**3. QTLs and genes of nitrogen use efficiency**

In soil, inorganic nitrogen is available for plants as nitrate (NO3 − ) in aerobic upland condition and ammonium (NH4 + ) in flooded wetland or acidic soils. Nitrogen use efficiency (NUE) is a complex trait that is controlled by multiple genes. Many genes and/QTLs associated with NUE have been identified in rice. Studying and understanding the mechanisms of N utilization at a molecular level may help to improve rice varieties for N deficiency tolerance under different abiotic stresses. Researchers [102] identified 14 putative QTLs for NUE components and 63 QTLs for 12 physiological and agronomic characteristics with six hotspot regions using 174 recombinant inbred lines derived from the IR64/Azucena cross at the

vegetative phase in the hydroponic Yoshida solution with three different N concentrations: 1X (standard), 1/4X and 1/8X. In line with this, it is reported that eight QTLs for plant height in hydroponics with two N supply levels in the Yoshida culture solution and 13 QTLs for plant height in a soil mediated experiment with two N supply treatments [103]. Twelve QTLs were detected for root weight, 14 for shoot weight and 12 for biomass from 239 rice recombinant inbreed lines (RILs) derived from a cross between two *indica* parents (Zhenshan97/Minghui63) under hydroponics medium using two N treatments [104]. In another pot experiment, seven QTLs were identified associated with nitrogen use and the yield on chromosome 3 [105]. Three candidate genes *Os05g0208000, Os07g0617800 and Os10g0189600* were identified through fine-mapping of four QTLs located on chromosomes 5, 7 and 10 accelerated yield performance under low N level [106].

Five QTLs were identified on chromosomes 1, 2, 7 and 11 for grain yield (GY) using 127 RILs derived from the cross Zhanshan 97/Minghui 63 [107]. The phenotypic and genetic associations between grain NUE and GY are positive and highly significant; thus, QTLs for both NUE and GY could be used to trigger NUE and GY in a breeding program [108]. Seven QTLs for the glutamine synthetase (GS1) protein content and six QTLs for the NADH-GOGAT protein content were detected using backcross inbred lines between Nipponbare and Kasalath. Some of these QTLs were fined mapped to get a structural gene for GS1 from chromosome 2 and chromosome 1 [109]. A QTL on chromosome 2 activates cytosolic GS1 for protein synthesis in older leaves, resulting in more active tillers during the vegetative stage and a more panicle number and total panicle weight [110]. Using 166 RIL populations, 22 single QTLs and 58 pairs of epistatic QTLs associated with physiological NUE in rice have been identified [111]. With the same mapping population, 28 main effect QTLs and 23 pairs of epistatic QTLs were detected [112]. It is reported that [113], using 38 chromosome segment substitution lines derived from a cross between "Koshihikari," a *japonica* variety, and "Kasalath," an *indica* variety, identified a major QTL *qRL6.1* on the long arm of chromosome 6 associated with root elongation under deficient and sufficient NH4<sup>+</sup> condition. The "Kasalath" allele at this QTL region promoted significant root elongation. The marker interval was C11635–P3A2 and phenotypic variance explained by this QTL was 76.4%.

A set of RILs grown in four different seasons in two locations with three nitrogen fertilization treatments was analyzed for QTL for grain yield components and two main effect QTLs were detected viz., grain yield per panicle on chromosome 4 and grain number per panicle on chromosome 12 under N zero level [114]. Four QTLs for trait differences of plant height and heading date between two N levels have been mapped on chromosomes 2 and 8 co-locating with reported QTLs for NUE [111]. In response to low nitrogen application for two years, 33 QTL have been identified in RIL population, out of which only ten QTLs were consistent under low N [115]. QTL mapping for NUE and nitrogen deficiency tolerance traits in RIL population for two years resulted in four common QTL on chromosomes 1, 3, 4 and 7 [116].

From a recombinant inbred population, 20 single QTLs (S-QTLs) and 58 pairs of epistatic loci (E-QTLs) were detected for the nitrogen concentration of grain, nitrogen concentration of straw, the nitrogen content of shoot, harvest index, grain yield, straw yield and physiological nitrogen use efficiency (PNUE) [117]. Researchers [118] identified seven chromosomal regions using 40 introgression lines (ILs) derived from a cross between "Ilpumbyeo," a temperate *japonica* variety, and "Moroberekan," a tropical *japonica* accession from seedlings grown in 0, 250 and 500 μM NH4 + . Among them, the *qRW6* QTL was detected on the long arm of chromosome 6 associated with root weight in temperate *japonica.*

Recently, a group of scientists reported [119] about a main effect QTL *qRD-WN6XB* (**Table 2**) on the long arm of chromosome 6, which positively confers

**147**

**Figure 2.**

**Table 2.**

*QTLs = quantitative trait loci.*

*Nitrogen Use Efficiency in Rice under Abiotic Stress: Plant Breeding Approach*

*qRL6.1* Root elongation under deficient and sufficient NH4

*Major QTLs/genes associated with nitrogen use efficiency under abiotic stresses.*

tolerance to N deficiency in the *Indica* rice variety XieqingzaoB, was identified using a chromosomal segment substitution line population using Zhonghui9308 and XieqingzaoB. Nine candidate genes were found in this region through fine mapping. Out of these genes, *Os06g15910* was seemed to be a strong candidate gene associated with root system improvement under low N status. However, putative

**QTLs/genes Special traits Chr. No Reference** *ARE1* High-yield under N limiting condition 8 [108]

*qRW6* Enhance root traits and yield potential 6 [118] *qRDWN6XB* Confers tolerance to N deficiency 6 [119] *qGYLN7* Increases grain yield under low N 7 [106] *qGYPP-4b* Increases grain yield per plant under low N 4 [114] *qGNPP-12* Increases grain number per panicle under low N 12 [114]

+

condition 6 [113]

*Holistic breeding approach for multiple abiotic stress tolerance in rice. F = flooding, D = drought, S = salinity,* 

*DOI: http://dx.doi.org/10.5772/intechopen.94038*

#### *Nitrogen Use Efficiency in Rice under Abiotic Stress: Plant Breeding Approach DOI: http://dx.doi.org/10.5772/intechopen.94038*

tolerance to N deficiency in the *Indica* rice variety XieqingzaoB, was identified using a chromosomal segment substitution line population using Zhonghui9308 and XieqingzaoB. Nine candidate genes were found in this region through fine mapping. Out of these genes, *Os06g15910* was seemed to be a strong candidate gene associated with root system improvement under low N status. However, putative


**Table 2.**

*Recent Advances in Rice Research*

vegetative phase in the hydroponic Yoshida solution with three different N concentrations: 1X (standard), 1/4X and 1/8X. In line with this, it is reported that eight QTLs for plant height in hydroponics with two N supply levels in the Yoshida culture solution and 13 QTLs for plant height in a soil mediated experiment with two N supply treatments [103]. Twelve QTLs were detected for root weight, 14 for shoot weight and 12 for biomass from 239 rice recombinant inbreed lines (RILs) derived from a cross between two *indica* parents (Zhenshan97/Minghui63) under hydroponics medium using two N treatments [104]. In another pot experiment, seven QTLs were identified associated with nitrogen use and the yield on chromosome 3 [105]. Three candidate genes *Os05g0208000, Os07g0617800 and Os10g0189600* were identified through fine-mapping of four QTLs located on chromosomes 5, 7 and 10

Five QTLs were identified on chromosomes 1, 2, 7 and 11 for grain yield (GY) using 127 RILs derived from the cross Zhanshan 97/Minghui 63 [107]. The phenotypic and genetic associations between grain NUE and GY are positive and highly significant; thus, QTLs for both NUE and GY could be used to trigger NUE and GY in a breeding program [108]. Seven QTLs for the glutamine synthetase (GS1) protein content and six QTLs for the NADH-GOGAT protein content were detected using backcross inbred lines between Nipponbare and Kasalath. Some of these QTLs were fined mapped to get a structural gene for GS1 from chromosome 2 and chromosome 1 [109]. A QTL on chromosome 2 activates cytosolic GS1 for protein synthesis in older leaves, resulting in more active tillers during the vegetative stage and a more panicle number and total panicle weight [110]. Using 166 RIL populations, 22 single QTLs and 58 pairs of epistatic QTLs associated with physiological NUE in rice have been identified [111]. With the same mapping population, 28 main effect QTLs and 23 pairs of epistatic QTLs were detected [112]. It is reported that [113], using 38 chromosome segment substitution lines derived from a cross between "Koshihikari," a *japonica* variety, and "Kasalath," an *indica* variety, identified a major QTL *qRL6.1* on the long arm of chromosome 6 associated with root

at this QTL region promoted significant root elongation. The marker interval was

A set of RILs grown in four different seasons in two locations with three nitrogen fertilization treatments was analyzed for QTL for grain yield components and two main effect QTLs were detected viz., grain yield per panicle on chromosome 4 and grain number per panicle on chromosome 12 under N zero level [114]. Four QTLs for trait differences of plant height and heading date between two N levels have been mapped on chromosomes 2 and 8 co-locating with reported QTLs for NUE [111]. In response to low nitrogen application for two years, 33 QTL have been identified in RIL population, out of which only ten QTLs were consistent under low N [115]. QTL mapping for NUE and nitrogen deficiency tolerance traits in RIL population for two

From a recombinant inbred population, 20 single QTLs (S-QTLs) and 58 pairs of epistatic loci (E-QTLs) were detected for the nitrogen concentration of grain, nitrogen concentration of straw, the nitrogen content of shoot, harvest index, grain yield, straw yield and physiological nitrogen use efficiency (PNUE) [117]. Researchers [118] identified seven chromosomal regions using 40 introgression lines (ILs) derived from a cross between "Ilpumbyeo," a temperate *japonica* variety, and "Moroberekan," a tropical *japonica* accession from seedlings grown in 0, 250

Recently, a group of scientists reported [119] about a main effect QTL *qRD-WN6XB* (**Table 2**) on the long arm of chromosome 6, which positively confers

. Among them, the *qRW6* QTL was detected on the long arm of

C11635–P3A2 and phenotypic variance explained by this QTL was 76.4%.

years resulted in four common QTL on chromosomes 1, 3, 4 and 7 [116].

chromosome 6 associated with root weight in temperate *japonica.*

condition. The "Kasalath" allele

accelerated yield performance under low N level [106].

elongation under deficient and sufficient NH4<sup>+</sup>

**146**

and 500 μM NH4

+

*Major QTLs/genes associated with nitrogen use efficiency under abiotic stresses.*

#### **Figure 2.**

*Holistic breeding approach for multiple abiotic stress tolerance in rice. F = flooding, D = drought, S = salinity, QTLs = quantitative trait loci.*

QTLs/genes needed for multiple abiotic stress tolerance, NUE and associated novel traits in rice could be discovered through a holistic breeding approach (**Figure 2**).
