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Identification of candidate genes for drought tolerance by whole-genome resequencing in maize

Jie Xu12, Yibing Yuan12, Yunbi Xu35, Gengyun Zhang4, Xiaosen Guo4, Fengkai Wu12, Qi Wang12, Tingzhao Rong12, Guangtang Pan12, Moju Cao12, Qilin Tang12, Shibin Gao12, Yaxi Liu6, Jing Wang12, Hai Lan12 and Yanli Lu12*

Author Affiliations

1 Maize Research Institute, Sichuan Agricultural University, Wenjiang 611130 Sichuan, China

2 Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Wenjiang 611130 Sichuan, China

3 Institute of Crop Science, the National Key Facilities for Crop Genetic Resources and Improvement, Chinese Academy of Agricultural Sciences, Beijing 100081, China

4 BGI-Shenzhen, Shenzhen 518083, China

5 International Maize and Wheat Improvement Center (CIMMYT), El Batan 56130 Texcoco, Mexico

6 Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130 Sichuan, China

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BMC Plant Biology 2014, 14:83  doi:10.1186/1471-2229-14-83

Published: 1 April 2014



Drought stress is one of the major limiting factors for maize production. With the availability of maize B73 reference genome and whole-genome resequencing of 15 maize inbreds, common variants (CV) and clustering analyses were applied to identify non-synonymous SNPs (nsSNPs) and corresponding candidate genes for drought tolerance.


A total of 524 nsSNPs that were associated with 271 candidate genes involved in plant hormone regulation, carbohydrate and sugar metabolism, signaling molecules regulation, redox reaction and acclimation of photosynthesis to environment were detected by CV and cluster analyses. Most of the nsSNPs identified were clustered in bin 1.07 region that harbored six previously reported QTL with relatively high phenotypic variation explained for drought tolerance. Genes Ontology (GO) analysis of candidate genes revealed that there were 35 GO terms related to biotic stimulus and membrane-bounded organelle, showing significant differences between the candidate genes and the reference B73 background. Changes of expression level in these candidate genes for drought tolerance were detected using RNA sequencing for fertilized ovary, basal leaf meristem tissue and roots collected under drought stressed and well-watered conditions. The results indicated that 70% of candidate genes showed significantly expression changes under two water treatments and our strategies for mining candidate genes are feasible and relatively efficient.


Our results successfully revealed candidate nsSNPs and associated genes for drought tolerance by comparative sequence analysis of 16 maize inbred lines. Both methods we applied were proved to be efficient for identifying candidate genes for complex traits through the next-generation sequencing technologies (NGS). These selected genes will not only facilitate understanding of genetic basis of drought stress response, but also accelerate genetic improvement through marker-assisted selection in maize.