Kaur Sarabjit, Shamshad M, Jindal Suruchi, Kaur Amandeep, Singh Satinder, Sharma Achla, Kaur Satinder
School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India.
Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India.
Front Genet. 2022 Mar 31;13:853910. doi: 10.3389/fgene.2022.853910. eCollection 2022.
High NUE (nitrogen use efficiency) has great practical significance for sustainable crop production. Wheat is one of the main cultivated crops worldwide for human food and nutrition. However, wheat grain productivity is dependent upon cultivars with high NUE in addition to the application of nitrogen fertilizers. In order to understand the molecular mechanisms exhibiting a high NUE response, a comparative transcriptomics study was carried out through RNA-seq analysis to investigate the gene expression that regulates NUE, in root and shoot tissue of N-efficient (PBW677) and N-inefficient (703) cultivars under optimum and nitrogen (N) stress. Differentially expressed gene analysis revealed a total of 2,406 differentially expressed genes (DEGs) present in both the contrasting cultivars under N stress. The efficient genotype PBW677 had considerably more abundant DEGs with 1,653 (903 roots +750 shoots) compared to inefficient cultivar PBW703 with 753 (96 roots +657 shoots). Gene ontology enrichment and pathway analysis of these DEGs suggested that the two cultivars differed in terms of adaptive mechanism. Gene enrichment analysis revealed that among the upregulated and downregulated genes the overrepresented and underrepresented gene categories belonged to biological processes like DNA binding, response to abiotic stimulus, photosynthesis, carbon fixation, carbohydrate metabolic process, nitrogen compound metabolic process, nitrate transport, and translation in cultivar PBW677, while the enriched biological processes were nucleosome assembly, chromatin remodeling, DNA packaging, lipid transport, sulfur compound metabolic process, protein modifications, and protein folding and refolding in N inefficient cultivar PBW703. We found several transcription factors (MYB, WRKY, RING finger protein, zinc finger protein, transporters, NRT1, amino acid transporters, sugar), protein kinases, and genes involved in N absorption, transportation, and assimilation to be highly expressed in high NUE cultivar PBW677. In our study, we report 13 potential candidate genes which showed alternate gene expression in the two contrasting cultivars under study. These genes could serve as potential targets for future breeding programs.
高氮利用效率(NUE)对作物可持续生产具有重要的现实意义。小麦是全球主要的栽培作物之一,为人类提供食物和营养。然而,除了施用氮肥外,小麦籽粒产量还取决于具有高氮利用效率的品种。为了了解表现出高氮利用效率响应的分子机制,通过RNA测序分析进行了一项比较转录组学研究,以调查在最佳和氮(N)胁迫条件下,氮高效(PBW677)和氮低效(703)品种的根和地上部组织中调节氮利用效率的基因表达。差异表达基因分析显示,在氮胁迫下,两个对比品种中共有2406个差异表达基因(DEG)。与低效品种PBW703的753个(96个根 + 657个地上部)相比,高效基因型PBW677具有相当多的丰富差异表达基因,有1653个(903个根 + 750个地上部)。对这些差异表达基因的基因本体富集和通路分析表明,两个品种在适应机制方面存在差异。基因富集分析显示,在PBW677品种中,上调和下调基因中过度表达和表达不足的基因类别属于生物过程,如DNA结合、对非生物刺激的反应、光合作用、碳固定、碳水化合物代谢过程、氮化合物代谢过程、硝酸盐运输和翻译,而在氮低效品种PBW703中,富集的生物过程是核小体组装、染色质重塑、DNA包装、脂质运输、硫化合物代谢过程、蛋白质修饰以及蛋白质折叠和重折叠。我们发现几个转录因子(MYB、WRKY、环指蛋白、锌指蛋白、转运蛋白、NRT1、氨基酸转运蛋白、糖)、蛋白激酶以及参与氮吸收、运输和同化的基因在高氮利用效率品种PBW677中高度表达。在我们的研究中,我们报告了13个潜在的候选基因,它们在两个研究的对比品种中表现出交替的基因表达。这些基因可以作为未来育种计划的潜在目标。