scholarly journals Genetic diversity analysis of the invasive gall pest Leptocybe invasa (Hymenoptera: Apodemidae) from China

PLoS ONE ◽  
2021 ◽  
Vol 16 (10) ◽  
pp. e0258610
Author(s):  
Xin Peng ◽  
Hantang Wang ◽  
Chunhui Guo ◽  
Ping Hu ◽  
Lei Xu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Phylogenetic Tree ◽  
Structure Analysis ◽  
Introgressive Hybridization ◽  
Invasive Pest ◽  
K Value ◽  
Leptocybe Invasa ◽  
And Diffusion ◽  
Amova Analysis

Leptocybe invasa Fisher et LaSalle is a global invasive pest that seriously damages Eucalyptus plants. Studying the genetic diversity, genetic structure and introgression hybridization of L. invasa in China is of great significance for clarifying the breeding strategy, future invasion and diffusion trends of L. invasa in China and developing scientific prevention and control measures. Genetic diversity and phylogenetic analyses of 320 L. invasa female adults from 14 geographic populations in China were conducted using 10 polymorphic microsatellite loci (SSRs) and mitochondrial DNA cytochrome oxidase I gene sequences (COIs). (1) The Bayesian phylogenetic tree and haplotype network diagram showed that only haplotype Hap3 existed in L. invasa lineage B in China, while haplotypes Hap1 and Hap2 existed in lineage A, among which haplotype Hap2 was found for the first time. The nucleotide and haplotype diversities of lineage A were higher than those of lineage B. (2) The SSR genetic diversity of the Wuzhou Guangxi, Ganzhou Jiangxi and Panzhihua Sichuan populations was higher than that of the other 11 populations, and the SSR genetic diversity of lineage A was higher than that of lineage B. (3) The AMOVA analysis of mitochondrial COI data showed that 75.55% of the variation was among populations, and 99.86% of the variation was between lineages, while the AMOVA analysis of nuclear SSR data showed that 35.26% of the variation was among populations, and 47.04% of the variation was between lineages. There were obvious differences in the sources of variation between the COI and SSR data. (4) The optimal K value of COI and SSR data in structure analysis was 2, and PCoA analysis also divided the dataset into two obvious categories. The UPMGA phylogenetic tree based on SSR data clustered 14 geographic species into two groups. The results of genetic structure analysis supported the existence of two lineages, A and B, in China. (5) Structural analysis showed that there was obvious introgressive hybridization in Wuzhou Guangxi, Ganzhou Jiangxi, Panzhihua Sichuan and other populations. These results suggest that lineage introgressive hybridization has occurred in the L. invasa population in China. The introgressive hybridization degree and genetic diversity of lineage A are obviously higher than those of lineage B. Lineage introgressive hybridization may be the driving force for further L. invasa invasion and diffusion in China in the future.

Genetic Diversity and Genetic Structure Analysis of the Natural Populations of Lilium brownii from Guangdong, China

2009 ◽  
Vol 47 (7-8) ◽  
pp. 503-510 ◽  
Author(s):  
Yong-fang Huang ◽  
Mao-xun Yang ◽  
Hao Zhang ◽  
Xue-ying Zhuang ◽  
Xue-hui Wu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Structure Analysis ◽  
Natural Populations

scholarly journals Association Mapping for Yield Attributing Traits and Yellow Mosaic Disease Resistance in Mung Bean [Vigna radiata (L.) Wilczek]

2022 ◽  
Vol 12 ◽  
Author(s):  
Versha Rohilla ◽  
Rajesh Kumar Yadav ◽  
Atman Poonia ◽  
Ravika Sheoran ◽  
Gita Kumari ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Association Mapping ◽  
Structure Analysis ◽  
Population Genetic Structure ◽  
Vigna Radiata ◽  
Mung Bean ◽  
Population Genetic ◽  
Mosaic Disease ◽  
Yellow Mosaic Disease

Mung bean [Vigna radiata (L.) Wilczek] is an important short-duration grain legume widely known for its nutritional, soil ameliorative, and cropping system intensification properties. This study aims at evaluating genetic diversity among mung bean genotypes and detecting genomic regions associated with various yield attributing traits and yellow mosaic disease (YMD) resistance by association mapping. A panel of 80 cultivars and advanced breeding lines was evaluated for 10 yield-related and YMD resistance traits during kharif (monsoon) and summer seasons of 2018–2019 and 2019–2020. A total of 164 genome-wide simple sequence repeat (SSR) markers were initially screened, out of which 89 were found polymorphic which generated 317 polymorphic alleles with an average of 3.56 alleles per SSR locus. The number of alleles at each locus varied from 2 to 7. The population genetic structure analysis grouped different genotypes in three major clusters and three genetically distinct subpopulations (SPs) (i.e., SP-1, SP-2, and SP-3) with one admixture subpopulation (SP-4). Both cluster and population genetic structure analysis categorized the advanced mung bean genotypes in a single group/SP and the released varieties in other groups/SPs, suggesting that the studied genotypes may have common ancestral history at some level. The population genetic structure was also in agreement with the genetic diversity analysis. The estimate of the average degree of linkage disequilibrium (LD) present at the genome level in 80 mung bean genotypes unveiled significant LD blocks. Over the four seasons, 10 marker-trait associations were observed significant for YMD and four seed yield (SY)-related traits viz., days to flowering, days to maturity, plant height, and number of pods per plant using the mixed linear model (MLM) method. These associations may be useful for marker-assisted mung bean yield improvement programs and YMD resistance.

Population genetic structure and migration patterns of Liriomyza sativae in China: moderate subdivision and no Bridgehead effect revealed by microsatellites

2015 ◽  
Vol 106 (1) ◽  
pp. 114-123 ◽  
Author(s):  
X.-T. Tang ◽  
Y. Ji ◽  
Y.-W. Chang ◽  
Y. Shen ◽  
Z.-H. Tian ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Genetic Structure ◽  
Population Genetic Structure ◽  
Population Genetic ◽  
Mantel Test ◽  
Invasive Pest ◽  
Migration Patterns ◽  
Liriomyza Sativae ◽  
And Migration

AbstractWhile Liriomyza sativae (Diptera: Agromyzidae), an important invasive pest of ornamentals and vegetables has been found in China for the past two decades, few studies have focused on its genetics or route of invasive. In this study, we collected 288 L. sativae individuals across 12 provinces to explore its population genetic structure and migration patterns in China using seven microsatellites. We found relatively low levels of genetic diversity but moderate population genetic structure (0.05 < FST < 0.15) in L. sativae from China. All populations deviated significantly from the Hardy–Weinberg equilibrium due to heterozygote deficiency. Molecular variance analysis revealed that more than 89% of variation was among samples within populations. A UPGMA dendrogram revealed that SH and GXNN populations formed one cluster separate from the other populations, which is in accordance with STRUCTURE and GENELAND analyses. A Mantel test indicated that genetic distance was not correlated to geographic distance (r = −0.0814, P = 0.7610), coupled with high levels of gene flow (M = 40.1–817.7), suggesting a possible anthropogenic influence on the spread of L. sativae in China and on the effect of hosts. The trend of asymmetrical gene flow was from southern to northern populations in general and did not exhibit a Bridgehead effect during the course of invasion, as can be seen by the low genetic diversity of southern populations.

scholarly journals ddRAD Sequencing: A Novel Arsenal Added to the Biosecurity Toolbox to Trace the Origin of Brown Marmorated Stink Bug, Halyomorpha Halys (Hemiptera: Pentatomidae)

2020 ◽  
Author(s):  
Juncong Yan ◽  
Gábor Vétek ◽  
Chandan Pal ◽  
Jinping Zhang ◽  
Rania Gmati ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Structure Analysis ◽  
Dna Sequences ◽  
Insect Pest ◽  
Economic Losses ◽  
Halyomorpha Halys ◽  
Invasion History ◽  
Stink Bug ◽  
Genetic Clusters

Abstract BackgroundBrown marmorated stink bug (BMSB), Halyomorpha halys (Hemiptera: Pentatomidae) is native to East Asia but has invaded many countries in the world. It is a polyphagous insect pest and causing significant economic losses to agriculture worldwide. Knowledge on the genetic diversity among BMSB populations is scarce but is essential to understand the patterns of colonization and invasion history of local populations. Efforts have been made to assess the genetic diversity of BMSB using partial mitochondrial DNA sequences but genetic divergence on mitochondria is not high enough to precisely identify and distinguish various BMSB populations. Therefore, in this study, we applied a ddRAD (double digest restriction-site associated DNA) sequencing approach to ascertain the genetic diversity of BMSB populations collected from 12 countries (2 native and 10 invaded) across four continents with the ultimate aim to trace the origin of BMSBs intercepted during border inspections and post-border surveillance.ResultA total of 1775 high confidence single nucleotide polymorphisms (SNPs) were identified from ddRAD sequencing data collected from 389 BMSB individuals. Principal component analysis (PCA) of the identified SNPs indicated the existence of two main distinct genetic clusters representing individuals sampled from regions where BMSB is native to, China and Japan, respectively, and one broad cluster comprised individuals sampled from countries which have been invaded by BMSB. The population genetic structure analysis further discriminated the genetic diversity among the BMSB populations at a higher resolution and distinguished them into five potential genetic clusters. ConclusionThe study revealed hidden genetic diversity among the studied BMSB populations across the continents. The BMSB populations from Japan were genetically distant from the other studied populations. Similarly, the BMSB populations from China were also separated from the Japanese and other populations. Further genetic structure analysis revealed the presence of at least three genetic clusters of BMSB in the invaded countries, possibly originating from multiple invasions. Furthermore, this study has produced novel set of SNP markers to enhance knowledge of genetic diversity among BMSB populations and demonstrate a great potential to trace the origin of BMSB individuals for future invasion events.

scholarly journals Study of genetic diversity of Iranian indigenous buffalo populations using microsatellite markers

Genetika ◽  
2019 ◽  
Vol 51 (1) ◽  
pp. 147-155
Author(s):  
Darestani Yousefi ◽  
Ashtiani Miraei ◽  
Mostafa Sadeghi
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Microsatellite Markers ◽  
Salting Out ◽  
Hair Samples ◽  
Pcr Products ◽  
Sustainable Conservation ◽  
High Level ◽  
Amova Analysis

Indigenous buffalo breeds represent a unique genetic resource, and understanding their variability, population structure and breeding units is important for their sustainable conservation. In the present study the genetic structure of Iranian buffalo populations was analyzed using ten microsatellite markers. Two hundred hair samples were collected and DNA was extracted using modified salting out method. After Polymerase Chain Reaction (PCR), the PCR products were electrophoresed using 9% polyacrylamide gel. Fifty- nine alleles were observed for all the loci. The average number of alleles was 5.90 and the effective average number of alleles was 4.86. The high level of mean heterozygosity index between three populations indicate that the genetic diversity is high in within and between populations. The mean of polymorphism information content (PIC) value for all loci was 0.70. The FST value for the total loci was 0.01, indicating a very low level of genetic structure among populations. The genetic structure AMOVA analysis showed that about 3% of the total genetic variation was explained by population differences and 97 percent was corresponded to differences among individuals. The obtained results at the present study indicated that characterization of genetic diversity by employing molecular tools is a prerequisite in developing strategies for conservation and utilization of buffalo genetic resources.

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

2020 ◽  
Author(s):  
Grimar Abdiel Perez ◽  
Pumipat Tongyoo ◽  
Julapark Chunwongse ◽  
Hans de Jong ◽  
Paweena Chuenwarin
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Phylogenetic Tree ◽  
Structure Analysis ◽  
Fruit Shape ◽  
Snp Markers ◽  
Distinguishing Characteristic ◽  
Breeding Programs ◽  
Unrooted Phylogenetic Tree ◽  
Luffa Acutangula

AbstractThis study explored a germplasm consisting of 112 Luffa acutangula (ridge gourd) accessions mainly from Thailand, and some accessions from Vietnam, China, Philippines, Indonesia, USA, Bangladesh and Laos for an analysis of the population structure and underlying genetic diversity using 2,834 SNPs. 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. The phylogenetic tree showed the diversity of L. acutangula in Thailand, and accessions from other countries apart from Thailand were grouped together in the same branches. In STRUCTURE, subpopulation 2 contained only accessions from Thailand while other subpopulations contained a combination of accessions from Thailand and from other countries. When plotted, the STRUCTURE bars to the area of collection, it revealed the geneflow from the surrounding places nearby as indicated by the admixed genetic in the STRUCTURE bars. AMOVA based on STRUCTURE clustering showed the variation between populations (12.83%) and confirmed the absence of population structure in subpopulations (−10.59%). There was a distinguishing characteristic fruit shape and length in each subpopulation. The ample genetic diversity found in the L. acutangula germplasm can be utilized in ridge gourd breeding programs to help meet the demands and needs of both consumers and farmers.

scholarly journals ddRAD sequencing: an emerging technology added to the biosecurity toolbox for tracing the origin of brown marmorated stink bug, Halyomorpha halys (Hemiptera: Pentatomidae)

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Juncong Yan ◽  
Gábor Vétek ◽  
Chandan Pal ◽  
Jinping Zhang ◽  
Rania Gmati ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Structure Analysis ◽  
Dna Sequences ◽  
Economic Losses ◽  
Halyomorpha Halys ◽  
Invasion History ◽  
Brown Marmorated Stink Bug ◽  
Stink Bug ◽  
Genetic Clusters

Abstract Background Brown marmorated stink bug (BMSB), Halyomorpha halys (Hemiptera: Pentatomidae) is native to East Asia but has invaded many countries in the world. BMSB is a polyphagous insect pest and causes significant economic losses to agriculture worldwide. Knowledge on the genetic diversity among BMSB populations is scarce but is essential to understand the patterns of colonization and invasion history of local populations. Efforts have been made to assess the genetic diversity of BMSB using partial mitochondrial DNA sequences but genetic divergence on mitochondria is not high enough to precisely accurately identify and distinguish various BMSB populations. Therefore, in this study, we applied a ddRAD (double digest restriction-site associated DNA) sequencing approach to ascertain the genetic diversity of BMSB populations collected from 12 countries (2 native and 10 invaded) across four continents with the ultimate aim to trace the origin of BMSBs intercepted during border inspections and post-border surveillance. Result A total of 1775 high confidence single nucleotide polymorphisms (SNPs) were identified from ddRAD sequencing data collected from 389 adult BMSB individuals. Principal component analysis (PCA) of the identified SNPs indicated the existence of two main distinct genetic clusters representing individuals sampled from regions where BMSB is native to, China and Japan, respectively, and one broad cluster comprised individuals sampled from countries which have been invaded by BMSB. The population genetic structure analysis further discriminated the genetic diversity among the BMSB populations at a higher resolution and distinguished them into five potential genetic clusters. Conclusion The study revealed hidden genetic diversity among the studied BMSB populations across the continents. The BMSB populations from Japan were genetically distant from the other studied populations. Similarly, the BMSB populations from China were also genetically differentiated from the Japanese and other populations. Further genetic structure analysis revealed the presence of at least three genetic clusters of BMSB in the invaded countries, possibly originating via multiple invasions. Furthermore, this study has produced novel set of SNP markers to enhance the knowledge of genetic diversity among BMSB populations and demonstrates the potential to trace the origin of BMSB individuals for future invasion events.

scholarly journals Species identification and population structure analysis in Geranium subg. Geranium (Geraniaceae)

Hacquetia ◽  
2018 ◽  
Vol 17 (2) ◽  
pp. 235-246 ◽  
Author(s):  
Somayeh Esfandani-Bozchaloyi ◽  
Masoud Sheidai ◽  
Maryam Keshavarzi ◽  
Zahra Noormohammadi
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Structure ◽  
Species Identification ◽  
Structure Analysis ◽  
Issr Markers ◽  
Morphological Studies ◽  
Population Structure Analysis ◽  
The World

AbstractSpecies identification is fundamentally important within the fields of biology, biogeography, ecology and conservation. The genusGeraniumL. (Geraniaceae) comprises about 430 species distributed throughout most parts of the world. According to the most recent treatments, subg.Geraniumis the largest subgenus with over 370 species classified in ten sections. The subg.Geraniumis represented in Iran by 13 species. These species are grouped 3 sections. In spite vast distribution of manyGeraniumspecies that grow in Iran, there are not any available report on their genetic diversity, mode of divergence and patterns of dispersal.Therefore, we performed molecular (ISSR markers) and morphological studies of 102 accessions from 13 species ofGeranium(subg.Geranium) that were collected from different habitats in Iran. The aims of present study are: 1) can ISSR markers identifyGeraniumspecies, 2) what is the genetic structure of these taxa in Iran, and 3) to investigate the species inter-relationship? The present study revealed that combination of morphological and ISSR data can identify the species.

Genetic structure and phylogeography of rice landraces in Yunnan, China, revealed by SSR

Genome ◽  
2007 ◽  
Vol 50 (1) ◽  
pp. 72-83 ◽  
Author(s):  
Hongliang Zhang ◽  
Junli Sun ◽  
Meixing Wang ◽  
Dengqun Liao ◽  
Yawen Zeng ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
Structure Analysis ◽  
Oryza Sativa L ◽  
Cropping System ◽  
Analysis Model ◽  
Cultivated Rice ◽  
Model Based ◽  
Rice Landraces ◽  
Southwest Region

Yunnan Province is one of the largest centers of genetic diversity of Oryza sativa L. in China, and in the world. Using a genetically representative core collection of 692 rice landraces from Yunnan, the genetic structure, differentiation, and geographic diversity of this rice germplasm were analyzed. The accessions were classified into different populations, according to the model-based structure analysis. Model-based populations were characterized through the reconstruction of a neighbor-joining tree, principal coordinate analysis, and the estimation of morphologic and SSR variations. Finally, the distribution of genetic diversity and differentiation among districts were studied. Seven model-based populations were identified on the basis of the structure analysis. This classification was partly consistent with Ting’s 5-level taxonomic system. Differentiation between 2 rice subspecies is the most apparent, with a clearer differentiation between soil-watery ecotypes in japonica than in indica; however, differentiation among seasonal ecotypes in indica is clearer than in japonica. Cropping system and man-made restricted-growth environments could be considered to be the main forces driving the intraspecific differentiation of cultivated rice. It has been suggested that, because it possesses the highest genetic diversity and all the necessary conditions as a center of genetic diversity, the southwest region of Yunnan, encompassing Simao, Lincang, and Xishuangbanna districts, is the center of genetic diversity of Yunnan rice landraces.

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