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Molecular Diversity and Expression Studies of Sub1 Gene Haplophyes of Rice, Differing in Tolerance to Submergence

Mr. ASM Masuduzzaman
Ph D Fellow
Department of Genetics and Plant Breeding,BAU, Mymensingh-2202

Abstract/ Executive Summary:

The varieties Madabaru, and Kottamali were moderately tolerant without the Sub1A1 allele, indicating the presence of novel genes for submergence tolerance. Comparison of Sub1 and non-Sub1 varieties under submergence indicated that ethylene response factor (ERF), Sub1A is the principal determinant in submergence tolerance that inhibited the elongation in Sub1 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 Sub1A and Sub1C affected elongation differentially and differential elongation had an influence on level of tolerance. Absence of Sub1A or presence of a Sub1A2 led to over expression of Sub1C and strong elongation. In IR42, suppression of Sub1A transcripts- favoured up regulation of Sub1C and expression of strong elongation responded towards high susceptibility. In Kottamali, a novel mechanism favored the expression of both the alleles. It is likely that expression of less deleterious medium elongation of Kottamali favoured the novel mechanism that indicated moderate level of tolerance. Selection of hybrid 2 (Kalukanda/Swarna Sub1) might led to improvement of tolerance having balanced level of Sub1A and Sub1C transcripts and moderate level of elongation.

Keywords: DIVERSITY, RICE, TOLERANCE, Halophyte

Location: Department of Genetics and Plant Breeding, BAU, Mymensingh

Start Date: 06-03-2004

End Date: 25-01-2009

Program Area: Variety and Species

Commodity: Rice

Objectives:

To improve submergence tolerance in rice cultivars for flood prone and rainfed areas of Asia.

Methodology:

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 Sub1A and Sub1C locus (conferring submergence tolerance) and to determine their functional influence on gene transcription variation. The SNP study, generated three patterns at Sub1A locus: Sub1A0 (null allele), Sub1 A1 (does not cut), and Sub1A2 (one SNP), and four patterns were generated at Sub1C locus: Sub1C1, Sub1C2, Sub1C3 and Sub1C4. Considering different combinations of SNPs (called haplotype), eight halophyte: A1C1, A1C2, A1C4, A2C2, A2C4, A0C2, A0C3 and A0C4 were detected - having increased power over single-allele studies.

Source of Information: PhD Thesis of Mr. ASM Masuduzzaman, Roll No.: 04 (2004-05),Reg. No.: 13166 (1984-85),Dept. of Genetics and Plant Breeding

Article Link (Online Journal):

Funding Source:

1. Government

Budget:

Total Budget (Tk.) :

Achievement/Findings:

The main achievement of the research work •Crossing of genotypes from SSR-based different clusters could be useful for the improvement of submergence tolerance in rice. Genotype Kottamali identified as a source of novel submergence tolerant gene suitable for developing improved rice varieties for stagnant flooding condition, where adaptation of semi-dwarf rice varieties are limited. •Hybrid-2 (Kalukanda/Swarna-Sub1) found to have balanced level of Sub1A and Sub1C transcripts as well as moderate level of elongation.

Knowledge Management: Thesis