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 BC₃F₄ 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.

Figure 1

Graphical representation of PB 1509-NILs carrying ‘Saltol’ depicting the extent of recovery of carrier chromosome (Chromosome 1).

Figure 2

Screening of Saltol-introgressed PB 1509-NILs (1-20) along with the recurrent parent (RP) PB 1509, susceptible check (SC) IR29 and the donor parent (DP) FL 478 for seedling stage salinity tolerance under field condition (micro-plot) at EC of 13.9 dS/m, (a) unstressed, (b) salt-stressed condition.

Figure 3

Effect of salt stress on parental lines and PB 1509-NILs for, (a) RWC: relative water content, (b) MSI: membrane stability index, and (c) Proline content. Student’s t-test was performed for statistical significance. An asterisk (*) above the bars refers significant difference from the RP-PB 1509 at P ≤ 0.05. The values represented are the mean of three biological replicates and standard error is shown as error bars.

Figure 4

(a) Shoot and (b) root Na⁺/K⁺ ratio of PB 1509-NILs compared with recurrent and donor parents under salt stress condition. Student’s t-test was performed to test the statistical significance. An asterisk (*) above the bars refers to the significant differences from PB 1509 at P ≤ 0.05. The values represented are the mean of three biological replicates. Standard error is shown as error bars.

Figure 5

Ranking of PB 1509-NILs carrying Saltol QTL and PB 1509 and FL478 relative to an “ideal genotype”. E1, Kharif 2017; E2, Kharif 2018, E3, Kharif 2019.

Figure 6

Expression profile of OsHKT1;5 in the parental lines (PB 1509 and FL478) and PB 1509-NILs (NIL9 and NIL18) at different time intervals after exposing to 50 mM of salt stress. Bar graphs were plotted between stress hours (x-axis) and relative expression level (log 2-ddCt) (y-axis). Student's t-test was performed for determining the statistical significance. An asterisk (*) above the bars refers to significant differences from their respective control at P ≤ 0.05. The values represented are the mean of three biological replicates and standard error is shown as error bar.

Figure 7

Marker assisted backcross breeding scheme used for introgression of Saltol in RP-PB 1509.