scholarly journals Employing Genome-Wide SNP Discovery to Characterize the Genetic Diversity in Cinnamomum camphora Using Genotyping by Sequencing

Forests ◽  
2021 ◽  
Vol 12 (11) ◽  
pp. 1511
Author(s):  
Xue Gong ◽  
Aihong Yang ◽  
Zhaoxiang Wu ◽  
Caihui Chen ◽  
Huihu Li ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
East Asia ◽  
Japanese Population ◽  
Eastern China ◽  
Genotyping By Sequencing ◽  
Central China ◽  
Western China ◽  
Cinnamomum Camphora ◽  
Ecological Value ◽  
Genome Wide

Cinnamomum camphora (L.) J.Presl is a representative tree species of evergreen broad-leafed forests in East Asia and has exceptionally high economic, ornamental, and ecological value. However, the excessive exploitation and utilization of C. camphora trees have resulted in the shrinking of wild population sizes and rare germplasm resources. In this study, we characterized 171 C. camphora trees from 39 natural populations distributed throughout the whole of China and one Japanese population. We investigated genetic diversity and population structure using genome-wide single-nucleotide polymorphism (SNP) identified by genotyping by sequencing (GBS) technology. The results showed the genetic diversity of the C. camphora populations from western China > central China > eastern China. Moreover, the Japanese population showed the highest diversity among all populations. The molecular variance analysis showed 92.03% of the genetic variation within populations. The average pairwise FST was 0.099, and gene flow Nm was 2.718, suggesting a low genetic differentiation among populations. Based on the genetic clustering analysis, the 40 C. camphora populations clustered into three major groups: Western China, Central China, and Eastern China + Japan. Eastern China’s population had the closest genetic relationship with the Japanese population, suggesting possible gene exchange between the two adjacent areas. This study furthers our understanding of the genetic diversity and genetic structure of C. camphora in East Asia and provides genetic tools for developing strategies of C. camphora germplasm utilization.

scholarly journals Does Mobile Phone Penetration Affect Divorce Rate? Evidence from China

2018 ◽  
Vol 10 (10) ◽  
pp. 3701 ◽  
Author(s):  
Jiaping Zhang ◽  
Mingwang Cheng ◽  
Xinyu Wei ◽  
Xiaomei Gong
Keyword(s):  
Mobile Phone ◽  
Eastern China ◽  
Divorce Rate ◽  
Central China ◽  
Western China ◽  
Explanatory Variables ◽  
Information And Communication ◽  
Lag Times ◽  
One Year ◽  
The Impact

Marital happiness is an important symbol of social harmony and can help promote sustainable economic and social development. In recent years, the rapid rise of the divorce rate in China, a country where the divorce rate had previously been low, has attracted wide attention. However, few articles have focused on the popularization of information and communication technology's impact on China’s rising divorce rate in recent years. As a first attempt, the provincial panel data during the period 2001–2016 is applied to study quantitatively the relationship between mobile phone penetration and the divorce rate. In order to get more reliable estimation results, this paper uses two indicators to measure the divorce rate, and quantile regression is applied for further analysis. Additionally, one-year to five-year lag times of the mobile phone penetration are used as the core explanatory variables in order to analyse the lagging effect of mobile phone penetration on divorce rate. The result shows that the correlation between the mobile phone penetration and the divorce rate was statistically positive significant in China during the period 2001–2016. Furthermore, the paper also finds that mobile phone penetration had the greatest impact on divorce rate in central China, followed by eastern China, but it was not obvious in western China during this period. From a technological perspective, this paper provides some possible explanations for the rising divorce rate in China in recent years, and further enriches the relevant research on the impact of the development of information and communication technology on societal changes.

scholarly journals Regional Green Development and Spatial Evolution in China: Abiding by Theory of Dissipative Structure

2018 ◽  
Vol 53 ◽  
pp. 04008
Author(s):  
Fumin Deng ◽  
Hui Zhu ◽  
Xuedong Liang
Keyword(s):  
Economic Development ◽  
Dissipative Structure ◽  
Eastern China ◽  
Indicator System ◽  
Entropy Method ◽  
Central China ◽  
Western China ◽  
Brusselator Model ◽  
Energy Factors ◽  
Green Development

Regional green development can commendably abide by the theory of dissipative structure. The relative dissipative characteristics taken on by regional development are analyzed, in which the energy factors and resources factors are incorporated into the green economic development and green environment support subsystems (2GE system) in line with the definite input characteristics. A more representative indicator system is established, with positive and negative entropy indexes involved. As Brusselator model and information entropy method are employed to calculate the data of 30 China’s provinces from 2008 to 2015, the findings bespeak that green development in China lays particular stress on green economic development assuming higher environment pressure and cost. The development among various regions is getting progressively and evidently different, which is manifested as potent economic base and abundant natural resources in the Eastern China; the backward green economic development and the progress of green environment in Central China; the pursuit of green economic development at the expense of the green environment in Western China and Northeastern China.

scholarly journals Comparing the Effectiveness of Exome Capture Probes, Genotyping by Sequencing and Whole-Genome Re-Sequencing for Assessing Genetic Diversity in Natural and Managed Stands of Picea abies

Forests ◽  
2020 ◽  
Vol 11 (11) ◽  
pp. 1185
Author(s):  
Helena Eklöf ◽  
Carolina Bernhardsson ◽  
Pär K. Ingvarsson
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Picea Abies ◽  
Norway Spruce ◽  
Large Scale ◽  
Genotyping By Sequencing ◽  
Complexity Reduction ◽  
Exome Capture ◽  
Genome Wide ◽  
Targeted Capture

Conifer genomes are characterized by their large size and high abundance of repetitive material, making large-scale genotyping in conifers complicated and expensive. One of the consequences of this is that it has been difficult to generate data on genome-wide levels of genetic variation. To date, researchers have mainly employed various complexity reduction techniques to assess genetic variation across the genome in different conifer species. These methods tend to capture variation in a relatively small subset of a typical conifer genome and it is currently not clear how representative such results are. Here we take advantage of data generated in the first large-scale re-sequencing effort in Norway spruce and assess how well two commonly used complexity reduction methods, targeted capture probes and genotyping by sequencing perform in capturing genome-wide variation in Norway spruce. Our results suggest that both methods perform reasonably well for assessing genetic diversity and population structure in Norway spruce (Picea abies (L.) H. Karst.). Targeted capture probes were slightly more effective than GBS, likely due to them targeting known genomic regions whereas the GBS data contains a substantially greater fraction of repetitive regions, which sometimes can be problematic for assessing genetic diversity. In conclusion, both methods are useful for genotyping large numbers of samples and they greatly reduce the cost involved with genotyping a species with such a complex genome as Norway spruce.

scholarly journals Occurrence and source apportionment of perfluoroalkyl acids (PFAAs) in the atmosphere in China

2019 ◽  
Vol 19 (22) ◽  
pp. 14107-14117 ◽  
Author(s):  
Deming Han ◽  
Yingge Ma ◽  
Cheng Huang ◽  
Xufeng Zhang ◽  
Hao Xu ◽  
...  
Keyword(s):  
Degradation Products ◽  
Southern China ◽  
Eastern China ◽  
Northern China ◽  
Central China ◽  
Western China ◽  
Perfluoroalkyl Acids ◽  
Average Value ◽  
Pmf Model ◽  
Air Sampler

Abstract. Perfluoroalkyl acids (PFAAs) are a form of toxic pollutant that can be transported across the globe and accumulated in the bodies of wildlife and humans. A nationwide geographical investigation considering atmospheric PFAAs via a passive air sampler (PAS) based on XAD (a styrene–divinylbenzene copolymer) was conducted in 23 different provinces/municipalities/autonomous regions in China, which provides an excellent chance to investigate their occurrences, spatial trends, and potential sources. The total atmospheric concentrations of 13 PFAAs (n=268) were 6.19–292.57 pg m−3, with an average value of 39.84±28.08 pg m−3, which were higher than other urban levels but lower than point source measurements. Perfluorooctanoic acid (PFOA) was the dominant PFAA (20.6 %), followed by perfluorohexanoic acid (PFHxA), perfluorooctane sulfonate (PFOS), and perfluoroheptanoic acid (PFPeA). An increasing seasonal trend of PFAA concentrations was shown as summer < autumn < spring < winter, which may be initiated by stagnant meteorological conditions. Spatially, the content of PFAAs displayed a declining gradient trend of central China > northern China > eastern China > north-eastern China > south-western China > north-western China > southern China, and Henan contributed the largest proportion of PFAAs. Four sources of PFAAs were identified using a positive matrix factorization (PMF) model, including PFOS-based products (26.1 %), products based on PFOA and perfluorononanoic acid (PFNA; 36.6 %), degradation products of fluorotelomer-based products (15.5 %), and an unknown source (21.8 %).

scholarly journals Dimethachlon Resistance in Sclerotinia sclerotiorum in China

Plant Disease ◽  
2014 ◽  
Vol 98 (9) ◽  
pp. 1221-1226 ◽  
Author(s):  
Feng Zhou ◽  
Xiao-Lei Zhang ◽  
Jin-Li Li ◽  
Fu-Xing Zhu
Keyword(s):  
Oilseed Rape ◽  
Sclerotinia Sclerotiorum ◽  
Eastern China ◽  
Gansu Province ◽  
Central China ◽  
Hunan Province ◽  
Western China ◽  
Current Status ◽  
Cross Resistance ◽  
Soybean Plants

The dicarboximide fungicide dimethachlon has been widely used for controlling Sclerotinia sclerotiorum in China for more than a decade. To assess the current status of dimethachlon resistance in S. sclerotiorum in China, 2,424 isolates were collected from disease-infected oilseed rape and soybean plants in five provinces of China in 2011 and 2012, and dimethachlon resistance was monitored by mycelial growth inhibition method on potato dextrose agar (PDA) media. Dimethachlon at 5 μg/ml was used as a discriminatory dose to detect resistance in all isolates, and 50% effective concentration values were determined for all dimethachlon-resistant isolates and some sensitive isolates. No dimethachlon resistance was detected in isolates from Anhui province (eastern China), Gansu province (northwestern China), and Qinghai province (western China). In Hunan province (central China), 3 of 268 (1.12%) isolates collected from oilseed rape plants in 2012 were resistant to dimethachlon, and the resistance ratios for the three resistant isolates were 4.56, 32.70, and 105.53, respectively. In Heilongjiang province (northeastern China), 8 of 243 (3.29%) isolates collected from soybean plants in 2011 were resistant to dimethachlon, with resistance ratios of 5.57 to 94.80; 11 of 409 (2.69%) isolates collected in 2012 were resistant to dimethachlon, with resistance ratios of 3.21 to 9.69. Cross-resistance studies showed that there was positive cross-resistance between dimethachlon and iprodione, procymidone, and the N-phenyl carbamate fungicide diethofencarb. No cross-resistance was found between dimethachlon and carbendazim, tebuconazole, kresoxim-methyl, thiram, and boscalid. Compared with the sensitive isolates of S. sclerotiorum, the field-dimethachlon-resistant isolates were more sensitive to osmotic pressure, grew more slowly on PDA media, and were less pathogenic on leaves of oilseed rape.

scholarly journals Patterns and trends of high-impact weather in China during 1959–2014

2016 ◽  
Vol 16 (3) ◽  
pp. 855-869 ◽  
Author(s):  
Jun Shi ◽  
Kangmin Wen ◽  
Linli Cui
Keyword(s):  
Southern China ◽  
Eastern China ◽  
High Impact ◽  
Northeastern China ◽  
Central China ◽  
Western China ◽  
Tibet Plateau ◽  
High Mountain ◽  
Mitigation And Adaptation ◽  
High Impact Weather

Abstract. The spatial and temporal characteristics of the frequencies of four types of high-impact weather (HIW), i.e. snowfall, thunderstorms, fog and hailstorms, were analysed in China during 1959–2014. Results indicate a significant decrease in the number of snowfall days, thunderstorm days and thunderstorm spells in all six regions of China, with regional decreasing rates of 0.1–3.4 days, 1.6–5.1 days and 0.23–0.77 times per decade respectively. The number of foggy days, hailstorm days and snowfall spells decreased at rates of 0.2–1.8 days, 0.1–0.7 days and 0.14–0.44 times per decade respectively in almost all regions and fog and hailstorm spells decreased at rates of 0.06–0.17 and 0.001–0.043 times per decade respectively in most regions of China. Spatially, there was more snowfall in northeastern China and western China, and more thunderstorms in southern China and southwestern China. The number of fog events was larger in some high mountain stations, eastern China and central China. Hailstorms were concentrated on Qinghai–Tibet Plateau. Over the past 56 years, snowfall days, thunderstorm days and thunderstorm spells decreased in most parts of China, and hailstorm days decreased in northeastern China, most parts of northern China and Tibet, southern Qinghai and western Sichuan. The spatial trends of foggy days, foggy spells, snowfall spells and hailstorm spells were not significant in most parts of China. With global warming, some types of HIW are likely to increase in their intensities, so more mitigation and adaptation strategies are still essential for local government and the public in China.

scholarly journals Genetic characterization of buckwheat accessions through genome-wide allele frequency fingerprints / Genetska karakterizacija vzorcev ajde z odtisi frekvence alelov v genomu

2020 ◽  
Vol 61 (1) ◽  
pp. 17-23
Author(s):  
Michelle M. Nay ◽  
Stephen L. Byrne ◽  
Eduardo A. Pérez ◽  
Achim Walter ◽  
Bruno Studer
Keyword(s):  
Genetic Diversity ◽  
Single Nucleotide Polymorphisms ◽  
Allele Frequency ◽  
Genotyping By Sequencing ◽  
Allele Frequencies ◽  
Fagopyrum Esculentum ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genome Wide ◽  
Fagopyrum Esculentum Moench

Genomics-assisted breeding of buckwheat (Fagopyrum esculentum Moench) depends on robust genotyping methods. Genotyping by sequencing (GBS) has evolved as a flexible and cost-effective technique frequently used in plant breeding. Several GBS pipelines are available to genetically characterize single genotypes but these are not able to represent the genetic diversity of buckwheat accessions that are maintained as genetically heterogeneous, open-pollinating populations. Here we report the development of a GBS pipeline which, rather than reporting the state of bi-allelic single nucleotide polymorphisms (SNPs), resolves allele frequencies within populations on a genome-wide scale. These genome-wide allele frequency fingerprints (GWAFFs) from 100 pooled individual plants per accession were found to be highly reproducible and revealed the genetic similarity of 20 different buckwheat accessions analysed in our study. The GWAFFs cannot only be used as an efficient tool to precisely describe buckwheat breeding material, they also offer new opportunities to investigate the genetic diversity between different buckwheat accessions and establish variant databases for key material. Furthermore, GWAFFs provide the opportunity to associate allele frequencies to phenotypic traits and quality parameters that are most reliably described on population level. This is the key to practically implement powerful genomics-assisted breeding concepts such as marker-assisted selection and genomic selection in future breeding schemes of allogamous buckwheat. Key words: Buckwheat (Fagopyrum esculentum Moench), genotyping by sequencing (GBS), population genomics, genome-wide allele frequency fingerprints (GWAFFs)   Izvleček Genomsko podprto žlahtnjenje ajde (Fagopyrum esculentum Moench) je odvisno od robustnih metod genotipiziranja. Genotipiziranje s spremljanjem sekvenc (genotyping by sequencing, GBS) se je razvilo kot fleksibilna in razmeroma poceni metoda, ki se jo uporablja pri žlahtnjenju rastlin. Uporabnih je več virov GBS za genetsko karakterizacijo posamičnih genotipov, toda te metode niso primerne za predstavitev genetske raznolikosti vzorcev ajde, ki jih vzdržujemo v heterozigotni obliki, kar velja za odprto oplodne populacije. Tu poročamo o razvoju GBS metode, ki, namesto prikazovanja bi-alelnega polimorfizma posameznih nukleotidov (single nucleotide polymorphisms, SNPs), pokaže frekvence alelov v populaciji na nivoju genoma. Ta prikaz frekvence alelov na nivoju genoma (genome-wide allele frequency fingerprints, GWAFFs) z združenimi sto posameznimi rastlinami vsakega vzorca se je pokazal kot visoko ponovljiv in je prikazal genetsko podobnost 20 različnih vzorcev ajde, ki smo jih analizirali v naši raziskavi. Metoda GWAFFs ni uporabna samo kot učinkovito orodje za natančen opis materiala za žlahtnjenje ajde, ponuja tudi možnosti raziskave  genetskih razlik med različnimi vzorci ajde in omogoča zbirke podatkov. Nadalje, metoda GWAFFs omogoča povezovanje frekvenc alelov s fenotipskimi lastnostmi in kvalitativnih parametrov, ki so najbolj zanesljivo opisani na nivoju populacij. To je ključ za praktično uporabo z genomiko podprtega žlahtnjenja, kot je z genskimi markerji podprta selekcija in genomska selekcija z GWAFFs. Ključne besede: ajda (Fagopyrum esculentum Moench), genotipizacija s sekvenciranjem (GBS), populacijska genomika, GWAFFs

scholarly journals Genotyping-by-sequencing and genome-wide association study reveal genetic diversity and loci controlling agronomic traits in triticale

2021 ◽  
Author(s):  
Dong Cao ◽  
Dongxia Wang ◽  
Shiming Li ◽  
Yun Li ◽  
Ming Hao ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Association Study ◽  
Genome Wide Association Study ◽  
Agronomic Traits ◽  
Genotyping By Sequencing ◽  
Genome Wide Association ◽  
Energy Crop ◽  
Hexaploid Triticale ◽  
Genome Wide ◽  
Genetic Mechanisms

Abstract Key message The genetic diversity and loci underlying agronomic traits were analysed by the reads coverage and genome-wide association study based genotyping-by-sequencing in a diverse population consisting of 199 accessions.Abstract Triticale (×Triticosecale Wittmack) is an economically important grain-forage and energy crop planted worldwide for its high biomass. Little is known about the genetic diversity and loci underlying agronomic traits in triticale. We performed genotyping-by-sequencing of 199 cultivars and mapped reads to the A, B, D, and R genomes for karyotype analysis. These cultivars could mostly be grouped into five types. Some chromosome abnormalities occurred with high frequency, such as 2D (2R) substitution, deletion of the long arm of chromosome 2D or the short arm of 5R, and translocation of the long arms of 7D/7A, the short arms of 6D/6A, or the long arms of 1D/1A. We chose only widely planted hexaploid triticale cultivars (153) for genome-wide association study. These cultivars could be divided into nine distinct groups, and the linkage disequilibrium decay was 25.4 kb in this population. We identified 253 significant marker-trait associations (MTAs) on 20 chromosomes, except 7R. Twenty-one reliable MTAs were identified repeatedly over two environments. We predicted 16 putative candidate genes involved in plant growth and development using the genome sequences of wheat and rye. These results provide a basis for understanding the genetic mechanisms of agronomic traits and will benefit the breeding of improved hexaploid triticale.

scholarly journals Genomic analysis reveals the genetic diversity, population structure, evolutionary history and relationships of Chinese pepper

2020 ◽  
Vol 7 (1) ◽  
Author(s):  
Shijing Feng ◽  
Zhenshan Liu ◽  
Yang Hu ◽  
Jieyun Tian ◽  
Tuxi Yang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Demographic History ◽  
Genomic Analysis ◽  
Genotyping By Sequencing ◽  
Gansu Province ◽  
Climatic Oscillations ◽  
Genome Wide ◽  
A Genome ◽  
Wild Accessions

Abstract Chinese pepper, mainly including Zanthoxylum bungeanum and Zanthoxylum armatum, is an economically important crop popular in Asian countries due to its unique taste characteristics and potential medical uses. Numerous cultivars of Chinese pepper have been developed in China through long-term domestication. To better understand the population structure, demographic history, and speciation of Chinese pepper, we performed a comprehensive analysis at a genome-wide level by analyzing 38,395 genomic SNPs that were identified in 112 cultivated and wild accessions using a high-throughput genome-wide genotyping-by-sequencing (GBS) approach. Our analysis provides genetic evidence of multiple splitting events occurring between and within species, resulting in at least four clades in Z. bungeanum and two clades in Z. armatum. Despite no evidence of recent admixture between species, we detected substantial gene flow within species. Estimates of demographic dynamics and species distribution modeling suggest that climatic oscillations during the Pleistocene (including the Penultimate Glaciation and the Last Glacial Maximum) and recent domestication events together shaped the demography and evolution of Chinese pepper. Our analyses also suggest that southeastern Gansu province is the most likely origin of Z. bungeanum in China. These findings provide comprehensive insights into genetic diversity, population structure, demography, and adaptation in Zanthoxylum.

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