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PMID: 16607031 Published · ppublish English Comparative Study Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

A comparative genomics strategy for targeted discovery of single-nucleotide polymorphisms and conserved-noncoding sequences in orphan crops.

Plant physiology ·Vol. 140 ·No. 4 ·2006-04-00 ·Pages 1183-91

Feltus FA, Singh HP, Lohithaswa HC, Schulze SR, Silva TD, Paterson AH

Abstract

Completed genome sequences provide templates for the design of genome analysis tools in orphan species lacking sequence information. To demonstrate this principle, we designed 384 PCR primer pairs to conserved exonic regions flanking introns, using Sorghum/Pennisetum expressed sequence tag alignments to the Oryza genome. Conserved-intron scanning primers (CISPs) amplified single-copy loci at 37% to 80% success rates in taxa that sample much of the approximately 50-million years of Poaceae divergence. While the conserved nature of exons fostered cross-taxon amplification, the lesser evolutionary constraints on introns enhanced single-nucleotide polymorphism detection. For example, in eight rice (Oryza sativa) genotypes, polymorphism averaged 12.1 per kb in introns but only 3.6 per kb in exons. Curiously, among 124 CISPs evaluated across Oryza, Sorghum, Pennisetum, Cynodon, Eragrostis, Zea, Triticum, and Hordeum, 23 (18.5%) seemed to be subject to rigid intron size constraints that were independent of per-nucleotide DNA sequence variation. Furthermore, we identified 487 conserved-noncoding sequence motifs in 129 CISP loci. A large CISP set (6,062 primer pairs, amplifying introns from 1,676 genes) designed using an automated pipeline showed generally higher abundance in recombinogenic than in nonrecombinogenic regions of the rice genome, thus providing relatively even distribution along genetic maps. CISPs are an effective means to explore poorly characterized genomes for both DNA polymorphism and noncoding sequence conservation on a genome-wide or candidate gene basis, and also provide anchor points for comparative genomics across a diverse range of species.

MeSH Terms
Base Sequence Chromosomes, Plant/genetics Conserved Sequence Crops, Agricultural/genetics Expressed Sequence Tags Genomics/methods Genotype Introns Molecular Sequence Data Poaceae/genetics Polymorphism, Single Nucleotide Sequence Alignment Untranslated Regions
Chemicals
Untranslated Regions
Authors & Affiliations
6 authors, click to expand affiliations / ORCID
Feltus F A
Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA.
Singh H P
Lohithaswa H C
Schulze S R
Silva T D
Paterson A H
References (32)
32 references, click to expand
  1. Methods and statistics for combining motif match scores.
    J Comput Biol. 1998 Summer;5(2):211-21 PMID: 9672829
  2. Conserved noncoding sequences in the grasses.
    Genome Res. 2003 Sep;13(9):2030-41 PMID: 12952874
  3. Convergent evolution of perenniality in rice and sorghum.
    Proc Natl Acad Sci U S A. 2003 Apr 1;100(7):4050-4 PMID: 12642667
  4. Convergent domestication of cereal crops by independent mutations at corresponding genetic Loci.
    Science. 1995 Sep 22;269(5231):1714-8 PMID: 17821643
  5. Human-zebrafish non-coding conserved elements act in vivo to regulate transcription.
    Nucleic Acids Res. 2005 Sep 22;33(17):5437-45 PMID: 16179648
  6. The genome sequence and structure of rice chromosome 1.
    Nature. 2002 Nov 21;420(6913):312-6 PMID: 12447438
  7. A draft sequence of the rice genome (Oryza sativa L. ssp. indica).
    Science. 2002 Apr 5;296(5565):79-92 PMID: 11935017
  8. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana.
    Nature. 2000 Dec 14;408(6814):796-815 PMID: 11130711
  9. Contrasting population structure from nuclear intron sequences and mtDNA of humpback whales.
    Mol Biol Evol. 1994 May;11(3):426-35 PMID: 7912407
  10. The correlation between intron length and recombination in drosophila. Dynamic equilibrium between mutational and selective forces.
    Genetics. 2000 Nov;156(3):1175-90 PMID: 11063693
  11. Highly conserved non-coding sequences are associated with vertebrate development.
    PLoS Biol. 2005 Jan;3(1):e7 PMID: 15630479
  12. Dwarf8 polymorphisms associate with variation in flowering time.
    Nat Genet. 2001 Jul;28(3):286-9 PMID: 11431702
  13. Comparative anchor tagged sequences (CATS) for integrative mapping of mammalian genomes.
    Nat Genet. 1997 Jan;15(1):47-56 PMID: 8988168
  14. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica).
    Science. 2002 Apr 5;296(5565):92-100 PMID: 11935018
  15. A general approach to single-nucleotide polymorphism discovery.
    Nat Genet. 1999 Dec;23(4):452-6 PMID: 10581034
  16. Comparative genetics in the grasses.
    Proc Natl Acad Sci U S A. 1998 Mar 3;95(5):1971-4 PMID: 9482816
  17. Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat.
    Plant Mol Biol. 2002 Mar-Apr;48(5-6):501-10 PMID: 11999831
  18. EMBOSS opens up sequence analysis. European Molecular Biology Open Software Suite.
    Brief Bioinform. 2002 Mar;3(1):87-91 PMID: 12002227
  19. Multiple sequence alignment with the Clustal series of programs.
    Nucleic Acids Res. 2003 Jul 1;31(13):3497-500 PMID: 12824352
  20. Toward a cytological characterization of the rice genome.
    Genome Res. 2001 Dec;11(12):2133-41 PMID: 11731505
  21. The genetic colinearity of rice and other cereals on the basis of genomic sequence analysis.
    Curr Opin Plant Biol. 2003 Apr;6(2):128-33 PMID: 12667868
  22. Comparative analysis of QTLs affecting plant height and maturity across the Poaceae, in reference to an interspecific sorghum population.
    Genetics. 1995 Sep;141(1):391-411 PMID: 8536986
  23. Intron evolution as a population-genetic process.
    Proc Natl Acad Sci U S A. 2002 Apr 30;99(9):6118-23 PMID: 11983904
  24. EC_oligos: automated and whole-genome primer design for exons within one or between two genomes.
    Bioinformatics. 2004 Dec 12;20(18):3668-9 PMID: 15271776
  25. Structure and evolution of cereal genomes.
    Curr Opin Genet Dev. 2003 Dec;13(6):644-50 PMID: 14638328
  26. Sequence and analysis of rice chromosome 4.
    Nature. 2002 Nov 21;420(6913):316-20 PMID: 12447439
  27. Intron size and natural selection.
    Nature. 1999 Sep 23;401(6751):344 PMID: 10517631
  28. Complete structure of the alpha B-crystallin gene: conservation of the exon-intron distribution in the two nonlinked alpha-crystallin genes.
    Proc Natl Acad Sci U S A. 1985 Sep;82(17):5819-23 PMID: 3862098
  29. Base-calling of automated sequencer traces using phred. I. Accuracy assessment.
    Genome Res. 1998 Mar;8(3):175-85 PMID: 9521921
  30. Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics.
    Proc Natl Acad Sci U S A. 2004 Jun 29;101(26):9903-8 PMID: 15161969
  31. An integrated genetic map and a new set of simple sequence repeat markers for pearl millet, Pennisetum glaucum.
    Theor Appl Genet. 2004 Nov;109(7):1485-93 PMID: 15322756
  32. An SNP resource for rice genetics and breeding based on subspecies indica and japonica genome alignments.
    Genome Res. 2004 Sep;14(9):1812-9 PMID: 15342564
Article Info
Journal
Plant physiology
Abbr.
Plant Physiol
ISSN
0032-0889
DOI
10.1104/pp.105.074203
Published
2006-04-00
Pages
1183-91
Language
English
Region
United States
NLM ID
0401224
PMCID
PMC1435799
Subset
IM
Databases
GENBANK
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