Expression analysis of some cold responsive ESTs in seedling- stage cold-tolerant QTL in rice (Oryza sativa l.)

A L Ranawake,C Nakamura

doi:10.4038/tare.v16i1.5268

Abstract

Recombinant inbred lines (RILs) derived from a Japonica parent Hygokithanishiki (HGKN) and Indica parent Hokuriku (HOK) were used to identify quantitative trait loci (QTLs) controlling cold tolerance at the seedling stage in rice (Oryza sativa L). Genetic map with 95 SSR markers were used for QTL analysis and 163 RILs were subjected to two consecutive cold stresses at 4 o C for cold tolerance evaluation. Five major QTLs were identified in two different cold stresses and among these QTLs, QTL on chromosome 11 scored 9.39 and 5.43 LOD values at the first and the second cold stresses respectively. In rice expression sequence tags (EST) data base, cold responsive ESTs were found in the QTL region of chromosome 11 and they were analyzed by reverse transcriptase polymerase chain reaction (RT-PCR). RT-PCR was done under cold stress and control conditions in parental rice cultivars and in selected cold tolerant RILs with relevant chromosome fragment from HGKN parent and in selected cold susceptible RILs with relevant chromosome fragment from HOK parent. Results showed that ESTs numbered CI047516.1, CI049555 and CI049229 expressed highly in cold tolerant parent and in selected cold tolerant RILs at cold stress giving evidence on possible candidate ESTs in cold tolerant QTL.

Highlights

Cold tolerance is a complex trait involving a number of biochemical and physiological events, which are controlled by major and minor quantitative trait loci (QTLs)
Genomic approaches for identification of expressed genes, namely expressed sequence tag (EST; Adams et al 1995), serial analysis of gene expression (SAGE; Velculescu et al 1995), and massively parallel signature sequencing (MPSS; Brenner et al 2000), have been widely used in gene expression studies in various organisms
In the present study cold responsive ESTs identified in the candidate region of the major seedling stage cold tolerant QTL were further studied to understand their contribution towards cold tolerance

Summary

Introduction

Cold tolerance is a complex trait involving a number of biochemical and physiological events, which are controlled by major and minor quantitative trait loci (QTLs). Cold tolerant QTLs at seed germination, vegetative and booting stages have been identified in different populations (Fujino et al 2004; Saito et al 2001; Andaya and MacKill 2003a; Andaya and MacKill 2003b; Andaya and Tai 2006; Andaya and Tai 2007; Zhang et al 2005). 16 RANAWAKE AL & NAKAMURA C : COLD RESPONSIVE ESTS IN A RICE COLD TOLERANT QTL

Results

Conclusion