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Bulked segregant RNA-seq reveals differential expression and SNPs of candidate genes associated with waterlogging tolerance in maize

Author: Hewei Du
Author: Jianxiong Zhu
Author: Hang Su
Author: Ming Huang
Author: Hongwei Wang
Author: Shuangcheng Ding
Author: Binglin Zhang
Author: An Luo
Author: Shudong Wei
Author: Xiaohai Tian
Author: Yunbi Xu
Year: 2017
URI: http://hdl.handle.net/10883/18874
Abstract: Waterlogging has increasingly become one of the major constraints to maize productivity in some maize production zones because it causes serious yield loss. Bulked segregant RNA-seq (BSR-seq) has been widely applied to profile candidate genes and map associated Single Nucleotide Polymorphism (SNP) markers in many species. In this study, 10 waterlogging sensitive and eight tolerant inbred lines were selected from 60 maize inbred lines with waterlogging response determined and preselected by the International Maize and Wheat Improvement Center (CIMMYT) from over 400 tropical maize inbred lines. BSR-seq was performed to identify differentially expressed genes and SNPs associated with waterlogging tolerance. Upon waterlogging stress, 354 and 1094 genes were differentially expressed in the tolerant and sensitive pools, respectively, compared to untreated controls. When tolerant and sensitive pools were compared, 593 genes were differentially expressed under untreated and 431 genes under waterlogged conditions, of which 122 genes overlapped. To validate the BSR-seq results, the expression levels of six genes were determined by qRT-PCR. The qRT-PCR results were consistent with BSR-seq results. Comparison of allelic polymorphism in mRNA sequences between tolerant and sensitive pools revealed 165 (normal condition) and 128 (waterlogged condition) high-probability SNPs. We found 18 overlapping SNPs with genomic positions mapped. Eighteen SNPs were contained in 18 genes, and eight and nine of 18 genes were responsive to waterlogging stress in tolerant and sensitive lines, respectively. Six alleles of the 18 originated from tolerant pool were significantly up-regulated under waterlogging, but not those from sensitive pool. Importantly, one allele (GRMZM2G055704) of the six genes was mapped between umc1619 and umc1948 on chromosome 1 where a QTL associated with waterlogging tolerance was identified in a previous research, strongly indicating that GRMZM2G055704 is a candidate gene responsive to waterlogging. Our research contributes to the knowledge of the molecular mechanism for waterlogging tolerance in maize.
Format: PDF
Language: English
Publisher: Frontiers Media
Copyright: CIMMYT manages Intellectual Assets as International Public Goods. The user is free to download, print, store and share this work. In case you want to translate or create any other derivative work and share or distribute such translation/derivative work, please contact CIMMYT-Knowledge-Center@cgiar.org indicating the work you want to use and the kind of use you intend; CIMMYT will contact you with the suitable license for that purpose.
Type: Article
Place of Publication: Switzerland
Pages: pages 1-13
Issue: 1022
Volume: v. 8
DOI: 10.3389/fpls.2017.01022
Keywords: RNA-seq
Keywords: Bulk Segregant Analysis
Keywords: Waterlogging Stress Tolerance
Keywords: SNPs
Agrovoc: RNA
Agrovoc: WATER TOLERANCE
Agrovoc: MAIZE
Agrovoc: SINGLE NUCLEOTIDE POLYMORPHISM
Agrovoc: ABIOTIC STRESS
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Related Datasets: https://www.frontiersin.org/articles/file/downloadfile/271916_supplementary-materials_images_1_tif/octet-stream/Image%201.TIF/1/271916
Journal: Frontiers in Plant Science


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  • Maize
    Maize breeding, phytopathology, entomology, physiology, quality, and biotech

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