**Abstract**

Agricultural land and resources reduced annually because of climate change thus it is necessary to further increase the productivity of the major staple food rice to sustain food security worldwide. However, rice productivity enhancement is one of the key challenges in abiotic stress-prone environments. The integration of cuttingedge breeding approaches and research management methods in the current varietal improvement pipelines can make a step-change towards varietal improvement for the abiotic stress-prone environments. Proper implementation of breeder's equations in the crop improvement pipeline can deliver a higher rate of genetic gain. Single Seed Descent based Rapid Generation Advance (RGA) technique in field and greenhouse is the most promising innovations and low-cost, highthroughput marker-assisted selection approaches are applied for rapid and efficient selection for abiotic stress-tolerances. Also improving efficiency, intensity, and accuracy of selection and reducing breeding cycle time through holistic rice breeding that can play an important role in developing climate-smart abiotic stresstolerant rice for target environments. This information can use as the future direction for rice breeders and other researchers.

**Keywords:** abiotic-stress tolerance, high-night temperature (HNT), holistic rice breeding, QTL, gene, product profile, rice

## **1. Introduction**

Rice is the major staple food for more than half of the world population that supplies 30–50% daily calorie intake. Rice security is synonymous with food security in Bangladesh. If rice production hampers because of different abiotic stresses then food security also become vulnerable. Abiotic stresses such as salinity, drought, flood, high-night temperature (HNT), and heat/high-temperature increase enormous challenges that limit agricultural production and food security.

Coastal agriculture faces these challenges because salinity affects directly more than one million hectares of agricultural land in Bangladesh. Salinity causes due to chemical weathering of minerals that release salts in the soils as Na, Ca, Mg ions; coastal agricultural land is inundated by salt-water during flash flood/tidal upsurge; unplanned saltwater intrusion into the shrimp gher (shallow shrimp cultivation pond) in the southern coastal zone and lifting groundwater with EC >3.0 dS/m for irrigation.

Several studies revealed that the detrimental effects and suitable genetic [1, 2] and physiological mechanisms of salt-stress tolerance in various sensitive growth stages of seedling stages like early seedling stage during seedling establishment in the field after transplanting, and different susceptible stages of reproductive phase such as panicle initiation/emergence, booting, flowering/heading, spikelet fertilitysterility, and seed set, yield and other salt tolerance-related traits [3–10].

For maintaining food security and sustainability in rice production, both drought and heat/high-temperature tolerance is important in the respective stress-prone ricegrowing areas for increasing rice production sustainably. However, steady growth in the rice sector is crucial during this pandemic situation to sustain self-sufficiency in different rice-growing countries in South Asia including Bangladesh.

Drought is also an important abiotic stress that threat for rainfed ecosystem. This stress adversely impacts on rice production. Drought tolerance is a complex polygenic trait with a complicated phenotype that affects various growth and developmental stages sensitive to drought-stress in rice. Different droughtresponsive QTLs and genes regulate the degree of sensitivity or tolerance of rice through triggering signal transduction pathways to several drought conditions [11].

High-night temperature (HNT), different abiotic stress from heat stress, is emerging abiotic stress because of climate change. This stress (HNT) is drawing the attention of plant breeders and physiologists due to its detrimental effects on rice productivity. HNT varies 25-30°C that adversely affects yield and grain quality such as chalkiness in rice. This stress was reported in the Rajshahi region of Bangladesh (M. A. Rahman, unpublished data).

Fragile flood-prone environments belong to 18% of areas of Bangladesh that suffer from varying degrees of flooding causes due to flash flood submergence, monsoon flood, and irregular rainfall. The flood adversely influences the rice production of more than a million ha of land in Bangladesh. Submergence tolerant high-yielding rice varieties are grown by the farmers of the flash flood-prone areas. However, deepwater rice (DWR) is cultivated in areas where flood water-depth varied from 1.5 to 2.0 m and these areas are more vulnerable to rice production as there is no high-yielding DWR variety for this harsh ecosystem in Bangladesh. Thus, rice-growing areas under unfavorable environments need to enhance productivity by developing climate-smart rice to cope with the harmful effects of climate change.

In this review, we discuss the abiotic stresses and the development of climate resilient rice addressing adverse effect of climate change.

#### **2. Abiotic stresses influencing rice production and food security**

#### **2.1 Heat tolerance**

#### *2.1.1 Strategies to enhance heat tolerance*

Heat/high temperature tolerance is important in the heat-prone rice growing areas for increasing rice production sustainably. To address climate change,

*Enhancing Abiotic Stress Tolerance to Develop Climate-Smart Rice Using Holistic Breeding… DOI: http://dx.doi.org/10.5772/intechopen.97283*

screening and breeding for higher level of heat tolerance is needed. Strategies such as agronomic intervention through sowing time adjustment, chemicals/plant hormones application, genetic and genomic approaches [12], breeding for heat resistant variety development, marker-assisted introgression of *qEMF3 QTL [13] for developing and selecting* cultivars with early morning flowering (EMF) before temperature rise are involved for improving heat tolerance.

QTLs associated with heat tolerance related traits using bulked segregant analysis in Rice to evaluate the genetic effect of QTLs controlling heat tolerance at flowering stage in rice. A population comprising 279 F2 individuals developed from 996 (heat tolerant)/4628 (heat-sensitive cultivar), was investigated for their segregation pattern of the difference in seed set rate under normal/optimum temperature condition and stress/high temperature condition that exhibited normal distribution, suggesting the polygenic control on the heat tolerance [14].

Eleven QTLs identified for heat tolerance using RIL population derived from IAPAR-9 (sensitive)/Liaoyan241 (heat tolerant) at the heading and flowering stage in rice. Four major QTLs such as *qNS1*, *qNS4*, *qNS6,* and *qRRS1* found stable in both seasons/years in various environments [15].

Jagadish [16] dissected QTLs for relative spikelet fertility during anthesis in rice *qtl\_1.1* (38.35 Mb) and *qtl\_11.1*, 24.16 Mb, QTL contributor is Azucena) and one (*qtl\_10.1*, 20.14 Mb from Bala). Total 24.1% phenotypic variation was explained by these three QTLs.

#### **2.2 Drought stress tolerance**

Improving grain yield is the key and universal objective of any crop breeding programs including rice. Identification of yield and yield-related traits and their introgression into adapted varieties is one of the best strategies to increase grain yield under drought. A number of yield QTLs identified in different chromosomes of rice under drought stress. QTL *qDTY12.1* was the first identified major grain yield QTL on chromosome 12 in rice under drought at the reproductive stage [17]. Another large-effect QTL for grain yield, *qDTY1.1*, was identified on chromosome 1 [18]. Moreover, other QTLs with major effect such as *qDTY2.2*, *qDTY3.1*, *qDTY3.2*, *qDTY4.1*, *qDTY6.1*, *qDTY9.1* controlling drought tolerance in rice were reported by several investigators [19–22]. The identified QTLs should be consistent in multiple genetic backgrounds and various target environments [23, 24]. Efficient QTL stacking of the major effect QTLs in the adapted varietal background is necessary to achieve higher grain yield under drought [25].

QTLs related to drought tolerance in rice have been shown in **Table 1**. However, only a few QTL studies on grain yield under drought stress have been reported. Most of the QTLs detected for regulating drought stress in rice analyzed for different important drought-related traits such as osmotic adjustment [48, 49], drought avoidance [32], root and shoot responses [50], photosynthesis and whole plant response [51] to drought tolerance.

#### **2.3 Flood/submergence tolerance**

Flood-prone ecosystems are fragile characterized by varying level of flooding, erratic precipitation that affect the rice production of more than one million ha in Bangladesh. Deepwater rice is cultivated more than 100000 ha in Bangladesh and the typical deepwater rice with nodal tillering, kneeing ability to keep the top three leaves in the air (above the water level) to capture and use solar energy for photosynthesis, internode elongation ability to prevent drowning with high yielding potential comparing with local varieties like Hijoldigha, Laxmidigha, Kartiksail,



*Enhancing Abiotic Stress Tolerance to Develop Climate-Smart Rice Using Holistic Breeding… DOI: http://dx.doi.org/10.5772/intechopen.97283*

#### **Table 1.**

*Useful QTLs responsible for drought-stress tolerance in rice.*

Khoiyamtor, Lalmohan, and Shishumati. These local germplasm has the ideal ideotype for deepwater ecosystem but only limitation is low yielding ability. To address sustainable development goals (SDGs) and maintain food security, we need to increase the production in the abiotic stress prone environments such as salinity, flood/submergence, drought and heat-prone areas through horizontal expansion (expansion of arable land in abiotic stress prone areas which are not yet under cultivation) of abiotic stress tolerant rice varieties in these areas. However, Floodprone ecosystems in Bangladesh are four types such as long time flooding zone (>35 days; 1.5–2.0 m water-depth), flash flood submergence zone (15–30 days; up to 1.5 m water depth), deepwater (> 2.0 m water-depth) zone and submergence during germination (10–12 cm depth) at relay Transplant Aman, direct seeded rice (DSR *Aus*) and broadcast Aman (B. Aman) Rice areas anaerobic germination In Asia, submergence affects rice yield adverselyin 20 million ha, causing food insecurity. The *SUB1*gene governing submergence tolerance cloned and introgressed into a number of rice varieties in South Asia, South East Asia and Africa. Yield advantages of Sub1 varieties ranged from 1.0 to >3.0 t ha�<sup>t</sup> after submergence comparing with non-Sub1 varieties. These submergence tolerant varieties reached more than 3.8 million farmers within 3 years of release in Asia [52].

Biosynthesis of growth regulator (Gibberellin) and signal transduction is important pathways for internode elongation of the deepwater rice [53]. Two large-effect QTLs located on chromosomes 3 (*qGTIL3,qGLEI3*, *qGNEI3* located between 38 and 87 cM) and chromosome 9 (*qGTIL9*, *qGLEI9*, *qGNEI9* positioned between 16 and 88 cM) are controlling traits such as total length of internode (TIL), lowest elongated internode (LEI) and number of elongated internode number (NEI). Three factors involved to characterize deepwater rice internode elongation ability: (1) total length of elongated internode (TLEI); (2) elongated internodes number (EIN); and (3) minimum elongated internode (MEI) [54–57]. Among these, MEI is the main parameter for initiating the internode elongation of deepwater rice [54] because MEI is leaf stage- dependent and first starts of internode elongation at the sixth leaf stage in deepwater rice.

Catling (1992) [58] described the genetic basis of internode elongation during submergence of deepwater rice that is regulated by several minor and two major genes. Suge [59] identified one gene with neither allele is found dominant (incomplete dominance) that responsible for elongation ability. Internode elongation depends on the increasing activity of cell division and cell elongation in specific areas of the internode.

#### **2.4 Salt tolerance**

Salt-stress entails changes in different physiological and metabolic pathways, based on severity and duration of the stress, and eventually decreases rice productivity [10, 60–62].

Genetic characterization of salt tolerance related traits is important to estimate phenotypic co-efficient of variation (PCV), genotypic co-efficient of variation (GCV), broad-sense heritability and genetic Advance (GA).

If sufficient variation with high heritability and genetic advance exists in the germplasm for salt tolerance related traits; consequently there is possibility to improve the traits related with salt tolerance in rice by exploiting salt tolerant landraces/germplasm in the breeding programs.

Genetic component analysis (GCA) study showed that both additive and dominance gene effects controlled low Na-K ratio [63]. The combining ability analysis shows that both general combing ability (GCA) and specific combining ability (SCA) effects are also important for deciphering the genetics of salt tolerance. They also revealed that selection may be made in later generation under controlled conditions for minimizing environmental effects for low heritable traits like Na-K ratio.

The additive effects could enhance fixation of the desirable combination of genes and also additive gene action is correlated to narrow sense heritability [64]. Thus, selection for salinity tolerance may be made in the early generation. Understanding the gene action for salt tolerance in rice will be useful in the future breeding program [65].

#### *2.4.1 Molecular basis of complex salt tolerance*

The molecular dissection of salt tolerance has considerably enhanced using the molecular platforms for identifying quantitative trait loci (QTL) controlling related genetic variation in crops including rice [1, 2, 8, 60, 66–72].

Moreover, several QTLs related with physiological, agronomic traits conferring salinity tolerance at seedling and reproductive stage have been reported [1, 8, 71, 73, 74] including major QTLs for salinity tolerance such as *SKC1* [75] (a sodium transporter *OsHKT1; 5* in the *SKC1* locus [76] and *Saltol* [71, 77] on chromosome 1


#### *Enhancing Abiotic Stress Tolerance to Develop Climate-Smart Rice Using Holistic Breeding… DOI: http://dx.doi.org/10.5772/intechopen.97283*


#### **Table 2.**

*Recently identified QTL for salt tolerance with controlling/responsible traits and phenotypic variation using different mapping populations at seedling and reproductive stages in rice.*

(**Table 2**). Recently unraveled molecular basis of various rice landraces such as Pokkali [71, 77], Nona Bokra [76], Hasawi [1], Capsule [2], Changmaogu [74] and Horkuch [72] can withstand different levels of salt-stress at various sensitive growth stages of rice.

## *2.4.2 Enhancing genetic gain for salt-stress*

Widely used tools for quantitative genetics such as genomic estimated breeding value (GEBV) and best linear unbiased predictions (BLUPs) are applied to evaluate the performance to construct high throughput new breeding populations for selecting the superior breeding lines when combined with genetic relatedness or kinship matrix/information (i.e. coefficient of coancestry) using pedigree information to calculate estimated breeding values (EBVs). This is a key parameter for selecting complex traits like salt tolerance and yield through estimating parents' genetic potential to produce better descendants on the basis of parent's own performance, pedigree information and progeny data. EBVs play important role to select parent for higher rate of genetic gain [83].

Theory of genetic gain in breeding and classical biometrical genetics indicates the improvement of performance compared to a standard or baseline. It is generally evaluated after advancing one generation to the subsequent generation and artificial selection is done [84]. However, genetic gain per year is also known as genetic trend that measured varietal performance over year by comparing benchmark or dominant varieties [85].

To maintain the food security under this Covid-19 situation horizontal expansion (increase of rice growing areas in high saline zone) of rice cultivation is needed areas in the coastal zone. Thus large areas will be brought under cultivation in high saline prone areas.

#### **2.5 Modern breeding**

Genomic assisted breeding (GAB) is regularly practiced for the genetic improvement of salt-tolerant rice applying various innovative tools for genomic breeding such as forward breeding, rapid breeding, and haplotype-based breeding [86]; 5G breeding methods such as genome sequence availability (genome assembly), characterization of germplasm at genomic and morpho-agronomic level, gene detection and understanding function, genomic breeding, and genome editing for enhancing superior performance of genotypes [87] could be used for enhancing efficiency and accuracy of breeding for complex traits related with abiotic stress tolerance. A precise SNP-assisted introgression of the *hst1*(*hitomebore salt-tolerant 1*) gene improved salt tolerance in the high-yielding rice variety was achieved through SNP based speed breeding [88].

Modern breeding emphasizes data-based parent selection. Local and exotic germplasms are subjected to genetic distance measurement, trait characterization through diagnostic trait markers, genomic selection, and breeding value estimation. Sometimes trait of interest (ToI) like salinity and submergence tolerance, aroma, disease resistance is found in local germplasm with low yield potential. Then that ToI is first transferred to an elite background possessing high yield potential for developing pre-breeding materials. After that, the elite line with the desired traits is used in breeding purposes to fulfill the product profile. **Figure 1** shows the schematic illustration for optimizing breeding scheme to achieve genetic gain.

We evaluated 1436 breeding lines for trait assay using 20-trait specific single nucleotide polymorphism (SNP) markers. These lines characterized for important traits such as disease (blast, bacterial leaf blight: BLB) and insect (brown plant

#### **Figure 1.**

*Varietal development through breeding modernization for rapid varietal turnover and replacement for rice growers of target regions.*

#### **Figure 2.**

*Genetically important lines (GILs) in the STR Breeding program,T. Aman, 2020-21.*

hopper: BPH; gall midge) resistance, grain quality (amylose content, chalkiness), grain number (*Gn1a*) and salinity tolerance at seedling stage (sodium exclusion, SES) traits. Out of 1436 breeding lines, 100 lines harbored the 7–10 QTLs/genes that regulating trait of interest (**Figure 2**) that designated as Genetically Important Lines (GILs). Each line assayed against QTLs and genes of interest to assess the presence or absence of useful traits. IRRI developed trait specific SNP markers used (https:// gsl.irri.org/) and SNP genotyping assay was carried out by Intertek as an external service provider. The trait-based SNP markers associated with the traits for


*Enhancing Abiotic Stress Tolerance to Develop Climate-Smart Rice Using Holistic Breeding… DOI: http://dx.doi.org/10.5772/intechopen.97283*

#### **Table 3.**

*Useful traits, trait-based SNP markers and their contributors of favorable allele.*

instance, snpOS00478 (*Pb1*), snpOS00451 (*Pi9*), and snpOS0054 (*xa5*), snpOS0061 (*Xa21*) etc. were applied for genotyping (**Table 3**).

These ten SNP markers produced 40% polymorphism across the *indica* germplasm derived pairwise combinations where in 95% of crosses made at least 1 polymorphic SNP marker was found within the IRRI rice breeding pool or *indica* subspecies (gsl@irri.org[https://sites.google.com/a/irri.org/snp-genotyping-mmal/ genotyping/quality-control-panel/indica-rice-qc-10-snp-panel).

Single seed descent method with the facility of rapid generation advance technique is expected to have better efficiency in the increment of genetic gain compared to pedigree and other methods of breeding [2]. From each cross, 200– 400 fixed lines evaluated in line stage testing (LST) trial and selection performed using high selection pressure. Then the selected lines are evaluated in yield trials and include in new variety release system (**Figure 1**).

Modern biometric tools are used in data analysis and field layout preparation of several experiment design e.g. P-rep, Augmented RCB, Alpha-Lattice, Latinized row-column, RCBD. Observation trials are mainly conducted using P-rep, Augmented RCB, Alpha-Lattice design of experiment based on the entry number and land availability. Selected genotypes are subjected to grain property analysis (e.g. grain size, shape, L/B ratio, etc) and physicochemical property analysis (e.g. amylose content). Selected genotypes that hold good agronomic traits, grain quality

characters and desired traits diagnosed through SNP markers are used as Elite parent in cyclic breeding program.

During this period phenotypic data collection is aided with data collection machine (Grain counter, Nondestructive moisture meter, destructive moisture meter, Phenoapp, CT5) and different software's like B4R (Breeding 4 Rice), FieldBook etc.

We need to explore a large number of cross combination derived fixed lines to experience a remarkable genetic gain with the shortest possible time. Line fixation can be accomplished within three years using the RGA [89, 90] facility which allows a breeder to contribute more in varietal development.


*Legend: 1= must have traits, 2= nice to have, 3= value added or game changer*

#### **Table 4.**

*Product profile with market demand-led traits for developing salinity tolerant rice (STR) variety for target region under STR breeding program at BRRI.*

*Enhancing Abiotic Stress Tolerance to Develop Climate-Smart Rice Using Holistic Breeding… DOI: http://dx.doi.org/10.5772/intechopen.97283*

However, promising breeding lines selected in OYT will be recycled to initiate next cycle of breeding for population improvement. By applying this transformed/ modernized breeding approach abiotic stress tolerant varieties with enhanced grain yield and quality traits will be developed.
