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PMID: 24684805 Published · epublish English Journal Article Research Support, Non-U.S. Gov't

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

BMC plant biology ·Vol. 14 ·2014-04-01 ·Pages 83

Xu J, Yuan Y, Xu Y, Zhang G, Guo X, Wu F, Wang Q, Rong T, Pan G, Cao M, Tang Q, Gao S, Liu Y, Wang J, Lan H, Lu Y

Abstract

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.

MeSH Terms
Adaptation, Physiological/genetics Chromosomes, Plant/genetics Cluster Analysis Dehydration Droughts Gene Ontology Genes, Plant Genetic Association Studies Genome, Plant/genetics Genotype Inbreeding Nucleic Acid Denaturation/genetics Polymerase Chain Reaction Polymorphism, Single Nucleotide/genetics Quantitative Trait Loci/genetics RNA, Messenger/genetics,metabolism Reproducibility of Results Sequence Analysis, DNA/methods Zea mays/genetics,physiology
Chemicals
RNA, Messenger
Authors & Affiliations
16 authors, click to expand affiliations / ORCID
Xu Jie
Yuan Yibing
Xu Yunbi
Zhang Gengyun
Guo Xiaosen
Wu Fengkai
Wang Qi
Rong Tingzhao
Pan Guangtang
Cao Moju
Tang Qilin
Gao Shibin
Liu Yaxi
Wang Jing
Lan Hai
Lu Yanli
Maize Research Institute, Sichuan Agricultural University, Wenjiang 611130 Sichuan, China. [email protected].
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Article Info
Journal
BMC plant biology
Abbr.
BMC Plant Biol
ISSN
1471-2229
DOI
10.1186/1471-2229-14-83
Email
[email protected]
Published
2014-04-01
Epub
2014-00-01
Pages
83
Language
English
Region
England
NLM ID
100967807
PMCID
PMC4021222
Subset
IM
External Links
PubMed source DOI: 10.1186/1471-2229-14-83 PMC Full Text View journal details
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