Features of the expressed sequences revealed by a large-scale analysis of ESTs from a normalized cDNA library of the elite indica rice cultivar Minghui 63

Jianwei - Zhang, Qi Feng, Caoqing Jin, Deyun Qiu, Lida Zhang, Kabin Xie, Dejun Yuan, Bin Han, Qifa Zhang, Shiping Wang

Research output: Contribution to journalArticle

37 Citations (Scopus)

Abstract

The indica subspecies of cultivated rice occupies the largest area of rice production in the world. However, a systematic analysis of cDNA sequences from the indica subspecies has not been performed. The aim of the present study was to collect and analyze the expressed sequence tags (ESTs) of indica rice on a large scale. A total of 39 208 raw sequences were generated from a normalized cDNA library prepared by use of 15 different tissues of the indica cultivar Minghui 63. After trimming, processing and analysis, 17 835 unique sequences were obtained, each of which presumably represents a unique gene. Of these sequences, 2663 were novel, and at least 70 were indica specific. Comparison of the Minghui 63 sequences with the ESTs/full-length cDNAs in GenBank revealed a large number of deletion/insertion/substitution (DIS) at both the inter- and intra-subspecific levels. The overall number of polymorphisms in the expressed sequences was higher in the inter-subspecific comparisons than in the intra-subspecific comparisons. However, the extent of DIS-based polymorphism was highly variable among different rice varieties. In total, 15 726 unique sequences, including 697 novel sequences, were assigned to regions where large numbers of quantitative trait loci (QTLs) for agronomic traits had been detected previously. These results may be useful for developing new molecular markers for genetic mapping, detecting allelic polymorphisms associated with phenotypic variations between rice varieties, and facilitating QTL cloning by providing the starting points for candidate-gene identification.

Original languageEnglish (US)
Pages (from-to)772-780
Number of pages9
JournalPlant Journal
Volume42
Issue number5
DOIs
StatePublished - Jun 2005
Externally publishedYes

Fingerprint

Expressed Sequence Tags
expressed sequence tags
Gene Library
cDNA libraries
rice
cultivars
Quantitative Trait Loci
genetic polymorphism
quantitative trait loci
Complementary DNA
Nucleic Acid Databases
Genetic Association Studies
phenotypic variation
agronomic traits
chromosome mapping
Sequence Analysis
Organism Cloning
Molecular Biology
molecular cloning
genes

Keywords

  • Expressed sequence tag
  • Indel
  • Indica rice
  • Mutator-like transposase
  • Quantitative trait locus
  • Single nucleotide polymorphism

ASJC Scopus subject areas

  • Plant Science

Cite this

Features of the expressed sequences revealed by a large-scale analysis of ESTs from a normalized cDNA library of the elite indica rice cultivar Minghui 63. / Zhang, Jianwei -; Feng, Qi; Jin, Caoqing; Qiu, Deyun; Zhang, Lida; Xie, Kabin; Yuan, Dejun; Han, Bin; Zhang, Qifa; Wang, Shiping.

In: Plant Journal, Vol. 42, No. 5, 06.2005, p. 772-780.

Research output: Contribution to journalArticle

Zhang, Jianwei - ; Feng, Qi ; Jin, Caoqing ; Qiu, Deyun ; Zhang, Lida ; Xie, Kabin ; Yuan, Dejun ; Han, Bin ; Zhang, Qifa ; Wang, Shiping. / Features of the expressed sequences revealed by a large-scale analysis of ESTs from a normalized cDNA library of the elite indica rice cultivar Minghui 63. In: Plant Journal. 2005 ; Vol. 42, No. 5. pp. 772-780.
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AU - Feng, Qi

AU - Jin, Caoqing

AU - Qiu, Deyun

AU - Zhang, Lida

AU - Xie, Kabin

AU - Yuan, Dejun

AU - Han, Bin

AU - Zhang, Qifa

AU - Wang, Shiping

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AB - The indica subspecies of cultivated rice occupies the largest area of rice production in the world. However, a systematic analysis of cDNA sequences from the indica subspecies has not been performed. The aim of the present study was to collect and analyze the expressed sequence tags (ESTs) of indica rice on a large scale. A total of 39 208 raw sequences were generated from a normalized cDNA library prepared by use of 15 different tissues of the indica cultivar Minghui 63. After trimming, processing and analysis, 17 835 unique sequences were obtained, each of which presumably represents a unique gene. Of these sequences, 2663 were novel, and at least 70 were indica specific. Comparison of the Minghui 63 sequences with the ESTs/full-length cDNAs in GenBank revealed a large number of deletion/insertion/substitution (DIS) at both the inter- and intra-subspecific levels. The overall number of polymorphisms in the expressed sequences was higher in the inter-subspecific comparisons than in the intra-subspecific comparisons. However, the extent of DIS-based polymorphism was highly variable among different rice varieties. In total, 15 726 unique sequences, including 697 novel sequences, were assigned to regions where large numbers of quantitative trait loci (QTLs) for agronomic traits had been detected previously. These results may be useful for developing new molecular markers for genetic mapping, detecting allelic polymorphisms associated with phenotypic variations between rice varieties, and facilitating QTL cloning by providing the starting points for candidate-gene identification.

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