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.
Highlights
Environmental abiotic stresses, such as drought, submergence or waterlogging, high salinity, and extreme temperatures, severely compromise crop production and productivity (Bray et al, 2000)
In order to map the genes associated with waterlogging stress adaptation, we identified the Single Nucleotide Polymorphism (SNP) present in RNAs contained in the RNA-seq data between the tolerant and sensitive pools
The maizeGDB and NCBI databases contain a large number of resources, including ESTs and gene expression, additional resources are needed for identification and mapping of the genes involved in waterlogging tolerance in maize
Summary
Environmental abiotic stresses, such as drought, submergence or waterlogging, high salinity, and extreme temperatures, severely compromise crop production and productivity (Bray et al, 2000). Plants have evolved several strategies to adapt to waterlogging or submergence stress. A large number of genes are induced under waterlogging or submergence conditions that may protect plants from damage caused by waterlogging or submergence. These genes present a valuable tool for improving waterlogging tolerance in maize and other crops. Maize uses a different strategy, including development of adventitious roots, to achieve waterlogging tolerance than rice and Arabidopsis, possibly because maize is cultivated in different agroclimatic zones. The above-mentioned genes isolated from rice and Arabidopsis may not be effective for improving waterlogging tolerance in maize. Identification of quantitative trait loci (QTL) and genes associated with waterlogging tolerance in maize is of critical importance for maize improvement
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