Abstract
Nitrogen-use efficiency (NUE) is a function of N-response and yield that is controlled by many genes and phenotypic parameters that are poorly characterized. This study compiled all known yield-related genes in rice and mined them from the N-responsive microarray data to find 1,064 NUE-related genes. Many of them are novel genes hitherto unreported as related to NUE, including 80 transporters, 235 transcription factors (TFs), 44 MicroRNAs (miRNAs), 91 kinases, and 8 phosphatases. They were further shortlisted to 62 NUE-candidate genes following hierarchical methods, including quantitative trait locus (QTL) co-localization, functional evaluation in the literature, and protein–protein interactions (PPIs). They were localized to chromosomes 1, 3, 5, and 9, of which chromosome 1 with 26 genes emerged as a hotspot for NUE spanning 81% of the chromosomes. Further, co-localization of the NUE genes on NUE-QTLs resolved differences in the earlier studies that relied mainly on N-responsive genes regardless of their role in yield. Functional annotations and PPIs for all the 1,064 NUE-related genes and also the shortlisted 62 candidates revealed transcription, redox, phosphorylation, transport, development, metabolism, photosynthesis, water deprivation, and hormonal and stomatal function among the prominent processes. In silico expression analysis confirmed differential expression of the 62 NUE-candidate genes in a tissue/stage-specific manner. Experimental validation in two contrasting genotypes revealed that high NUE rice shows better photosynthetic performance, transpiration efficiency and internal water-use efficiency in comparison to low NUE rice. Feature Selection Analysis independently identified one-third of the common genes at every stage of hierarchical shortlisting, offering 6 priority targets to validate for improving the crop NUE.
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Claims 16
Claim · model-written summary
1,064 NUE-related genes were identified in rice from yield-related genes and N-responsive microarray data
- Taxon
- Rice
Oryza sativat0 - Outcome
- NUE-related genese1
- Value
- 1,064e1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Nitrogen-Use Efficiency in Rice”
e1“to find 1,064 NUE-related genes”
Claim · model-written summary
Rice NUE-related genes include 80 transporters
- Taxon
- RiceOryza sativat0
- Outcome
- transporterse2
- Value
- 80e2
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Nitrogen-Use Efficiency in Rice”
e2“including 80 transporters, 235 transcription factors (TFs), 44 MicroRNAs (miRNAs), 91 kinases, and 8 phosphatases”
Claim · model-written summary
Rice NUE-related genes include 235 transcription factors
- Taxon
- RiceOryza sativat0
- Outcome
- transcription factorse2
- Value
- 235e2
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Nitrogen-Use Efficiency in Rice”
e2“including 80 transporters, 235 transcription factors (TFs), 44 MicroRNAs (miRNAs), 91 kinases, and 8 phosphatases”
Claim · model-written summary
Rice NUE-related genes include 44 MicroRNAs
- Taxon
- RiceOryza sativat0
- Outcome
- MicroRNAse2
- Value
- 44e2
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Nitrogen-Use Efficiency in Rice”
e2“including 80 transporters, 235 transcription factors (TFs), 44 MicroRNAs (miRNAs), 91 kinases, and 8 phosphatases”
Claim · model-written summary
Rice NUE-related genes include 91 kinases
- Taxon
- RiceOryza sativat0
- Outcome
- kinasese2
- Value
- 91e2
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Nitrogen-Use Efficiency in Rice”
e2“including 80 transporters, 235 transcription factors (TFs), 44 MicroRNAs (miRNAs), 91 kinases, and 8 phosphatases”
Claim · model-written summary
Rice NUE-related genes include 8 phosphatases
- Taxon
- RiceOryza sativat0
- Outcome
- phosphatasese2
- Value
- 8e2
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Nitrogen-Use Efficiency in Rice”
e2“including 80 transporters, 235 transcription factors (TFs), 44 MicroRNAs (miRNAs), 91 kinases, and 8 phosphatases”
Claim · model-written summary
The NUE-related genes were shortlisted to 62 NUE-candidate genes in rice
- Taxon
- RiceOryza sativat0
- Outcome
- NUE-candidate genese3
- Value
- 62e3
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Nitrogen-Use Efficiency in Rice”
e3“They were further shortlisted to 62 NUE-candidate genes”
Claim · model-written summary
Chromosome 1 with 26 genes is a hotspot for NUE in rice
- Taxon
- RiceOryza sativat0
- Outcome
- hotspot for NUEe4
- Value
- 26 genese4
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Nitrogen-Use Efficiency in Rice”
e4“chromosome 1 with 26 genes emerged as a hotspot for NUE”
Claim · model-written summary
The NUE-related genes were localized to chromosomes 1, 3, 5 and 9 in rice
- Taxon
- RiceOryza sativat0
- Outcome
- localizede5
- Value
- chromosomes 1, 3, 5, and 9e5
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Nitrogen-Use Efficiency in Rice”
e5“They were localized to chromosomes 1, 3, 5, and 9”
Claim · model-written summary
Co-localization of NUE genes on NUE-QTLs resolved differences found in earlier studies that relied on N-responsive genes
- Taxon
- RiceOryza sativat0
- Outcome
- differences in the earlier studiese6
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Nitrogen-Use Efficiency in Rice”
e6“co-localization of the NUE genes on NUE-QTLs resolved differences in the earlier studies”
Claim · model-written summary
Functional annotation and protein-protein interaction analysis revealed several prominent processes among NUE-related genes in rice
- Taxon
- RiceOryza sativat0
- Outcome
- prominent processese7
- Qualifier
- transcription, redox, phosphorylation, transport, development, metabolism, photosynthesis, water deprivation, and hormonal and stomatal functione7
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Nitrogen-Use Efficiency in Rice”
e7“revealed transcription, redox, phosphorylation, transport, development, metabolism, photosynthesis, water deprivation, and hormonal and stomatal function among the prominent processes”
Claim · model-written summary
In silico expression analysis confirmed differential expression of the 62 NUE-candidate rice genes in a tissue- or stage-specific manner
- Taxon
- RiceOryza sativat0
- Organ / stage
- tissue/stage-specifice1
- Outcome
- differential expressione1
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Nitrogen-Use Efficiency in Rice”
e1“In silico expression analysis confirmed differential expression of the 62 NUE-candidate genes in a tissue/stage-specific manner”
Claim · model-written summary
High-NUE rice shows better photosynthetic performance, transpiration efficiency and internal water-use efficiency than low-NUE rice
- Taxon
- RiceOryza sativat0
- Material
- two contrasting genotypese2
- Outcome
- photosynthetic performance, transpiration efficiency and internal water-use efficiencye2
- Direction
- bettere2
- Comparator
- low NUE ricee2
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Nitrogen-Use Efficiency in Rice”
e2“Experimental validation in two contrasting genotypes revealed that high NUE rice shows better photosynthetic performance, transpiration efficiency and internal water-use efficiency in comparison to low NUE rice”
Claim · model-written summary
Feature selection independently identified one-third of the common genes at every stage of hierarchical shortlisting
- Taxon
- RiceOryza sativat0
- Outcome
- common genese3
- Value
- one-thirde3
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Nitrogen-Use Efficiency in Rice”
e3“Feature Selection Analysis independently identified one-third of the common genes at every stage of hierarchical shortlisting”
Claim · model-written summary
The study offers 6 priority rice targets to validate for improving crop NUE
- Taxon
- RiceOryza sativat0
- Outcome
- priority targets to validatee4
- Value
- 6e4
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Nitrogen-Use Efficiency in Rice”
e4“offering 6 priority targets to validate for improving the crop NUE”
Claim · model-written summary
Many of the NUE-related rice genes are novel and were previously unreported as related to NUE
- Taxon
- RiceOryza sativat0
- Outcome
- novel genese5
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
t0“Nitrogen-Use Efficiency in Rice”
e5“Many of them are novel genes hitherto unreported as related to NUE”