Novel plant breeding techniques to advance nitrogen use efficiency in rice: A review

Figures & data

Figure 1. Illustration explaining various traits essential for the identification of NUE genotypes and different OMIC_S for the functional characterization of genes controlling NUE in rice.

Table 1. A list of genes available in rice genome controlling NUE

Gene	Function	Source	Reference
NRT1.1 [NPF 6.3,CHL1)	Nitrate transporter	Oryza sativa L.	^Citation41
NRT2.1	Nitrate transporter	Oryza sativa L.	^Citation42
NRT3.1 [NAR2.1]	Nitrate transport component	Oryza sativa L.	^Citation43
AMT1.1	Ammonium transporter	Oryza sativa L.	^Citation44
GS1	Glutamine synthetase [cytosolic]	Oryza sativa L.	^Citation45
GS2	Glutamine synthetase [plastidic]	Oryza sativa L.	^Citation46
GOGAT	Glutamate synthase	Oryza sativa L.	^Citation47
AlaAT	Aminotransferase	Oryza sativa L.	^Citation48
ENOD93–1	Early nodulin	Oryza sativa L.	^Citation49
OsGOGAT1, OsAMT1	Increase NUpE in low N conditions	Oryza sativa L.	^Citation50
glnA	Grain yield in high, moderate and low N conditions	Oryza sativa L.	^Citation51
ASN1	N content in grains	Oryza sativa L.	^Citation52
SHMT1	Photosynthesis and grain number per panicle	Oryza sativa L.	^Citation53
AAP1	Tiller number and grain yield	Oryza sativa L.	^Citation54
AAP3	Tiller number and grain yield	Oryza sativa L.	^Citation55
AAP5	Tiller number and grain yield	Oryza sativa L.	^Citation56
AAP6	Amino acid uptake from roots, Amino acid transport and grain protein content	Oryza sativa L.	^Citation57
Pup1/OsPupK46 2/PSTOL1	Tissue P concentration and relative tiller number	Oryza sativa L.	^Citation58
qNGR9/DEP1	Plant height response to N	Oryza sativa L.	^Citation59
TOND1	Relative plant dry weight under N-deficient to N-sufficient conditions	Oryza sativa L.	^Citation60
qNGR2/GRF4	Ammonium uptake	Oryza sativa L.	^Citation61
DRO1	N uptake and leaf N concentration after heading	Oryza sativa L.	^Citation62
MADS25	Increase the expressions of NO3 ^– transporter genes	Oryza sativa L.	^Citation63
DEP1	Ammonium uptake and assimilation	Oryza sativa L.	^Citation59
NAP	NAC transcription factor positively regulating leaf senescence	Oryza sativa L.	^Citation64

Figure 2. Genes/Gene families involved in plant NUE (modified from.^31,40

Figure 3. The basic flow chart of genome editing scheme for rice NUE improvement. (1) Selection of desirable germplasm. (2) The extraction of genomic DNA from selected germplasm. (3) Primarily analysis of genome through bioinformatics techniques to identify genes controlling NUE. (4) Selection of gene/genes of interest identified through bioinformatics analysis, available literature/online database. (5) Selection of target site based on GETs and availability/selection of vector. (6) Construction of vector holding gene of interest/target site. (7) Vector transformation through different transformation techniques (protoplast, agrobacterium transformation, and particle bombardment etc. (8) Utilization of Cas genome engineering machinery for targeted modification and extraction of genomic DNA from transgenic plants for mutation identification analysis. (9) The utilization of designed primers for PCR amplification of the target gene site to get Sanger sequencing results. (10) Screening of transgenic mutant plants based on Sanger sequencing results (type of mutation) and phenotypic changes. (11) Selection of transgene-free mutant plants for further collection of (morphological, physiological and biochemical) phenotypic data and interpretation of results.

Table 2. Transgenic approaches manipulating genes controlling amino acid metabolism and transport to improve nitrogen use efficiency in rice

Gene	Source	Promoter used	Phenotype observed	Reference
PTR6	Oryza sativa L.	Ubiquitin	Increased plant growth	^Citation30
AMT1.1	Oryza sativa L.	Ubiquitin	Increased ammonium, uptake and seed yield	^Citation121
AMT2.1	Oryza sativa L.	CaMV 35S	Increased Ammonium uptake	^Citation98
GS1	Oryza sativa L.	CaMV 35S	Increased N, decreased seed yield	^Citation107
GS2	Oryza sativa L.	CaMV 35S	Photorespiration capacity up	^Citation46
GOGAT	Oryza sativa L.	CaMV 35S	Increased grain weight	^Citation47
AlaAT	Hordeum vulgare L.	OsAnt1	Increased biomass and seed yield	^Citation122
GDHA	Aspergillus	CaMV 35S	Increased DW, N, yield in field	^Citation51
DOF1	Zea mays L.	CaMV 35S	Increase nitrogen content 30%, enhance growth rate under low N, reduced glucose level	^Citation123
ENOD93–1	Oryza sativa L.	Ubiquitin	Increased shoot biomass and seed yield	^Citation49
glnA	Escherichia col	CaMV 35S	Increase grain yield under high, moderate and low N conditions	^Citation124
GS1.1, GS2	Oryza sativa L.	CaMV 35S	Increase N assimilation and plant biomass	^Citation125
OsGOGAT1	Oryza sativa L.	Activation tagging lines	Increase NUpE in low N conditions; increase N content of grains	^Citation126
ASN1	Oryza sativa L.	Ubiquitin	Increase N content of grains; no impact on grain yield	^Citation127
gdhA	Aspergillus niger	CaMV 35S	Increase ammonia assimilation and plant biomass under high N conditions	^Citation51
GDH	Trichurus	Ubiquitin	Increase N assimilation, thousand grain weight, grain number and seed protein content under high, moderate and low N field conditions	^Citation128
SHMT1	Oryza sativa L.	Actin	Increased photosynthesis and grain number per panicle	^Citation53
ALAAT	Hordeum vulgare L.	Ant1	Increase plant biomass, NUpE and final seed yield under high N conditions independently of soil N source [ammonia/nitrate]	^Citation122
ALAAT2	Cucumis sativa L.	Ant1	Increase NUpE and grain yield in high and moderate N conditions	^Citation129
AAP1	Oryza sativa L.	CaMV 35S	Increase tiller number and grain yield	^Citation54
AAP3	Oryza sativa L.	CaMV 35S	Decrease tiller number and grain yield	^Citation55
AAP5	Oryza sativa L.	CaMV 35S	Decrease tiller number and grain yield	^Citation130
AAP6	Oryza sativa L.	CaMV 35S	Increase amino acid uptake from roots, amino acid transport and grain protein content at final harvest; maintain grain yield	^Citation57

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