Analysis of DRO1 expression under water deficit stress and its relationship with root angle phenotype in Indian rice accessions
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Date
2017
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DIVISION OF MOLECULAR BIOLOGY AND BIOTECHNOLOGY ICAR-INDIAN AGRICULTURAL RESEARCH INSTITUTE NEW DELHI
Abstract
Deeper Rooting 1 (DRO1) gene identified from a major QTL on chromosome
9 is associated with increasing the root growth angle (RGA) in rice. This gene is a
major player in providing wider RGA and facilitates survival under water deficit
stress conditions. To understand the allelic status and expression of DRO1 and its
association with RGA phenotype in rice the present research work was undertaken.
The study material comprising of 24 major Indian upland and lowland genotypeswere
grown in well-watered control (WC) and water-deficit stress (WS) conditions. Root
length increased under WS across the accessions wherein the genotypes Azucena and
Satti showed almost 40% increase.For root length, ANOVA revealed that the
genotype differences were not significant but treatment differences were. In case of
root angle, however, the means were statistically non-significant between the
treatments while genotype differences did exist based on which the study material
could be grouped into two classes (9 wide angle and 15 narrow angle genotypes).
Expression analysis revealed that the gene was upregulated in all genotypes by 1- 4.5
fold and verified the grouping in seven of the nine wider angle genotypes. DRO1 gene
(3058bp) was amplified using four pairs of overlapping primers and sequenced. In the
756 bp long CDS of DRO1, a total of 52 SNPs but no InDels were identified across
the 24 genotypes. The SNP position 375 was triallelic and transversions were almost
2.5 folds more common than transitions. Among the genotypes, donor of DTY 3.1(1
SNP) showed the least number of changes, whereas DTY 9.1(19 SNPs) showed the
most. In the 251 amino acid long protein, substitutions were found in 19 positions,
wherein position 92 was the most frequent. Based on the allele mining, all the 24
genotypes can be grouped into 16 haplotypes covering the variation from functional
allele (Satti, IR36 and DTY 3.1) to truncated non-functional alleles in PMK2, IR64,
IR20 and Swarna. The information obtained in the present investigation regarding the
allelic and expression status of the DRO1 gene will be very useful for the breeders in
their crop improvement programme on drought tolerance.
Key words: Rice, root angle, DRO1, allele mining, expression profiling
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t-9658
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