A genomic walking method for screening sequence length polymorphism

2006 ◽  
Vol 6 (2) ◽  
pp. 563-567 ◽  
Author(s):  
JEAN-CLAUDE WALSER ◽  
MICHAEL B. EVGEN'EV ◽  
MARTIN E. FEDER
Keyword(s):  
Length Polymorphism ◽  
Sequence Length ◽  
Genomic Walking

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 New molecular markers for the distal end of the t-complex and their relationships to mutations affecting mouse development.

Genetics ◽  
1992 ◽  
Vol 131 (1) ◽  
pp. 175-182 ◽  
Author(s):  
T Ebersole ◽  
F Lai ◽  
K Artzt
Keyword(s):  
Molecular Markers ◽  
Mouse Chromosome ◽  
Length Polymorphism ◽  
Rflp Analysis ◽  
Chromosome 17 ◽  
Cosmid Library ◽  
Sequence Length ◽  
Mouse Development ◽  
T Complex ◽  
T Haplotype

Abstract Many mutations affecting mouse development have been mapped to the t-complex of mouse chromosome 17. We have obtained 17 cosmid clones as molecular markers for this region by screening a hamster-mouse chromosome 17 and 18 cell hybrid cosmid library with mouse-specific repetitive elements and mapping positive clones via t-haplotype vs. C3H restriction fragment length polymorphism (RFLP) analysis. Twelve of the clones mapping distal to Leh66B in t-haplotypes are described here. Using standard RFLP analysis or simple sequence length polymorphism between t-haplotypes, exceptional partial t-haplotypes and nested sets of inter-t-haplotype recombinants, five cosmids have been mapped in or around In(17)3 and seven in the most distal inversion In17(4). More precise mapping of four of the cosmids from In(17)4 shows that they will be useful in the molecular identification of some of the recessive lethals mapped to the t-complex: two cosmids map between H-2K and Crya-1, setting a distal limit in t-haplotypes for the position of the tw5 lethal, one is inseparable from the tw12 lethal, and one maps distal to tf near the t0(t6) lethal and cld.

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.

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