Microsatellite polymorphism for molecular characterization of pomelo (Citrus maxima) accessions from Indonesia

Abstract. Susandarini R, Subandiyah S, Daryono BS, Rugayah. 2020. Microsatellite polymorphism for molecular characterization of pomelo (Citrus maxima) accessions from Indonesia. Biodiversitas 21: 2390-2395. Citrus maxima (Burm.) Merr. (pomelo) as a minor fruit crop deserve attention on its phenotypic and genotypic variability to avoid the risk of extinction. Previous study showed that pomelo from Indonesia has high morphological variability, and thus it is interesting to explore its genotypic variability using molecular markers. Microsatellite is a molecular marker widely used in Citrus taxonomy studies. This study aimed at revealing microsatellite polymorphism and its potential application in cultivar characterization of C .maxima. Eighty accessions of C. maxima consisting of registered cultivars and landraces from Indonesia were used in this study. Analysis of microsatellite sequences from genomic DNA amplified using DY296883 primer showed that C. maxima microsatellite has high polymorphism in the form of repeat length variation of (GA)n, ranging from (GA)7 to (GA)19. This study proved the existence of high genotypic variability in C. maxima, and confirmed the role of microsatellite as a useful molecular marker for uncovering variability at intraspecific level. Observation of the microsatellite polymorphisms indicated that variability of (GA)n can be used to distinguish some pomelo cultivars.

Download Full-text

Molecular Characterization of the Dwarf53 Gene Homolog in Dasypyrum Villosum

Plants ◽

10.3390/plants9020186 ◽

2020 ◽

Vol 9 (2) ◽

pp. 186

Author(s):

Mikhail Bazhenov ◽

Anastasiya Chernook ◽

Pavel Kroupin ◽

Gennady Karlov ◽

Mikhail Divashuk

Keyword(s):

Molecular Marker ◽

Molecular Characterization ◽

Common Wheat ◽

Physiological Response ◽

Stem Growth ◽

Dasypyrum Villosum ◽

Physiological Processes ◽

Monosomic Addition ◽

Wheat Lines

The Dwarf53 (D53) gene, first studied in rice, encodes a protein that acts as a repressor of the physiological response of plants to strigolactones—substances that regulate the activity of axillary buds, stem growth, branching of roots and other physiological processes. In this work, we isolated and sequenced the homolog of the D53 gene in several accessions of the wild grass Dasypyrum villosum of different geographical origins, resulting in the discovery of large allelic variety. A molecular marker was also created that allows us to differentiate the D. villosum D53 gene from common wheat genes. Using this marker and monosomic addition, substitution and translocation wheat lines carrying the known D. villosum chromosomes, the D53 gene was localized on the long arm of the 5V chromosome.

Download Full-text

Caracterización molecular de Heliconia sp. Utilizando la técnica RAPD.

Revista ECIPeru ◽

10.33017/reveciperu2011.0051/ ◽

2019 ◽

pp. 230-233

Keyword(s):

Molecular Marker ◽

Molecular Characterization ◽

Genomic Dna ◽

Average Quality ◽

Expected Heterozygosity ◽

Apartado Postal ◽

Pcr Products ◽

Version 2.0

Caracterización molecular de Heliconia sp. Utilizando la técnica RAPD. Molecular characterization of Heliconia sp. using RAPD technique. Freddy Gutierrez, Roberson Ramirez, Pedro Adrianzén, Marianela Cobos, Sergio Pinedo, Sixto Imán, Juan Castro Centro de Investigaciones de Recursos Naturales de la Amazonia (CIRNA), 496S. Universidad Nacional de la Amazonia Peruana-UNAP. Apartado postal 496S Facultad de Ciencias Biológicas. Instituto Nacional de Innovación Agraria (INIA), C.P. 609. DOI: https://doi.org/10.33017/RevECIPeru2011.0051/ RESUMEN Este trabajo se realizó entre los meses de Julio a Setiembre del 2010, con el objetivo de caracterizar molecularmente a la especie Heliconia sp. Utilizando el marcador molecular RAPD. Para esto, se realizó la purificación del ADN genómico de la especie en estudio obteniéndose buenos resultados en cuanto a la calidad y la cantidad del ADN purificado, el cual fue verificado con los métodos electroforético y espectrofotométrico, la cantidad de ADN obtenido en promedio fue de 92.8 ng/ μl, asimismo el ratio de calidad promedio fue de 2.2. Para la amplificación de los productos de la PCR se empleó el iniciador MT3R, obteniéndose mucho polimorfismo. Los productos de la PCR tuvieron tamaños de 750 pb hasta 2050 pb. En cuanto a la caracterización molecular, se realizó un dendograma (UPGMA) utilizando el programa estadístico NTSIS versión 2.0. Asimismo se obtuvo la formación de 2 grupos (clusters) y 2 fugas donde se observó la aparición de “aparentes duplicados” en algunos de ellos, es decir, que comparten el mismo patrón genético con un 100% de similitud. Además el valor de la heterocigosidad esperada fue de 0.14, valor relativamente bajo, posiblemente al tipo de reproducción que posee este género, el cual es la autogamica. Descriptores: ADN genómico, Heliconia sp, electroforético, espectrofotométrico. ABSTRACT This work was carried out between the months of July to September 2010 with the objective of molecular characterization of the species heliconia sp using the RAPD molecular marker. For this, we performed the purification of genomic DNA, of the species under study with good results in terms of quality and quantity of purified DNA, which was verified by electrophoretic and spectrophometric methods, the amount of DNA obtained was on average 92.8 ng/ l, also the ratio of average quality was 2.2. For amplification of PCR products was used MT3R initiator, obtaining much polymorphism. PCR products had sizes of 750 bp to 2050 bp. as for the molecular characterization, we performed a dendrogram (UPGMA) using the statiscal sofwar version 2.0 NTSIS. It also obtained the formation of 2 groups (clusters) and 2 leaks where we the appearance of “apparent duplicates” in some of them, ie they share the same genetic patern with 100% similarity. Also, the value of expected heterozygosity was 0.14, relatively low value, possibly the type of reproduction that has this kind, which is the autogamous. Keywords: genomic DNA, Heliconia sp, electrophoretic, spectrophometric.

Download Full-text

Molecular characterization of the Rs-Rf 1 gene and molecular marker-assisted development of elite radish (Raphanus sativus L.) CMS lines with a functional marker for fertility restoration

Molecular Breeding ◽

10.1007/s11032-012-9756-1 ◽

2012 ◽

Vol 30 (4) ◽

pp. 1727-1736 ◽

Cited By ~ 1

Author(s):

Xinju Sun ◽

Yang Liu ◽

Liangju Wang ◽

Xianwen Zhu ◽

Yiqin Gong ◽

...

Keyword(s):

Molecular Marker ◽

Molecular Characterization ◽

Raphanus Sativus ◽

Fertility Restoration ◽

Functional Marker ◽

Raphanus Sativus L

Download Full-text

Molecular characterization of Porcine circovirus type 2 isolates from post-weaning multisystemic wasting syndrome-affected and non-affected pigs

Journal of General Virology ◽

10.1099/vir.0.19536-0 ◽

2004 ◽

Vol 85 (2) ◽

pp. 293-304 ◽

Cited By ~ 84

Author(s):

Claire de Boisséson ◽

Véronique Béven ◽

Laurent Bigarré ◽

Richard Thiéry ◽

Nicolas Rose ◽

...

Keyword(s):

Molecular Marker ◽

Molecular Characterization ◽

Porcine Circovirus Type ◽

Nucleotide Identity ◽

Porcine Circovirus ◽

Wasting Syndrome ◽

New Genotype ◽

Complete Sequences

Porcine circovirus type 2 (PCV2) is recognized as a primary cause in post-weaning multisystemic wasting syndrome (PMWS). In this study, both PCV1 and PCV2 types were studied in pigs originating from PMWS-affected (+) and non-affected (−) herds from Brittany. PCV2 was identified by PCR in 100 % of animals from PMWS(+) herds and in 76 % from PMWS(−) herds, while PCV1 was not detected. The complete sequences of 38 PCV2 isolates were determined and 23 new variants were identified, displaying between 94·6 and 99·9 % nucleotide identity with one another. Although highly related to all the PCV2 sequences available in databases, the isolates from France gathered in a distinct subcluster. Compared with the 13 PCV2 from PMWS(+) farms, the 10 PMWS(−) sequences exhibited a slightly higher variability. No viral molecular marker specific to a pathogenic state could be identified, even by including other PCV2 variants isolated from PMWS-suffering animals from other countries. We concluded that the PMWS outbreaks in Brittany are most likely not due to the emergence of a new genotype of circovirus.

Download Full-text