Retrospective Determination of the Parental Population of Superior Cacao (Theobroma cacao L.) Seedlings and Association of Microsatellite Alleles with Productivity

Commercial production of cacao in Hawaii is increasing, and this trend is expected to continue over the next several years. The increased acreages are being planted with seedlings from introduced and uncharacterized cacao populations from at least three initial introductions of cacao into the islands. Productive seedlings have been selected from a planting at Waialua, Oahu. The parents of these selections were believed to be the population at the Hawaii Agriculture Research Center (HARC) at Kunia; however, potential parental populations also exist at Univ. of Hawaii research stations at Waimanalo and Malama Ki. Using microsatellite markers, we analyzed the potential parental populations to identify the parents and determine the genetic background for 99 productive and 50 unproductive seedlings from the Waialua site. Based on 19 polymorphic microsatellite loci the parental population was identified as trees from Waimanalo and not trees from Malama Ki or Kunia. The Kunia and Malama Ki populations were very similar with low allelic diversity (A = 1.92) and low unbiased gene diversity (Hnb) of 0.311 and 0.329, respectively, and were determined to be Trinitario in type. The Waimanalo, productive seedling, and unproductive seedling populations had much higher levels of genetic diversity with Hnb of 0.699, 0.686, and 0.686, respectively, and were determined to be upper Amazon Forastero hybridized with Trinitario in type. An additional 46 microsatellite markers were amplified and analyzed in the Waimanalo parents, productive, and unproductive seedlings for a total of 65 loci. Seventeen loci contained alleles that were significantly associated with productive seedlings as determined by Armitage's trend test. Of these, 13 loci (76.4%) co-located with previously reported quantitative trait loci for productivity traits. These markers may prove useful for marker assisted selection and demonstrate the potential of association genetic studies in perennial tree crops such as cacao.

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Molecular characterization of wheat (Triticum aestivum L.) genotypes through SSR markers

Bangladesh Journal of Agricultural Research ◽

10.3329/bjar.v37i3.12082 ◽

2012 ◽

Vol 37 (3) ◽

pp. 389-398 ◽

Cited By ~ 3

Author(s):

S Islam ◽

MS Haque ◽

RM Emon ◽

MM Islam ◽

SN Begum

Keyword(s):

Genetic Diversity ◽

Triticum Aestivum ◽

Genetic Distance ◽

Microsatellite Markers ◽

Gene Diversity ◽

Polymorphic Information Content ◽

Allelic Diversity ◽

Triticum Aestivum L ◽

Allele Number ◽

Average Gene

A study was undertaken to examine the genetic diversity of 12 wheat (Triticum aestivum L.) genotypes, using 4 simple sequence repeats (SSRs). A total of 10 alleles were found. Allele number per locus ranged from 2 to 4 with an average of 2.5. The polymorphic information content (PIC) values ranged from 0.2755 to 0.5411 with an average of 0.3839. The average gene diversity over all SSR loci for the 12 wheat genotypes was 0.4688, ranging from 0.3299 to 0.6042. Cluster analysis based on microsatellite allelic diversity discriminated the varieties into different clusters. Genetic diversity was the highest between variety Gourab and Akbar as well as Gourab and BAW-1064, showing a genetic distance value of 0.4697. The genetic distance was lowest between Balaka and Aghrani as well as Triticale and BAW-1036. Positive correlations were found between gene diversity, number of alleles, the allele size range and the types of repeat motif of microsatellite markers. It was found from this study that microsatellite markers could characterize and discriminate all of the genotypes. More primers should be used for saturation of different regions in further studies. Bangladesh J. Agril. Res. 37(3): 389-398, September 2012 DOI: http://dx.doi.org/10.3329/bjar.v37i3.12082

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Characterization of simple sequence repeat loci for Peltigera membranacea (lichenized Ascomycota) and its Nostoc photobiont

The Lichenologist ◽

10.1017/s0024282921000384 ◽

2021 ◽

Vol 53 (6) ◽

pp. 457-465

Author(s):

Silke Werth ◽

Stefán Þór Pálsson ◽

Ólafur S. Andrésson

Keyword(s):

Simple Sequence Repeat ◽

Population Genetic ◽

Common Ground ◽

Gene Diversity ◽

Similar Species ◽

Sequence Repeat ◽

Genetic Studies ◽

Unbiased Gene ◽

Simple Sequence

AbstractTo facilitate population-genetic studies, we developed simple sequence repeat (SSR) markers and a molecular species identification assay for Peltigera membranacea (Ascomycota, Peltigerales), a common ground-dwelling lichen of forest and tundra ecosystems. Additional markers were developed for its Nostoc photobiont. Twenty-one fungal markers for P. membranacea were found to be polymorphic, with the number of alleles ranging from 3–21. Nei's unbiased gene diversity ranged from 0.588 to 0.640 in four significantly structured (FST = 0.059) mycobiont populations. For the Nostoc photobiont, 14 polymorphic SSR were developed, yielding 4–14 alleles each, with gene diversity ranging from 0.062 to 0.771 in four populations showing substantial population structure (FST = 0.278). The new markers developed are suitable for population genetic studies of Peltigera membranacea and of its cyanobiont, and at the same time allowed us to distinguish 98.5% of P. membranacea specimens from morphologically similar species of Peltigera.

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Development and characterization of fungal specific microsatellite markers in the lichenLobarina scrobiculata(Lobariaceae, Ascomycota)

The Lichenologist ◽

10.1017/s0024282915000109 ◽

2015 ◽

Vol 47 (3) ◽

pp. 183-186 ◽

Cited By ~ 6

Author(s):

Maria Prieto ◽

Lidia Romera ◽

Sonia Merinero ◽

Gregorio Aragón ◽

Isabel Martínez

Keyword(s):

Microsatellite Markers ◽

Iberian Peninsula ◽

Population Studies ◽

Gene Diversity ◽

Conservation Status ◽

Natural Populations ◽

Conservation Strategies ◽

Unbiased Gene ◽

Effective Conservation

AbstractLobarina scrobiculata(better known asLobaria scrobiculata) is a widespread lichen, threatened and Red-Listed in various European countries. Microsatellite markers for the mycobiont ofL. scrobiculatawere developed in order to investigate its genetic diversity in the Iberian Peninsula and Europe and to design effective conservation strategies. A total of 7 polymorphic markers were isolated and characterized. These microsatellites were tested in natural populations found in the Iberian Peninsula. The number of observed alleles ranged from 3 to 8, and the Nei's unbiased gene diversity from 0·26 to 0·59. These microsatellite markers are the first to be developed forL. scrobiculataand they will be useful for population studies and for the assessment of the conservation status of this species.

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Polymorphic fungus-specific microsatellite markers ofBactrospora dryinareveal multiple colonizations of trees

The Lichenologist ◽

10.1017/s0024282917000548 ◽

2017 ◽

Vol 49 (6) ◽

pp. 561-577 ◽

Cited By ~ 1

Author(s):

Olga NADYEINA ◽

Daria ZARABSKA-BOŻEJEWICZ ◽

Andrea WIEDMER ◽

Carolina CORNEJO ◽

Christoph SCHEIDEGGER

Keyword(s):

Population Genetics ◽

Microsatellite Markers ◽

Habitat Restoration ◽

Gene Diversity ◽

Spatial Scales ◽

Pedunculate Oak ◽

Epiphytic Lichen ◽

Oak Trees ◽

Forest Remnants ◽

Unbiased Gene

AbstractBactrospora dryinais an epiphytic lichen-forming fungus specifically related to old-growth floodplain forests, which have dramatically declined in Europe over the past centuries. In order to promote conservation management of such forest remnants, we aimed to study population genetics of this rare and threatened lichen. The newly developed 16 microsatellite markers are specific for the mycobiont ofB. dryinaand reliably amplify either single fruiting bodies or a sterile thallus. This allows the use of these markers for the identification of sterile crusts and for quantification of recent dispersal of the species into restored habitats. We tested the markers in 264 samples collected from 10 pedunculate oak trees growing in three localities in north-eastern Switzerland. All markers were polymorphic and showed two to five alleles per locus, and unbiased gene diversity varied from 0·06 to 0·71 over three populations. The relatively low number of alleles inB. dryinais possibly the consequence of colonization of secondary habitats created by forest management. Although oaks were largely covered with a single, continuousB. dryinacolony, the microsatellite markers identified single or complex multi-genotype colonizations per tree. For future population genetic studies, we recommend collection of 5–15 specimens from one tree which would enable detection of 60–80% of the multilocus genotypes present. Hierarchical AMOVA revealed high variation (70%) on host trees, and a relatively high differentiation (12%) among the three locations in NE Switzerland indicated limited gene flow between those regions. Thus, the newly developed markers showed their applicability in population genetics at different spatial scales. They will play an important role in monitoring habitat restoration for the conservation ofB. dryinaand associated forests and riverscapes.

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Genetic variability in a population of Astyanax scabripinnis: recent bottleneck and the possible influence of individuals with B chromosomes

Acta Scientiarum Biological Sciences ◽

10.4025/actascibiolsci.v41i1.47323 ◽

2019 ◽

Vol 41 ◽

pp. e47323

Author(s):

Daniel Meneguello Limeira ◽

Mateus Henrique Santos ◽

Rogério Pincela Mateus ◽

Mara Cristina de Almeida ◽

Roberto Ferreira Artoni

Keyword(s):

Genetic Variability ◽

Microsatellite Markers ◽

Allelic Diversity ◽

B Chromosomes ◽

Isolated Populations ◽

Population Genetic Analysis ◽

Genetic Studies ◽

Astyanax Scabripinnis ◽

Heterozygosity Excess ◽

Recent Bottleneck

Access the genetic variability of endangered and isolated populations has become an important conservation tool. Astyanax scabripinnis is a well-known fish model for genetic studies, forming very isolated populations in headwaters. Besides that, this species frequently presents supernumerary chromosomes, which elevates the interest on genetic studies. Genetic diversity of an Astyanax scabripinnis population from the Atlantic Forest (Serra da Mantiqueira region, Brazil) was assessed with microsatellite markers for the first time. Since microsatellite markers are not described for this species, we tested markers described for a related species for transferability to A. scabripinnis. Six polymorphic loci were sufficiently reliable for population genetic analysis. We found that this population passed through a recent bottleneck because of the presence of an excess of heterozygotes, low allelic diversity, heterozygosity excess, and small effective population size. Individuals with and without B chromosomes were previously identified in this population and our study found private alleles in the individuals without B chromosomes. Furthermore, when individuals without B chromosomes were removed from the analysis, the population did not present heterozygosity excess, suggesting that the bottleneck event was driven by individuals with B chromosomes. Our results provide an insight into the value of microsatellite markers as molecular tools and is the first genetic study using molecular data of A. scabripinnis from this area.

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