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 Nadarajah, Soon-Joo Yap, Wickneswari Ratnam

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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
JournalFunct Integr Genomics
Volume9
Issue number1
DOIs
Publication statusPrint publication - Jul 2008
Externally publishedYes

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sequence analysis
Oryza rufipogon
genomics
wild rice
loci
DNA
quantitative trait loci
Oryza sativa
genes
rice
complementary DNA
expressed sequence tags
intergenic DNA
transposons
protein kinases
nucleotides
phenotype
receptors
breeding
proteins

Cite this

Song, Beng-Kah ; Hein, Ingo ; Druka, Arnis ; Waugh, Robbie ; Marshall, David ; Nadarajah, Kalaivani ; Yap, Soon-Joo ; Ratnam, Wickneswari. / 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. In: Funct Integr Genomics. 2008 ; Vol. 9, No. 1. pp. 97-108.
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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.",
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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; Nadarajah, Kalaivani; Yap, Soon-Joo; Ratnam, Wickneswari.

In: Funct Integr Genomics, Vol. 9, No. 1, 07.2008, p. 97-108.

Research output: Contribution to journalArticleResearchpeer-review

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