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Applications of single nucleotide polymorphisms in crop genetics.
Rafalski A. Rafalski A. Curr Opin Plant Biol. 2002 Apr;5(2):94-100. doi: 10.1016/s1369-5266(02)00240-6. Curr Opin Plant Biol. 2002. PMID: 11856602 Review.
SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines.
Ching A, Caldwell KS, Jung M, Dolan M, Smith OS, Tingey S, Morgante M, Rafalski AJ. Ching A, et al. Among authors: rafalski aj. BMC Genet. 2002 Oct 7;3:19. doi: 10.1186/1471-2156-3-19. Epub 2002 Oct 7. BMC Genet. 2002. PMID: 12366868 Free PMC article.
A small number (2-8) of distinct and highly diverse haplotypes can be distinguished at all loci examined. Within genes, SNP loci comprising the haplotypes are in linkage disequilibrium with each other. CONCLUSIONS: No decline of linkage disequilibrium within a few h
A small number (2-8) of distinct and highly diverse haplotypes can be distinguished at all loci examined. Within genes, SNP loci comp
The complete sequence of 340 kb of DNA around the rice Adh1-adh2 region reveals interrupted colinearity with maize chromosome 4.
Tarchini R, Biddle P, Wineland R, Tingey S, Rafalski A. Tarchini R, et al. Among authors: rafalski a. Plant Cell. 2000 Mar;12(3):381-91. doi: 10.1105/tpc.12.3.381. Plant Cell. 2000. PMID: 10715324 Free PMC article.
This gene mapped to maize chromosome 1, indicating a possible translocation of Adh1 after the evolutionary divergence leading to maize and sorghum. ...Seven retrotransposons and eight transposons were identified in this rice segment, including a Tc1/Mariner-like ele …
This gene mapped to maize chromosome 1, indicating a possible translocation of Adh1 after the evolutionary divergence leading to maiz …
High-throughput identification, database storage and analysis of SNPs in EST sequences.
Useche FJ, Gao G, Harafey M, Rafalski A. Useche FJ, et al. Among authors: rafalski a. Genome Inform. 2001;12:194-203. Genome Inform. 2001. PMID: 11791238
It uses a Bayesian engine for SNP detection (PolyBayes), selects relevant polymorphism information which is then uploaded into a database. We detected 2439 SNPs and 822 insertion deletions (INDELs) with a PolyBayes probability higher than 0.99 on the public s …
It uses a Bayesian engine for SNP detection (PolyBayes), selects relevant polymorphism information which is then uploaded into a
Whole genome scan detects an allelic variant of fad2 associated with increased oleic acid levels in maize.
Beló A, Zheng P, Luck S, Shen B, Meyer DJ, Li B, Tingey S, Rafalski A. Beló A, et al. Among authors: rafalski a. Mol Genet Genomics. 2008 Jan;279(1):1-10. doi: 10.1007/s00438-007-0289-y. Epub 2007 Oct 13. Mol Genet Genomics. 2008. PMID: 17934760
A single locus with major effect on oleic acid was mapped between 380 and 384 cM in the IBM2 neighbors genetic map on chromosome 4 and confirmed in a biparental population. ...This is the first report of the use of a high resolution whole genome scan associat
A single locus with major effect on oleic acid was mapped between 380 and 384 cM in the IBM2 neighbors genetic map on chromosome 4 an
Origins, genetic organization and transcription of a family of non-autonomous helitron elements in maize.
Brunner S, Pea G, Rafalski A. Brunner S, et al. Among authors: rafalski a. Plant J. 2005 Sep;43(6):799-810. doi: 10.1111/j.1365-313X.2005.02497.x. Plant J. 2005. PMID: 16146520
One of these elements, the Mo17-specific helitron on chromosome 1 (bin 1.07), is transcriptionally active, probably as a result of insertion in the vicinity of a promoter. ...During the course of evolution, transcribed helitrons containing multiple gene fragments ma …
One of these elements, the Mo17-specific helitron on chromosome 1 (bin 1.07), is transcriptionally active, probably as a result of in …
Evolution of DNA sequence nonhomologies among maize inbreds.
Brunner S, Fengler K, Morgante M, Tingey S, Rafalski A. Brunner S, et al. Among authors: rafalski a. Plant Cell. 2005 Feb;17(2):343-60. doi: 10.1105/tpc.104.025627. Epub 2005 Jan 19. Plant Cell. 2005. PMID: 15659640 Free PMC article.
By contrast, miniature inverted terminal repeats (MITEs) occur at a similar frequency in the shared and nonshared fractions. ...Frequently, retroelement insertions create a different sequence environment adjacent to conserved genes....
By contrast, miniature inverted terminal repeats (MITEs) occur at a similar frequency in the shared and nonshared fractions. ...Frequ …
Linkage disequilibrium and sequence diversity in a 500-kbp region around the adh1 locus in elite maize germplasm.
Jung M, Ching A, Bhattramakki D, Dolan M, Tingey S, Morgante M, Rafalski A. Jung M, et al. Among authors: rafalski a. Theor Appl Genet. 2004 Aug;109(4):681-9. doi: 10.1007/s00122-004-1695-8. Theor Appl Genet. 2004. PMID: 15300382
A set of 32 was chosen to represent most of the genetic diversity in the cultivated North American elite maize breeding pool. ...The presence of this exceptionally long segment of high LD may be suggestive of selection acting on one of the genes in the vicinity of adh1 or
A set of 32 was chosen to represent most of the genetic diversity in the cultivated North American elite maize breeding pool. ...The
Contrasting effects of selection on sequence diversity and linkage disequilibrium at two phytoene synthase loci.
Palaisa KA, Morgante M, Williams M, Rafalski A. Palaisa KA, et al. Among authors: rafalski a. Plant Cell. 2003 Aug;15(8):1795-806. doi: 10.1105/tpc.012526. Plant Cell. 2003. PMID: 12897253 Free PMC article.
We investigated the effects of human selection for yellow endosperm color, representing increased carotenoid content, on two maize genes, the Y1 phytoene synthase and PSY2, a putative second phytoene synthase. ...The strong sequence haplotype conservation within yellows at …
We investigated the effects of human selection for yellow endosperm color, representing increased carotenoid content, on two maize genes, th …
Rapid genetic mapping of ESTs using SNP pyrosequencing and indel analysis.
Ching A, Rafalski A. Ching A, et al. Among authors: rafalski a. Cell Mol Biol Lett. 2002;7(2B):803-10. Cell Mol Biol Lett. 2002. PMID: 12378241
The genotyping of SNPs is performed by pyrosequencing, a sequencing-by-synthesis method that has been used successfully in SNP diagnostics. SNP analysis of up to 96 samples, a number required to produce meaningful genetic segregation data, can be rapidly accomplishe …
The genotyping of SNPs is performed by pyrosequencing, a sequencing-by-synthesis method that has been used successfully in SNP diagno …
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