Meta-analysis of quantitative trait loci for grain yield and component traits under reproductive-stage drought stress in an upland rice population.

Kurniawan R. Trijatmiko,Sugiono Moeljopawiro,Andy Pereira,Michael J. Thomson,Casiana M. Vera Cruz,Joko Prasetiyono,Supriyanta Supriyanta

doi:10.1007/s11032-013-0012-0

Abstract

A recombinant inbred population developed from a cross between high-yielding lowland rice (Oryza sativa L.) subspecies indica cv. IR64 and upland tropical rice subspecies japonica cv. Cabacu was used to identify quantitative trait loci (QTLs) for grain yield (GY) and component traits under reproductive-stage drought stress. One hundred fifty-four lines were grown in field trials in Indonesia under aerobic conditions by giving surface irrigation to field capacity every 4 days. Water stress was imposed for a period of 15 days during pre-flowering by withholding irrigation at 65 days after seeding. Leaf rolling was scored at the end of the stress period and eight agronomic traits were evaluated after recovery. The population was also evaluated for root pulling force, and a total of 201 single nucleotide polymorphism markers were used to construct the molecular genetic linkage map and QTL mapping. A QTL for GY under drought stress was identified in a region close to the sd1 locus on chromosome 1. QTL meta-analysis across diverse populations showed that this QTL was conserved across genetic backgrounds and co-localized with QTLs for leaf rolling and osmotic adjustment (OA). A QTL for percent seed set and grains per panicle under drought stress was identified on chromosome 8 in the same region as a QTL for OA previously identified in three different populations.Electronic supplementary materialThe online version of this article (doi:10.1007/s11032-013-0012-0) contains supplementary material, which is available to authorized users.

Highlights

Rice (Oryza sativa L.) is susceptible to water deficit compared to other crop species, and this sensitivity is especially severe around flowering (Lafitte et al 2004)
The mean and range of values for days to heading (DTH), plant height (PH), per plant (PPL), spikelets per panicle (SPP), grains per panicle (GPP), percent seed set (PSS), grain weight (GW), grain yield (GY), root pulling force (RPF), and leaf rolling scores (LRS) in the recombinant inbred line (RIL) population are summarized in Table 1 and phenotype data are presented in Online Resource 1
Under the given drought stress, the GY of IR64 was similar to Cabacu with means of 17.5 g and 16.0 g per plant, respectively

Summary

Introduction

Rice (Oryza sativa L.) is susceptible to water deficit compared to other crop species, and this sensitivity is especially severe around flowering (Lafitte et al 2004). In South and Southeast Asia, more than 50 % of a total of 40 million ha rainfed lowland areas is affected by drought annually. These areas are found mainly in northeast Thailand, eastern India, Bangladesh, and Indonesia (Sarkarung and Pantuwan 1999). Drought tolerance requires an analytical approach of dissecting and studying the contribution of different trait components using a quantitative trait locus (QTL)-based model. This approach is suited to crops like rice for which dense genetic linkage maps are already available (Harushima et al 1998; McCouch et al 2002). Along with the availability of the map-based sequence of the rice genome (IRGSP 2005), the dense genetic linkage map allows rice molecular geneticists to narrow down the location of QTLs into a small region and predict the putative candidate genes in the region for gene cloning and validation by reverse genetics approaches (Hattori et al 2009)

Methods

Results

Conclusion