Marker aided introgression of ‘Saltol’, a major QTL for seedling stage salinity tolerance into an elite Basmati rice variety ‘Pusa Basmati 1509’

Abstract

Marker assisted backcross breeding was used to transfer Saltol, a major QtL for seedling stage salinity tolerance from the donor FL478 to Pusa Basmati 1509 (PB 1509), a high yielding and early maturing Basmati rice variety. Foreground selection was carried out using three markers namely, AP3206f, RM3412b and RM10793, linked to Saltol. In addition, 105 genome-wide SSR markers polymorphic between FL478 and PB 1509 were used in background selection. Among the BC 3 f 4 near isogenic lines (NILs) developed, recurrent parent genome recovery ranged from 96.67 to 98.57%. Multi-season evaluation identified some of the NILs showing significantly higher yield with grain and cooking quality comparable to PB 1509. All the NILs exhibited tolerance to salinity with significantly higher relative water content, membrane stability index and proline content as compared to PB 1509. the root and shoot concentration of na + , K + and na + /K + in NILs was at par with FL478 under stress conditions. the gene OsHKT1;5 located in the Saltol region showed higher expression levels under stress indicating its role in conferring salinity tolerance. Salt tolerant NILs of PB 1509 will be useful in stabilizing production in salt affected areas. Rice is highly sensitive to salinity stress at seedling and reproductive stages. The symptoms of salt injury in rice are stunted growth, rolling of leaves, white tips, drying of older leaves and grain sterility. The most common injuries are attributed to the destabilization of the membrane, osmotic imbalance and disruption of photosynthetic mechanism 1,2. Water uptake by rice plant is also hindered due to salt stress which causes leaf damage 3,4. Soil salinity limits the rice plant's growth and development, resulting in yield losses of more than 50% 5. Though salinity affects all stages of the growth and development of the rice plant, its effect on young seedlings is highly detrimental as it directly influences plant establishment, thus affecting yield. With every dS/m increase of electrical conductivity (EC) beyond the threshold salt level of 3.0 dS/m, the rice yield is decreased by 12% which implies a yield reduction up to 50% at EC 7.2 dS/m 6. Therefore, development of varieties with seedling stage salinity tolerance can sustain the production of the crop in salt affected areas by promoting the good initial establishment of plants, leading to healthy vegetative growth that can increase crop yield 7. In India, rice is grown on 44 million ha with an annual production of 110 million tons of milled rice. Basmati is premium quality rice which is grown in ~ 2 million ha across seven states of India which has been earmarked as the Geographical Indication (GI) area for the cultivation 8. Basmati rice is well-known worldwide for its exquisite quality traits, superfine grains, fluffy cooked rice with superior eating quality and pleasant aroma 9. It is a valuable agricultural export commodity, which earned foreign exchange worth US$ 4.72 billion during 2018-2019 10 .

Molecular Breeding for Improving Productivity of Oryza sativa L. cv. Pusa 44 under Reproductive Stage Drought Stress through Introgression of a Major QTL, qDTY12.1

“…This has been a conspicuous deviation from our earlier approaches wherein background selection was augmented with phenotypic selection to ensure better RPG as well as recurrent parent phenome (RPP) recovery [ 34 , 35 , 36 ]. Ultimately, deferred background selection provided a recovery of 94.7–98.7%, closely similar to the level of recovery that was previously reported [ 37 , 38 ]. This provided us with two advantages: (i) considerable time could be saved on screening the background markers, which helped us to shuttle the breeding materials between New Delhi and Aduthurai in time, and (ii) considerable resources could be saved as the background recovery was tested on a small panel of selected lines at BC 3 F 4 .…”

Genome-Wide Association Study Reveals Marker–Trait Associations for Early Vegetative Stage Salinity Tolerance in Rice

“…Under salt stress conditions, due to accumulation of Na + , there is significant decrease in chlorophyll concentration which limits the photosynthetic capacity of salt-sensitive plants, leading to chlorosis and reduced growth of seedlings [4,20,63]. This strong association of low Na + uptake, high K + uptake and low Na + /K + ratio with salt tolerance was formerly reported in many studies [28,62,64]. The SKC1 gene from Nona Bokra regulates Na + /K + homeostasis in the shoot under salt stress conditions [59].…”

“…Therefore, development of rice varieties with tolerance to salinity stress is of utmost importance. Huge genetic variability for seedling and reproductive stage salinity tolerance has been reported in rice [4,28,50,51], thus making it acquiescent to genetic manipulation for improving tolerance to salinity stress [52,53]. In the present study, we have evaluated a set of genotypes consisting of landraces, cultivars, and breeding lines for seedling-stage salinity tolerance.…”

“…Several QTLs have been identified, of which Saltol a major QTL for seedling stage salinity tolerance from landrace Pokkali was identified on chromosome 1 which regulates shoot Na + /K + under salt stress [17,20,24]. Saltol is widely used in rice breeding programs aiming towards the development of varieties suited for salinity conditions [28].…”

Toward Integrated Multi-Omics Intervention: Rice Trait Improvement and Stress Management

“…It is well established that salinity tolerance is autonomous at the seedling stage and reproductive stage (Mohammadinezhad et al, 2010). The major salt-tolerant QTL identified is Saltol QTL which has been extensively deployed worldwide to generate better performing rice cultivars (Gregorio, 1997;Krishnamurthy et al, 2020;Yadav et al, 2020). Saltol QTL was identified in IR29 (sensitive variety) and Pokkali (tolerant variety) RIL population which mapped on chromosome 1.…”