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Plant Molecular Biology

, Volume 60, Issue 1, pp 87–94 | Cite as

Fine Mapping and in silico Isolation of the EUI1 Gene Controlling Upper Internode Elongation in Rice

  • Hongli Ma
  • Shubiao Zhang
  • Lan Ji
  • Hongbo Zhu
  • Shulan Yang
  • Xuanjun FangEmail author
  • Rencui YangEmail author
Article

Abstract

Upper internode elongation in rice is an important agronomic trait. Well-known mutants with an elongated uppermost internode (eui) are important germplasms for developing unsheathed-panicle male-sterile lines in hybrid rice breeding. We finely mapped the eui1 gene and identified its candidate gene using in silico analysis based on previous research work and rice genomic sequence data. The rice eui1 gene was mapped to two overlapping BAC clones, OSJNBa0095J22 and OSJNBb0099O15, between the markers AC40 and AC46, that were 0.64 cM apart and spanned approximately 152 kb. A simple sequence repeat (SSR) marker AC41 that cosegregated with eui1 was located in an intron of a putative cytochrome P450-related gene. In silico analysis suggested that this encoded the cytochrome CYP714D1. Allelic sequencing confirmed that EUI1 corresponded to this P450 gene. A gamma ray-induced eui1 mutant carried a deletion in exon II of the EUI1 gene, and resulted in a frame-shift deletion that produced a truncated polypeptide. We conclude that the EUI1 gene controlling the upper internode elongation in rice is 9804 bp long, and comprises two exons and one intron. The length of the cDNA is 1931 bp containing a 1734 bp ORF, a 110 bp 5′-UTR and a 87 bp 3′-UTR. The ORF encodes an unknown 577 amino acid functional protein, that appears to be a member of the cytochrome P450 family.

Keywords

elongated uppermost internode (euiEUI1 gene; fine mapping in silico cloning rice (Oryza sativa L) 

Abbreviations

BAC

bacteria artificial chromosome

bp

base pair

cDNA

complementary DNA

cM

centi Morgan

dNTPs

deoxyribonucleotide triphosphates

EST

expressed sequence tags

eui

elongated uppermost internode

NCBI

national center of biotechnology information

ORF

open reading frame

PA64 eS1

Pei’ai 64 eS1

PCR

polymerase chain reaction

PDB

protein data bank

SSR

simple sequence repeat

STS

sequence tagged site

UTR

untranslated region

XQZ eB1

Xieqingzao eB1

ZH15

Zhonghua 15

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Copyright information

© Springer 2006

Authors and Affiliations

  1. 1.Institute of Genetics and Crop BreedingFujian Agriculture and Forestry UniversityFuzhouChina
  2. 2.Hainan Institute of Tropical Agricultural ResourcesSanyaChina

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