Species Boundaries and Molecular Markers for the Classification of 16SrI Phytoplasmas Inferred by Genome Analysis

In the present study, morphological and molecular markers (RAPD primers) were used to analyze the genetic diversity and genetic relationships among 21 accessions of Echinochloa spp. complex comprising the wild and cultivated species collected from Melghat and adjoining regions of Vidarbha, Maharashtra. The availability of diverse genetic resources is a prerequisite for genetic improvement of any crop including barnyard millet. A high degree of molecular diversity among the landraces was detected. Among the 21 genotypes, two major groups (A and B) were formed, at 67.28 % similarity, which clearly encompasses 15 accessions of E. frumentacea and 6 accessions of E. colona. Higher similarity was observed in accessions of E. frumentacea. The accessions IC 597322 and IC 597323 also IC 597302 and IC 597304 showed more than 94% similarity among themselves. The classification of genetic diversity has enabled clear-cut grouping of barnyard millet accessions into two morphological races (E. frumentacea and E. colona).

Download Full-text

Reexamining the Classification of Theobroma cacao L. Using Molecular Markers

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.119.5.1078 ◽

1994 ◽

Vol 119 (5) ◽

pp. 1073-1082 ◽

Cited By ~ 19

Author(s):

Antonio Figueira ◽

Jules Janick ◽

Morris Levy ◽

Peter Goldsbrough

Keyword(s):

Molecular Markers ◽

Theobroma Cacao ◽

Rapd Markers ◽

Continuous Variation ◽

Clear Distinction ◽

Species Separation ◽

Theobroma Cacao L ◽

Rdna Polymorphism

Genetic similarities among eight Theobroma and two Herrania species, including 29 genotypes of T. cacao, were estimated by rDNA polymorphism. A phenogram based on these genetic similarities significantly separated two clusters: one cluster included all Herrania and Theobroma species, except T. cacao, while the second contained 28 of 29 T. cacao genotypes. There was no clear distinction between Herrania and Theobroma species. Separation of 29 T. cacao genotypes, representing all races and various origins, had no congruency with the conventional classification into three horticultural races: Criollo, Forastero, and Trinitario. Genetic similarities in T. cacao, estimated with RAPD markers, indicated continuous variation among the generally similar but heterogeneous genotypes. The wild genotypes formed an outgroup distinct from the cultivated genotypes, a distinction supported by the rDNA data. The phenograms constructed from RAPD and rDNA data were not similar within the wild and cultivated cacao subsets.

Download Full-text

Identification of European and Japanese Larch and Their Interspecific Hybrid with Morphological Markers: Application to Young Seedlings

Silvae Genetica ◽

10.1515/sg-2006-0018 ◽

2006 ◽

Vol 55 (1-6) ◽

pp. 123-134 ◽

Cited By ~ 7

Author(s):

L. E. Pâques ◽

G. Philippe ◽

D. Prat

Keyword(s):

Molecular Markers ◽

Parental Species ◽

Correct Classification ◽

Morphological Markers ◽

Hybrid Features ◽

Pure Species ◽

Seed Orchards ◽

Linear Discriminant ◽

Non Destructive

Abstract Open-pollinated hybridisation seed orchards of European and Japanese larches produce mixed progenies combining a highly variable proportion of hybrids along with pure parental species. For several reasons, it is desirable to identify and to sort out hybrids from pure species at the seedling stage. Taxa identification of 1-2 yr-old seedlings was attempted using non-destructive assessment of several traits, including morphology, phenology, growth and architecture parameters. Two sets of progenies originating from 10 open-pollinated hybridisation seed orchards were used, relying in a first step on taxa identification of individual seedlings with diagnostic molecular markers. Based on 21 traits assessed, some clear trends in pure species and hybrid features were apparent but due to the large and overlapping ranges of taxa characteristics, no single parameter allowed unambiguous identification of taxa. Combination of traits through linear discriminant analysis made possible correct classification of 90.2% to 98.6% of individuals depending on the orchard although there were a few problematic orchards. Two traits appeared particularly pertinent for discriminating young plants taxa, namely 1st-yr leaf retention (marcescence) and the bark colour of 2nd-year shoot increments. Results were corroborated using progenies from several orchards and over two experimental periods.

Download Full-text

Molecular Markers

Advances in Environmental Engineering and Green Technologies - Molecular Plant Breeding and Genome Editing Tools for Crop Improvement ◽

10.4018/978-1-7998-4312-2.ch002 ◽

2021 ◽

pp. 16-52

Keyword(s):

Molecular Markers ◽

Nucleotide Sequence ◽

Genetic Analysis ◽

Plant Breeding ◽

Genome Analysis ◽

Morphological Difference ◽

Basic Principles ◽

Versatile Tool ◽

New Varieties ◽

Rate Of Success

Conventionally, establishment of relationship between the genotype and phenotype through genetic analysis was considered as key to success in plant breeding. The discovery of molecular markers has changed the entire scenario of genome analysis. Coinheritance of a gene of interest and a marker suggests that they are physically close on the chromosome. A marker must be polymorphic in nature for their identification and utilization. Such polymorphism can be detected at three levels: phenotype (morphological), difference in biomolecules (biochemical), or differences in the nucleotide sequence of DNA (molecular). These markers act as a versatile tool and find their importance in taxonomy, plant breeding, gene mapping, cultivar identification, and forensic science. They have several advantages over the conventional methods of plant breeding for developing new varieties with higher rate of success. This chapter covers the basic principles and applications of various types of markers with special emphasis on molecular markers.

Download Full-text

High-grade gliomas and molecular biology of neurosurgical oncology

Oxford Textbook of Neurological Surgery ◽

10.1093/med/9780198746706.003.0007 ◽

2019 ◽

pp. 89-106

Author(s):

Stephen J Price ◽

Harry Bulstrode ◽

Richard Mair

Keyword(s):

Molecular Markers ◽

Who Classification ◽

High Grade Glioma ◽

High Grade ◽

Optimal Management ◽

Who Grade ◽

Normal Human ◽

Who Grade Iii ◽

Grade Iii

The term high-grade glioma (HGG) encompasses a number of histological entities that are considered by the WHO Classification as WHO Grade III and IV tumours. They have traditionally been considered as having similar behaviour and had been treated in a similar manner but recent advances in our understanding of tumour biology have led to the identification of molecular markers that are now central to the classification of these tumours. Normal human cells develop into cancer cells through a stepwise accumulation of genomic and epigenomic alterations and this chapter considers the molecular markers of gliomas and explains their significance before going on to discuss the optimal management.

Download Full-text

SPInDel Analysis of the Non-Coding Regions of cpDNA as a More Useful Tool for the Identification of Rye (Poaceae: Secale) Species

International Journal of Molecular Sciences ◽

10.3390/ijms21249421 ◽

2020 ◽

Vol 21 (24) ◽

pp. 9421

Author(s):

Lidia Skuza ◽

Ewa Filip ◽

Izabela Szućko ◽

Jan Bocianowski

Keyword(s):

Mitochondrial Dna ◽

Molecular Markers ◽

Related Species ◽

Economic Importance ◽

Closely Related Species ◽

Coding Sequences ◽

Coding Regions ◽

Genomic Regions ◽

Tribe Triticeae

Secale is a small but very diverse genus from the tribe Triticeae (family Poaceae), which includes annual, perennial, self-pollinating and open-pollinating, cultivated, weedy and wild species of various phenotypes. Despite its high economic importance, classification of this genus, comprising 3–8 species, is inconsistent. This has resulted in significantly reduced progress in the breeding of rye which could be enriched with functional traits derived from wild rye species. Our previous research has suggested the utility of non-coding sequences of chloroplast and mitochondrial DNA in studies on closely related species of the genus Secale. Here we applied the SPInDel (Species Identification by Insertions/Deletions) approach, which targets hypervariable genomic regions containing multiple insertions/deletions (indels) and exhibiting extensive length variability. We analysed a total of 140 and 210 non-coding sequences from cpDNA and mtDNA, respectively. The resulting data highlight regions which may represent useful molecular markers with respect to closely related species of the genus Secale, however, we found the chloroplast genome to be more informative. These molecular markers include non-coding regions of chloroplast DNA: atpB-rbcL and trnT-trnL and non-coding regions of mitochondrial DNA: nad1B-nad1C and rrn5/rrn18. Our results demonstrate the utility of the SPInDel concept for the characterisation of Secale species.

Download Full-text

Using Color to Define Species Boundaries: Quantitative Analysis in the Orchard Oriole Complex Supports the Recognition of two Species

The Condor ◽

10.1093/condor/109.3.692 ◽

2007 ◽

Vol 109 (3) ◽

pp. 692-697 ◽

Cited By ~ 1

Author(s):

Lynna M. Kiere ◽

Christopher M. Hofmann ◽

Ian E. Tracy ◽

Thomas W. Cronin ◽

Jeff Leips ◽

...

Keyword(s):

Adult Male ◽

Spectral Characteristics ◽

Color Measurement ◽

Species Boundaries ◽

Plumage Color ◽

Separate Species ◽

Reflectance Spectrometry ◽

Ideal System ◽

Molecular Studies

Abstract Abstract. The recent divergence of Orchard (Icterus spurius spurius) and Fuertes's Orioles (I. s. fuertesi) makes them an ideal system for investigating species boundaries. Orchard and Fuertes's Orioles differ in several respects. They have distinct breeding ranges—Fuertes's Orioles breed in eastern coastal Mexico, whereas Orchard Orioles breed throughout eastern and central North America—and differ in plumage coloration, with adult male Orchard Orioles appearing “chestnut” and Fuertes's Orioles “ochre.” However, no detailed quantitative color analyses have been conducted. To characterize these differences we quantitatively measured plumage color using reflectance spectrometry. The colored plumages of adult male Orchard and Fuertes's Orioles have unique spectral characteristics, with no color overlap between them. Combined with life history differences and previous molecular studies, these findings support the classification of Orchard and Fuertes's Orioles as separate species. Additionally, this study demonstrates the utility of quantitative color measurement as a tool for examining species boundaries.

Download Full-text

Clinical importance of molecular markers of adult diffuse glioma

Practical Neurology ◽

10.1136/practneurol-2018-002116 ◽

2019 ◽

Vol 19 (5) ◽

pp. 412-416 ◽

Cited By ~ 1

Author(s):

Emanuela Molinari ◽

Olimpia E Curran ◽

Robin Grant

Keyword(s):

Molecular Markers ◽

Molecular Genetic ◽

Clinical Importance ◽

Response To Treatment ◽

Low Grade ◽

Diffuse Glioma ◽

Wild Type ◽

Genetic Classification ◽

Cns Tumours

In 2016, the WHO incorporated molecular markers, in addition to histology, into the diagnostic classification of central nervous system (CNS) tumours. This improves diagnostic accuracy and prognostication: oligo-astrocytoma no longer exists as a clinical entity; isocitrate dehydrogenase (IDH) mutant and 1p/19q co-deleted oligodendroglioma is a smaller category with better prognosis; IDH wild-type ‘low-grade’ glioma has a much poorer prognosis; and glioblastoma is divided into IDH mutant (with an better prognosis than pre-2016 glioblastoma) and IDH wild type (with a poorer prognosis). Previous advice based on phenotype alone will change with respect to median survival, best management plan and response to treatment. There are implications for routine neuropathology reporting and future trial design. Cases that are difficult to classify may need more advanced molecular genetic classification through DNA methylation-based classification of CNS tumours (Heidelberg Classifier). We discuss the practical implications.

Download Full-text