**5. Salt-tolerant germplasm in Sri Lanka**

Sri Lanka was the first country to recommend rice varieties for salinity-prone areas whereby the first variety released was an improved land race "Pokkali" [73]. Presently, there are four elite locally improved rice varieties recommended for cultivation in salt-affected areas namely Bg369, Bg310, At401, and At354 [33]. Salt- tolerant germplasm Pokkali [74] and Nona Bokra [75] are extensively used in local salinity tolerance breeding programs. Pokkali is an immediate parent of Bg310, At401, and At354, whereas Nona Bokra is an immediate parent of Bg369. In addition, tolerant and moderately tolerant local rice germplasm that express Na<sup>+</sup> exclusion at root surface, Na<sup>+</sup> exclusion at root xylem parenchyma, and capacity to maintain shoot water status under saline stress were identified [76].

Pokkali and Nona Bokra are known to withstand salinity EC > 12 dSm<sup>1</sup> from seedling to harvesting [68, 77–79] and were also reported to express high to moderate salinity tolerance throughout the crop life. Pokkali and Nona Bokra seedlings recorded salinity susceptibility scores of three compared to a score of seven in susceptible checks [80]. The concentration of NaCl inhibiting 50% of shoot growth (IC50) in 72 hours is 305 mM in Nona Bokra and 272 mM in Pokkali but significantly low in susceptible IR64 (188 mM) and IR29 (243 mM). Shoot Na<sup>+</sup> accumulation after 2 hours of 200 mM salinity stress at the seedling stage was 50% in Pokkali (2629.6 ppm) compared to that in the susceptible variety IR64 (5674.3 ppm). Similarly, plant Na+ concentration and Na<sup>+</sup> /K<sup>+</sup> ratio were 2.4 and 2.5 folds lower in Pokkali seedlings compared to that in the salt-sensitive, IR64 [81]. Nona Bokra and Pokkali report low shoot Na<sup>+</sup> content of 5 mg/g by shoot dry weight compared to IR64 (13 mg/g) and IR29 (12 mg/g) [82]. Nona Bokra, Pokkali, and IR28 reported 0.6 mg, 4.0 mg, and 5.8 mg reduction of dry weight of a fertile spikelet at 15 dSm<sup>1</sup> , indicating the presence of tolerance mechanisms that are effective over the growth period. [83]

Pokkali and Nona Bokra express "Na+ exclusion," and therefore the phenotypes are "high Na+ in the culm and low Na+ in the leaf" [76]. Evidence found on additional resistance traits such as efficient photosynthesis, adaptive defense mechanisms, osmolyte accumulation, membrane integrity, and optimum biochemical environment in the cells of Pokkali may provide whole-life resistance [84–87]. Furthermore, multiple Quantitative Trait Loci (QTLs) associated with salinity tolerance were predicted in Pokkali [88–92], including the *Saltol* locus [93–97], which is collocated with a major QTL, *SKC1* from the salt-tolerant landrace, Nona Bokra [98]. *Saltol*/*SKC1* is a major QTL associated with low Na+ uptake, high K+ uptake, and Na+ /K+ homeostasis in shoots in the seedling stage. *Saltol/SKC1* was collocated with an important candidate gene *OsHKT1;5*, a high-affinity K transporter gene [99–101] that is expressed in xylem parenchyma cells, and retrieves Na+ ions from xylem sap under salinity. Furthermore, root QTLs associated with the total Na+ in the root (*qRNTQ-1*) and K+ concentration in root (*qRKC-4*) that contribute to salt tolerance were reported in a cross between Nona Bokra/Koshihikari [102]. The physiological, genetic,

*The Scale and Complexity of Salinity Impacts on Sri Lankan Rice Farming Systems:… DOI: http://dx.doi.org/10.5772/intechopen.112651*

and genomic studies, therefore, revealed multiple tolerance mechanisms expressed at different growth stages in Pokkali, Nona Bokra, and in the local varieties derived from those parents.

Although the four recommended local varieties expressed comparable saline tolerance at specific crop growth stages, overall tolerance levels during the crop life were not comparable with that of Pokkali and Nona Bokra. Based on the percentage germination of seeds soaked at 45 dSm<sup>1</sup> salt solution for 9 days [103], At 354 (21–30% germination) was moderately susceptible for salinity compared to Pokkali (51–70% germination); however, Bg369 was highly susceptible (>10% germination) [68, 78, 104]. Evidence from multiple studies found that based on susceptibility scores at 12 dSm<sup>1</sup> At354 and Bg369 were tolerant and comparable with Pokkali at seedling stage [68, 76]. Nona Bokra and Pokkali seedlings survived (100% survival rate) up to 8 dSm<sup>1</sup> ; however, above 4 dSm<sup>1</sup> survival rates declined by 50% in IR28 [105]. Based on the survival percentage of plants treated at 12 dSm<sup>1</sup> from 3 weeks to flowering, Bg369 and At354 were comparable with Pokkali [68]. Additionally, the yield reduction at 8 dSm<sup>1</sup> based on grain yield per panicle, At354 was low compared to Pokkali and Nona Bokra (per panicle grain yield reduction was 0.72 g, 0.43 g, and 0.38 g respectively) [78]. A F5, RILs population of At354 Bg352 (susceptible check), predicted six QTLs on chromosomes 1 and 4 from At 354, contributing to 10–16% of the total phenotypic variability. The six QTLS were collocated with 10 tolerant haplotypes of Os01g0581400, Os10g0107000, Os11g0655900, Os12g0622500, and Os12g0624200, highlighting the genetic potential of At354 as a salinity tolerant variety [106]. Therefore, it is clear that the full potential of Pokkali, Nona Bokra, and the related germplasm is yet to be explored and incorporated into local elite rice varieties.

Several reports have identified unique local rice germplasm that can be used in base broadening for salinity tolerance [68, 78, 104]. In a study, using 102 rice accessions from local germplasm including both traditional and improved varieties five susceptibility/tolerance categories were identified based on growth parameters during the initial phase (Phase I) of osmotic stress caused by reduced water uptake due to excess salts in the external soil solution at 100 mM Na<sup>+</sup> (**Figure 6**) [65]. Interestingly, in this study Pokkali was categorized as "tolerant," whereas six phenotypically superior germplasm were categorized in the "highly tolerant" category. Multiple tolerance traits were expressed in 7% of the germplasm [76]. Interestingly, unique germplasm

#### **Figure 6.**

*Salinity tolerance mechanisms in 54 selected traditional and improved rice germplasms from Sri Lanka at the seedling stage (based on [76]).*

superior to Pokkali at different development stages were also reported. Bg406 records 70% germination under 12 dSm<sup>1</sup> EC, expressing similar or more tolerance than Pokkali (51–70%); At402, performed equal or better at the seedling stage and reproductive stages [68]. Similarly, At303, Bg350, and Bg450 have a high tolerance compared to Pokkali at the osmotic phase of salinity stress [76] owing to their ability to maintain high relative growth rate at early stages of salinity (24 hours after final salinization at 10 dSm-1). The unique varieties namely Bw400, At402, and Bg406 expressed tolerance compatible with Pokkali at varying degrees throughout the crop life [107]. As these traits and associated alleles are distinct from Pokkali and Nona Bokra parental germplasm, these provide unique germplasm base for increasing salinity tolerance in elite rice genotypes without compromising crop vigor. Therefore, further analysis of the local germplasm will identify novel physiological and genetic tolerance mechanisms, and the associated genotypes can be used in base-broadening for salinity tolerance breeding in rice.
