Development of microsatellite markers and characterization of simple sequence length polymorphism (SSLP) in rice (Oryza sativa L.)

1996 ◽  
Vol 252 (5) ◽  
pp. 597-607 ◽  
Author(s):  
O. Panaud ◽  
X. Chen ◽  
S. R. McCouch
Keyword(s):  
Oryza Sativa ◽  
Microsatellite Markers ◽  
Length Polymorphism ◽  
Oryza Sativa L ◽  
Simple Sequence Length Polymorphism ◽  
Sequence Length ◽  
Simple Sequence

Comparative evaluation of within-cultivar variation of rice (Oryza sativa L.) using microsatellite and RFLP markers

Genome ◽  
1997 ◽  
Vol 40 (3) ◽  
pp. 370-378 ◽  
Author(s):  
Johnson O. Olufowote ◽  
Yunbi Xu ◽  
Xiuli Chen ◽  
Mak Goto ◽  
Susan R. McCouch ◽  
...  
Keyword(s):  
Microsatellite Markers ◽  
Length Polymorphism ◽  
Oryza Sativa L ◽  
Simple Sequence Length Polymorphism ◽  
Sequence Length ◽  
Rflp Markers ◽  
Rice Varieties ◽  
Germplasm Collections ◽  
Cultivar Variation ◽  
Simple Sequence

The objective of this study was to determine an efficient way of detecting within-cultivar variation in rice varieties obtained from national and international germplasm collections. Seventy-one rice cultivars were evaluated for within-cultivar variation using a combination of phenotypic, RFLP, and microsatellite or simple sequence length polymorphism (SSLP). Variation between individuals within an accession and between duplicate accessions within a cultivar was detected even in cultivars that had been purified by phenotypic evaluation. Landrace cultivars were more heterogeneous and displayed a larger number of both RFLP and SSLP alleles than did modern cultivars. Microsatellite markers detected a greater number of alleles and were able to discriminate between even closely related individuals more efficiently than RFLPs. Some microsatellite markers were more informative than others for assessing genetic diversity. Single markers revealed 5.6–61.1% of the total variation detected by the 10 SSLP markers. Some marker combinations were complementary, providing more information than others. Several combinations of 4 SSLP markers detected as much as 94% of the total within-cultivar variation detected by the 10 SSLP markers. These results suggest that the use of four well-chosen microsatellites would be an efficient method for evaluating the heterogeneity of rice accessions.Key words: genetic variation, RFLP, microsatellite markers, simple sequence length polymorphism, SSLP, rice.

Nuclear- and chloroplast-microsatellite variation in A-genome species of rice

Genome ◽  
2001 ◽  
Vol 44 (4) ◽  
pp. 658-666 ◽  
Author(s):  
T Ishii ◽  
Y Xu ◽  
S R McCouch
Keyword(s):  
Oryza Sativa ◽  
Length Polymorphism ◽  
Allelic Diversity ◽  
Sequence Length ◽  
Chloroplast Microsatellites ◽  
Microsatellite Variation ◽  
Chloroplast Microsatellite ◽  
Genome Species ◽  
A Genome ◽  
Simple Sequence

Simple sequence length polymorphism analysis was carried out to reveal microsatellite variation and to clarify the phylogenetic relationships among A-genome species of rice. Total DNA from 29 cultivars (23 Oryza sativa and 6 O. glaberrima) and 30 accessions of wild A-genome species (12 O. rufipogon, 5 O. glumaepatula, 2 O. longistaminata, 6 O. meridionalis, and 5 O. barthii) was used as a template for PCR to detect 24 nuclear and 10 chloroplast microsatellite loci. Microsatellite allelic diversity was examined based on amplified banding patterns. Microsatellites amplified clearly in all 59 accessions, with an average of 18.4 alleles per locus. The polymorphism information content (PIC) value ranged from 0.85 to 0.94, with an average of 0.89. At the species level, high average PIC values were observed in O. sativa (0.79) and O. rufipogon (0.80). For chloroplast microsatellites, the average number of alleles per locus and the average PIC value were 2.9 and 0.38, respectively. While the magnitude of diversity was much greater for nuclear microsatellites than for chloroplast microsatellites, they showed parallel patterns of differentiation for each taxonomic group. Using the ratio of common alleles (estimated as size of amplified fragments) as a similarity index, the average percentages of common microsatellite alleles were calculated between taxa. For both nuclear and chloroplast microsatellites, O. sativa showed the highest similarity values to O. rufipogon, and O. glaberrima was most similar to O. barthii. These data support previous evidence that these cultivars originated from the corresponding wild ancestral species.Key words: simple sequence length polymorphism, SSLP, microsatellite marker, rice, Oryza sativa, allelic diversity, phylogenetics.

scholarly journals Validation of Simple Sequence Length Polymorphism Regions of Commonly Used Mouse Strains for Marker Assisted Speed Congenics Screening

2015 ◽  
Vol 2015 ◽  
pp. 1-17 ◽  
Author(s):  
Channabasavaiah B. Gurumurthy ◽  
Poonam S. Joshi ◽  
Scott G. Kurz ◽  
Masato Ohtsuka ◽  
Rolen M. Quadros ◽  
...  
Keyword(s):  
Length Polymorphism ◽  
Snp Array ◽  
Genetically Engineered ◽  
Simple Sequence Length Polymorphism ◽  
Sequence Length ◽  
Mouse Strains ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Sophisticated Equipment ◽  
Simple Sequence

Marker assisted speed congenics technique is commonly used to facilitate backcrossing of mouse strains in nearly half the time it normally takes otherwise. Traditionally, the technique is performed by analyzing PCR amplified regions of simple sequence length polymorphism (SSLP) markers between the recipient and donor strains: offspring with the highest number of markers showing the recipient genome across all chromosomes is chosen for the next generation. Although there are well-defined panels of SSLP makers established between certain pairs of mice strains, they are incomplete for most strains. The availability of well-established marker sets for speed congenic screens would enable the scientific community to transfer mutations across strain backgrounds. In this study, we tested the suitability of over 400 SSLP marker sets among 10 mouse strains commonly used for generating genetically engineered models. The panel of markers presented here can readily identify the specified strains and will be quite useful in marker assisted speed congenic screens. Moreover, unlike newer single nucleotide polymorphism (SNP) array methods which require sophisticated equipment, the SSLP markers panel described here only uses PCR and agarose gel electrophoresis of amplified products; therefore it can be performed in most research laboratories.

scholarly journals Morphomolecular Characterization of Local Boro Rice (Oryza Sativa L.) Germplasm

2016 ◽  
Vol 29 (2) ◽  
pp. 01-09
Author(s):  
T. Halder ◽  
M. E. Hoque ◽  
M. M. Islam ◽  
L. Ali ◽  
A. K. Chowdhury
Keyword(s):  
Oryza Sativa ◽  
Morphological Traits ◽  
Oryza Sativa L ◽  
Polymorphic Information Content ◽  
Growth Duration ◽  
Allele Number ◽  
Simple Sequence ◽  
1000 Grain Weight ◽  
Boro Rice

An investigation was carried out to analysis the genetic diversity of 12 Bangladeshi local Boro rice (Oryza sativa L.) germplasm using morphological traits and molecular markers. Eight morphological traits (viz., days to 50 percent flowering, growth duration, plant height, filled grain/panicle, 1000 grain weight and grain yield) and eight Simple Sequence Repeat (SSR) markers were used for this analysis. The plant morphological traits exhibited more variation among the genotypes tested. Several traits were found to be significantly positive in correlation coefficient analysis and thus those traits can be considered stable as demonstrated by their coefficient of variability. A set of eight SSR primer pairs was used for molecular characterization resulting 49 alleles, where average of allele number was 6.13. The polymorphic information content (PIC) values ranged from 0.67 (RM1) to 0.86 (RM314) with an average of 0.76. The highest PIC value (0.86) was obtained for RM314 which also gave maximum alleles. The PIC value revealed that RM314 was the best marker for 12 genotypes tested. The cluster analysis based on UPGMA system grouped 12 genotypes into four clusters.

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