Serial analysis of gene expression study of a hybrid rice strain (LYP9) and its parental cultivars

Jing Yue Bao, Sanggyu Lee, Chen Chen, Xiu Qing Zhang, Yu Zhang, Si Qi Liu, Terry Clark, Jian Wang, Meng Liang Cao, Huan Ming Yang, San Ming Wang, Jun Yu

Research output: Contribution to journalReview article

72 Citations (Scopus)

Abstract

Using the serial analysis of gene expression technique, we surveyed transcriptomes of three major tissues (panicles, leaves, and roots) of a super-hybrid rice (Oryza sativa) strain, LYP9, in comparison to its parental cultivars, 93-11 (indica) and PA64s (japonica). We acquired 465,679 tags from the serial analysis of gene expression libraries, which were consolidated into 68,483 unique tags. Focusing our initial functional analyses on a subset of the data that are supported by full-length cDNAs and the tags (genes) differentially expressed in the hybrid at a significant level (P < 0.01), we identified 595 up-regulated (22 tags in panicles, 228 in leaves, and 345 in roots) and 25 down-regulated (seven tags in panicles, 15 in leaves, and three in roots) in LYP9. Most of the tag-identified and up-regulated genes were found related to enhancing carbon- and nitrogen-assimilation, including photosynthesis in leaves, nitrogen uptake in roots, and rapid growth in both roots and panicles. Among the down-regulated genes in LYP9, there is an essential enzyme in photorespiration, alanine:glyoxylate aminotransferase 1. Our study adds a new set of data crucial for the understanding of molecular mechanisms of heterosis and gene regulation networks of the cultivated rice.

Original languageEnglish (US)
Pages (from-to)1216-1231
Number of pages16
JournalPlant Physiology
Volume138
Issue number3
DOIs
StatePublished - Dec 1 2005

Fingerprint

inflorescences
Gene Expression
rice
gene expression
cultivars
Nitrogen
Genes
Hybrid Vigor
leaves
genes
Gene Regulatory Networks
Photosynthesis
Gene Library
Transcriptome
photorespiration
transaminases
nitrogen
Carbon
Complementary DNA
heterosis

ASJC Scopus subject areas

  • Physiology
  • Genetics
  • Plant Science

Cite this

Bao, J. Y., Lee, S., Chen, C., Zhang, X. Q., Zhang, Y., Liu, S. Q., ... Yu, J. (2005). Serial analysis of gene expression study of a hybrid rice strain (LYP9) and its parental cultivars. Plant Physiology, 138(3), 1216-1231. https://doi.org/10.1104/pp.105.060988

Serial analysis of gene expression study of a hybrid rice strain (LYP9) and its parental cultivars. / Bao, Jing Yue; Lee, Sanggyu; Chen, Chen; Zhang, Xiu Qing; Zhang, Yu; Liu, Si Qi; Clark, Terry; Wang, Jian; Cao, Meng Liang; Yang, Huan Ming; Wang, San Ming; Yu, Jun.

In: Plant Physiology, Vol. 138, No. 3, 01.12.2005, p. 1216-1231.

Research output: Contribution to journalReview article

Bao, JY, Lee, S, Chen, C, Zhang, XQ, Zhang, Y, Liu, SQ, Clark, T, Wang, J, Cao, ML, Yang, HM, Wang, SM & Yu, J 2005, 'Serial analysis of gene expression study of a hybrid rice strain (LYP9) and its parental cultivars', Plant Physiology, vol. 138, no. 3, pp. 1216-1231. https://doi.org/10.1104/pp.105.060988
Bao, Jing Yue ; Lee, Sanggyu ; Chen, Chen ; Zhang, Xiu Qing ; Zhang, Yu ; Liu, Si Qi ; Clark, Terry ; Wang, Jian ; Cao, Meng Liang ; Yang, Huan Ming ; Wang, San Ming ; Yu, Jun. / Serial analysis of gene expression study of a hybrid rice strain (LYP9) and its parental cultivars. In: Plant Physiology. 2005 ; Vol. 138, No. 3. pp. 1216-1231.
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