scholarly journals Development of KASP Markers for Germplasm Characterization and Fingerprinting Identification of Broccoli in China

2020 ◽  
Author(s):  
Yusen Shen ◽  
Jiansheng Wang ◽  
Huifang Yu ◽  
Xiaoguang Sheng ◽  
Zhenqing Zhao ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Marker Assisted Selection ◽  
Genetic Relationships ◽  
Cost Effective ◽  
Germplasm Characterization ◽  
2D Barcode ◽  
New Type ◽  
Generation Sequencing ◽  
Kasp Markers ◽  
Selection Of

Abstract Background: Broccoli (Brassica oleracea var. italica) is a vegetable widely cultivated in China. Many new-type broccoli cultivars were bred and developed by Chinese breeders during the recent three decades. However, the broccoli cultivar nomenclature and detailed information of genetic relationships among broccoli germplasms are unclear. Results: The present study identified millions of SNPs by next-generation sequencing of 23 representative broccoli lines. Through several steps of selection, 100 SNPs were successfully converted into KASP markers, and used to evaluate the genetic diversity, genetic relationship, and population structure of 392 broccoli accessions, which represent the mainly broccoli breeding materials in China. The initial, introduced and improved accessions were well clustered, though some accessions were overlapped between groups, probably reflecting the fact that breeding activities led to genetic similarities. To make the KASP genotyping more efficient and cost-effective, 25 of the 100 KASPs were selected for fingerprinting of all accessions, and the 2D barcode contained fingerprinting information were generated for elite varieties. Conclusion: The KASP markers developed in this study provided an efficient way for germplasm characterization, DNA fingerprinting, seed purity identification, and marker-assisted selection of broccoli in China.

New type F lineage-related Tn1546and avanA/vanBtype vancomycin-resistantEnterococcus faeciumisolated from patients in Dammam, Saudi Arabia during 2006–2007

2012 ◽  
Vol 141 (5) ◽  
pp. 1109-1114 ◽  
Author(s):  
M. A. KHAN ◽  
M. SHORMAN ◽  
J. AL-TAWFIQ ◽  
J. P. HAYS
Keyword(s):  
Saudi Arabia ◽  
Antimicrobial Resistance ◽  
Clinical Setting ◽  
Genetic Relationships ◽  
Middle Eastern ◽  
Vancomycin Resistant Enterococci ◽  
Genetic Clusters ◽  
New Type ◽  
Vancomycin Resistant ◽  
Selection Of

SUMMARYKnowledge regarding vancomycin-resistant enterococci (VRE) from Middle Eastern countries is scarce. We therefore investigated the antimicrobial resistance profiles and genetic relationships of VREEnterococcus faeciumisolates obtained from patients attending the King Fahad Specialist Hospital, Dammam, during 2006–2007. The predominant VRE comprised 20vanB, fivevanAand onevanA/vanBtype isolates, which tended to fall into two genetic clusters that were identifiable phenotypically by their susceptibility to tetracycline. Multi-locus sequence typing of a random selection of isolates showed that they were part of clonal cluster 17, showing the importance of this genotype in nosocomial VRE infections in Saudi Arabia. Further analysis showed that four of thevanAgenotype isolates possessed a new type F Tn1546transposon, associated with IS1216Vand IS1251. Finally,E. faecium vanA/Bisolates are rarely reported in the clinical setting including in Saudi Arabia.

scholarly journals Genetic Diversity and Relationship of China’s Bergenia Germplasm Revealed by Intersimple Sequence Repeat Markers

2021 ◽  
pp. 1-7
Author(s):  
Xiuli Lv ◽  
Yuan Guan ◽  
Jian Wang ◽  
Yanwei Zhou ◽  
Qunlu Liu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Cluster Analysis ◽  
Phylogenetic Relationship ◽  
Theoretical Basis ◽  
Genetic Relationships ◽  
Issr Markers ◽  
Similarity Coefficient ◽  
Sequence Repeat ◽  
Relationship Of ◽  
Selection Of

To reveal the genetic diversity and genetic relationships of China’s Bergenia germplasm, 28 Bergenia accessions from different regions in China were analyzed by 24 intersimple sequence repeat (ISSR) markers. The results showed that 318 sites were amplified in all germplasm, including 307 polymorphic sites, and the percentage of polymorphic sites was 96.54%. Cluster analysis showed that the 28 accessions were divided into three categories, with a similarity coefficient of 0.5475. Bergenia purpurascens was clustered into one category; B. scopulosa was clustered into one category; and B. tianquaninsis, B. emeiensis, B. stracheyi, and B. crassifolia were clustered into one category. The results of the cluster analysis indicated that the 28 accessions were not completely classified by origin. Using the ISSR marker technique to analyze the phylogenetic relationship of Bergenia germplasm is helpful for identifying valuable resources and providing a theoretical basis for the selection of breeding parents.

scholarly journals Efficient curation of genebanks using next generation sequencing reveals substantial duplication of germplasm accessions

2018 ◽  
Author(s):  
Narinder Singh ◽  
Shuangye Wu ◽  
W. John Raupp ◽  
Sunish Sehgal ◽  
Sanu Arora ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Next Generation Sequencing ◽  
Crop Improvement ◽  
Aegilops Tauschii ◽  
Cost Effective ◽  
Ex Situ ◽  
Next Generation ◽  
Sequencing Platform ◽  
Efficient Management ◽  
Generation Sequencing

ABSTRACTGenebanks are valuable resources for crop improvement through the acquisition, ex-situ conservation and sharing of unique germplasm among plant breeders and geneticists. With over seven million existing accessions and increasing storage demands and costs, genebanks need efficient characterization and curation to make them more accessible and usable and to reduce operating costs, so that the crop improvement community can most effectively leverage this vast resource of untapped novel genetic diversity. However, the sharing and inconsistent documentation of germplasm often results in unintentionally duplicated collections with poor characterization and many identical accessions that can be hard or impossible to identify without passport information and unmatched accession identifiers. Here we demonstrate the use of genotypic information from these accessions using a cost-effective next generation sequencing platform to find and remove duplications. We identify and characterize over 50% duplicated accessions both within and across genebank collections of Aegilops tauschii, an important wild relative of wheat and source of genetic diversity for wheat improvement. We present a pipeline to identify and remove identical accessions within and among genebanks and curate globally unique accessions. We also show how this approach can also be applied to future collection efforts to avoid the accumulation of identical material. When coordinated across global genebanks, this approach will ultimately allow for cost effective and efficient management of germplasm and better stewarding of these valuable resources.

Genetic Relationships and Principal Component Analysis in Elite Chickpea (Cicer arietinum L.) Genotypes for Seed Yield and Its Component Traits

2020 ◽  
Author(s):  
D. K. Janghel ◽  
Krishan Kumar ◽  
S. S. Verma ◽  
A. K. Chhabra
Keyword(s):  
Genetic Diversity ◽  
Cicer Arietinum ◽  
Seed Yield ◽  
Genetic Relationships ◽  
Component Analysis ◽  
Yield Improvement ◽  
Cicer Arietinum L ◽  
Effective Selection ◽  
Component Traits ◽  
Selection Of

Background: Chickpea (Cicer arietinum L.) is the important Rabi season food legume crop ranked third after common bean and field pea. The degree and extent of trait variability, genetic relationship and genetic diversity in promising chickpea genotypes should be known for possible yield improvement. Realizing the importance of genetic relationships and genetic diversity in key economic traits, the present investigation envisaged to measure the genetic relationships in the yield component traits to make effective selection for yield improvement in chickpea breeding programme. Methods: The experimental material comprised of 60 chickpea genotypes (both Desi and Kabuli types), grown in RBD with three replications at Pulses Section of Department of Genetics and Plant Breeding, CCSHAU, Hisar during Rabi 2014-15. The data on 11 quantitative traits was analysed for ANOVA, correlation coefficient, path coefficient, regression and principle component analysis. Result: The present study has led the understanding of many inter-related traits involved in the genetic variation of chickpea seed yield. This would certainly provide guidelines for selection of parents as well as effective selection of promising chickpea genotypes, and also have paramount importance in formulating plant model for selection of segregating generations in chickpea breeding programmes for development of high yielding varieties.

Analysis of genetic diversity in a sweetpotato (Ipomoea batatas) germplasm collection using DNA amplification fingerprinting

Genome ◽  
1995 ◽  
Vol 38 (5) ◽  
pp. 938-945 ◽  
Author(s):  
Guohao He ◽  
C. S. Prakash ◽  
R. L. Jarret
Keyword(s):  
Genetic Diversity ◽  
Ipomoea Batatas ◽  
Genetic Relationships ◽  
Germplasm Collection ◽  
Dna Amplification ◽  
Taq Polymerase ◽  
Plant Introductions ◽  
Vinyl Polymer ◽  
High Level ◽  
Selection Of

A DNA amplification fingerprinting (DAF) approach was employed to develop individual-specific profiles and analyze genetic relationships among 73 plant introductions of sweetpotato (Ipomoea batatas (L.) Lam.) including unadapted lines from around the world and a few selected U.S.A. cultivars. Reliable and informative fingerprint profiles were obtained employing single octamer primers and Stoffel fragment Taq polymerase in the polymerase chain reaction, polyacrylamide-based vinyl polymer for electrophoresis, and silver staining to visualize the DNA. Using seven highly informative octamer primers, individual-specific DAF profiles were obtained for all accessions tested. The degree of polymorphism in the sweetpotato collection was very large, indicating a high level of genetic variability. Several accessions clustered together based on their geographic source. Most U.S.A. cultivars formed a separate cluster in the phenogram, while accessions from Papua New Guinea exhibited the highest genetic diversity. The wild species I. triloba and tetraploid I. batatas formed a group distinct from the cultivated sweetpotato. DAF appears to be useful in sweetpotato germplasm characterization and may be employed to identify duplicate accessions or for creation of core subsets. DAF data may also be useful for facilitating the selection of parents for a breeding program to ensure a broad genetic base.Key words: DNA fingerprinting, DNA markers, germplasm, genetic diversity, RAPD markers.

scholarly journals The use of iPBS markers to study the genetic diversity of known stock grape varieties

2020 ◽  
pp. 11-17
Author(s):  
D. S. Savenkova ◽  
V. O. Mindiarova ◽  
Yu. O. Filippova ◽  
S. A. Volkova ◽  
A. V. Мilovanov ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Dna Markers ◽  
Genetic Relationships ◽  
Common Stock ◽  
Plant Pests ◽  
The World ◽  
Different Types ◽  
The Common ◽  
Grape Varieties ◽  
Selection Of

The expansion of viticulture in the world is accompanied by the spread of diseases and plant pests. Phylloxera is one of those organisms causing enormous damage to the world’s viticulture. The discovery of the possibility of grafting varieties on stock has led to the development of the breeding of stock originating from North America. Currently, the active use of different types of molecular markers for the identification and study of the genetic diversity of grapes allows to more accurately and efficiently study the biological peculiarities and genetics of plants. Obtaining good reproducibility of the analysis results and revealing the polymorphism between varieties and clones when using different types of markers, you can further use this knowledge for breeding in the selection of crossed pairs. The aim of the study in the present article was to study the common stock grape varieties - hybrids of American species. The article presents a study of the five most famous stock grape varieties: Kober 5BB and 420-A, Paulsen 1103, 101-14 and Richter 57 to identify genetic relationships and polymorphism between samples, based on the use of IRAP and iPBS primers. We used thirteen selected DNA markers that generated a total of 308 polymorphic DNA bands with 54.95 % polymorphism. The effectiveness of iPBS markers was comparable or even more effective than the markers based on retrotransposons. As a result of research, differences and commonality between stocks were clearly demonstrated by both cluster analysis and PCoA analysis.

scholarly journals Application of molecular markers in livestock improvement

2010 ◽  
Vol 26 (3-4) ◽  
pp. 135-154 ◽  
Author(s):  
A. Teneva ◽  
M.P. Petrovic
Keyword(s):  
Genetic Diversity ◽  
Molecular Markers ◽  
Biochemical Markers ◽  
Marker Assisted Selection ◽  
Distance Estimation ◽  
Breeding Strategies ◽  
New Class ◽  
Recent Developments ◽  
Selection Of ◽  
Synteny Mapping

With recent developments in DNA technologies, a large number of genetic polymorphisms at DNA sequence level has been introduced over the last decades as named DNA-based markers. The discovery of new class of DNA profiling markers has facilitated the development of marker-based gene tags, mapbased cloning of livestock important genes, variability studies, phylogenetic analysis, synteny mapping, marker-assisted selection of favourable genotypes, etc. The most commonly used DNA-based markers have advantages over the traditional phenotypic and biochemical markers since they provide data that can be analyzed objectively. In this article the main applications of molecular markers in present-day breeding strategies for livestock improvement - parentage determination, genetic distance estimation, genetic diversity, gene mapping and marker-assisted selection have been reviewed.

Medical Literature Searches -How Many Bibliographic Databases are Needed for Sufficient Retrieval in Medical Topics?

1985 ◽  
Vol 24 (03) ◽  
pp. 163-165 ◽  
Author(s):  
K. John
Keyword(s):  
Medical Literature ◽  
Cost Effective ◽  
Medical Faculty ◽  
Bibliographic Databases ◽  
Literature Searches ◽  
Selection Of

SummaryAs many bibliographic services in medicine are offered, literature searches in eight databases at DIMDI were performed to find out which database is most important in medicine. The distribution of publications from members of the medical faculty of Frankfurt University was examined. No save prediction is possible as to which database will yield most articles. Overlapping from different databases is often rather low. The selection of an appropriate database mix for sufficient recall and in a cost-effective manner.is a task for an experienced searcher.

Selection of worm species and packing in a new type of biologic reactor for sludge reduction

2014 ◽  
Author(s):  
S.X. Li ◽  
Z.H. Wang ◽  
D.M. Li ◽  
W.W. Duan ◽  
S. Mei ◽  
...  
Keyword(s):  
Sludge Reduction ◽  
New Type ◽  
Selection Of

Teknologi Esktrasi dan Cara Pemisahannya untuk Mendapatkan Kembali Karotenoid dari Minyak Sawit : Suatu Tinjauan

2016 ◽  
Vol 9 (1) ◽  
pp. 80-95
Author(s):  
Agus Sudibyo ◽  
Sardjono Sardjono
Keyword(s):  
Vitamin A ◽  
Palm Oil ◽  
Beta Carotene ◽  
Cost Effective ◽  
Raw Material ◽  
Extraction And Separation ◽  
Molecular Product ◽  
Industrial Use ◽  
Palm Oil Mill ◽  
Selection Of

Crude palm oil (CPO)is the richest natural plant source of carotenoids in terms of retinol (pro-vitamin A) equivalent, whereas palm oil mill effluent (POME) is generated from palm oil industry that contains oil and carotenes that used to be treated before discharge. Carotenoids are importance in animals and humans for the purpose of the enhancement of immune response, conversion of vitamin A and scavenging of oxygen radicals. This component has different nutritional  functions and benefits to humaan health. The growing interest in the other natural sources of beta-carotene and growing awareness to prevent pollution has stimulated the industrial use of CPO and POME as a raw material for carotenoids extraction. Various technologies of extraction and separation have been developed in order to recover of carotenoids.This article reports on various technologies that have been developed in order to recover of carotenoids from being destroyed in commercial refining of palm oil and effects of some various treatments on the extraction end separation for carotenoid from palm oil and carotenoids concentration. Principally, there are different technologies, and there is one some future which is the use of solvent. Solvent plays important role  in the most technologiest, however the problem of solvents which are used is that they posses potentiaal fire health and environmental hazards. Hence selection of the  most safe, environmentally friendly and cost effective solvent is important to design of alternative extraction methods.Chemical molecular product design is one of the methods that are becoming more popular nowadays for finding solvent with the desired properties prior to experimental testing.ABSTRAKMinyak sawit kasar merupakan sumber karotenoid terkaya yang berasal dari tanaman sawit sebagai senyawa yang sama dengan retinol atau pro-vitamin A; sedangkan limbah pengolahan minyak sawit dihasilkan dari industri pengolahan minyak sawit yang berisi minyak dan karotene yang perlu diberi perlakuan terlebih dahulu sebelum dibuang. Karotenoid merupakan bahan penting yang diperlukan pada hewan dan manusia guna memperkuat tanggapan terhadap kekebalan, konversi ke vitamin A dan penangkapan gugus oksigen radikal. Dengan berkembangnya ketertarikan dalam mencari beta-karotene yang bersumber dari alam lain dan meningkatnya kesadaran untuk mencegah adanya pencemaran lingkungan, maka mendorong suatu industri untuk menggunakan CPO dan POME sebagai bahan baku untuk diekstrak karotenoidnya. Berbagai macam teknologi guna mengekstrak dan memisahkan karotenoid telah dikembangkan untuk mendapatkan kembali karotenoidnya. Makalah ini melaporkan dan membahas berbagai jenis teknologi yang telah dikembangkan guna mendapatkan kembali senyawa karotenoid dari kerusakan di dalam proses pemurnian minyak sawit secara komersial dan pengaruh beberapa perlakuan terhadap ekstrasi dan pemisahan karotenoid dari minyak sawit dan konsentrasi karotenoidnya. Pada prinsipnya, berbagai teknologi yang digunakan untuk mengekstrak dan memisahkan karotenoid terdapat perbedaan, dan terdapat salah satu teknologi yang digunakan untuk esktrasi dan pemisahan karotenoid adalah menggunakan bahan pelarut. Pelarut yang digunakan mempunyai peranan yang penting dalam teknologi ekstrasi; namun pelarut yang digunakan untuk mengekstrak tersebut mempunyai persoalan karena berpotensi mengganggu kesehatan dan membahayakan cemaran lingkungan. Oleh karena itu, pemilihan jenis teknologi yang aman, ramah terhadap lingkungan dan biaya yang efektif untuk penggunaan pelarut merupakan hal penting sebelum dilakukan desain metode/teknologi alternatif untuk esktrasi karotenoid. Pola produk molekuler kimia merupakan salah satu metode yang saat ini menjadi lebih populer untuk mencari pelarut dengan sifat-sifat yang dikehendaki sebelum diujicobakan. Kata kunci :    karotenoid, ekstrasi, pemisahan, teknologi, minyak sawit kasar, limbah industri pengolahan sawit.

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