Asian Journal of Bio Science

B. P. Niranjan Reddy ¹, R. K. Deshmukh ², Bhavna Gupta ³, N. K. Deshmukh ², G. Bhaganagare ³, S. M. Shivraj ³, T. Singh ³, A. S. Kotashane ³

Affiliations
1 National Research Center on Plant Biotechnology, IARI, New Delhi, IN
2 Dept. of Boitechnology, Swamy Ramanand Teerth Marathwada University, Nanded (M.S.), IN
3 Dept. of Boitechnology, Indira Gandhi Krishi Vishwavidhyalaya., Raipur, (C.G.), IN

Abstract

To identify putative candidate genes involved in BLB disease resistance, we performed in silico anchoring of the generated QTL genetic marker data to the rice physical map. In total, one QTL responsible for resistance specificity to Xanthomonas oryzae pv. oryzae iso 6 was identified using CT 9993-5-10-1-M / IR 62266-42-6-2 double haploid population. The QTL qBB 10.1, on chromosome 10 RG 4561-EM 14-10 was saturated with 108 markers, 1097 ESTs, and 201 genes. In total, 28 putative positional candidate genes were identified and were classified based on their function. it is suggested that, the generated data can further be used for the dissection and validation of the QTL to understand the molecular mechanisms of the plant pathogen interaction and to develop a resistant variety.

Keywords

QTL, Bacterial Leaf Blight, Expressed Sequence Tags, Candidate Genes, Physical Map.

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R. K. Deshmukh ¹, N. K. Deshmukh ², G. B. Patil ¹, S. B. Kadam ¹, H. Sonah ¹, R. N. Gacche ²

Affiliations
1 Department of Biotechnology, Indira Gandhi Krishi Vishwavidyalaya, Raiur (C.G.), IN
2 Department of Biotechnology, Swami Ramanand Teerth Marathwada University, Nanded (M.S.), IN

Abstract

The term promoter is used to designate a region in the genome sequence upstream of a gene transcription start site (TSS). Most promoter elements regulating TSS are localized in the proximal promoter, is a region of several hundreds nucleotides around the TSS. If the SNP occurs within coding sequence, which may or may not alter amino acid sequence. Where as, SNPs occur within the proximal promoter region has more impact on gene expression. The publication of whole genome sequences for the japonica (Nipponbare) and indica (93-11) types of rice enables the determination of common SNPs occurring between them. In present study we used 31 non-redundant proximal promoter sequences in rice, from previous studies which are experimentally determined transcription start site for RNA polymerase II. When proximal promoters of japonica were compared with the corresponding proximal promoters of indica using BLAST alignment programme, a total of 69 SNPs were identified. Out of these 32 SNPs (46.3%) were transitions (A/G, T/C) and 37 SNPs (53.6 %) were transversions (A/C, A/T, G/C, G/T). Maximum frequency of SNPs was found in the region -50 to -150 (61.2 %). Minimum frequency found in region -151 to -201(9.6 %). It demonstrate that functional cis-regulatory polymorphisms segregate within sub species of rice and there is abundant SNP present in proximal promoter region. SNPs in proximal promoter may one of the causes of fictional variation. In addition, study indicates that SNPs are not evenly distributed. Selection pressure is always more for a region having more fictional impact and theoretically should have conserved, in contrast nonfunctional regions acting as reservoir of mutation.

Keywords

Cis Acting Elements, Proximal Promoter, SNP.

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