Genome-wide identification of the peptide transporter family in rice and analysis of the PTR expression modulation in two near-isogenic lines with different nitrogen use efficiency

Abstract

Background: Nitrogen (N) is a major nutrient element for crop growth. In plants, the members of the peptide transporter (PTR) gene family are involved in nitrate uptake and transport. Here, we identied PTR gene family in rice and analyzed their expression level in near-isogenic lines. Results: We identified 96, 85 and 78 PTR genes in Nipponbare, R498and Oryza glaberrima , and the phylogenetic were similar in Asian cultivated rice and African cultivated rice. The number of PTR genes was higher in peanuts (125) and soybeans (127). The 521 PTR genes in rice, maize, sorghum, peanut, soybean and Arabidopsis could be classified into 4 groups, and their distribution was different between monocots and dicots. In Nipponbare genome, the 25 PTR genes were distributed in 5 segmental duplication regions on chromosome 1, 2, 3, 4, 5, 7, 8, 9, and 10. The PTR genes in rice have 0-11 introns and 1-12 exons , and 16 of them have the NPF (NRT1/PTR family) domain. The results of RNA-Seq showed that the number of differentially expressed genes (DEGs) between NIL15 and NIL19 at three stages were 928, 1467, and 1586, respectively. Under low N conditions, the number of differentially expressed PTR genes increased significantly. The RNA-Seq data was analyzed using WGCNA to predict the potential interaction between genes. We classified the genes with similar expression pattern into one module, and obtained 25 target modules. Among these modules, three modules may be involved in rice nitrogen uptake and utilization, especially the brown module, in which hub genes were annotated as protein kinase that may regulate rice N metabolism. Conclusions: In this study, we comprehensively analyzed the PTR gene family in rice. 96 PTR genes were identified in Nippobare genome and 25 of them were located on five large segmental duplication regions. The Ka/Ks ratio indicated that many PTR genes had undergone positive selection. The RNA-seq results showed that many PTR genes were involved in riceNUE, and protein kinases might play an important role in this process. These results provide a fundamental basis to improve the rice NUE via molecular breeding.

OsTTG1, a WD40 repeat gene, regulates anthocyanin biosynthesis in rice

“…The extraction of total RNA and cDNA synthesis was performed as previously described (Yang et al, 2020). The CFX96 quantitative PCR machine (Bio-Rad, Berkeley, CA, USA) was used for qPCR reactions.…”

“…We collected DLMM grain samples at 9, 14 and 19 DAF, with three biological replicates. The procedures of RNA extraction, and detection of concentration, purity and RNA integrity were done as previously described (Yang et al, 2020). The Illumina Truseq TM RNA sample prep kit was used to construct the library, and the Illumina NovaSeq 6000 was used for transcriptome sequencing.…”