scholarly journals Analyses of Genetic Diversity, Differentiation and Geographic Origin of Natural Provenances and Land Races of Casuarina equisetifolia Based on EST-SSR Markers

Forests ◽  
2020 ◽  
Vol 11 (4) ◽  
pp. 432
Author(s):  
Yong Zhang ◽  
Pan Hu ◽  
Chonglu Zhong ◽  
Yongcheng Wei ◽  
Jingxiang Meng ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Distances ◽  
The Philippines ◽  
Coastal Protection ◽  
Casuarina Equisetifolia ◽  
Land Races ◽  
Seed Sources ◽  
Land Race ◽  
The Pacific ◽  
Resistant Genotypes

Research Highlights: High variation of genetic diversity and differentiation among 27 seed sources within 14 natural provenances and 13 land race samples of Casuarina equisetifolia were found. High proportions of monoecious individuals may be present in some populations, as indicated by severe heterozytote deficiency and inbreeding found in many provenances and land races. The most probable origins of the land races were inferred according to the values of pairwise provenance differentiation and Nei’s genetic distances. Targeted introductions and testing of unrelated new accessions of C. equisetifolia from the Pacific and Philippines was proposed to identify Ralstonia-resistant genotypes. Background and Objectives: Casuarina equisetifolia was introduced to China a hundred years ago and has become a critically important tree species in coastal protection since the 1950s. Despite its importance, patterns of genetic variation, genetic relationships among natural provenances and probable origins of the land races remain unresolved. This has become a concern in China where Ralstonia solanacearum bacterial wilt has devastated plantations that are known to be from a narrow genetic base that urgently needs to be broadened. Materials and Methods: Fourteen natural provenances from Australia, Pacific islands and Southeast Asia, and 13 land race samples from parts of Asia and Africa outside the natural range were genotyped using 13 SSR (Simple Sequence Repeats) markers to characterize their allelic variation and genetic relationship. Results: Significant genetic diversity and differentiation among 27 seed sources within 14 provenances and 13 land race samples of C. equisetifolia was indicated. Significant heterozygote deficiency and inbreeding was indicated for a number of provenances, perhaps indicating a high proportion of monoecious parents in these populations. The most probable origins of the land races of the introduced countries were suggested according to the values of pairwise provenance differentiation (FST) and Nei’s genetic distances. Conclusions: We found significant genetic diversity and genetic differentiation among seed sources of C. equisetifolia. While individual land races do not appear to lack diversity, we were able to infer the origins of some, allowing targeted introductions of unrelated material to be made. In the case of the Chinese land race, targeting and testing new accessions from the Pacific and the Philippines may be a good strategy to identify Ralstonia-resistant genotypes.

Genetic diversity, species phylogeny and historical biogeography of the Aquarius paludum group (Heteroptera: Gerridae)

2003 ◽  
Vol 34 (3) ◽  
pp. 313-327 ◽  
Author(s):  
Herbert Zettel ◽  
Jakob Damgaard
Keyword(s):  
Genetic Diversity ◽  
Sequence Data ◽  
Mitochondrial Gene ◽  
Taxonomic Status ◽  
Species Group ◽  
Genetic Distances ◽  
The Philippines ◽  
Disjunct Distribution ◽  
Gene Encoding ◽  
Vicariance Event

AbstractWe investigated genetic diversity and phylogeny of all water strider species assigned to the Aquarius paludum species group on basis of 425 bp DNA sequence data from the mitochondrial gene encoding cytochrome oxidase subunit I (COI). Parsimony analyses and genetic distances confirmed the taxonomic status of the two recently described species Aquarius lili Polhemus & Polhemus, 1994 from Timor and A. philippinensis Zettel & Ruiz, 2003 from the Philippines as being separate from the widespread Oriental A. adelaidis (Dohrn, 1860). Molecular clock estimates suggest that the disjunct zoogeographical pattern among the three species is due to a Pliocene/Pleistocene long-range dispersal, rather than a Mesozoic vicariance event as previously suggested. However, when we superimposed the disjunct distribution of Southern Hemisphere representatives of the paludum-group onto their phylogenetic relationship, the pattern indicated vicariance events following the break-up of Gondwana.

scholarly journals Combining Quantitative Data on Growth, Wood Density and Other Traits with SSR Markers to Evaluate Genetic Diversity and Structure in a Planted Population of Eucalyptus camaldulensis Dehn.

Forests ◽  
2019 ◽  
Vol 10 (12) ◽  
pp. 1090
Author(s):  
Xiuhua Shang ◽  
Roger J. Arnold ◽  
Zhihua Wu ◽  
Peijian Zhang ◽  
Guo Liu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Differentiation ◽  
Ssr Markers ◽  
Quantitative Trait ◽  
Eucalyptus Camaldulensis ◽  
Genetic Distances ◽  
Bark Thickness ◽  
Seed Sources ◽  
Pilodyn Penetration ◽  
Ssr Loci

Eucalyptus camaldulensis Dehn. is one of the most morphologically and genetically variable Eucalyptus species. Growth, Leptocybe invasa Fisher & La Salle susceptibility, pilodyn penetration and other traits up to age 36 months were assessed in a seed source/family trial in China comprising 112 seedlots representing five natural stand and six exotic seed sources. Genetic diversity and population structure of this trial population were also analyzed using 48 simple sequence repeat (SSR) markers. The key objective was to examine whether the genomic data could provide value over information obtained from just quantitative trait data. Significant genetic variation was found among seed sources and among families within seed sources for most quantitative traits. The ratio of variance among seed sources to variance among families within seed sources, based on variances estimated from quantitative trait data, varied from 0.1% (height at 9 months) up to 75.2% (bark thickness). Equivalent ratios estimated from the AMOVA on SSR loci data were similar for height (ages 24 and 36 months) and also pilodyn penetration at 36 months, but not for 9-month height or 36-month bark thickness. From 48 SSR loci examined, the genetic differentiation coefficient (among seed sources) was 0.086, indicating low genetic differentiation among seed sources. While overall genetic diversity in the trial population examined was high, the levels within the different seed sources varied markedly. Prior to this study, genetic distances among families from the three exotic seed sources (from domesticated Indian populations) in the trial, along with their genetic distances from, and relatedness to, families from five natural stand seed sources (Australian) in the trial were unknown. The SSR loci data removed uncertainties and revealed that the exotic sources increased the breadth of genetic origins represented in the trial population—information that could not have been obtained from just the quantitative trait data.

Genetic diversity of native cultivated cacao accessions (Theobroma cacao L.) in Nicaragua

2012 ◽  
Vol 10 (3) ◽  
pp. 254-257
Author(s):  
Erwin Aragon ◽  
Claudia Rivera ◽  
Helena Korpelainen ◽  
Aldo Rojas ◽  
Paula Elomaa ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Theobroma Cacao ◽  
Phytophthora Palmivora ◽  
Genetic Composition ◽  
Breeding Programmes ◽  
Black Pod ◽  
Black Pod Disease ◽  
Parental Lines ◽  
Resistant Genotypes ◽  
Theobroma Cacao L

A total of 60 farmers' cacao accessions (Theobroma cacao L.) from Nicaragua were investigated using microsatellite markers to reveal their genetic composition and to identify potentially resistant genotypes against the black pod disease caused by Phytophthora palmivora. These accessions were compared with 21 breeders' accessions maintained locally, two Criollo accessions from Costa Rica and two accessions from Ecuador. The analyses showed a low level of differentiation among groups of farmers' accessions (FST = 0.06) and that six Nicaraguan accessions were genetically closely related to the two Criollo accessions used as a reference. In addition, seven distinct genotypes were found to have allelic composition that may indicate linkage to resistance alleles, thus being potential parental lines in future breeding programmes.

scholarly journals Genetic Diversity Among Some Walnut (Juglans regia L.) Genotypes by SSR Markers

2021 ◽  
Vol 13 (12) ◽  
pp. 6830
Author(s):  
Murat Guney ◽  
Salih Kafkas ◽  
Hakan Keles ◽  
Mozhgan Zarifikhosroshahi ◽  
Muhammet Ali Gundesli ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Plant Genetic Resources ◽  
Juglans Regia ◽  
Genetic Distances ◽  
Mean Value ◽  
Central Anatolia ◽  
Group Method ◽  
Arithmetic Average ◽  
Pair Group ◽  
Principal Coordinates

The food needs for increasing population, climatic changes, urbanization and industrialization, along with the destruction of forests, are the main challenges of modern life. Therefore, it is very important to evaluate plant genetic resources in order to cope with these problems. Therefore, in this study, a set of ninety-one walnut (Juglans regia L.) accessions from Central Anatolia region, composed of seventy-four accessions and eight commercial cultivars from Turkey, and nine international reference cultivars, was analyzed using 45 SSR (Simple Sequence Repeats) markers to reveal the genetic diversity. SSR analysis identified 390 alleles for 91 accessions. The number of alleles per locus ranged from 3 to 19 alleles with a mean value of 9 alleles per locus. Genetic dissimilarity coefficients ranged from 0.03 to 0.68. The highest number of alleles was obtained from CUJRA212 locus (Na = 19). The values of polymorphism information content (PIC) ranged from 0.42 (JRHR222528) to 0.86 (CUJRA212) with a mean PIC value of 0.68. Genetic distances were estimated according to the UPGMA (Unweighted Pair Group Method with Arithmetic Average), Principal Coordinates (PCoA), and the Structure-based clustering. The UPGMA and Structure clustering of the accessions depicted five major clusters supporting the PCoA results. The dendrogram revealed the similarities and dissimilarities among the accessions by identifying five major clusters. Based on this study, SSR analyses indicate that Yozgat province has an important genetic diversity pool and rich genetic variance of walnuts.

scholarly journals LC–MS/MS Analysis of Ciguatoxins Revealing the Regional and Species Distinction of Fish in the Tropical Western Pacific

2021 ◽  
Vol 9 (3) ◽  
pp. 299 ◽  
Author(s):  
Naomasa Oshiro ◽  
Takumi Tomikawa ◽  
Kyoko Kuniyoshi ◽  
Akira Ishikawa ◽  
Hajime Toyofuku ◽  
...  
Keyword(s):  
Fish Species ◽  
The Philippines ◽  
Western Pacific ◽  
Tropical Region ◽  
Northern Coast ◽  
Coastal Regions ◽  
Main Island ◽  
Tropical Western Pacific ◽  
The Pacific ◽  
Fish Samples

Ciguatera fish poisoning (CFP) is one of the most frequently reported seafood poisoning diseases. It is endemic to the tropical region and occurs most commonly in the regions around the Pacific Ocean, Indian Ocean, and Caribbean Sea. The principal toxins causing CFP are ciguatoxins (CTXs). In the Pacific region, more than 20 analogs of CTXs have been identified to date. Based on their skeletal structures, they are classified into CTX1B-type and CTX3C-type toxins. We have previously reported species-specific and regional-specific toxin profiles. In this study, the levels and profiles of CTXs in fish present in the tropical western Pacific regions were analyzed using the liquid chromatography–tandem mass spectrometry (LC–MS/MS) technique. Forty-two fish specimens, belonging to the categories of snappers, groupers, Spanish mackerel, and moray eel, were purchased from various places such as Fiji, the Philippines, Thailand, and Taiwan. Only the fish captured from Fijian coastal waters contained detectable amounts of CTXs. The toxin levels in the fish species found along the coastal regions of the Viti Levu Island, the main island in Fiji, and the toxin profiles were significantly different from those of the fish species present in other coastal regions. The toxin levels and profiles varied among the different fish samples collected from different coastal areas. Based on the toxin levels and toxin profiles, the coast was demarcated into three zones. In Zone-1, which covers the northern coast of the main island and the regions of the Malake Island and Korovau, CTXs in fish were below the detection level. In Zone-2, CTX3C-type toxins were present in low levels in the fish. CTX1B-type and CTX3C-type toxins co-occurred in the fish present in Zone-3. The toxin profiles may have reflected the variation in Gambierdiscus spp.

scholarly journals Genetic diversity and kinship relationships in one of the largest South American fur seal ( Arctocephalus australis ) populations of the Pacific Ocean

2021 ◽  
Author(s):  
Josefina Gutiérrez ◽  
Mauricio Seguel ◽  
Pablo Saenz‐Agudelo ◽  
Gerardo Acosta‐Jamett ◽  
Claudio Verdugo
Keyword(s):  
Genetic Diversity ◽  
Pacific Ocean ◽  
South American ◽  
The Pacific ◽  
Fur Seal ◽  
The Pacific Ocean

scholarly journals Diversity Assessment of Some Sesame (Sesamum indicum L.) Genotypes Cultivated in Northern Ghana Using Morphological and Simple Sequence Repeat (SSR) Markers

2019 ◽  
Vol 2019 ◽  
pp. 1-10 ◽  
Author(s):  
Raphael Adu-Gyamfi ◽  
Ruth Prempeh ◽  
Issahaku Zakaria
Keyword(s):  
Genetic Diversity ◽  
Plant Height ◽  
Ssr Markers ◽  
Analysis Of Variance ◽  
Morphological Data ◽  
Northern Ghana ◽  
Land Races ◽  
Diversity Assessment ◽  
Parental Lines ◽  
Number Of Seeds

In Ghana, sesame is cultivated in some districts of northern Ghana. Genotypes cultivated are land races that are low yielding leading to decline in production. There is the need for improvement of these land races to generate high yielding cultivars. Characterization of genetic diversity of the sesame land races will be of great value in assisting in parental lines selection for sesame breeding programmes in Ghana. Twenty-five sesame land races were collected from five districts in northern Ghana noted for sesame cultivation. Seeds collected were planted in three replicates in randomized complete block design and were evaluated for a number of morphological characters. Data collected were subjected to Principal Component Analysis (PCA) and a dendrogram showing similarity between the accessions were drawn. Data on number of capsules per plant, number of seeds per capsule, and plant height at flowering were subjected to analysis of variance using GenStat Discovery Edition 4. Molecular genetic diversity was assessed by using thirty eight SSR markers widely distributed across sesame genome to characterize the materials. Twenty-one out of the 38 primers were polymorphic. Cluster analyses using the Euclidean similarity test and a complete link clustering method were used to make a dendrogram out of the morphological data. Analysis of variance showed that capsule number was significantly different; a range of 54.9 and 146.7 was produced. The number of seeds per capsule varied significantly and the variation between highest and lowest accession in seed production was 33%. Plant height was also significantly different ranging from 60.6 to 94.1 cm. Using morphological traits the accessions clustered into two major groups and two minor groups and variation among accessions were 10-61%. On the other hand, SSR marker-based dendrogram revealed five major and two minor groups. It showed that variation among the accessions was low, 10-20%. Heterozygosity was 0.52, total alleles produced were 410, and average allele per locus was 19.52. Six accessions, C3, C4, S5, W1, W3, and W5 fell in five different clusters in the SSR dendrogram and in six clusters in the morphomolecular based dendrogram. These accessions were noted for high capsule number per plant and seeds number per capsule and are recommended for consideration as potential parental lines for breeding programme for high yield.

scholarly journals Genetic diversity and population structure of rice stripe virus in China

2009 ◽  
Vol 90 (4) ◽  
pp. 1025-1034 ◽  
Author(s):  
Tai-Yun Wei ◽  
Jin-Guang Yang ◽  
Fu-Long Liao ◽  
Fang-Luan Gao ◽  
Lian-Ming Lu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Yunnan Province ◽  
Southwest China ◽  
Eastern China ◽  
Rice Stripe Virus ◽  
Genetic Distances ◽  
Geographical Regions ◽  
Strong Negative Selection ◽  
Recent Outbreak

Rice stripe virus (RSV) is one of the most economically important pathogens of rice and is repeatedly epidemic in China, Japan and Korea. The most recent outbreak of RSV in eastern China in 2000 caused significant losses and raised serious concerns. In this paper, we provide a genotyping profile of RSV field isolates and describe the population structure of RSV in China, based on the nucleotide sequences of isolates collected from different geographical regions during 1997–2004. RSV isolates could be divided into two or three subtypes, depending on which gene was analysed. The genetic distances between subtypes range from 0.050 to 0.067. The population from eastern China is composed only of subtype I/IB isolates. In contrast, the population from Yunnan province (southwest China) is composed mainly of subtype II isolates, but also contains a small proportion of subtype I/IB isolates and subtype IA isolates. However, subpopulations collected from different districts in eastern China or Yunnan province are not genetically differentiated and show frequent gene flow. RSV genes were found to be under strong negative selection. Our data suggest that the most recent outbreak of RSV in eastern China was not due to the invasion of new RSV subtype(s). The evolutionary processes contributing to the observed genetic diversity and population structure are discussed.

scholarly journals Chance long-distance or human-mediated dispersal? How Acacia s.l. farnesiana attained its pan-tropical distribution

2017 ◽  
Vol 4 (4) ◽  
pp. 170105 ◽  
Author(s):  
Karen L. Bell ◽  
Haripriya Rangan ◽  
Manuel M. Fernandes ◽  
Christian A. Kull ◽  
Daniel J. Murphy
Keyword(s):  
The Philippines ◽  
Historical Sources ◽  
Long Distance ◽  
Old World ◽  
South Central ◽  
The Pacific ◽  
The Pacific Ocean ◽  
Spanish Explorers ◽  
The Tropics ◽  
Old World Tropics

Acacia s.l. farnesiana , which originates from Mesoamerica, is the most widely distributed Acacia s.l. species across the tropics. It is assumed that the plant was transferred across the Atlantic to southern Europe by Spanish explorers, and then spread across the Old World tropics through a combination of chance long-distance and human-mediated dispersal. Our study uses genetic analysis and information from historical sources to test the relative roles of chance and human-mediated dispersal in its distribution. The results confirm the Mesoamerican origins of the plant and show three patterns of human-mediated dispersal. Samples from Spain showed greater genetic diversity than those from other Old World tropics, suggesting more instances of transatlantic introductions from the Americas to that country than to other parts of Africa and Asia. Individuals from the Philippines matched a population from South Central Mexico and were likely to have been direct, trans-Pacific introductions. Australian samples were genetically unique, indicating that the arrival of the species in the continent was independent of these European colonial activities. This suggests the possibility of pre-European human-mediated dispersal across the Pacific Ocean. These significant findings raise new questions for biogeographic studies that assume chance or transoceanic dispersal for disjunct plant distributions.

Sign in / Sign up

Export Citation Format

Share Document