Open Access Open Badges Research article

Rapid EST isolation from chromosome 1R of rye

Ruo-Nan Zhou14, Rui Shi15, Shu-Mei Jiang12, Wei-Bo Yin1, Huang-Huang Wang1, Yu-Hong Chen1, Jun Hu1, Richard RC Wang3, Xiang-Qi Zhang1 and Zan-Min Hu1*

Author Affiliations

1 Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, P. R. China

2 South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, P. R. China

3 USDA-ARS, FRRL, Utah State University, Logan, UT 84322-6300, USA

4 Graduate University of Chinese Academy of Sciences, Beijing 100049, P. R. China

5 Forest Biotechnology Group, N.C. State University, Campus Box 7247, Raleigh, NC 27695-7247, USA

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BMC Plant Biology 2008, 8:28  doi:10.1186/1471-2229-8-28

Published: 18 March 2008



To obtain important expressed sequence tags (ESTs) located on specific chromosomes is currently difficult. Construction of single-chromosome EST library could be an efficient strategy to isolate important ESTs located on specific chromosomes. In this research we developed a method to rapidly isolate ESTs from chromosome 1R of rye by combining the techniques of chromosome microdissection with hybrid specific amplification (HSA).


Chromosome 1R was isolated by a glass needle and digested with proteinase K (PK). The DNA of chromosome 1R was amplified by two rounds of PCR using a degenerated oligonucleotide 6-MW sequence with a Sau3AI digestion site as the primer. The PCR product was digested with Sau3AI and linked with adaptor HSA1, then hybridized with the Sau3AI digested cDNA with adaptor HSA2 of rye leaves with and without salicylic acid (SA) treatment, respectively. The hybridized DNA fragments were recovered by the HSA method and cloned into pMD18-T vector. The cloned inserts were released by PCR using the partial sequences in HSA1 and HSA2 as the primers and then sequenced. Of the 94 ESTs obtained and analyzed, 6 were known sequences located on rye chromosome 1R or on homologous group 1 chromosomes of wheat; all of them were highly homologous with ESTs of wheat, barley and/or other plants in Gramineae, some of which were induced by abiotic or biotic stresses. Isolated in this research were 22 ESTs with unknown functions, probably representing some new genes on rye chromosome 1R.


We developed a new method to rapidly clone chromosome-specific ESTs from chromosome 1R of rye. The information reported here should be useful for cloning and investigating the new genes found on chromosome 1R.