Dataset Information

Genome-wide associated study identifies NAC42-activated nitrate transporter conferring high nitrogen use efficiency in rice.

ABSTRACT: Over-application of nitrogen fertilizer in fields has had a negative impact on both environment and human health. Domesticated rice varieties with high nitrogen use efficiency (NUE) reduce fertilizer for sustainable agriculture. Here, we perform genome-wide association analysis of a diverse rice population displaying extreme nitrogen-related phenotypes over three successive years in the field, and identify an elite haplotype of nitrate transporter OsNPF6.1^HapB that enhances nitrate uptake and confers high NUE by increasing yield under low nitrogen supply. OsNPF6.1^HapB differs in both the protein and promoter element with natural variations, which are differentially trans-activated by OsNAC42, a NUE-related transcription factor. The rare natural allele OsNPF6.1^HapB, derived from variation in wild rice and selected for enhancing both NUE and yield, has been lost in 90.3% of rice varieties due to the increased application of fertilizer. Our discovery highlights this NAC42-NPF6.1 signaling cascade as a strategy for high NUE and yield breeding in rice.

SUBMITTER: Tang W

PROVIDER: S-EPMC6872725 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Genome-wide associated study identifies NAC42-activated nitrate transporter conferring high nitrogen use efficiency in rice.

Tang Weijie W Ye Jian J Yao Xiangmei X Zhao Pingzhi P Xuan Wei W Tian Yunlu Y Zhang Yuanyan Y Xu Shuang S An Hongzhou H Chen Gaoming G Yu Jun J Wu Wei W Ge Yuwei Y Liu Xiaolan X Li Jin J Zhang Hanzhi H Zhao Yaqin Y Yang Bing B Jiang Xingzhou X Peng Chao C Zhou Cong C Terzaghi William W Wang Chunming C Wan Jianmin J

Nature communications 20191121 1

Over-application of nitrogen fertilizer in fields has had a negative impact on both environment and human health. Domesticated rice varieties with high nitrogen use efficiency (NUE) reduce fertilizer for sustainable agriculture. Here, we perform genome-wide association analysis of a diverse rice population displaying extreme nitrogen-related phenotypes over three successive years in the field, and identify an elite haplotype of nitrate transporter OsNPF6.1<sup>HapB</sup> that enhances nitrate up ...[more]

PMID: 31754193

Similar Datasets

Project description:BACKGROUND:Nitrogen (N) is a major nutrient element for crop growth. In plants, the members of the peptide transporter (PTR) gene family may involve in nitrate uptake and transport. Here, we identified PTR gene family in rice and analyzed their expression profile in near-isogenic lines. RESULTS:We identified 96, 85 and 78 PTR genes in Nipponbare, R498 and Oryza glaberrima, and the phylogenetic trees were similar in Asian cultivated rice and African cultivated rice. The number of PTR genes was higher in peanut (125) and soybean (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 N 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 rice nitrogen use efficiency (NUE), 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.

Project description:Mulching and nitrogen are critical drivers of crop production for smallholders of the Loess Plateau in China. The purpose of this study was to investigate the effect of mulching and nitrogen fertilizer on the soil water content, soil nitrate-N content and vertical distribution in maize root-zone. The experiment was conducted over two consecutive years and used randomly assigned field plots with three replicates. The six treatments consisted of no fertilizer without plastic film (CK), plastic film mulching with no basal fertilizer and no top dressing (MN0), basal fertilizer with no top dressing and no mulching (BN1), plastic film mulching and basal fertilizer with no top dressing (MN1), basal fertilizer and top dressing with no mulching (BN2) and plastic film mulching with basal fertilizer and top dressing (MN2). In the top soil layers, the soil water content was a little high in the plastic film mulching than that without mulching. The mean soil water content from 0 to 40 cm without mulching were 3.35% lower than those measured in the corresponding mulching treatments in 31 days after sowing in 2012. The mulching treatment increased the soil nitrate-N content was observed in the 0-40-cm soil layers. The results indicate that high contents of soil nitrate-N were mainly distributed at 0-20-cm at 31 days after sowing in 2012, and the soil nitrate-N concentration in the MN2 treatment was 1.58 times higher than that did not receive fertilizer. The MN2 treatment greatly increased the soil nitrate-N content in the upper layer of soil (0-40-cm), and the mean soil nitrate-N content was increased nearly 50 mg kg-1 at 105 days after sowing compared with CK treatment in 2012. The soil nitrate-N leaching amount in MN1 treatment was 28.61% and 39.14% lower than BN1 treatment, and the mulch effect attained to 42.55% and 65.27% in MN2 lower than BN2 in both years. The yield increased with an increase in the basal fertilizer, top dressing and plastic film mulching, and the grain yield increase ranged from 31.41% to 83.61% in two consecutive years. The MN1 and MN2 treatment is recommended because it increased the grain yield and improved the fertilizer use efficiency, compared with the no-mulching treatment.

Dataset Information

Genome-wide associated study identifies NAC42-activated nitrate transporter conferring high nitrogen use efficiency in rice.

Publications

Genome-wide associated study identifies NAC42-activated nitrate transporter conferring high nitrogen use efficiency in rice.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure