Seedling stage salt stress response specific characterization of genetic polymorphism and validation of SSR markers in rice

Abstract

Salt tolerance status at early seedling stage in 30 rice varieties including two tolerant (Pokkali and CSR-36) and two susceptible (IR-29 and IR-64) checks was assessed under different levels of salinity (0, 4, 8 and 16 dS m^-1) created by salt mixture of NaCl, CaCl₂, Na₂SO₄ in 7:2:1 ratio. Overall salinity tolerance indices clearly reflected that 17 varieties including the two tolerant checks were highly tolerant, seven varieties exhibited moderately tolerant, whereas six varieties including the two susceptible checks had highly susceptible response to salt stress. Molecular profiling of 13 tolerant and 5 susceptible rice varieties by using 24 SSR markers revealed 8.5 alleles per primer with altogether 114 shared and 91 unique allelic variants. Considering the allele number, polymorphism information content and polymorphism percent, SSR primers RM 302, RM 8094, RM 10665, RM 10694, RM 10748 and RM 10825 appeared to be highly polymorphic and comparatively more informative. Hierarchical classification and spatial distribution patterns based on amplification profiles dependent similarity indices unambiguously discriminated these 18 varieties in accordance with their salt tolerance response. Sequential exclusion of primers in further analysis led to validation of RM 140, RM 1287, RM 3412, RM 10745, RM 10764 and RM 10772 for their efficiency to distinguish salt tolerant varieties from susceptible ones. A specific combination of either four (RM 1287, RM 3412, RM 10764 and RM 10772) or even two markers (RM 1287 and RM 3412) also seemed to be equally effective in discrimination of entries according to their salt stress responsiveness. Principal coordinate analysis completely corroborated hierarchical classification of the varieties. Salt tolerance donors identified and SSR primers validated in the present study may be further utilized in the development of salt stress tolerant varieties of rice.

Keywords: Principal component analysis; Principal coordinate analysis; Rice; SSR markers; Salt tolerance.

Fig. 1

Principal component analysis based two dimensional spatial distributions of 30 rice varieties along orthogonal coordinate axes

Fig. 2

Amplification pattern of targeted genomic regions in 18 varieties of rice

Fig. 3

Hierarchical classification of 18 rice varieties using 24 SSR primers based similarity indices

Fig. 4

Spatial two-dimensional distribution of 24 SSR primers based genetic profiles of 18 rice varieties

Fig. 5

Hierarchical classification of 18 rice varieties using six SSR primers (RM 140, RM 1287, RM 3412, RM 10745, RM 10764 and RM 10772) based similarity indices

Fig. 6

Spatial two-dimensional distribution of six SSR primers (RM 140, RM 1287, RM 3412, RM 10745, RM 10764 and RM 10772) based genetic profiles of 18 rice varieties

Fig. 7

a Position and arrangement of utilized SSR markers (*Marker position expressed in cM). b Position and arrangement of validated SSR markers

Fig. 8

Hierarchical classification of 18 rice varieties using four SSR (RM 1287, RM 3412, RM 10764 and RM 10772) primers based similarity indices

Fig. 9

Spatial two-dimensional distribution of four SSR primers (RM 1287, RM 3412, RM 10764 and RM 10772) based genetic profiles of 18 rice varieties

Fig. 10

Hierarchical classification of 18 rice varieties using two SSR primers (RM 1287 and RM 3412) based similarity indices

Fig. 11

Spatial distribution of two SSR primers (RM 1287 and RM 3412) based genetic profiles of 18 rice varieties