Transcriptome Analysis Reveals Differences in Key Genes and Pathways Regulating Carbon and Nitrogen Metabolism in Cotton Genotypes under N Starvation and Resupply

Abstract

Nitrogen (N) is the most important limiting factor for cotton production worldwide. Genotype-dependent ability to cope with N shortage has been only partially explored in cotton, and in this context, the comparison of molecular responses of cotton genotypes with different nitrogen use efficiency (NUE) is of particular interest to dissect the key molecular mechanisms underlying NUE. In this study, we employed Illumina RNA-Sequencing to determine the genotypic difference in transcriptome profile using two cotton genotypes differing in NUE (CCRI-69, N-efficient, and XLZ-30, N-inefficient) under N starvation and resupply treatments. The results showed that a large genetic variation existed in differentially expressed genes (DEGs) related to amino acid, carbon, and nitrogen metabolism between CCRI-69 and XLZ-30. Further analysis of metabolic changes in cotton genotypes under N resupply showed that nitrogen metabolism and aromatic amino acid metabolism pathways were mainly enriched in CCRI-69 by regulating carbon metabolism pathways such as starch and sucrose metabolism, glycolysis/gluconeogenesis, and pentose phosphate pathway. Additionally, we performed an expression network analysis of genes related to amino acid, carbon, and nitrogen metabolism. In total, 75 and 33 genes were identified as hub genes in shoots and roots of cotton genotypes, respectively. In summary, the identified hub genes may provide new insights into coordinating carbon and nitrogen metabolism and improving NUE in cotton.

Physiological and Transcriptomic Responses of Antioxidant System and Nitrogen Metabolism in Tomato Roots Treated With Nitrogen Starvation and Re-Supply

“…In our study, the differentially expressed genes are mainly involved in the pathways of phenylpropanoid biosynthesis, amino sugar and nucleotide sugar metabolism, cysteine and methionine metabolism, starch and sucrose metabolism, N metabolism and other pathways. In previous report, cotton under N starvation and re-supply treatment, enriched to a pathway similar to the results of our experiment (Iqbal et al 2020). The KEGG pathways revealed that 15 unigenes, including one NRT gene, two NR genes, one NiR gene, two GDH genes, six GS genes and three GOGAT genes, were related to nitrogen metabolism and signi cantly differentially expressed in response to nitrate starvation and a nitrate re-supply treatment (Chen et al 2018).…”

“…This indicated that tomato roots in N de ciency state can uptake an adequate supply of nitrate within 24 h of its being N resupplied, which are consistent with earlier reports(Chen et al 2018;Richard-Molard et al 2008). In previous reports, NR activity decreased under N de ciency stress in cotton(Iqbal et al 2020), rice (Sinha et al 2018), and wheat(Sinha et al 2015), which was consistent with the results in this paper. In this study, tomato seedlings after two days of N de ciency, GOGAT genes were up-regulated, while the expression of SlGS, SlNR, and SlNiR genes were down-regulated in tomato roots.…”

“…Re-supplying nitrate to the nitrate-starved Arabidopsis seedlings within 30 min, markedly and extensively alters the expression levels of genes involved in primary and secondary metabolism, cellular growth, hormone responses, protein synthesis, signal transduction and transcriptional regulation(Scheible et al 2004). Iqbal et al (2020) reported the genotypic difference in transcriptome pro le using two cotton genotypes differing in NUE under N starvation and resupply treatments. A large genetic variation existed in DEGs related to amino acid, carbon, and nitrogen metabolism.…”

Amino Acid Transporters in Plants: Identification and Function

“…In general, N partitioning between source and sink organs balances N uptake and metabolism in source organs, and transport potential from source to sink organs [ 5 ]. Moreover, the balance between carbon (C) and N is critical to improving N use efficiency (NUE): N levels can significantly affect C fixation, as photosynthetic proteins, such as Rubisco and PEP carboxylase, constitute a large N sink [ 119 ]. Alterations in amino acid phloem loading and unloading can regulate N and C acquisition and metabolism.…”

Recent Advances in Carbon and Nitrogen Metabolism in C3 Plants

“…The authors also suggested the reasonable regulation of C and N metabolism as a way to improve NUE [ 275 ] and the reprogramming of primary and secondary metabolism under the future climatic scenario [ 276 ]. The study in [ 277 ] was carried out to identify the molecular networks of C and N metabolism in cotton. These authors identified several hub genes that might provide novel insights into coordinating C and N metabolism, which could serve as the basis for high NUE.…”