scholarly journals Genetic Diversity and Population Structure of the Spring Orchid Cymbidium goeringii in Korean Distant Islands

Diversity ◽  
2020 ◽  
Vol 12 (12) ◽  
pp. 486
Author(s):  
Seung Woo Noh ◽  
Jun-Kyu Park ◽  
Jin Seok Yu ◽  
Da Eun Nam ◽  
Yuno Do ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Northeast Asia ◽  
Population Genetic Study ◽  
Small Islands ◽  
Important Species ◽  
Mainland Population ◽  
Ulleung Island ◽  
Cymbidium Goeringii ◽  
China And Japan

The spring orchid (Cymbidium goeringii), found in northeast Asia, is one of the most popular and horticulturally important species of the orchid family. This study analyzed the genetic diversity and population structure of the spring orchid populations in the small islands and mainland South Korea using 11 microsatellite markers. The genetic diversities of spring orchid populations in the distant islands (Heuksan Island and Ulleung Island) were slightly lower than that of the mainland population (Yeonggwang-gun). The population structure in the mainland was genetically separated from the populations in the islands. The population of Ulleung Island, located in the eastern part of the Korean peninsula, was genetically closer to the populations from China and Japan than to the populations from Yeonggwang-gun and Heuksan Island, which are geographically close to China. These results imply that the populations of spring orchids distributed in Yeonggwang-gun and Heuksan Island appear not to be influenced by the yellow dust winds. As the first population genetic study of spring orchids distributed in small distant islands, our study will be useful for understanding the genetic diversity and population structure of isolated C. goeringii populations.

scholarly journals Genetic variation and structure of Sclerotinia sclerotiorum populations from soybean in Brazil

2018 ◽  
Author(s):  
Anthony Pannullo ◽  
Zhian N. Kamvar ◽  
Thomas J.J. Miorini ◽  
James R Steadman ◽  
Sydney E Everhart
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Sclerotinia Sclerotiorum ◽  
Population Genetic ◽  
The United States ◽  
Multilocus Genotype ◽  
Population Genetic Study ◽  
Population Genetic Analysis ◽  
Moderate Amount ◽  
Multilocus Genotypes

The clonal, necrotrophic plant pathogen, Sclerotinia sclerotiorum is the causal agent of white mold on soybean, causing significant losses for Brazilian farmers each year. While assessments of population structure and clonal dynamics can be beneficial for determining effective management strategies, few studies have been performed. In this paper, we present a broad-scale population genetic analysis with 11 microsatellite loci of 94 isolates of S. sclerotiorum from soybean fields in nine Brazilian states (N=74) with Argentina (N=5) and the United States (N=15) as outgroups. Genotyping identified 87 multilocus genotypes with 81 represented by a single isolate. The pattern of genetic diversity observed suggested populations were not strongly differentiated because despite the high genetic diversity, there were few private alleles/genotypes and no multilocus genotypes were identified in both South and North America while one multilocus genotype was shared between Argentina and Brazil. Pairwise analysis of molecular variance between populations in Brazil revealed nine out of 15 pairs significantly different (P > 0.05). The population from the U.S. was most strongly differentiated in across all measures of population differentiation. Overall, our results found evidence for gene flow across populations with a moderate amount of population structure within states in Brazil. We additionally found shared genotypes across populations in Brazil and Argentina, suggesting that sclerotia may be transferred across states either through seeds or shared equipment. This represents the first population genetic study to cover a wide area in Brazil.

scholarly journals Genetic variation and structure of Sclerotinia sclerotiorum populations from soybean in Brazil

2018 ◽  
Author(s):  
Anthony Pannullo ◽  
Zhian N. Kamvar ◽  
Thomas J.J. Miorini ◽  
James R Steadman ◽  
Sydney E Everhart
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Sclerotinia Sclerotiorum ◽  
Population Genetic ◽  
The United States ◽  
Multilocus Genotype ◽  
Population Genetic Study ◽  
Population Genetic Analysis ◽  
Moderate Amount ◽  
Multilocus Genotypes

The clonal, necrotrophic plant pathogen, Sclerotinia sclerotiorum is the causal agent of white mold on soybean, causing significant losses for Brazilian farmers each year. While assessments of population structure and clonal dynamics can be beneficial for determining effective management strategies, few studies have been performed. In this paper, we present a broad-scale population genetic analysis with 11 microsatellite loci of 94 isolates of S. sclerotiorum from soybean fields in nine Brazilian states (N=74) with Argentina (N=5) and the United States (N=15) as outgroups. Genotyping identified 87 multilocus genotypes with 81 represented by a single isolate. The pattern of genetic diversity observed suggested populations were not strongly differentiated because despite the high genetic diversity, there were few private alleles/genotypes and no multilocus genotypes were identified in both South and North America while one multilocus genotype was shared between Argentina and Brazil. Pairwise analysis of molecular variance between populations in Brazil revealed nine out of 15 pairs significantly different (P > 0.05). The population from the U.S. was most strongly differentiated in across all measures of population differentiation. Overall, our results found evidence for gene flow across populations with a moderate amount of population structure within states in Brazil. We additionally found shared genotypes across populations in Brazil and Argentina, suggesting that sclerotia may be transferred across states either through seeds or shared equipment. This represents the first population genetic study to cover a wide area in Brazil.

scholarly journals Shining light on a deep-sea bacterial symbiont population structure with CRISPR

2021 ◽  
Vol 7 (8) ◽  
Author(s):  
Maëva Perez ◽  
Bernard Angers ◽  
C. Robert Young ◽  
S. Kim Juniper
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Dna Sequences ◽  
Deep Sea ◽  
Bacterial Species ◽  
Housekeeping Genes ◽  
Immune Memory ◽  
Population Genetic Study ◽  
Mining Operations ◽  
Gene Markers

Many foundation species in chemosynthesis-based ecosystems rely on environmentally acquired symbiotic bacteria for their survival. Hence, understanding the biogeographic distributions of these symbionts at regional scales is key to understanding patterns of connectivity and predicting resilience of their host populations (and thus whole communities). However, such assessments are challenging because they necessitate measuring bacterial genetic diversity at fine resolutions. For this purpose, the recently discovered clustered regularly interspaced short palindromic repeats (CRISPR) constitutes a promising new genetic marker. These DNA sequences harboured by about half of bacteria hold their viral immune memory, and as such, might allow discrimination of different lineages or strains of otherwise indistinguishable bacteria. In this study, we assessed the potential of CRISPR as a hypervariable phylogenetic marker in the context of a population genetic study of an uncultured bacterial species. We used high-throughput CRISPR-based typing along with multi-locus sequence analysis (MLSA) to characterize the regional population structure of the obligate but environmentally acquired symbiont species Candidatus Endoriftia persephone on the Juan de Fuca Ridge. Mixed symbiont populations of Ca. Endoriftia persephone were sampled across individual Ridgeia piscesae hosts from contrasting habitats in order to determine if environmental conditions rather than barriers to connectivity are more important drivers of symbiont diversity. We showed that CRISPR revealed a much higher symbiont genetic diversity than the other housekeeping genes. Several lines of evidence imply this diversity is indicative of environmental strains. Finally, we found with both CRISPR and gene markers that local symbiont populations are strongly differentiated across sites known to be isolated by deep-sea circulation patterns. This research showed the high power of CRISPR to resolve the genetic structure of uncultured bacterial populations and represents a step towards making keystone microbial species an integral part of conservation policies for upcoming mining operations on the seafloor.

scholarly journals Conservation Genomics of Wild Red Sage (Salvia miltiorrhiza) and Its Endangered Relatives in China: Population Structure and Interspecific Relationships Revealed From 2b-RAD Data

2021 ◽  
Vol 12 ◽  
Author(s):  
Xuan Zhou ◽  
Zhi-Cheng Zhang ◽  
Yan-Bo Huang ◽  
Han-Wen Xiao ◽  
Jun-Jie Wu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Related Species ◽  
Salvia Miltiorrhiza ◽  
Eastern China ◽  
Genetic Research ◽  
Market Demand ◽  
Conservation Genomics ◽  
High Genetic Diversity ◽  
Important Species

Red sage (Salvia miltiorrhiza) is a widely used medicinal plant for treatment of cardiovascular and cerebrovascular diseases. Because of excessive excavation by huge market demand and habitat loss by human activities, the wild population resources of S. miltiorrhiza have reduced drastically in recent years. Meanwhile, population status of two closely related species S. bowleyana and S. paramiltiorrhiza were in a trend of decreasing due to their potential replacement of S. miltiorrhiza. Particularly, S. paramiltiorrhiza was threatened and endemic to a small region in eastern China. However, to date there has been no conservation genetic research reported for wild S. miltiorrhiza population and its endangered relatives. Assess the wild germplasm diversity for S. miltiorrhiza and its related species would provide fundamental genetic background for cultivation and molecular breeding of this medicinally important species. In the present study, we investigated the genetic diversity, population structure, and intra/inter-specific differentiation of S. miltiorrhiza and above two relatives using 2b-RAD genome-wide genotyping method. By investigating 81 individuals of S. miltiorrhiza, 55 individuals of S. bowleyana and 15 individuals of S. paramiltiorrhiza from 23 locations in China, we obtained 23,928 SNPs in total. A comparatively high genetic diversity was observed in S. miltiorrhiza (π = 0.0788, He = 0.0783 ± 0.0007). The observed and expected heterozygosity in populations of these three species ranged from 0.0297 to 0.1481 and 0.0251 to 0.831, respectively. Two major lineage groups were detected in the examined S. miltiorrhiza populations. The results indicated that Dabie Mountain as a genetic diversity center of S. miltiorrhiza and possible complex inter-specific genetic exchange/hybridization occurred between S. miltiorrhiza and the two relatives. We suggest that strategic conservation and germplasm preservation should be considered not only for wild populations of S. miltiorrhiza, but also for its related S. bowleyana and S. paramiltiorrhiza.

Analysis of genetic diversity and population structure of rice cultivars from Korea, China and Japan using SSR markers

2009 ◽  
Vol 31 (4) ◽  
pp. 283-292 ◽  
Author(s):  
Weiguo Zhao ◽  
Jong-Wook Chung ◽  
Kyung-Ho Ma ◽  
Tae-San Kim ◽  
Seung-Min Kim ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Ssr Markers ◽  
Rice Cultivars ◽  
China And Japan

Genetic diversity and population structure of Populus yunnanensis revealed by SSR markers

2020 ◽  
Vol 52 (6) ◽  
Author(s):  
Anpei Zhou ◽  
Dan Zong ◽  
Peihua Gan ◽  
Yao Zhang ◽  
Dan Li ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Ssr Markers
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