scholarly journals Selective Amplification of Start codon Polymorphic Loci (SASPL): a new PCR-based molecular marker in olive

Plant Omics ◽  
2017 ◽  
Vol 10 (02) ◽  
pp. 64-77 ◽  
Author(s):  
Alsamman M. Alsamman ◽  
◽  
S. S. Adawy ◽  
S. D. Ibrahim ◽  
B. A. Hussein ◽  
...  
Keyword(s):  
Molecular Marker ◽  
Start Codon ◽  
Selective Amplification ◽  
Polymorphic Loci ◽  
Pcr Based Molecular Marker

scholarly journals Amplified fragment length polymorphisms (AFLP's)

2017 ◽  
pp. 119 ◽  
Author(s):  
June Simpson
Keyword(s):  
Molecular Marker ◽  
Restriction Fragment ◽  
Restriction Enzyme ◽  
Fragment Length ◽  
Polymorphic Loci ◽  
Length Polymorphisms ◽  
Amplified Fragment Length Polymorphisms ◽  
Pcr Conditions

AFLP is a combination restriction fragment/PCR molecular marker technique which detects polymorphisms due to changes at or in the vicinity of restriction enzyme sites. The technique detects multiple polymorphic loci throughout the genome and may be used for fingerprinting and mapping purposes. The main advantages of the method are the consistency and reliability of the technique due to stringent PCR conditions and the ability to rapidly detect many polymorphic loci.

Development of a PCR-Based Molecular Marker to Select for Nematode Resistance in Peanut

Crop Science ◽  
2007 ◽  
Vol 47 (2) ◽  
pp. 841-845 ◽  
Author(s):  
Y. Chu ◽  
C. C. Holbrook ◽  
P. Timper ◽  
P. Ozias-Akins
Keyword(s):  
Molecular Marker ◽  
Nematode Resistance ◽  
Pcr Based Molecular Marker

scholarly journals Development and Application of a PCR-Based Molecular Marker for the Identification of High Temperature Tolerant Cabbage (Brassica oleracea var. capitata) Genotypes

Agronomy ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 116
Author(s):  
Hayoung Song ◽  
Myungjin Lee ◽  
Byung-Ho Hwang ◽  
Ching-Tack Han ◽  
Jong-In Park ◽  
...  
Keyword(s):  
High Temperature ◽  
Molecular Marker ◽  
Brassica Oleracea ◽  
Inbred Line ◽  
Genetic Basis ◽  
Soft Rot ◽  
Inbred Lines ◽  
Rna Seq ◽  
F2 Population ◽  
Pcr Based Molecular Marker

Global warming accelerates the development of high temperature (HT)- and high humidity (HH)-tolerant varieties. This is further facilitated by the identification of HTHH-tolerant genes and the development of molecular markers based on these genes. To identify genes involved in HTHH tolerance in cabbage (Brassica oleracea var. capitata), we performed RNA-seq analysis of two inbred lines, BN1 (HTHH-tolerant) and BN2 (HTHH-susceptible), and selected trehalose 6- phosphate phosphatase I-2 (BoTPPI-2) as one of the HTHH-tolerant-associated genes. We also developed a segregating F2 population from a cross between BN1 and BN2. RNA-seq results showed that BoTPPI-2 transcript levels were high in the HTHH-tolerant inbred line BN1, but not detectable in the HTHH-susceptible inbred line BN2. The expression pattern of BoTPPI-2 was not related to the expression of heat shock-related genes. Soft rot resistance, used as an indicator of HTHH tolerance, was higher in BN1 than in BN2. F2 individuals similar to BN1 with respect to phenotype appeared to be HTHH-tolerant, whereas BN2-types were susceptible to HTHH. Analysis of the genomic DNA revealed the presence of a long terminal repeat (LTR; ca. 4.6 kb) in the ninth intron of the BoTPPI-2_BN2 allele, thereby suppressing its transcription and exhibiting HTHH phenotype. Except for the LTR insertion, the sequence of BoTPPI-2_BN2 was almost identical to that of BoTPPI-2_BN1. On the basis of the LTR and BoTPPI-2 sequences, we developed a molecular marker to identify HTHH-tolerant genotypes and validated its efficiency using F2 individuals, inbred lines, and cultivars from diverse sources. The marker explained the genetic basis of HTHH tolerance in at least 80%, but not 100%, of the cabbage genotypes. Thus, additional markers associated with HTHH tolerance are needed for perfect selection.

scholarly journals Genetic diversity and structure of Capsicum annuum as revealed by start codon targeted and directed amplified minisatellite DNA markers

Hereditas ◽  
2019 ◽  
Vol 156 (1) ◽  
Author(s):  
David O. Igwe ◽  
Celestine A. Afiukwa ◽  
George Acquaah ◽  
George N. Ude
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Capsicum Annuum ◽  
Genetic Parameters ◽  
Polymorphic Information Content ◽  
Start Codon ◽  
Minisatellite Dna ◽  
Cross River ◽  
Polymorphic Loci ◽  
Genetic Diversity And Structure

Abstract Background Identification of high resolving DNA-based markers is of paramount importance to unlock the potential of genetic diversity and selection of unique accessions of Capsicum annuum L., within Cross River and Ebonyi States of Nigeria, for breeding and conservation. Therefore, we comparatively explored the effectiveness of start codon targeted (SCoT) and directed amplified minisatellite DNA (DAMD) markers for diversity analysis of the accessions. Fifteen accessions were collected for DNA extraction and amplifications with the markers. Results Dendrograms from SCoT and DAMD categorized the accessions into five and three genetic groups, respectively, while the principal component analysis identified five genetic clusters, each from the markers. The average values of allele, gene diversity and polymorphic information content detected with SCoT and DAMD demonstrate that the two markers were effective and efficient, especially, SCoT in genetic diversity study of the accessions of pepper. Number of polymorphic loci (NPL) and percentage polymorphic loci (PPL) from SCoT (NPL = 64, PPL = 80.00–95.73%) and DAMD (NPL = 56, PPL = 53.33–86.67%) were high, but higher in SCoT markers. Other effective genetic parameters (effective number of alleles, Nei’s genetic diversity and Shannon’s information indices) identified with the two marker systems elucidated the allelic richness, rich genetic diversity within the populations and informative nature of the markers, especially SCoT. The intraspecific genetic diversity, interspecific genetic diversity, and coefficient of differentiation obtained with SCoT and DAMD further exposed the genetic structure with more genetic divergence within than among the populations of the accessions. Estimate of gene flow from the SCoT markers was 3.8375 and 0.6.2042 for the DAMD markers. The estimate of gene flow values from the markers indicated extensiveness with SCoT (Nm = 3.8375) and extremely extensive with DAMD (Nm = 6.2042) among the populations. Conclusion This study shows that SCoT markers may be more useful and informative than DAMD in measuring genetic diversity and differentiation of the accessions of the genus Capsicum. Genetic parameters obtained with SCoT showed that the accessions from Cross River were more genetically diverse than the ones from Ebonyi State. Therefore, SCoT may be a preferred marker in evaluating genetic diversity for improvement and conservation of this spicy crop, C. capsicum.

PCR-based molecular marker for the Bdv2 Thinopyrum intermedium source of barley yellow dwarf virus resistance in wheat

2001 ◽  
Vol 52 (12) ◽  
pp. 1383 ◽  
Author(s):  
P. Stoutjesdijk ◽  
S. J. Kammholz ◽  
S. Kleven ◽  
S. Matsay ◽  
P. M. Banks ◽  
...  
Keyword(s):  
Molecular Marker ◽  
Barley Yellow Dwarf Virus ◽  
Wheat Breeding ◽  
Addition Line ◽  
Thinopyrum Intermedium ◽  
Barley Yellow Dwarf ◽  
Pcr Product ◽  
Partial Amphiploid ◽  
Yellow Dwarf Virus ◽  
Pcr Based Molecular Marker

Because of the importance of BYDV in wheat production worldwide, and given the difficulties of bioassaying for resistance, a molecular marker was developed for the resistance known as Bdv2 that originates on the long arm of chromosome 7Ai1 of Thinopyrum intermedium. This resistance was identified in a partial amphiploid line TAF46, a disomic addition line to wheat (L1), a telosomic addition line (7Ai1 L), and a series of recombinants and translocations. A RAPD (random amplified polymeric DNA) marker for the resistant germplasm was cloned and sequenced, and primers were designed against that sequence to produce a sequence characterised amplified region (SCAR) marker. A single PCR product is produced only with genotypes carrying the resistance from any of the available recombinants. The cloned sequence, recommended primers, and PCR protocols are described. The usefulness of the marker has been demonstrated for following Bdv2 in segregating wheat breeding germplasm, with the imminent release of a BYDV-resistant cultivar.

scholarly journals Genetic Diversity Analysis of Tomato (Solanum lycopersicum L.) with Morphological, Cytological, and Molecular Markers under Heat Stress

Horticulturae ◽  
2021 ◽  
Vol 7 (4) ◽  
pp. 65
Author(s):  
Ahmed B. EL-Mansy ◽  
Diaa Abd El-Moneim ◽  
Salha Mesfer ALshamrani ◽  
Fatmah Ahmed Alsafhi ◽  
Mohamed A. Abdein ◽  
...  
Keyword(s):  
Heat Stress ◽  
Molecular Marker ◽  
Solanum Lycopersicum ◽  
High Temperatures ◽  
Random Amplified Polymorphic Dna ◽  
Resolving Power ◽  
Start Codon ◽  
Molecular Characteristics ◽  
Solanum Lycopersicum L ◽  
Karyotype Asymmetry

Tomatoes are usually consumed daily in the human diet. High temperatures reduce the number of tomato yields per year. Heat stress has been considered one of the most prominent causes of alterations in morphological and molecular characteristics in crops that decrease normal growth, production, and yield in diverse plants, including tomatoes (Solanum lycopersicum L.). In this study, we evaluated six tomato lines, namely G1, G2, G3, G4, G5, and G6, at morphological, molecular, and cytological levels under heat stress. The average results of two seasons (2018 and 2019) clarified that the G6, G1, and G2 lines recorded the highest flowering values, as well as some fruit and vegetative growth traits. Furthermore, G6 and G2 had the maximum number of fruits/plant, whereas G2 and G1 produced the highest yield/plant under high temperatures. The number of chromosomes in all lines was 2n = 24, except for G5, in which the number was 2n = 26, whereas chromosome sizes were small, ranging from 323.08 to 464.48 µm. The G1 cultivar was a symmetrical cultivar (primitive), having the highest total form percentage (TF%) and symmetry index (Syi) values and the minimum karyotype asymmetry index (ASK) value, whereas G4 was asymmetrical (advanced). Molecular marker analysis demonstrated that intersimple sequence repeat (ISSR) primers 49A, HB-14, 49A, 49B, and 89B presented the highest values for polymorphism percentage P%, marker index (MI), effective multiplex ratio (EMR), and polymorphism information content (PIC), respectively. In contrast, OP-A3, OP-B3, SCoT 2, and SCoT 12 primers showed the highest PIC, EMR, MI, P%, and resolving power (Rp) values across the studied random amplified polymorphic DNA (RAPD) and start codon-targeted (SCoT) primers. Moreover, ISSR revealed the highest number of unique specific markers (6), followed by RAPD (4) and SCoT (3) markers. Cluster analysis of combined cytological data and data relating to molecular marker attributes separated the G1, G2, and G3 lines into one group, whereas the other lines were clustered in another group. On the whole, the application of combined analysis using morphological, cytological, and molecular genetics techniques could be considered to provide suitable parameters for studying the evolution of the genetic divergence between the studied tomato lines.

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