Morphological, Molecular and Genomic Characterization of Two Inter-Subspecific Hybrids between Olive Cultivars and Olive Subspecies

Two inter-subspecific F1 hybrids have been obtained by crossing olive cultivars (‘Frantoio’ and ‘Coratina’) with pollen donors from olive subspecies (Olea europaea subsp. cuspidata) to enrich the germplasm of cultivated olive in southern China. This study aimed to investigate the characterization of morphological traits and molecular markers in the two hybrids and their parents of crosses. The morphological study showed a significant difference between genotypes according to the main discriminative parameters on qualitative and quantitative traits of leaf, fruit, and endocarp. A set of six co-dominant polymorphic simple sequence repeats (SSRs) were used for molecular identification, and SSR analysis confirmed that two progenies were the offspring of their cited parents based on the presence of parental specific SSR alleles. Three single-copy nuclear loci (SCNL) primer pairs were used for amplification of single-copy genes in the two progenies and their parents and after then PCR products were sequenced. Sequence alignment analysis on the effective data showed a total of 15 different base sites between two progenies, which were confirmed as true inter-specific hybrids between olive cultivars and subsp. cuspidata.

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Genomic characterization of lumpy skin disease virus in southern China

Transboundary and Emerging Diseases ◽

10.1111/tbed.14432 ◽

2021 ◽

Author(s):

Jun Ma ◽

Yaoxian Yuan ◽

Jianwei Shao ◽

Minghui Sun ◽

Wei He ◽

...

Keyword(s):

Disease Virus ◽

Skin Disease ◽

Southern China ◽

Lumpy Skin Disease ◽

Lumpy Skin Disease Virus ◽

Genomic Characterization

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Molecular characterization of indigenous olive genotypes based on SSR analysis

Genetika ◽

10.2298/gensr1603017u ◽

2016 ◽

Vol 48 (3) ◽

pp. 1017-1025

Author(s):

Hulya Unver ◽

Ebru Sakar ◽

Mehmet Ulas ◽

Sezai Ercisli ◽

Bekir Ak

Keyword(s):

Genetic Diversity ◽

Simple Sequence Repeat ◽

Sequence Repeat ◽

Ssr Analysis ◽

Olive Cultivars ◽

Ssr Loci ◽

Similarity Ratio ◽

Repeat Primer ◽

Simple Sequence

Trees of 25 widely grown olive genotypes were analyzed using a set of 10 SSR (simple sequence repeat) primer pairs and to evaluate genetic diversity and reveal inter-cultivar relationships. Two well-known international olive cultivars (Chetoni and Manzanilla) and four widely grown Turkish standard cultivars (Aycalik, Edincik Su, Gemlik, Kilis Yaglik) are also included in the study to compare Kilis genotypes. The 10 polymorphic SSR loci exhibited 4 (UDO4) to 17 alleles (UDO43), with expected heterozygozity (He) ranging from 0.510 to 0.887 and a mean of 0.692 presenting high polymorphism. In this study we did not determine identical genotypes and Polateli4 and Kilis Ya?l?k (0.75), Polateli3 and Polateli7 (0.75) and Polateli6 and Manzanilla (0.70) revealed the highest similarity ratio each other. The most genetically divergent cultivars were Elbeyli8 and Musabeyli5 (0.10); Elbeyli3 and Musabeyli7 (0.15) and Musabeyli6 and Elbeyli7 (0.15), respectively.

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Isolation and complete genomic characterization of H1N1 subtype swine influenza viruses in southern China through the 2009 pandemic

Virology Journal ◽

10.1186/1743-422x-8-129 ◽

2011 ◽

Vol 8 (1) ◽

pp. 129 ◽

Cited By ~ 6

Author(s):

Yizhi Liu ◽

Jun Ji ◽

Qingmei Xie ◽

Jing Wang ◽

Huiqin Shang ◽

...

Keyword(s):

Southern China ◽

Swine Influenza ◽

Influenza Viruses ◽

H1n1 Subtype ◽

Genomic Characterization ◽

Complete Genomic

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Identification and characterization of anonymous nuclear markers for the double-striped cockroach, Blattella bisignata

Bulletin of Entomological Research ◽

10.1017/s0007485312000375 ◽

2012 ◽

Vol 103 (1) ◽

pp. 29-35 ◽

Cited By ~ 1

Author(s):

Q.-P. Ren ◽

Z. Fan ◽

X.-M. Zhou ◽

G.-F. Jiang ◽

Y.-T. Wang ◽

...

Keyword(s):

Southwest China ◽

Genomic Library ◽

Southern China ◽

Average Length ◽

Single Copy ◽

Small Scale ◽

Nuclear Markers ◽

Representative Species ◽

Identification And Characterization

AbstractDuring the last decade, multilocus analysis has gradually become a powerful tool for the studies of population genetics and phylogeography. The double-striped cockroach, Blattella bisignata, is endemic to southeast Asia, and there is currently little genetic information available for the species. We chose it as the target species to investigate a biodiversity hotspot in southwest China. Here, we report the identification and characterization of 11 single-copy anonymous nuclear markers with an average length of 378bp. These loci, isolated from a genomic library of B. bisignata, can amplify in two additional Blattella species (B. germanica and B. lituricollis). While testing these markers in representative species of Blattellidae, Blattidae and Epilampridae, some of them can cross-amplify successfully. After sequencing 30 individuals collected from southern China per locus, we found relatively high variability (approximately 3.6 SNPs per 100bp). Finally, a small-scale study was also performed to show that these markers do indeed fulfill the expectations as phylogeographic markers.

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Genomic characterization of influenza A (H7N9) viruses isolated in Shenzhen, Southern China, during the second epidemic wave

Archives of Virology ◽

10.1007/s00705-016-2872-1 ◽

2016 ◽

Vol 161 (8) ◽

pp. 2117-2132 ◽

Cited By ~ 2

Author(s):

Shisong Fang ◽

Xin Wang ◽

Fangyuan Dong ◽

Tao Jin ◽

Guang Liu ◽

...

Keyword(s):

Influenza A ◽

Southern China ◽

Genomic Characterization ◽

Epidemic Wave

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Molecular Epidemiology and Evolution of Influenza Viruses Circulating within European Swine between 2009 and 2013

Journal of Virology ◽

10.1128/jvi.00840-15 ◽

2015 ◽

Vol 89 (19) ◽

pp. 9920-9931 ◽

Cited By ~ 88

Author(s):

Simon J. Watson ◽

Pinky Langat ◽

Scott M. Reid ◽

Tommy Tsan-Yuk Lam ◽

Matthew Cotten ◽

...

Keyword(s):

Influenza Virus ◽

North America ◽

Large Scale ◽

Southern China ◽

Influenza Viruses ◽

European Countries ◽

Avian Virus ◽

Pdm09 Virus ◽

Genomic Characterization

ABSTRACTThe emergence in humans of the A(H1N1)pdm09 influenza virus, a complex reassortant virus of swine origin, highlighted the importance of worldwide influenza virus surveillance in swine. To date, large-scale surveillance studies have been reported for southern China and North America, but such data have not yet been described for Europe. We report the first large-scale genomic characterization of 290 swine influenza viruses collected from 14 European countries between 2009 and 2013. A total of 23 distinct genotypes were identified, with the 7 most common comprising 82% of the incidence. Contrasting epidemiological dynamics were observed for two of these genotypes, H1huN2 and H3N2, with the former showing multiple long-lived geographically isolated lineages, while the latter had short-lived geographically diffuse lineages. At least 32 human-swine transmission events have resulted in A(H1N1)pdm09 becoming established at a mean frequency of 8% across European countries. Notably, swine in the United Kingdom have largely had a replacement of the endemic Eurasian avian virus-like (“avian-like”) genotypes with A(H1N1)pdm09-derived genotypes. The high number of reassortant genotypes observed in European swine, combined with the identification of a genotype similar to the A(H3N2)v genotype in North America, underlines the importance of continued swine surveillance in Europe for the purposes of maintaining public health. This report further reveals that the emergences and drivers of virus evolution in swine differ at the global level.IMPORTANCEThe influenza A(H1N1)pdm09 virus contains a reassortant genome with segments derived from separate virus lineages that evolved in different regions of the world. In particular, its neuraminidase and matrix segments were derived from the Eurasian avian virus-like (“avian-like”) lineage that emerged in European swine in the 1970s. However, while large-scale genomic characterization of swine has been reported for southern China and North America, no equivalent study has yet been reported for Europe. Surveillance of swine herds across Europe between 2009 and 2013 revealed that the A(H1N1)pdm09 virus is established in European swine, increasing the number of circulating lineages in the region and increasing the possibility of the emergence of a genotype with human pandemic potential. It also has implications for veterinary health, making prevention through vaccination more challenging. The identification of a genotype similar to the A(H3N2)v genotype, causing zoonoses at North American agricultural fairs, underlines the importance of continued genomic characterization in European swine.

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Construction and characterization of chromosome 1B specific DNA library of wheat

Canadian Journal of Plant Science ◽

10.4141/p04-006 ◽

2005 ◽

Vol 85 (2) ◽

pp. 309-316

Author(s):

Fa-Yun Zhang ◽

Wei-Bo Yin ◽

Rui Shi ◽

Ying-Kao Hu ◽

Yue-Ming Yan ◽

...

Keyword(s):

Blot Hybridization ◽

Wheat Chromosome ◽

Single Copy ◽

Triticum Aestivum L ◽

Dot Blot ◽

Insert Size ◽

Pcr Products ◽

Chromosome Specific Library

Chromosome 1B was microdissected and collected from chromosome spreads of wheat (Triticum aestivum L. ‘Jing 411’), using a glass needle. DNA of the isolated chromosome was amplified in vitro by Sau3A linker adaptor-mediated polymerase chain reaction (LA-PCR). The second-round PCR products were verified by Southern hybridization using DIG-labeled genomic DNA of wheat. The results initially showed the DNA was from wheat genome. A pair of SSR primers specific to chromosome 1B was used to verify the origin of the PCR products from the isolated chromosome. The results confirmed that the PCR products originated from chromosome 1B. The second round of PCR products from chromosome 1B were cloned into plasmid pUCm-T vectors to create a chromosome-specific library, which included approximately 248 000 recombinant clones. Characterization of 100 randomly selected clones of the library showed that the insert size ranged between 0.5 and 2.0 kb, with an average of 1 kb. Randomly selected 288 clones were characterized with dot blot hybridization, of which 57.2% were medium/high copy clones and 42.8% low/single copy clones. The application of this technique to establish high-density molecular maps for chromosome 1B is discussed. Key words: Wheat, chromosome microdissection, chromosome-specific library

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Epigenetic characterization of the H19/IGF2 locus in calf clones placenta

Pesquisa Veterinária Brasileira ◽

10.1590/1678-5150-pvb-6491 ◽

2020 ◽

Vol 40 (12) ◽

pp. 1063-1072

Author(s):

Natalia S. Costa ◽

Márcia M. Silveira ◽

Luna N. Vargas ◽

Alexandre R. Caetano ◽

Rodolfo Rumpf ◽

...

Keyword(s):

Methylation Pattern ◽

Significant Difference ◽

Pcr Products ◽

H19 Gene ◽

Imprinting Control Region ◽

Low Efficiency ◽

Genomic Regions ◽

Methylation Patterns ◽

Exon 10

ABSTRACT: Somatic Cell Nuclear Transfer (SCNT-Cloning) is a promising technique in many areas and is based on genetically identical individuals. However, its efficiency is low. Studies suggest that the leading cause is inadequate epigenetic reprogramming. This study aimed to characterize the methylation pattern of the exon 10 regions of the IGF2 gene and the Imprinting Control Region (ICR) of the H19 gene in the placenta of cloned calves. For this study, female and male cloned calves presenting different phenotypes were used. Genomic DNA from these animals’ placenta was isolated, then treated with sodium bisulfite and amplified to the ICR/H19 and IGF2 loci. PCR products were cloned into competent bacteria and finally sequenced. A significant difference was found between controls and clones with healthy phenotypes for the ICR/H19 region. In this region, controls showed a hemimethylated pattern, as predicted in the literature due to this region has an imprinted control, while clones were showed less methylated. For the IGF2, no significant differences were found between controls and clones. These results suggest that different genomic regions in the genome may be independently reprogrammed and that failures in reprogramming the DNA methylation patterns of imprinted genes may be one of the causes of the low efficiency of SCNT.

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