Abstract
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.
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Claims 17
Claim · model-written summary
The contrasting wheat cultivars had 2,406 differentially expressed genes under N stress.
- Taxon
- Wheat
Triticum aestivumt0 - Treatment
- N stresse0
- Outcome
- differentially expressed genes (DEGs)e0
- Value
- 2,406e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Differentially expressed gene analysis revealed a total of 2,406 differentially expressed genes (DEGs) present in both the contrasting cultivars under N stress.”
t0“Wheat Cultivars”
Claim · model-written summary
Efficient wheat genotype PBW677 had 1,653 DEGs, more than PBW703.
- Taxon
- WheatTriticum aestivumt0
- Material
- PBW677e0
- Outcome
- DEGse0
- Direction
- more abundante0
- Value
- 1,653e0
- Comparator
- PBW703e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“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).”
t0“Wheat Cultivars”
Claim · model-written summary
Inefficient wheat cultivar PBW703 had 753 DEGs.
- Taxon
- WheatTriticum aestivumt0
- Material
- PBW703e0
- Outcome
- inefficient cultivar PBW703e0
- Value
- 753e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“inefficient cultivar PBW703 with 753 (96 roots +657 shoots)”
t0“Wheat Cultivars”
Claim · model-written summary
In PBW677, 903 DEGs were in roots.
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“PBW677 had considerably more abundant DEGs with 1,653 (903 roots +750 shoots)”
t0“Wheat Cultivars”
Claim · model-written summary
In PBW677, 750 DEGs were in shoots.
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“PBW677 had considerably more abundant DEGs with 1,653 (903 roots +750 shoots)”
t0“Wheat Cultivars”
Claim · model-written summary
In PBW703, 96 DEGs were in roots.
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“PBW703 with 753 (96 roots +657 shoots)”
t0“Wheat Cultivars”
Claim · model-written summary
In PBW703, 657 DEGs were in shoots.
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“PBW703 with 753 (96 roots +657 shoots)”
t0“Wheat Cultivars”
Claim · model-written summary
Pathway analysis suggested different adaptive mechanisms in the two wheat cultivars.
- Taxon
- WheatTriticum aestivumt0
- Material
- two cultivarse0
- Outcome
- adaptive mechanisme0
- Direction
- differede0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Gene ontology enrichment and pathway analysis of these DEGs suggested that the two cultivars differed in terms of adaptive mechanism.”
t0“Wheat Cultivars”
Claim · model-written summary
PBW677 enriched categories included DNA binding, abiotic stimulus response and photosynthesis.
- Taxon
- WheatTriticum aestivumt0
- Material
- PBW677e0
- Outcome
- DNA binding, response to abiotic stimulus, photosynthesise0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“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”
t0“Wheat Cultivars”
Claim · model-written summary
PBW677 enriched categories included carbon fixation, carbohydrate and nitrogen metabolism.
- Taxon
- WheatTriticum aestivumt0
- Material
- PBW677e0
- Outcome
- carbon fixation, carbohydrate metabolic process, nitrogen compound metabolic processe0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“carbon fixation, carbohydrate metabolic process, nitrogen compound metabolic process, nitrate transport, and translation in cultivar PBW677”
t0“Wheat Cultivars”
Claim · model-written summary
PBW677 enriched categories included nitrate transport and translation.
- Taxon
- WheatTriticum aestivumt0
- Material
- PBW677e0
- Outcome
- nitrate transport, and translatione0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“nitrate transport, and translation in cultivar PBW677”
t0“Wheat Cultivars”
Claim · model-written summary
PBW703 enriched categories included nucleosome assembly, chromatin remodeling and DNA packaging.
- Taxon
- WheatTriticum aestivumt0
- Material
- PBW703e0
- Outcome
- nucleosome assembly, chromatin remodeling, DNA packaginge0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“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”
t0“Wheat Cultivars”
Claim · model-written summary
PBW703 enriched categories included lipid transport, sulfur metabolism and protein modification.
- Taxon
- WheatTriticum aestivumt0
- Material
- PBW703e0
- Outcome
- lipid transport, sulfur compound metabolic process, protein modificationse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“lipid transport, sulfur compound metabolic process, protein modifications, and protein folding and refolding in N inefficient cultivar PBW703”
t0“Wheat Cultivars”
Claim · model-written summary
PBW703 enriched categories included protein folding and refolding.
- Taxon
- WheatTriticum aestivumt0
- Material
- PBW703e0
- Outcome
- protein folding and refoldinge0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“protein folding and refolding in N inefficient cultivar PBW703”
t0“Wheat Cultivars”
Claim · model-written summary
Several transcription factors, kinases, transporters and N assimilation genes were highly expressed in high NUE wheat cultivar PBW677.
- Taxon
- WheatTriticum aestivumt0
- Material
- PBW677e0
- Outcome
- transcription factorse0
- Direction
- highly expressede0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“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.”
t0“Wheat Cultivars”
Claim · model-written summary
Thirteen candidate wheat genes showed alternate expression in the two contrasting cultivars.
- Taxon
- WheatTriticum aestivumt0
- Material
- two contrasting cultivarse0
- Outcome
- potential candidate genese0
- Direction
- alternate gene expressione0
- Value
- 13e0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“we report 13 potential candidate genes which showed alternate gene expression in the two contrasting cultivars under study.”
t0“Wheat Cultivars”
Claim · model-written summary
The authors proposed these candidate genes as potential future breeding targets.
- Taxon
- WheatTriticum aestivumt0
- Outcome
- potential targets for future breeding programse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“These genes could serve as potential targets for future breeding programs.”
t0“Wheat Cultivars”