Bulked Segregant RNA-seq Reveals Differential Expression and SNPs of Candidate Genes Associated with Waterlogging Tolerance in Maize

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.

BSR-Seq Analysis Provides Insights into Cold Stress in Actinidia Arguta F1 Populations

“…Each pool, or bulk, contains individuals who are identical in a particular trait or genomic region but arbitrary at all unlinked regions [16]. Bulked segregant RNA-seq (BSR-Seq) possesses the advantage of BSA and RNA-seq together, which has the full capability to identify differentially expressed genes (DEGs) and the ability to identify SNPs between different pools [17]. This method does not require genome information.…”

Rapid identification of a candidate gene related to fiber strength using a superior chromosome segment substitution line from Gossypium hirsutum ×Gossypium barbadense via bulked segregant RNA-sequencing

“…Due to saving plenty of manpower, material resources, and shortening the breeding cycle, BSR-seq has attracted more and more attentions in recent years, which has been an efficient strategy for rapid QTL mapping and efficient identification of candidate genes in connection with key traits in plants (Liu et al, 2012;Trick et al, 2012;Wang et al, 2013a;Yates et al, 2014). Through performing BSA-seq on waterlogging sensitive and resistant pools in maize, a candidate gene (GRMZM2G055704) in the key QTL located in umc1619-umc1948onchromosome1 was identified to response waterlogging (Du et al, 2017). In order to screen the genes responsive to early and late flowering, BSR-seq association analysis on the extreme pools in tree peony obtained 291 unigenes, of which 7 DEGs (c42942.graph_c0, c58332.graph_c0, c58361.graph_c0, c57417.graph_c0, c46352.graph_c0, c53143.graph_c0, and c58526.graph_c0) were confirmed to relate with early and late flowering (Hou et al, 2018).…”

iTRAQ-based Comparative Proteomic Analysis of Flag Leaves of Two Wheat (Triticum aestivum L.) Genotypes Differing in Waterlogging Tolerance at Anthesis

“…Great efforts were taken to study the mechanism of WL tolerance at the molecular level. Expression levels of many genes were found to change in response to WL by RNA-seq analysis in cotton [8,9], rapes [10], maize [11,12], cucumber [13]. Fifty-two and 146 proteins were differentially expressed in tomato leaves and cucumber adventitious roots in response to WL stress, respectively [14,15].…”