Physiological and Comparative Transcriptomic Analysis Provide Insight Into Cotton (Gossypium hirsutum L.) Root Senescence in Response

Nitrogen (N) deficiency is one of the pivotal environmental factors that induce leaf senescence. However, little is known regarding the impact of low N on root senescence in cotton. Thus, the objective of this study was to investigate the effect of low nitrogen on root senescence. In this study, the molecular mechanism of cotton root senescence in response to nitrogen deficiency was investigated by combing physiological and transcriptomic analysis when no nitrogen and normal nitrogen (138mg N·kg−1 soil). The results showed that: (1) nitrogen starvation induced the premature senescence of leaf, while delaying root senescence. (2) The increase in catalase (CAT) activity at 60, 80, and 100days after emergence (DAE), combined with decrease of malonaldehyde content at 60, 80, and 100 DAE, and the content of abscisic acid (ABA), all of these contributed to the delay of root senescence by low nitrogen treatment. (3) To study the molecular mechanisms underlying root senescence, the gene expression profiling between low nitrogen and normal nitrogen treatments were compared pairwise at 20, 40, 60, 80, and 100 DAE. A total of 14,607 genes were identified to be differentially expressed at these five points. (5) Most genes involved in glutathione (GSH) and ascorbate peroxidase (APX) synthesis were upregulated, while ABA, apoptosis, caspase, and cell cycle-related differentially expressed genes (DEGs) were downregulated. Coupled with the physiology data, these results provide new insights into the effect of nitrogen starvation on root senescence.

Transcriptome Analysis of Two Near-Isogenic Lines with Different NUE under Normal Nitrogen Conditions in Wheat

Nitrogen (N) is an essential nutrient element for crop productivity. Unfortunately, the nitrogen use efficiency (NUE) of crop plants gradually decreases with the increase of the N application rate. Nevertheless, little has been known about the molecular mechanisms of differences in NUE among genotypes of wheat. In this study, we used RNA-Sequencing (RNA-Seq) to compare the transcriptome profiling of flag leaves at the stage of anthesis in wheat NILs (1Y, high-NUE, and 1W, low-NUE) under normal nitrogen conditions (300 kg N ha−1, corresponding to 1.6 g N pot−1). We identified 7023 DEGs (4738 upregulated and 2285 downregulated) in the comparison between lines 1Y and 1W. The responses of 1Y and 1W to normal N differed in the transcriptional regulatory mechanisms. Several genes belonging to the GS and GOGAT gene families were upregulated in 1Y compared with 1W, and the enhanced carbon metabolism might lead 1Y to produce more C skeletons, metabolic energy, and reductants for nitrogen metabolism. A subset of transcription factors (TFs) family members, such as ERF, WRKY, NAC, and MYB, were also identified. Collectively, these identified candidate genes provided new information for a further understanding of the genotypic difference in NUE.

Morphological and physiological plasticity response to low nitrogen stress in black cottonwood (Populus deltoides Marsh.)

It is important to evaluate nitrogen use efficiency and nitrogen tolerance of trees in order to improve their productivity. In this study, both were evaluated for 338 Populus deltoides genotypes from six provenances. The plants were cultured under normal nitrogen (750 μM NH4NO3) and low nitrogen (5 μM NH4NO3) conditions for 3 months. Growth, chlorophyll content and glutamine synthetase activity of each genotype were measured. Under low nitrogen, heights, ground diameter, leaf area, leaf and root biomass, and chlorophyll contents were significantly lower than those under normal nitrogen level. Correlation analysis showed that nutrient distribution changed under different nitrogen treatments. There was a negative correlation between leaf traits and root biomass under normal nitrogen level, however, the correlation became positive in low nitrogen treatment. Moreover, with the decrease of nitrogen level, the negative correlation between leaf morphology and chlorophyll levels became weakened. The growth of the genotypes under the two treatments was evaluated by combining principal component analysis with a fuzzy mathematical membership function; the results showed that leaf traits accounted for a large proportion of the variation in the evaluation model. According to the results of comprehensive evaluation of plants under the two treatments, the 338 P. deltoides genotypes could be divided into nine categories, with wide genotypic diversity in nitrogen use efficiency and low nitrogen tolerance. As a result, 26 N-efficient genotypes and 24 N-inefficient genotypes were selected. By comparative analysis of their morphological and physiological traits under the two treatments, leaf traits could be significant indicators for nitrogen use efficiency and nitrogen tolerance, which is of considerable significance for breeding poplar varieties with high nitrogen use efficiencies.

Novel QTL Associated with Shoot Branching Identified in Doubled Haploid Rice (Oryza sativa L.) under Low Nitrogen Cultivation

Shoot branching is considered as an important trait for the architecture of plants and contributes to their growth and productivity. In cereal crops, such as rice, shoot branching is controlled by many factors, including phytohormones signaling networks, operating either in synergy or antagonizing each other. In rice, shoot branching indicates the ability to produce more tillers that are essential for achieving high productivity and yield potential. In the present study, we evaluated the growth and development, and yield components of a doubled haploid population derived from a cross between 93-11 (P1, indica) and Milyang352 (P2, japonica), grown under normal nitrogen and low nitrogen cultivation open field conditions. The results of the phenotypic evaluation indicated that parental lines 93-11 (P1, a high tillering indica cultivar) and Milyang352 (P2, a low tillering japonica cultivar) showed distinctive phenotypic responses, also reflected in their derived population. In addition, the linkage mapping and quantitative trait locus (QTL) analysis detected three QTLs associated with tiller number on chromosome 2 (qTNN2-1, 130 cM, logarithm of the odds (LOD) 4.14, PVE 14.5%; and qTNL2-1, 134 cM, LOD: 6.05, PVE: 20.5%) and chromosome 4 (qTN4-1, 134 cM, LOD 3.92, PVE 14.5%), with qTNL2-1 having the highest phenotypic variation explained, and the only QTL associated with tiller number under low nitrogen cultivation conditions, using Kompetitive Allele-Specific PCR (KASP) and Fluidigm markers. The additive effect (1.81) of qTNL2-1 indicates that the allele from 93-11 (P1) contributed to the observed phenotypic variation for tiller number under low nitrogen cultivation. The breakthrough is that the majority of the candidate genes harbored by the QTLs qTNL2-1 and qTNN4-1 (here associated with the control of shoot branching under low and normal nitrogen cultivation, respectively), were also proposed to be involved in plant stress signaling or response mechanisms, with regard to their annotations and previous reports. Therefore, put together, these results would suggest that a possible crosstalk exists between the control of plant growth and development and the stress response in rice.

QTL Mapping and Favorable Allele Mining of Nitrogen Deficiency Tolerance Using an Interconnected Breeding Population in Rice

Nitrogen is one of the most important nutrients for rice growth and development. Breeding of nitrogen deficiency tolerance (NDT) variety is considered to be the most economic measure to solve the constrain of low nitrogen stress on grain yield in rice. An interconnected breeding (IB) population of 497 lines developed using Huanghuazhan (HHZ) as the recurrent parent and eight elite lines as the donor parents were tested for five traits including grain yield, biomass, harvest index, thousand grain weight, and spikelet fertility under two nitrogen treatments in three growing seasons. Association analysis using 7,388 bins generated by sequencing identified a total of 14, 14, and 12 QTLs for the five traits under low nitrogen (LN), normal nitrogen (NN), and LN/NN conditions, respectively, across three seasons. Favorable alleles were dissected for the 40 QTLs at the 10 NDT regions, and OM1723 was considered as the most important parent with the highest frequency of favorable alleles contributing to NDT-related traits. Six superior lines all showed significantly higher GY in LN environments and similar GY under NN environments except for H10. Substitution mapping using near-isogenic introgression lines delimited the qTGW2-1, which was identified on chromosome 2 under LN, NN, and LN/NN conditions into two QTLs, which were located in the two regions of about 200 and 350 kb with different favorable alleles. The bins 16, 1301, 1465, 1486, 3464, and 6249 harbored the QTLs for NDT detected in this study, and the QTLs/genes previously identified for NDT or nitrogen use efficiency (NUE) could be used for enhancing NDT and NUE by marker-assisted selection (MAS).

Transcriptomic Analysis Reveals the Contribution of QMrl-7B to Wheat Root Growth and Development

Backgound: Roots are the major organs for water and nutrient acquisition and substantially affect plant growth, development and reproduction. Improvements to root system architecture are highly important for increasing yield potential of bread wheat. QMrl-7B, a major stable quantitative trait locus (QTL) that controls maximum root length (MRL), strongly contributes to an improved root system in wheat. Results: To further analyse the biological functions of QMrl-7B in root development, two types of Triticum aestivum near isogenic lines (NILs), one with superior QMrl-7B alleles from cultivar Kenong 9204 (KN9204) and another with inferior QMrl-7B alleles from cultivar Jing 411 (J411), were subjected to transcriptomic analysis. Among all the mapped genes analysed, 4871 genes were identified as being differentially expressed between the pairwise NILs under different nitrogen (N) conditions, with 3543 genes expressed under normal-nitrogen (NN) condition and 2689 genes expressed under low-nitrogen (LN) condition. These genes encode proteins that include mainly NO3- transporters, phytohormone signalling components and transcription factors (TFs), indicating the presence of a complex regulatory network involved in root determination. In addition, among the 13524 LN-induced differentially expressed genes (DEGs) detected in this assay, 4308 were specifically expressed in the A-NIL which brings superior alleles, and 2463 were expressed specifically in the B-NIL which brings inferior alleles. These DEGs reflect different responses of the two types of NILs to varying N supplies, which likely involve LN-induced root growth. Conclusions: These results explain the better-developed root system and increased root vitality provided by the superior alleles of QMrl-7B and provide a deeper understanding of the genetic underpinnings of root traits, pointing to a valuable locus suitable for future breeding efforts for sustainable agriculture.

Exploring the Potential of Overexpressed OsCIPK2 Rice as a Nitrogen Utilization Efficient Crop and Analysis of Its Associated Rhizo-Compartmental Microbial Communities

Nitrogen (N) is one of the indispensable factors in rice growth and development. China holds a premier position in the production of rice and at the same time also faces higher N fertilizer costs along with serious damage to the environment. A better solution is much needed to address these issues, without disrupting the production of rice as an important cereal, while minimizing all the deleterious effects on the environment. Two isogenic lines Kitaake (WT) and its genetically modified line CIPK2 (RC), overexpressing the gene for Calcineurin B-like interacting protein kinase 2 (OsCIPK2) with better nitrogen use efficiency (NUE), were compared for their growth and development under low versus normal levels of N. NUE is a complex trait mainly related to a plant’s efficiency in extraction, assimilation, and recycling of N from soil. The microbial population was analyzed using high-throughput Illumina Miseq 16S rRNA sequencing and found that RC with CIPK2, specifically expressed in rice root, not only performed better without nitrogen fertilizer (LN) but also increased the diversity of bacterial communities in rice rhizosphere compartments (rhizosphere, rhizoplane, and endosphere). The relative abundance of beneficial bacteria phyla increased, which are known to promote the circulation and transformation of N in rhizosphere soil. To further explore the potential of RC regarding better performance under LN, the ion fluxes in root apical were detected by non-invasive micro-test technique (NMT). We found that RC can absorb more Ca2+ and NO3− under LN as compared to WT. Finally, compared to WT, RC plants exhibited better growth of root and shoot, and increased yield and N uptake under LN, whereas there was no significant difference in the growth of two rice lines under normal nitrogen (NN) treatment. We are able to get preliminary results, dealing with the OsCIPK2 overexpressed rice line, by studying the rice molecular, physiological, and chemical parameters related to NUE. The results laid the foundation for further research on N absorption and utilization in rice from the soil and the interaction with microbial communities.

Transcriptome analysis for Fraxinus mandshurica seedlings from different carbon fixation and growth provenances in response to nitrogen deficiency

Background The carbon fixation characteristic of F. mandshurica seedlings from 20 provenances has been evaluated by our research group. In order to explore whether growth and carbon sequestration are related to nutritional adaptability, the foliage and roots of the annual Wuchang (WC) seedlings with high carbon content and Hailin (HL) seedlings with low carbon content which were grown in nitrogen-deficient nutrition and total nutrition were used for RNA-seq determination. Results Eight transcriptome libraries by high-throughput sequence were analysis. 1,235,174,984 clean reads and 88,655 unigenes with N50 length of 1,259 bp were obtained. Under normal nitrogen condition, 783 differentially expressed genes (DEGs) between WC and HL were identified, the number in foliage (669) of DEGs between HL and WC was more than that in roots (149). The number of transcription factors (TFs), hormone, and Protein kinase (PK) genes was significantly more in WC than that in HL. Compared to the normal nitrogen, 8173 DEGs related to nitrogen deficiency were identified and the number of DEGs in roots (6999) was more than that in foliage (1616). Several nitrogen deficiency-related metabolic pathways and many DEGs involved in nitrogen absorption and assimilation, carbon metabolism, hormones, transcription factors and kinases were identified. The numbers of DEGs encoding nitrate transporters, PK, TFs and hormone in WC were less than that in HL, which indicated the response of HL provenance seedlings to nitrogen deficiency was stronger than that of WC provenance seedlings. However, under nitrogen deficiency, the number of up-regulated DEGs in the WC provenance seedlings is more than that in the HL, which indicated that the WC provenance seedlings were more tolerant to nitrogen deficiency than HL. Conclusions The data showed that high carbon content and high growth rate of WC provenance seedlings are mainly attributed to the high transcriptional expression of many metabolic genes in foliage. The response of HL provenance seedlings to nitrogen deficiency is significantly greater than that of WC provenances seedlings, but WC provenance seedlings were more tolerant to nitrogen deficiency than HL. Many genes related to nitrogen deficiency were identified, which will expand our current understanding of nitrogen responses.