Characterizing the Saltol Quantitative Trait Locus for Salinity Tolerance in Rice

Michael J Thomson,Dante L Adorada,Marjorie De Ocampo,Abdelbagi M Ismail,Eduardo Blumwald,Rakesh K Singh,Andres Godwin Sajise,M Akhlasur Rahman,Glenn B Gregorio,Ellen Tumimbang-Raiz,James Egdane,Zeba I Seraj

doi:10.1007/s12284-010-9053-8

Abstract

Abstract This study characterized Pokkali-derived quantitative trait loci (QTLs) for seedling stage salinity tolerance in preparation for use in marker-assisted breeding. An analysis of 100 SSR markers on 140 IR29/Pokkali recombinant inbred lines (RILs) confirmed the location of the Saltol QTL on chromosome 1 and identified additional QTLs associated with tolerance. Analysis of a series of backcross lines and near-isogenic lines (NILs) developed to better characterize the effect of the Saltol locus revealed that Saltol mainly acted to control shoot Na+/K+ homeostasis. Multiple QTLs were required to acquire a high level of tolerance. Unexpectedly, multiple Pokkali alleles at Saltol were detected within the RIL population and between backcross lines, and representative lines were compared with seven Pokkali accessions to better characterize this allelic variation. Thus, while the Saltol locus presents a complex scenario, it provides an opportunity for marker-assisted backcrossing to improve salt tolerance of popular varieties followed by targeting multiple loci through QTL pyramiding for areas with higher salt stress.

Highlights

Salt stress is a major constraint across many rice production areas because of the high sensitivity of modern rice varieties
A follow-up study categorized the recombinant inbred lines (RILs) into sensitive and tolerant groups and mapped the position of Saltol between RM23 and RM140 (10.7–12.2 Mb on chromosome 1), and confirmed the effect of the shoot Na–K ratio with an LOD of 6.6 and R2 of 43% using 54 RILs (Bonilla et al 2002). While neither of these studies presented the percent variation explained for visual standard evaluation system (SES) tolerance scores or survival, it was assumed that by controlling the key mechanism of Na+/K+ homeostasis under stress, Saltol is a major contributor to seedling stage tolerance
The data from the current study confirmed that Saltol contributes to Na+/K+ homeostasis with an LOD of 7.6 and R2 of 27% across the 140 RILs and a 30% decrease in the shoot Na–K ratio, from 1.7 to 1.2 in the IR29/Pokkali backcross lines, while the Saltol effect on SES scores in the QTL population and backcross lines was much smaller

Summary

Introduction

Salt stress is a major constraint across many rice production areas because of the high sensitivity of modern rice varieties. Salinity is a major problem in coastal regions in the tropics where rice-based farming systems predominate. This is because of the intrusion of brackish water during the dry season and at the start of the wet season. Salt stress is a worsening problem in inland areas because of the buildup of salinity as a consequence of excessive use of irrigation water with improper drainage. Electronic supplementary material The online version of this article (doi:10.1007/s12284-010-9053-8) contains supplementary material, which is available to authorized users.

Objectives

Methods

Results

Conclusion