Mining for low-nitrogen tolerance genes by integrating meta-analysis and large-scale gene expression data from maize

Abstract

Nitrogen (N) is the most important macronutrient for plant growth and development. Hence, understanding genetic architectures and functional genes involved in the response to N deficiency can greatly facilitate the development of low-Ntolerant cultivars. In this study, we collected 212 quantitative trait loci (QTL) of agronomically important traits under low-N stress conditions in maize. We then identified 21 consensus QTL (cQTL) strongly induced for low-N tolerance after excluding overlapping cQTL containing QTL simultaneously identified in meta-analyses of studies performed under other environmental conditions. Among the 21 cQTL, 30 candidate maize genes were identified from maize large-scale differential expression data derived from analyses of low-N stress, and the 12 most important maize orthologs were identified using homologous BLAST analyses of genes with known functions in N use efficiency in model plants. Furthermore, maize orthologs associated with low-N tolerance and metabolism were also predicted using large-scale expression data from other model plants. The present genetic loci and candidate genes indicate the molecular mechanisms of low-N tolerance in maize and may provide information for QTL fine mapping and molecular marker-assisted selection.

Maize Combined Insect Resistance Genomic Regions and Their Co-localization With Cell Wall Constituents Revealed by Tissue-Specific QTL Meta-Analyses

“…Although the number of original QTL in each tissue was substantially reduced, the resulting MQTL are relatively large constituting a limitation for their introgression using MAS. Large CIs resulting from a meta-analysis is not seldom for studies conducted in similar conditions (Jin et al, 2015 ; Luo et al, 2015 ; Zhao et al, 2015 ; Jiang et al, 2016 ). In fact, the IBM 2 2008 neighbors is a result of intermating lines from a bi-parental cross between B73 and Mo17, and as such, has a size increase of nearly four-fold in the genetic map distance, but also it substantially increases resolution up to 91% (Lee et al, 2002 ).…”

Comparative Transcriptomics of Rice Genotypes with Contrasting Responses to Nitrogen Stress Reveals Genes Influencing Nitrogen Uptake through the Regulation of Root Architecture

“…Although many genes involved in N uptake and assimilation are known, information on transcriptional regulation and signal transduction processes, associated with improvements in NUE, is limited. Many QTLs from NUE mapping studies in rice and other crops overlapped with genes that were involved in nitrogen uptake and assimilation [23][24][25]. For a complex trait like NUE, which is controlled by many genes with several interacting environmental factors, we applied a genome-wide expression profiling technique, using a japonica genotype "Bengal" and an indica genotype "Pokkali", with contrasting responses to nitrogen availability to discover candidate genes with the potential to improve the NUE in rice.…”

Transcriptomic and Genome-wide Association Study Reveal Long Noncoding RNAs Responding to Nitrogen Deficiency in Maize

“…The expression levels of candidate genes in which GWAS-identi ed SNPs located were evaluated in 255 maize lines through RNA-Seq of root at the maize seedling stage under LN stress. This includes the discovery of two genes in the integration of meta-analysis and large-scale gene expression pro le data of maize under LN stress [21]. For example, Zm00001d051804 plays an important role in glutamine biosynthesis in response to exogenous nitrogen during seed germination in maize and Arabidopsis [22].…”

“…Of these lncRNAs, we found LNC_002984, LNC_002985, and LNC_002986 located upstream of Zm00001d051804 that could potentially regulate the expression levels of neighboring genes in a cis manner. Zm00001d051804 was reported to be related to the response to low nitrogen stress [21]. Moreover, the homologous gene in Arabidopsis was shown to play an important redundant role in ammonium assimilation under ammonium-de cient conditions and in facilitating nitrogen remobilization in root [27,28].…”