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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
Author(s) -
Zhang Jianwei,
Feng Qi,
Jin Caoqing,
Qiu Deyun,
Zhang Lida,
Xie Kabin,
Yuan Dejun,
Han Bin,
Zhang Qifa,
Wang Shiping
Publication year - 2005
Publication title -
the plant journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.058
H-Index - 269
eISSN - 1365-313X
pISSN - 0960-7412
DOI - 10.1111/j.1365-313x.2005.02408.x
Subject(s) - biology , expressed sequence tag , genbank , subspecies , quantitative trait locus , genetics , cdna library , oryza sativa , complementary dna , cultivar , gene , candidate gene , botany , paleontology
Summary 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.