Journal of Integrative Agriculture ›› 2014, Vol. 13 ›› Issue (6): 1216-1229.DOI: 10.1016/S2095-3119(13)60614-0

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Genome-Wide Expression Profile of Maize Root Response to Phosphorus Deficiency Revealed by Deep Sequencing

 SU Shun-zhong, WU Ling, LIU Dan, LU Yan-li, LIN Hai-jian, ZHANG Shu-zhi, SHEN Ya-ou, LIU Hai-lan, ZHANG Zhi-ming, RONG Ting-zhao, ZHANG Xiao, TIAN Yue-hui, NIE Zhi , GAO Shi-bin   

  1. Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture/Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, P.R.China
  • 收稿日期:2013-04-03 出版日期:2014-06-01 发布日期:2014-06-06
  • 通讯作者: GAO Shi-bin, Tel: +86-28-86290915, Fax: +86-28-86290912, E-mail: shibingao@163.com
  • 基金资助:

    This work supported by the National Basic Research Program of China (2009CB118400), the 948 Project of Ministry of Agriculture of China (2011-G15-2 and 2013-Z38), the National Natural Science Foundation of China (31361140364 and 31171566) and the Key Technologies R&D Program of China during the 12th Five-Year Plan period (2011BAD35B01).

Genome-Wide Expression Profile of Maize Root Response to Phosphorus Deficiency Revealed by Deep Sequencing

 SU Shun-zhong, WU Ling, LIU Dan, LU Yan-li, LIN Hai-jian, ZHANG Shu-zhi, SHEN Ya-ou, LIU Hai-lan, ZHANG Zhi-ming, RONG Ting-zhao, ZHANG Xiao, TIAN Yue-hui, NIE Zhi , GAO Shi-bin   

  1. Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture/Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, P.R.China
  • Received:2013-04-03 Online:2014-06-01 Published:2014-06-06
  • Contact: GAO Shi-bin, Tel: +86-28-86290915, Fax: +86-28-86290912, E-mail: shibingao@163.com
  • Supported by:

    This work supported by the National Basic Research Program of China (2009CB118400), the 948 Project of Ministry of Agriculture of China (2011-G15-2 and 2013-Z38), the National Natural Science Foundation of China (31361140364 and 31171566) and the Key Technologies R&D Program of China during the 12th Five-Year Plan period (2011BAD35B01).

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摘要： Phosphorus (P) is one of the three primary macronutrients that are required in large amounts for plant growth and development. To better understand molecular mechanism of maize and identify relevant genes in response to phosphorus deficiency, we used Solexa/Illumina’s digital gene expression (DGE) technology to investigate six genome-wide expression profiles of seedling roots of the low-P tolerant maize inbred line 178. DGE studies were conducted at 6, 24 and 72 h under both phosphorus deficient and sufficient conditions. Approximately 3.93 million raw reads for each sample were sequenced and 6 816 genes exhibited significant levels of differential expressions in at least one of three time points in response to P starvation. The number of genes with increased expression increased over time from 6 to 24 h, whereas genes with decreased expression were more abundant at 72 h, suggesting a gradual response process for P deficiency at different stages. Gene annotations illustrated that most of differentially expressed genes (DEGs) are involved in different cellular and molecular processes such as environmental adaptation and carbohydrate metabolism. The expression of some known genes identified in other plants, such as those involved in root architecture, P metabolism and transport were found to be altered at least two folds, indicating that the mechanisms of molecular and morphological adaptation to P starvation are conserved in plants. This study provides insight into the general molecular mechanisms underlying plant adaptation to low-P stress and thus may facilitate molecular breeding for improving P utilization in maize.

关键词: maize , phosphorus efficiency , root , digital gene expression

Abstract: Phosphorus (P) is one of the three primary macronutrients that are required in large amounts for plant growth and development. To better understand molecular mechanism of maize and identify relevant genes in response to phosphorus deficiency, we used Solexa/Illumina’s digital gene expression (DGE) technology to investigate six genome-wide expression profiles of seedling roots of the low-P tolerant maize inbred line 178. DGE studies were conducted at 6, 24 and 72 h under both phosphorus deficient and sufficient conditions. Approximately 3.93 million raw reads for each sample were sequenced and 6 816 genes exhibited significant levels of differential expressions in at least one of three time points in response to P starvation. The number of genes with increased expression increased over time from 6 to 24 h, whereas genes with decreased expression were more abundant at 72 h, suggesting a gradual response process for P deficiency at different stages. Gene annotations illustrated that most of differentially expressed genes (DEGs) are involved in different cellular and molecular processes such as environmental adaptation and carbohydrate metabolism. The expression of some known genes identified in other plants, such as those involved in root architecture, P metabolism and transport were found to be altered at least two folds, indicating that the mechanisms of molecular and morphological adaptation to P starvation are conserved in plants. This study provides insight into the general molecular mechanisms underlying plant adaptation to low-P stress and thus may facilitate molecular breeding for improving P utilization in maize.

Key words: maize , phosphorus efficiency , root , digital gene expression