An integrated nitrogen utilization gene network and transcriptome analysis reveal candidate genes in response to nitrogen deficiency in Brassica napus

Pengfeng Li; Runjie Du; Zhaopeng Li; Zhuo Chen; Jiana Li; Hai Du

doi:10.3389/fpls.2023.1187552

An integrated nitrogen utilization gene network and transcriptome analysis reveal candidate genes in response to nitrogen deficiency in Brassica napus

Front Plant Sci. 2023 May 9:14:1187552. doi: 10.3389/fpls.2023.1187552. eCollection 2023.

Authors

Pengfeng Li^{1

2}, Runjie Du^{1

2}, Zhaopeng Li^{1

2}, Zhuo Chen^{1

2}, Jiana Li^{1

2}, Hai Du^{1

2}

Affiliations

¹ College of Agronomy and Biotechnology, Chongqing Engineering Research Center for Rapeseed, Southwest University, Chongqing, China.
² Academy of Agricultural Sciences, Southwest University, Chongqing, China.

Abstract

Nitrogen (N) is an essential factor for crop yield. Here, we characterized 605 genes from 25 gene families that form the complex gene networks of N utilization pathway in Brassica napus. We found unequal gene distribution between the A_n- and C_n-sub-genomes, and that genes derived from Brassica rapa were more retained. Transcriptome analysis indicated that N utilization pathway gene activity shifted in a spatio-temporal manner in B. napus. A low N (LN) stress RNA-seq of B. napus seedling leaves and roots was generated, which proved that most N utilization related genes were sensitive to LN stress, thereby forming co-expression network modules. Nine candidate genes in N utilization pathway were confirmed to be significantly induced under N deficiency conditions in B. napus roots, indicating their potential roles in LN stress response process. Analyses of 22 representative species confirmed that the N utilization gene networks were widely present in plants ranging from Chlorophyta to angiosperms with a rapid expansion trend. Consistent with B. napus, the genes in this pathway commonly showed a wide and conserved expression profile in response to N stress in other plants. The network, genes, and gene-regulatory modules identified here represent resources that may enhance the N utilization efficiency or the LN tolerance of B. napus.

Keywords: Brassica napus; RNA-seq; evolution; expression; genes; nitrogen.

Grants and funding

This work was supported by the National Key Research and Development Program of China (2018YFD1000900). We appreciate Dr. Wei Xin and Ji-Ping Gao for providing the rice N tress RNA-seq dataset for us. We thank Yun-Ke Zhu for analyzing the RNA-seq data.