The 172-kb genomic DNA region of the O. rufipogon yld1.1 locus

Comparative sequence analysis with O. sativa ssp. japonica and O. sativa ssp. indica

Beng Kah Song, Ingo Hein, Arnis Druka, Robbie Waugh, David Marshall, Kalaivani K. Nadarajah, Soon Joo Yap, R Wickneswari V Ratnam

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

Common wild rice (Oryza rufipogon) plays an important role by contributing to modern rice breeding. In this paper, we report the sequence and analysis of a 172-kb genomic DNA region of wild rice around the RM5 locus, which is associated with the yield QTL yld1.1. Comparative sequence analysis between orthologous RM5 regions from Oryza sativa ssp. japonica, O. sativa ssp. indica and O. rufipogon revealed a high level of conserved synteny in the content, homology, structure, orientation, and physical distance of all 14 predicted genes. Twelve of the putative genes were supported by matches to proteins with known function, whereas two were predicted by homology to rice and other plant expressed sequence tags or complementary DNAs. The remarkably high level of conservation found in coding, intronic and intergenic regions may indicate high evolutionary selection on the RM5 region. Although our analysis has not defined which gene(s) determine the yld1.1 phenotype, allelic variation and the insertion of transposable elements, among other nucleotide changes, represent potential variation responsible for the yield QTL. However, as suggested previously, two putative receptor-like protein kinase genes remain the key suspects for yld1.1.

Original languageEnglish
Pages (from-to)97-108
Number of pages12
JournalFunctional and Integrative Genomics
Volume9
Issue number1
DOIs
Publication statusPublished - 2009

Fingerprint

Sequence Analysis
DNA
Genes
Synteny
Intergenic DNA
DNA Transposable Elements
Expressed Sequence Tags
Oryza
Protein Kinases
Breeding
Nucleotides
Complementary DNA
Phenotype
Proteins

Keywords

  • Comparative sequence analysis
  • Microcolinearity
  • Oryza rufipogon
  • Yield QTL yld1.1

ASJC Scopus subject areas

  • Genetics

Cite this

The 172-kb genomic DNA region of the O. rufipogon yld1.1 locus : Comparative sequence analysis with O. sativa ssp. japonica and O. sativa ssp. indica. / Song, Beng Kah; Hein, Ingo; Druka, Arnis; Waugh, Robbie; Marshall, David; K. Nadarajah, Kalaivani; Yap, Soon Joo; V Ratnam, R Wickneswari.

In: Functional and Integrative Genomics, Vol. 9, No. 1, 2009, p. 97-108.

Research output: Contribution to journalArticle

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