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Strategies for Identification of Genes Toward Enhancing Nitrogen Utilization Efficiency in Cereals

  • Alka Bharati
  • Pranab Kumar Mandal
Chapter

Abstract

Global cereal demand will increase up to 38% by 2025, and to achieve it in a sustainable way, 60% increase in global nitrogen (N) use will be necessary. In cereals ~30 to 50% of the applied N is taken up by the crop, and the rest is lost in the environment causing pollution. Hence, improvement of N use efficiency (NUE) in cereals is really important. The NUE is the total biomass or grain yield produced per unit of applied N fertilizer. Soil and plant management practices play a key role toward enhancing N recovery, but again it greatly depends on environmental conditions. Another option for improvement of NUE is the genetic strategy. Broadly, NUE has two components, N uptake efficiency (NUpE), which is N acquisition by the plant per unit of available N in the soil, and N utilization efficiency (NUtE), which is yield per unit of acquired N by the plant. As NUtE is directly related to the crop yield, it depends on subcomponent N assimilation, remobilization, and finally efficient utilization of assimilated N for starch biosynthesis in the grain. Understanding the mechanisms and gene regulating of these processes, exploiting genotypic variant in each subcomponent (N uptake, assimilation, and remobilization) to find genes and superior alleles is crucial for the improvement of NUE in crop plants. In addition, the studies on starch metabolism during grain filling are an important factor for N utilization. To study this, genotypes with similar background of uptake and assimilation but differing in grain filling should be taken into consideration. Global metabolomic profiling of these genotypes, transcriptome profiling, identification, and mapping of quantitative trait loci (QTLs) in combination with marker-assisted selection (MAS), analyzing mutants defective in their normal response to N limitation, and studying plants that show better growth under N-limiting conditions are different options to study the N-utilization efficiency and gene identification. In the first topic, we have highlighted the N application and its effect on yield in cereals. Introduction of N-responsive genotype during green revolution has enhanced yield, but indiscriminate use of fertilizer mainly N fertilizer has caused severe damage to environment. In the subsequent topic, we have defined NUE as a whole; later the main focus was on biological NUE and their different components. Thereafter we described strategies for genetic improvement to reduce N use without much compromising yield. Primarily we tried to highlight candidate genes and their role in NUE reported in cereals as well as model plant system. We have also described the advance molecular techniques to identify the gene in strategic manner. As a part of molecular breeding, QTL identification and its introgression are described in one of the topics at the last part.

Keywords

Candidate genes Cereals Nitrogen use efficiency 

Abbreviation

AAP

Amino acid permease

ABA

Abscisic acid

ADP

Adenosine diphosphate

AE

Agronomic efficiency

AFG

Auxin signaling F-box

AGPase

ADP glucose pyrophosphorylase

AlaAT

Alanine aminotransferase

AMT

Ammonium transporter

ARE

Apparent recovery efficiency

AS

Asparagine synthase

ATF

Amino acid transporter

BE

Branching enzyme

BNF

Biological nitrogen fixation

C

Carbon

CaMV

Cauliflower mosaic virus

cDNA

Complimentary DNA

CGs

Candidate genes

CLC

Chloride channel family

CPSase

Carbamoyl phosphate synthase

CRISPR-Cas9

Clustered regularly interspaced short palindromic repeats

DNA

Deoxyribonucleic acid

Dof

DNA binding with one zinc finger

EMS

Ethyl methanesulfonate

G-1-P

Glucose-1-phospate

GBSS

Granule-bound starch synthase

GDH

Glutamate dehydrogenase

GMPase

GDP mannose pyrophosphorylase

GOGAT

Glutamine-2-oxoglutarate aminotransferase or glutamate synthase

GS

Glutamine synthetase

H+

Hydrogen

HAT

High-affinity transport system

HSN1

Hypersensitive to \( {\mathrm{NH}}_4^{+} \)

HYVs

High-yielding varieties

ISA

Isoamylase

LATS

Low-affinity transport

LHT

Lysine/histidine transporter

MAS

Marker-assisted selection

miR

micro RNA

MPSS

Massively parallel signature sequencing

mQTLs

Metabolic QTLs

N

Nitrogen

N2O

Nitrogen oxide

NAD(P)H

Nicotinamide adenine dinucleotide phosphate

NAGK

N-acetyl glutamate kinase

NH3

Ammonia

NIL

Near-isogenic lines

NiR

Nitrite reductase

NO

Nitric oxide

\( {\mathrm{NO}}_3^{-} \)

Nitrate

NPF

Peptide transporter family

NpUE

N physiological use efficiency

NR

\( {\mathrm{NO}}_3^{-} \) reductase

NRA

\( {\mathrm{NO}}_3^{-} \) reductase activity

NRT

\( {\mathrm{NO}}_3^{-} \) transporter

NUE

Nitrogen use efficiency

NUpE

N uptake efficiency

NUtE

N utilization efficiency

PEP

Partial factor productivity

PEPC

Phosphoenolpyruvate carboxylase

PNB

Partial nutrient balance

PTST

Protein targeting to starch

QTL

Quantitative trait loci

RNA

Ribonucleic acid

RNAi

RNA interference

RS

Root system

RSA

Root system architecture

SAGE

Serial analysis of gene expression

SAV

Senescence associated vacuoles

SBE

Soluble starch branching enzymes

SG

Starch granules

SLAC/SLAH

Slow anion-associated channel homolog

SS

Starch synthase

SSH

Suppression subtractive hybridization

T-DNA

Transfer DNA

TALEN

Transcription activator-like effector nucleases

TCA

Tricarboxylic acid

TIP

Tonoplast intrinsic protein

TOR

Target of rifampicin

UI

Usage index

WUE

Water use efficiency

ZFN

Zinc finger nucleus

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© Springer Nature Singapore Pte Ltd. 2020

Authors and Affiliations

  • Alka Bharati
    • 1
  • Pranab Kumar Mandal
    • 1
  1. 1.ICAR-National Research Center on Plant BiotechnologyNew DelhiIndia

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