Abstract
Breeding for improving submergence tolerance in rice cultivars is a major objective for flood prone and rainfed areas of Asia. A cluster of three ERF like genes at the Sub1 locus (chromosome 9) has been identified from a rice variety, FR13A that confer tolerance to complete submergence for about 14 days. Further, genetic diversity is one of the important issues to find additional sources of tolerance. In the present investigation, SSR-based clustering and submergence screening among 160 flood prone rice accessions showed that a diverse collection of accessions could provide additional diversity with submergence tolerance sources for further studies. Additional objectives were to study the haplotype variation, based on a set of single nucleotide polymorphisms (SNPs) at the SublA and Sub1C locus (conferring submergence tolerance) and to determine their functional influence on gene transcription variation. The SNP study, generated three patterns at SublA locus: Sub1A0 (null allele), SublAl (does not cut), and Sub1A2 (one SNP), and four patterns were generated at SublC locus: Sub1C1, Sub1 C2, Sub1C3 and Subl C4. Considering different combinations of SNPs (called haplotype), eight haplotypes: A1C1, A1C2, A1C4, A2C2, A2C4, A0C2, A0C3 and A0C4 were detected having increased power over single-allele studies. Varieties of A1C1 haplotype were found as more tolerant than other haplotypes. Further, the varieties Madabaru, and Kottamali (A2C2) were moderately tolerant without the SublA1 allele, indicating the presence of novel genes for submergence tolerance in these varieties. Comparison of Subl and non-Subl varieties under submergence indicated that ethylene response factor (ERF), Sub1A is the principal determinant in submergence tolerance that inhibited the elongation in Subl lines. It is likely that submergence primarily triggers elongation and variation in tolerance which was related with differential expression of elongation within and between haplotypes. Further expression studies also demonstrated that different patterns of expression of SublA and SublC affected elongation differentially and differential elongation had an influence on level of tolerance. SublA and SublC transcripts in relation with elongation might be critical, as excessive elongation confers rapid leaf chlorosis followed by seedling death. In A1C1 haplotype (IR4093), higher Sub1A expression, lower Sub1C transcripts, lower elongation and higher survival were found. In tolerant varieties, the expression of SublA reduced the elongation; suppressed elongation improved the level of survival. Absence of SublA (A0C2 haplotype) or presence of a Sub1A2 (A2C2 haplotype) led to over expression of SublC and strong elongation. In IR42, suppression of SublA transcripts- favoured up regulation of SubIC and expression of strong elongation responded towards high susceptibility. In Kottamali, a novel mechanism favored the expression of both the alleles (a welcome situation over other varieties in A2C2 haplotype). A balance between Sub1A and Sub1C transcripts in shoot of Kottamali expressed a moderate level of elongation and caused limited leaf chlorosis. It is likely that expression of less deleterious medium elongation of Kottamali favoured the novel mechanism that indicated moderate level of tolerance. These studies also demonstrated that two hybrids had unequal expression of Sub1A and Sub1C alleles that also affected the elongation patterns differentially. Selection of hybrid 2 (Kalukanda/Swarna Subl) might led to improvement of tolerance having balanced level of Sub1A and Sub1C transcripts and moderate level of elongation.