Combining drought and submergence tolerance in rice: marker-assisted breeding and QTL combination effects
Mol Breeding
Combining drought and submergence tolerance in rice: marker-assisted breeding and QTL combination effects
Shalabh Dixit 0 1
Anshuman Singh 0 1
Nitika Sandhu 0 1
Aditi Bhandari 0 1
Prashant Vikram 0 1
Arvind Kumar 0 1
0 P. Vikram International Maize and Wheat Improvement Center (CIMMYT) , Km. 45, Carretera México-Veracruz, El Batán, 56237 Texcoco, CP , Mexico
1 A. Singh Rani Lakshmi Bai Central Agriculture University , Jhansi , India
2 International Rice Research Institute (IRRI) , DAPO Box 7777, Metro Manila , Philippines
TDK1 is a popular rice variety from the Lao PDR. Originally developed for irrigated conditions, this variety suffers a high decline in yield under drought conditions. Studies have identified three quantitative trait loci (QTLs) for grain yield under drought conditions, qDTY3.1, qDTY6.1, and qDTY6.2, that show a high effect in the background of this variety. We report here the pyramiding of these three QTLs with SUB1 that provides 2-3 weeks of tolerance to complete submergence, with the aim to develop drought- and submergence-tolerant near-isogenic lines (NILs) of TDK1. We used a tandem approach that combined marker-assisted backcross breeding with phenotypic selection to develop NILs with high yield under drought stress and non-stress conditions and preferred grain quality. The effect of different QTL combinations on yield and yield-related traits under drought stress and non-stress conditions is also reported. Our results show qDTY3.1 to be the largest and most consistent QTL affecting yield under drought conditions, followed by qDTY6.1 and qDTY6.2, respectively. QTL class analysis also showed that lines with a combination of qDTY3.1 and qDTY6.1 consistently showed a higher tolerance to drought than those in which one of these QTLs was missing. In countries such as Lao PDR, where large areas under rice cultivation suffer vegetative-stage submergence and reproductive-stage drought, these lines could ensure yield stability. These lines can also serve as valuable genetic material to be used for further breeding of high-yielding, drought- and submergence-tolerant varieties in local breeding programs.
Rice; Drought; Yield; Submergence; QTL; MABB
Introduction
Drought and flooding are considered to be two of the
most important abiotic stresses that affect rice
production globally. A total of approximately 40 million
hectares of rice area are affected by different forms of the
two stresses occurring at different crop stages. Under
natural conditions, both of these stresses are expected to
occur at different levels in the topographic sequence.
However, in rainfed rice ecosystems, these two stresses
are often observed to occur in the same area within a
growing season. This combination of stresses is
especially relevant in South and Southeast Asia where
rainfed rice ecosystems are major natural disaster
hotspots prone to drought and flood risks
(Dilley et al.
2005)
. For example, in eastern India, the onset of the
monsoon may bring heavy rains in July–August that
cause flash floods at the vegetative stage of the rice
crop. However, early withdrawal of the monsoon or
prolonged dry phases at the reproductive stage may
cause considerable yield loss due to drought. Similarly,
in the Mekong River basin in Southeast Asia, rainfed
areas in countries such as Lao PDR, Thailand, Vietnam,
and Cambodia are prone to submergence and drought
within or across seasons and locations. Among these
countries, Lao PDR is likely the most affected by
drought and flood. The rainfed lowland ecosystem
dominates rice cultivation in the country and is highly prone
to natural disasters. In 2004, rainfed lowlands accounted
for about 75% of the total area and 78% of the
production (www.irri.org). Although floods are a common
phenomenon in this region due to the presence of the
Mekong River, an increase in drought incidences has
also been observed in the past two decades
(Komany
2004)
. TDK1 is a popular rice variety that is cultivated
in a large part of the rainfed lowland ecosystems in Lao
PDR. A submergence-tolerant version of this variety
(TDK1-Sub1) has been developed which provides
considerable tolerance to flash floods; however, both TDK1
and TDK1-Sub1 are highly susceptible to drought.
SUB1 is a major quantitative trait locus (QTL) derived
from landrace FR13A that provides tolerance of 2–
3 weeks of complete submergence
(Septiningsih et al.
2014)
. This QTL was found to account for 69% of the
phenotypic variance in the original identification study
(Xu and Mackill 1996)
and has been used extensively in
marker-assisted backcross breeding (MABB) programs
to improve mega-varieties with tolerance of
submergence
(Neeraja et al. 2007; Septiningsih et al. 2014;
Toledo et al. 2015)
.
Similar to the advances made in submergence
tolerance, considerable progress has also been made in
understanding the genetics of grain yield under drought
conditions in the past decade at the International Rice
Research (...truncated)