High levels of population differentiation in two New Caledonian Scaevola species (Goodeniaceae) and its implications for conservation prioritisation and restoration

2017 ◽  
Vol 65 (2) ◽  
pp. 140
Author(s):  
Adrien S. Wulff ◽  
Peter M. Hollingsworth ◽  
Marie Piquet ◽  
Antje Ahrends ◽  
Laurent L'Huillier ◽  
...  
Keyword(s):  
Population Differentiation ◽  
New Caledonia ◽  
Gene Diversity ◽  
Allelic Diversity ◽  
Insect Pollination ◽  
Mining Sites ◽  
Seed Sources ◽  
Close Proximity ◽  
Ultramafic Substrates ◽  
Conservation Prioritisation

Population genetic structure was studied in two Scaevola (Goodeniaceae) species across their ranges in New Caledonia. Scaevola montana is locally common and distributed primarily on ultramafic substrates, and is used for ecological restoration of mining sites. Scaevola coccinea is a narrow endemic restricted to ultramafic soils in a single valley, where intensive mining activity occurs. We compared levels of diversity and differentiation in the two species using nuclear microsatellites, so as to understand the spatial scale at which populations become isolated. We also measured environmental distances among sites as a crude proxy to estimate where adaptive differentiation may occur. Populations of S. montana were sampled over a total distance of ~500 km. In contrast, the total range of S. coccinea is 12 × 6 km. Greater allelic diversity and gene diversity was detected within populations of S. montana than S. coccinea. Both species show high levels of population differentiation (S. montana FʹST = 0.437; S. coccinea FʹST = 0.54). The marked population structure in S. coccinea despite the close proximity of the sampled populations is associated with its pollination by territorial birds and no observed seed-dispersal agents, compared with the greater vagility of insect pollination and bird dispersal of S. montana. In S. coccinea, given the high levels of differentiation, we highlight the importance of each individual population for the conservation of intra-specific biodiversity in this species. In S. montana, we used a combination of the genetic data and environmental characteristics of each of the sample sites to outline general guidelines on seed sources for restoration programs.

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

2012 ◽  
Vol 37 (3) ◽  
pp. 389-398 ◽  
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

The nature of diversity and diversification at the ABO locus

Blood ◽  
2003 ◽  
Vol 102 (8) ◽  
pp. 3035-3042 ◽  
Author(s):  
Axel Seltsam ◽  
Michael Hallensleben ◽  
Anke Kollmann ◽  
Rainer Blasczyk
Keyword(s):  
Phylogenetic Analysis ◽  
Sequence Data ◽  
Gene Diversity ◽  
Allelic Diversity ◽  
Antigen Expression ◽  
Genomic Sequences ◽  
Coding Sequence ◽  
Intron 1 ◽  
Sequence Variations ◽  
Genotype Correlation

Abstract In this study we analyzed the complete genomic sequences, except intron 1, and 2 regulatory regions of 6 common (ABO*A101, ABO*A201, ABO*B101, ABO*O01, ABO*O02, and ABO*O03) and 18 rare ABO alleles, 3 of which were new. This was done by phylogenetic analysis and correlating sequence data with the ABO phenotypes. The study revealed multiple polymorphisms in noncoding regions. The intron-based phylogenetic analysis revealed 5 main lineages: ABO*A, ABO*B, ABO*O01, ABO*O02, and ABO*O03. The genomic sequences of most rare ABO alleles differed slightly from those of the common alleles. Singular mutations or hybrid alleles were most common, but a few exhibited mosaic sequence pattern containing multiple exon and/or intron motifs from other ABO lineages. Thus, both an accumulation of mutations as well as an assortment of the mutations by recombination seems to be responsible for the ABO gene diversity. The prevalence of replacement mutations indicates positive selection for allelic diversity. Phenotype-genotype correlation showed that sequence variations within the complete coding sequence can affect A- and B-antigen expression. All variant ABO*A/B alleles and one new ABO*O03-like allele were associated with weak ABO phenotypes. These findings are suggestive of the requirement of a comprehensive coding sequence database for sequence-based phenotype prediction.

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

2005 ◽  
Vol 130 (2) ◽  
pp. 181-190 ◽  
Author(s):  
R.J. Schnell ◽  
C.T. Olano ◽  
J.S. Brown ◽  
A.W. Meerow ◽  
C. Cervantes-Martinez ◽  
...  
Keyword(s):  
Microsatellite Markers ◽  
Gene Diversity ◽  
Allelic Diversity ◽  
Trend Test ◽  
Parental Population ◽  
Genetic Studies ◽  
Unbiased Gene ◽  
Microsatellite Alleles ◽  
Theobroma Cacao L

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.

scholarly journals Manganese distribution in the Mn-hyperaccumulator Grevillea meisneri from New Caledonia

2021 ◽  
Author(s):  
Camille Bihanic ◽  
Eddy Petit ◽  
Roseline Perrot ◽  
Lucie Cases ◽  
Armelle Garcia ◽  
...  
Keyword(s):  
Large Scale ◽  
New Caledonia ◽  
Tissue Level ◽  
Cluster Roots ◽  
Transport Pathways ◽  
X Ray ◽  
Mining Sites ◽  
Rehabilitation Programs ◽  
Primary Roots ◽  
Preferential Uptake

Abstract • Grevillea meisneri, an endemic New Caledonian Mn-hyperaccumulator, is used in rehabilitation of degraded mining sites on the island. Large-scale programs require transplanting nursery-grown seedlings, but effects of the nursery environment on Mn tolerance of transplants and their capacity to hyper-accumulate Mn are unknown, slowing rehabilitation efforts.• We studied tissue-level distribution of Mn and other elements in different tissues of G. meisneri using micro-X-Ray Fluorescence spectroscopy (μXRF), comparing nursery-grown plants transplanted into the site and sampled seven years later, and similar-sized plants that had grown spontaneously in the site. • Mirroring patterns in other Mn-hyperaccumulators, Mn was preferentially accumulated in leaves but was also present in roots. Concentrations were highest in leaf epidermal tissues, in cortex and vascular tissues of stems and primary roots, and in phloem and pericycle-endodermis of parent cluster roots. Although abundant in soil, Ni was absent from all tissues of G. meisneri. Ca was always co-localised with Mn. Preferential uptake of Mn vs Ni in roots implies as-yet-uncharacterized specific Mn-transporters, while Ca and Mn co-localisation suggests shared transport pathways. • No differences were observed in concentration and distribution of Mn in transplanted and spontaneously-growing plants. Nursery-grown transplants should be highly suitable for large-scale, high-throughput rehabilitation programs.

scholarly journals Genetic Diversity and Differentiation inPhoma betaePopulations on Table Beet in New York and Washington States

Plant Disease ◽  
2019 ◽  
Vol 103 (7) ◽  
pp. 1487-1497 ◽  
Author(s):  
Lori B. Koenick ◽  
Niloofar Vaghefi ◽  
Noel L. Knight ◽  
Lindsey J. du Toit ◽  
Sarah J. Pethybridge
Keyword(s):  
Genetic Diversity ◽  
New York ◽  
Mating Type ◽  
Gene Diversity ◽  
Management Strategies ◽  
Allelic Diversity ◽  
Genotypic Diversity ◽  
Reproduction Mode ◽  
Inoculum Source ◽  
Seed Crops

Phoma betae is an important seedborne pathogen of table beet worldwide that is capable of causing foliar, root, and damping-off diseases. Ten microsatellite and mating type markers were developed to investigate the genetics of P. betae populations in table beet root crops in New York and in table beet seed crops in Washington, from where table beet seed is predominantly sourced. The markers were used to characterize 175 isolates comprising five P. betae populations (two from New York and three from Washington), and they were highly polymorphic with an allelic range of 4 to 33 and an average of 11.7 alleles per locus. All populations had high genotypic diversity (Simpson’s complement index = 0.857 to 0.924) and moderate allelic diversity (Nei’s unbiased gene diversity = 0.582 to 0.653). Greater differentiation observed between populations from the two states compared with populations within the same state suggested that an external inoculum source, such as windblown ascospores, may be homogenizing the populations. However, most genetic diversity (87%) was among individual isolates within populations (pairwise index of population differentiation = 0.127; P = 0.001), suggesting that local within-field inoculum source(s), such as infested field debris or infected weeds, may also be important in initiating disease outbreaks. Standardized index of association, proportion of compatible pairs of loci, and mating type ratio calculations showed evidence for a mixed reproduction mode in all populations. These findings could be useful in designing more effective management strategies for diseases caused by P. betae in table beet production.

scholarly journals Molecular Genetic Diversity and Population Structure of Ginseng Germplasm in RDA-Genebank: Implications for Breeding and Conservation

Agronomy ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 68 ◽  
Author(s):  
Kyung Jun Lee ◽  
Jung-Ro Lee ◽  
Raveendar Sebastin ◽  
Gyu-Taek Cho ◽  
Do Yoon Hyun
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Ssr Markers ◽  
Gene Diversity ◽  
Research Effort ◽  
Molecular Genetic ◽  
Allelic Diversity ◽  
Perennial Herb ◽  
Molecular Evidence ◽  
Breeding Lines

Ginseng (Panax ginseng C.A. Meyer), commonly known as Korean or Asian ginseng, is a perennial herb native to Korea and China. There has been limited research effort to analyze the genetic diversity and population structure of ginseng germplasm because of its growth habits. In the present study, genetic diversity and population structure of ginseng germplasm conserved in the National Agrobiodiversity Center (NAC) of South Korea were analyzed to provide basic data for future preservation and breeding of ginseng genetic resources. Seventeen simple sequence repeat (SSR) markers were used to assess the genetic diversity and population structure of 1109 ginseng accessions. Among 1109 ginseng accessions, 1042 (94.0%) accessions were landraces and 66 (6.0%) accessions were breeding lines (61 accessions, 5.5%) or cultivars (5 accessions, 0.5%). SSR markers revealed 56 different alleles with an average of 3.29 alleles per locus. The average gene diversity was 0.49. Analysis of molecular variance showed that 91% of allelic diversity was attributed to individual accessions within clusters while only 9% was distributed among clusters. Using discriminant analysis of principal components, 12 clusters were detected in 1109 ginseng accessions. The results of this study provide molecular evidence for the narrow genetic base of ginseng germplasm in NAC. For the broad understanding and efficient use of ginseng germplasm, it is necessary to analyze functional factors and to evaluate morphological traits.

Five new species and a systematic synopsis of Pycnandra (Sapotaceae), the largest endemic genus in New Caledonia

2016 ◽  
Vol 29 (1) ◽  
pp. 1 ◽  
Author(s):  
Ulf Swenson ◽  
Jérôme Munzinger
Keyword(s):  
New Species ◽  
Conservation Management ◽  
New Caledonia ◽  
Iucn Red List ◽  
Specific Substrate ◽  
Leaf Venation ◽  
Endemic Genus ◽  
Substrate Preferences ◽  
Wide Range ◽  
Ultramafic Substrates

Pycnandra Benth. (Sapotaceae) is the largest endemic genus in New Caledonia and is subdivided into six subgenera. An addition of five species are here described in four subgenera, viz. P. comptonioides Swenson & Munzinger, P. kouakouensis Swenson & Munzinger, P. montana Swenson & Munzinger, P. poindimiensis Swenson & Munzinger and P. versicolor Swenson & Munzinger. Another seven to nine taxa are discussed but remain undescribed owing to the lack of adequate collections (and may remain undescribed pending the interpretation of the Nagoya Protocol). Pycnandra is characterised by a non-areolate higher leaf venation, sepals glabrous on the inner surface, no staminodes, and a single-seeded fruit. The members occur in a wide range of habitats and most species have very specific substrate requirements, growing on ultramafic, non-ultramafic or calcareous substrates. Almost 40 species are restricted to ultramafic substrates and many are now at risk of extinction because of deforestation, deliberately set fires and mining. We provide a systematic synopsis with keys to subgenera and species, phenology, substrate preferences, altitudinal ranges and preliminary IUCN Red List assessments for all described taxa. Four of the five new species are assessed as Critically Endangered. Pycnandra versicolor is in urgent need of conservation management beacuse its entire distribution is inside an active mine on the Koniambo massif.

scholarly journals Genetic Diversity of Aromatic Rice Germplasm Revealed By SSR Markers

2018 ◽  
Vol 2018 ◽  
pp. 1-11 ◽  
Author(s):  
Saba Jasim Aljumaili ◽  
M. Y. Rafii ◽  
M. A. Latif ◽  
Siti Zaharah Sakimin ◽  
Ibrahim Wasiu Arolu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Diversity Index ◽  
Gene Diversity ◽  
Allelic Diversity ◽  
Peninsular Malaysia ◽  
Breeding Program ◽  
Aromatic Rice ◽  
Information Index ◽  
Rice Germplasm

Aromatic rice cultivars constitute a small but special group of rice and are considered the best in terms of quality and aroma. Aroma is one of the most significant quality traits of rice, and variety with aroma has a higher price in the market. This research was carried out to study the genetic diversity among the 50 aromatic rice accessions from three regions (Peninsular Malaysia, Sabah, and Sarawak) with 3 released varieties as a control using the 32 simple sequence repeat (SSR) markers. The objectives of this research were to quantify the genetic divergence of aromatic rice accessions using SSR markers and to identify the potential accessions for introgression into the existing rice breeding program. Genetic diversity index among the three populations such as Shannon information index (I) ranged from 0.25 in control to 0.98 in Sabah population. The mean numbers of effective alleles and Shannon’s information index were 0.36 and 64.90%, respectively. Similarly, the allelic diversity was very high with mean expected heterozygosity (He) of 0.60 and mean Nei’s gene diversity index of 0.36. The dendrogram based on UPGMA and Nei’s genetic distance classified the 53 rice accessions into 10 clusters. Analysis of molecular variance (AMOVA) revealed that 89% of the total variation observed in this germplasm came from within the populations, while 11% of the variation emanated among the populations. These results reflect the high genetic differentiation existing in this aromatic rice germplasm. Using all these criteria and indices, seven accessions (Acc9993, Acc6288, Acc6893, Acc7580, Acc6009, Acc9956, and Acc11816) from three populations have been identified and selected for further evaluation before introgression into the existing breeding program and for future aromatic rice varietal development.

scholarly journals SSR allelic diversity in relation to morphological traits and resistance to grain mould in sorghum

2010 ◽  
Vol 61 (3) ◽  
pp. 230 ◽  
Author(s):  
Rajan Sharma ◽  
S. P. Deshpande ◽  
S. Senthilvel ◽  
V. P. Rao ◽  
V. Rajaram ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Morphological Traits ◽  
Ssr Marker ◽  
Allelic Variation ◽  
Gene Diversity ◽  
Polymorphic Information Content ◽  
Allelic Diversity ◽  
Average Score ◽  
Marker Loci

Allelic variation at 46 simple sequence repeat (SSR) marker loci well distributed across the sorghum genome was used to assess genetic diversity among 92 sorghum lines, 74 resistant and 18 susceptible to grain mould. Of the 46 SSR markers, 44 were polymorphic, with the number of alleles ranging from 2 to 20 with an average of 7.55 alleles per locus. Genetic diversity among the sorghum lines was high as indicated by polymorphic information content (PIC) and gene diversity values. PIC values of polymorphic SSR markers ranged from 0.16 to 0.90, with an average of 0.54. Gene diversity among the sorghum lines varied from 0.16 to 0.91, with an average score of 0.58 per SSR marker. AMOVA indicated that 12% of the total variation observed among the sorghum lines was accounted for between grain mould resistant and susceptible types. Diversity based on six morphological traits and grain mould scores indicated major roles of panicle type and glumes coverage, followed by grain colour, in clustering of the lines. Seven grain mould resistant/susceptible pairs with dissimilarity indices >0.50, but with similar flowering time, plant height, and panicle type/inflorescence within each pair, were selected for use in developing recombinant inbred line mapping populations to identify genomic regions (and quantitative trait loci) associated with sorghum grain mould resistance.

scholarly journals Portable Raman Spectrometer for In Situ Analysis of Asbestos and Fibrous Minerals

2020 ◽  
Vol 11 (1) ◽  
pp. 287
Author(s):  
Jasmine Rita Petriglieri ◽  
Danilo Bersani ◽  
Christine Laporte-Magoni ◽  
Mario Tribaudino ◽  
Alessandro Cavallo ◽  
...  
Keyword(s):  
New Caledonia ◽  
Fluorescence Emission ◽  
Workplace Safety ◽  
Mining Sites ◽  
Raman Spectrometer ◽  
Fibrous Minerals ◽  
Mining Front ◽  
In Situ Detection ◽  
Portable Raman

Asbestos inhalation is associated with fatal respiratory diseases and raises concerns from the perspective of workplace safety and environmental impacts. Asbestos and asbestos-like minerals naturally occur in rocks and may become airborne when outcrops or soils are disturbed by anthropic activities. In situ detection of these minerals is a crucial step for the risk evaluation of natural sites. We assess here whether a portable Raman spectrometer (pRS) may be used in the identification of asbestos and asbestos-like minerals at the mining front during exploitation. pRS performance was tested at three geologically different mining sites in Italy and New Caledonia and compared with a high-resolution micro-Raman spectrometer (HRS). About 80% of the overall in situ analyses at the mining front were successfully identified by pRS, even when intermixed phases or strongly disaggregated and altered samples were analyzed. Chrysotile and tremolite asbestos, asbestos-like antigorite, and balangeroite were correctly detected during surveys. The major difficulties faced during in situ pRS measurements were fluorescence emission and focussing the laser beam on non-cohesive bundles of fibers. pRS is adequate for discriminating asbestos and asbestos-like minerals in situ. pRS may support risk assessment of mining sites to better protect workers and environment.

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