 ◽  
Vol 43 (1) ◽  
pp. 38-42
Author(s):  
Kavungal Priya ◽  
◽  
Indira . ◽  
Vadakkethil Balakrishnan Sreekumar ◽  
Renuka . ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Western Ghats ◽  
Rapd Markers ◽  
Gene Diversity ◽  
Issr Markers ◽  
High Genetic Diversity ◽  
Western Ghats Of India ◽  
The Mean ◽  
Two Parameters ◽  
Two Populations

Calamus brandisii Becc. is one of the endemic slender rattans found in the Western Ghats of India. The genetic diversity of two main populations available in Kerala was investigated using 20 RAPD and 9 ISSR markers. Two parameters viz., gene diversity and genetic diversity within and among populations were analyzed. ISSR analysis showed quite high genetic diversity in Pandimotta compared to Bonacaud population whereas in RAPD markers both these populations were moderately diverse. The percentage of total genetic differentiation (Gst) among two populations is relatively higher than the mean Gst value indicating high genetic diversity within the populations. The genetic distance between these two populations was 0.1739 with ISSR markers and 0.1971 with RAPD markers. Because of its high genetic diversity, Pandimotta population can be treated as an important population of gene diversity with potentially useful genes. This may be included in the high priority reservoir for genetic conservation also.

scholarly journals Keragaman Genetik 96 Aksesi Plasma Nutfah Padi Berdasarkan 30 Marka SSR Terpaut Gen Pengatur Waktu Pembungaan (HD Genes)

2016 ◽  
Vol 7 (2) ◽  
pp. 76
Author(s):  
Dwinita Wikan Utami ◽  
Sutoro Sutoro ◽  
Nurul Hidayatun ◽  
Andari Risliawati ◽  
Ida Hanarida
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Ssr Markers ◽  
Heading Date ◽  
Germplasm Collection ◽  
Dna Fingerprint ◽  
Early Maturity ◽  
Plant Variety ◽  
Variety Protection ◽  
Genetic Analyzer

<p>Genetic Diversity of 96 Accession of Rice Germplasm<br />Using 30 SSR Markers Linked to Heading Date Genes (HD<br />Genes). Dwinita W. Utami, Sutoro, Nurul Hidayatun,<br />Andari Risliawati, and Ida Hanarida. Rice with early<br />maturity is one of an important genetic resources in rice<br />germplasm collection. Characterization and identification of<br />genetic diversity is an important issue for plant variety protection.<br />Molecular identification by microsatellite markers<br />using Genetic Analyzer enables resolve of this issue. The<br />objective of this research is to identify the genetic diversity of<br />96 rice accessions based on their specific DNA fingerprint<br />using microsatellite markers. A total of 96 accessions consisting<br />of a diverse variety of maturity classification were<br />genotyped with 30 SSR markers linked to HD genes which<br />spread out in 12 chromosomes of rice geneome. The total<br />297 alleles were detected indicated the level of marker<br />informativeness. RM5607 generated 7 allele with the size<br />range from 103 to 197 and the highest PIC at 0.90. RM3571<br />(linked to HD12 gene) has a significant value associated with<br />varieties which have early maturity trait. Clustering analysis<br />showed the cluster based on Sub Species genome background<br />and on early maturity trait.</p>

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

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.

scholarly journals Genetic diversity in Brazilian tall coconut populations by microsatellite markers

2013 ◽  
Vol 13 (4) ◽  
pp. 356-362 ◽  
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.

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