Molecular screening of traditional rice varieties using tsv1-linked simple sequence repeat markers

2019 ◽  
Vol 157 (03) ◽  
pp. 211-216
Author(s):  
X. G. I. Caguiat
Keyword(s):  
Molecular Markers ◽  
Simple Sequence Repeat ◽  
Abiotic Stress Tolerance ◽  
Sequence Repeat ◽  
Biotic And Abiotic Stress ◽  
Rice Varieties ◽  
Simple Sequence Repeat Markers ◽  
Breeding Programmes ◽  
Simple Sequence ◽  
Traditional Rice

AbstractGenebanks offer vast amounts of traditional germplasm with potential sources of novel genes against biotic and abiotic stresses. In order to utilize the germplasm in rice breeding programmes, there should be a fast screening approach such as the use of molecular markers. Thus, the current study aimed to evaluate the use of tsv1 resistance-linked simple sequence repeat markers (SSR) for the preliminary screening of Philippine traditional rice germplasm against rice tungro spherical virus (RTSV). The tsv1 resistance-linked SSR markers consisted of two to four repeat motifs with 5–24 base repeats. Expected sizes ranged from 123 to 465 base pairs (bp) with polymorphism information content ranging from 0.23 to 0.73. Genetic analysis showed six major clusters at 50%: Clusters A, B and C had individual accessions, Cluster D had three accessions, Cluster E had 55 and Cluster F had 42 accessions. The study showed the germplasm with alleles linked to tsv1 but should be validated in the future with induced screening. In general, the material consisted of selected germplasm showing the presence of alleles linked to the tsv1 gene. These rice accessions could be a source of resistance to RTSV following further validation. Furthermore, molecular markers provide a useful tool to accelerate the screening of genetic resources for biotic and abiotic stress tolerance.

scholarly journals Simple Sequence Repeat (SSR) Markers for Raspberry and Blackberry

HortScience ◽  
2004 ◽  
Vol 39 (4) ◽  
pp. 785D-785 ◽  
Author(s):  
Kim S. Lewers* ◽  
Eric T. Stafne ◽  
John R. Clark ◽  
Courtney A. Weber ◽  
Julie Graham
Keyword(s):  
Molecular Markers ◽  
Simple Sequence Repeat ◽  
Mapping Population ◽  
Black Raspberry ◽  
Sequence Repeat ◽  
Red Raspberry ◽  
Simple Sequence Repeat Markers ◽  
Cultivar Development ◽  
Pcr Product ◽  
Simple Sequence

Some raspberry and blackberry breeders are interested in using molecular markers to assist with selection. Simple Sequence Repeat markers (SSRs) have many advantages, and SSRs developed from one species can sometimes be used with related species. Six SSRs derived from the weed R. alceifolius, and 74 SSRs from R. idaeus red raspberry `Glen Moy' were tested on R. idaeus red raspberry selection NY322 from Cornell Univ., R. occidentalis `Jewel' black raspberry, Rubus spp. blackberry `Arapaho', and blackberry selection APF-12 from the Univ. of Arkansas. The two raspberry genotypes are parents of an interspecific mapping population segregating for primocane fruiting and other traits. The two blackberry genotypes are parents of a population segregating for primocane fruiting and thornlessness. Of the six R. alceifolius SSRs, two amplified a product from all genotypes. Of the 74 red raspberry SSRs, 56 (74%) amplified a product from NY322, 39 (53%) amplified a product from `Jewel', and 24 (32%) amplified a product from blackberry. Of the 56 SSRs that amplified a product from NY322, 17 failed to amplify a product from `Jewel' and, therefore, detected polymorphisms between the parents of this mapping population. Twice as many detected polymorphisms of this type between blackberry and red raspberry, since 33 SSRs amplified a product from NY322, but neither of the blackberry genotypes. Differences in PCR product sizes from these genotypes reveal additional polymorphisms. Rubus is among the most diverse genera in the plant kingdom, so it is not surprising that only 19 of the 74 raspberry-derived SSRs amplified a product from all four of the genotypes tested. These SSRs will be useful in interspecific mapping and cultivar development.

scholarly journals Molecular Characterization of Moroccan Fig Germplasm Using Intersimple Sequence Repeat and Simple Sequence Repeat Markers To Establish A Reference Collection

HortScience ◽  
2005 ◽  
Vol 40 (1) ◽  
pp. 29-32 ◽  
Author(s):  
B. Khadari ◽  
A. Oukabli ◽  
M. Ater ◽  
A. Mamouni ◽  
J.P. Roger ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Molecular Characterization ◽  
Molecular Analysis ◽  
Simple Sequence Repeat ◽  
Germplasm Collection ◽  
Sequence Repeat ◽  
Simple Sequence Repeat Markers ◽  
Reference Collection ◽  
Simple Sequence

A study was conducted to identify genotypes present in a Moroccan fig germplasm collection and provide the first database for a reference collection in northern Morocco. In total, 75 fig samples were analyzed using 8 intersimple sequence repeat primers and 6 simple sequence repeat loci. From these samples, we identified 72 fig genotypes. In genetically heterogeneous cultivars, genotypes under the same denomination were distinguished by both molecular markers and pomological traits. Molecular analysis was used to classify the germplasm into 46 well-defined cultivars and 6 caprifig trees. The remaining genotypes were not clearly identified due to three cases of mislabeling and four cases of homonymy. No evidence was found for the occurrence of geographically widespread genotypes.

Identification of New Sources of Rust Resistance in Cowpea (Vigna Unguiculata L. Walp) Germplasm Using Simple Sequence Repeat Markers

2019 ◽  
Author(s):  
A. T. Asare ◽  
T. A. Mensah ◽  
S. M.A. Tagoe ◽  
D. K.A. Asante
Keyword(s):  
Fungal Pathogen ◽  
Simple Sequence Repeat ◽  
Rust Resistance ◽  
Gene Diversity ◽  
Yield Losses ◽  
Sequence Repeat ◽  
Simple Sequence Repeat Markers ◽  
Breeding Programmes ◽  
Moderate Resistance ◽  
Simple Sequence

The demand for resistance cowpea to rust infection has currently increased due to considerable yield losses caused by the fungal pathogen. The study assessed available cowpea genotypes for rust resistance using simple sequence repeat (SSR) markers. Out of 100 cowpea genotypes screened, 97% showed presence of the markers whilst 3% showed absence of the markers. Among the cowpea were 72% resistance, 16% moderate resistance and 9% low resistance to rust. The markers revealed mean high allele frequency (0.86) and low gene diversity (0.24) and polymorphism information content (0.21) among the cowpea genotypes. The markers co-inherited with mean regression value greater than 0.1. There was no clear pattern of clustering among the cowpea genotypes. The cowpea genotypes with rust resistance traits could serve as good sources of germplasm for cultivation or resilient genes with rust target in breeding programmes to improve the crop.

scholarly journals Optimization of the choice of molecular markers for identification of commercially used rice varieties in India using rapid DNA extraction protocol

2016 ◽  
Vol 8 (2) ◽  
pp. 1028-1034
Author(s):  
Pravas Ranjan Kole ◽  
Rajeev Singh Rana ◽  
Kangila Venkataramana Bhat
Keyword(s):  
Molecular Marker ◽  
Simple Sequence Repeat ◽  
Cultivar Identification ◽  
Genetic Identification ◽  
Sequence Repeat ◽  
Genetic Purity ◽  
Traditional Practice ◽  
Rice Varieties ◽  
Simple Sequence Repeat Markers ◽  
Simple Sequence

The present investigating aimed at the development of molecular marker for cultivar identification and genetic purity assessment. A total of four SSR markers and six SRAP primer were developed for the identification of sixteen different commercial varieties of rice. Traditional practice like grow-out-test based on morphological traits is time consuming and sometimes environmentally influenced. After development of molecular marker, it is using as an alternative to grow –out –test because of its rapid, accurate detection. We have assessed the potential of simple sequence repeat and sequence-related amplified polymorphism markers in distinguishing rice varieties and four simple sequence repeat markers namely CT-14, CT-25 CT XY-1 and ATC-3 and six sequence-related amplified polymorphism markers primers could be clearly distinguished sixteen commercially cultivar rice varieties. In addition to single markers, it’s better to try with marker combinations, which were amenable for PCR and capable of distinguishing the varieties. Larger differences for each crop were found between cultivers from different seed companies than within the same company. These DNA markers can provide an easier and faster reliable genetic identification of rice cultivars.

scholarly journals Genotyping of Peach and Nectarine Cultivars with SSR and SRAP Molecular Markers

2004 ◽  
Vol 129 (2) ◽  
pp. 204-210 ◽  
Author(s):  
Riaz Ahmad ◽  
Dan Potter ◽  
Stephen M. Southwick
Keyword(s):  
Molecular Markers ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Sweet Cherry ◽  
Prunus Persica ◽  
Sequence Repeat ◽  
Srap Markers ◽  
Upgma Cluster Analysis ◽  
Commercially Important ◽  
Simple Sequence

Simple sequence repeat (SSR) and sequence related amplified polymorphism (SRAP) molecular markers were evaluated for detecting intraspecific variation in 38 commercially important peach and nectarine (Prunus persica) cultivars. Out of the 20 SSR primer pairs 17 were previously developed in sweet cherry and three in peach. The number of putative alleles revealed by SSR primer pairs ranged from one to five showing a low level of genetic variability among these cultivars. The average number of alleles per locus was 2.2. About 76% of cherry primers produced amplification products in peach and nectarine, showing a congeneric relationship within Prunus species. Only nine cultivars out of the 38 cultivars could be uniquely identified by the SSR markers. For SRAP, the number of fragments produced was highly variable, ranging from 10 to 33 with an average of 21.8 per primer combination. Ten primer combinations resulted in 49 polymorphic fragments in this closely related set of peaches and nectarines. Thirty out of the 38 peach and nectarine cultivars were identified by unique SRAP fingerprints. UPGMA Cluster analysis based on the SSR and SRAP polymorphic fragments was performed; the relationships inferred are discussed with reference to the pomological characteristics and pedigree of these cultivars. The results indicated that SSR and SRAP markers can be used to distinguish the genetically very close peach and nectarine cultivars as a complement to traditional pomological studies. However, for fingerprinting, SRAP markers appear to be much more effective, quicker and less expensive to develop than are SSR markers.

scholarly journals Assessment of the Genetic Diversity of Rice Germplasms Characterized by Black-Purple and Red Pericarp Color Using Simple Sequence Repeat Markers

Plants ◽  
2019 ◽  
Vol 8 (11) ◽  
pp. 471
Author(s):  
Jae-Ryoung Park ◽  
Won-Tae Yang ◽  
Yong-Sham Kwon ◽  
Hyeon-Nam Kim ◽  
Kyung-Min Kim ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Germplasm Collection ◽  
Group Method ◽  
Sequence Repeat ◽  
Rice Varieties ◽  
Red Pericarp ◽  
Simple Sequence ◽  
Colored Rice

The assessment of the genetic diversity within germplasm collections can be accomplished using simple sequence repeat (SSR) markers and association mapping techniques. The present study was conducted to evaluate the genetic diversity of a colored rice germplasm collection containing 376 black-purple rice samples and 172 red pericarp samples, conserved by Dong-A University. There were 600 pairs of SSR primers screened against 11 rice varieties. Sixteen informative primer pairs were selected, having high polymorphism information content (PIC) values, which were then used to assess the genetic diversity within the collection. A total of 409 polymorphic amplified fragments were obtained using the 16 SSR markers. The number of alleles per locus ranged from 11 to 47, with an average of 25.6. The average PIC value was 0.913, ranging from 0.855 to 0.964. Four hundred and nine SSR loci were used to calculate Jaccard’s distance coefficients, using the unweighted pair-group method with arithmetic mean cluster analysis. These accessions were separated into several distinctive groups corresponding to their morphology. The results provided valuable information for the colored rice breeding program and showed the importance of protecting germplasm resources and the molecular markers that can be derived from them.

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