Drought regularly affects 23 million ha of rainfed rice in South and Southeast Asia. In the eastern Indian states of Jharkhand, Orissa, and Chattisgarh alone, rice production losses during severe droughts (about one in five years) average about 40% of total production, with an estimated value of US$800 million. Drought is considered a major constraint in both upland and rainfed lowland rice production in South and Southeast Asia, and the presence of drought tolerance in African rice Oryza glaberrima was an important objective for developing new varieties.
THE STRASA SOLUTION
QTLs combinations for marker-assisted breeding
The project identified the best lines from QTL pyramiding in a range of genetic backgrounds that confer a yield advantage of 1 t/ha over the recurrent parent. This activity provided important lessons that are now used as guides for current breeding strategies: (i) it is not always that the more QTLs pyramided, the better the yield; (ii) the same physiological traits are not always seen when a QTL is pyramided or introgressed into a different genetic background, but in some cases these are evident; (iii) on strategically pyramiding QTLs with physiological mechanisms thought to be complementary: the qDTY1.1 + qDTY3.1 combination did appear to confer a synergistic effect by combining complementary mechanisms that resulted in higher panicle numbers under drought. On the other hand, dissection of qDTY2.2 + qDTY4.1 lines revealed that these QTLs do not appear to be conferring distinct mechanisms that complement each other, but rather additive effects on similar mechanisms (root architecture and hydraulics). These lessons provided a better explanation on the importance of epistasis effects on QTL introgression and in fact have helped guide recent breeding strategies away from QTL pyramiding efforts. Meanwhile, several notable products of QTL pyramiding were released as varieties through STRASA Phase 3: qDTY2.2 + qDTY4.1 - DRR dhan 42 (India), Sukha dhan 4 (Nepal), and qDTY1.1 + qDTY3.1 + Sub1 - Bahuguni dhan 1 (Nepal).
The science of STRASA Project on developing drought-tolerant rice varieties at IRRI, Philippines
Root phenotypes related to qDTY12.1 candidate genes
Canopy temperature effect of qDTY2.2 + qDTY4.1
QTLs that were pyramided
Over the last 10+ years, work on the drought stress component of the STRASA project led to many new insights and developments to benefit rice farmers in drought-prone regions. A systematic field protocols for applying reproductive stage drought stress as well as evaluation of pathogen response, a breeding pipeline (OYT, AYT, PVS) for improving drought tolerance of rice was implemented, and advanced research through the identification, molecular/physiological characterization, and pyramiding of drought-yield QTLs, was conducted. Such work saw the progressive improvement of rice productivity under drought as well as the continuous advancement of research facilities for NARES partners, including the development of molecular laboratories and rainout shelters (photos at left).
Donor identification and line development
Breeding populations have been developed from new drought-tolerant O. glaberrima accessions, leading to the identification of progenies with good drought tolerance and high yield potential. Polymorphism has been detected between genomes of sister lines NERICA 3 (drought sensitive) and NERICA 4 (highly drought tolerant) in populations developed between the two, revealing 27 homozygous SNPs, 12 indels, and 13 validated SNPs so far (Figure at right). The IRRI ESA breeding team identified 15 accessions which showed consistent drought tolerance in Tanzania for two seasons in rainfed lowland trials. These could be new sources of drought tolerance.
Donor variety identification: The project screened 500 Aus and traditional varieties at IRRI for tolerance to seedling stage upland drought, reproductive stage upland drought, and reproductive stage lowland drought, together with resistance to blast and bacterial blight.
These trials were conducted during the dry seasons from 2014 to 2018. Each year, selected donor genotypes were sent to NARES partner sites for testing under a range of conditions. In 2018DS and 2019DS, the project trialed the 60 "Best Donors", identified from 2014 to 2017, at IRRI under reproductive stage drought with the mentioned tolerant traits.
These were also shared with CRURRS Hazaribagh for blast and bacterial blight evaluation in the 2018 Kharif season to compare the pathogen resistance of the drought donors in response to strains at IRRI with their response to strains in Jharkhand, India.
Throughout STRASA Phase 3, these Best Donors have been used in drought breeding programs in NARES partner sites, and are being used to develop new material for the trait development breeding pipeline for marginal environments at IRRI.
Head to head trial in a project site in India
A participatory varietal selection (PVS) in Institute of Agriculture and Animal Science (IAAS), Lamjung, Nepal
A field ready for harvest in Tripura, India
QTL identification: The project identified five consistent QTLs (qDTY1.1, qDTY2.3, qDTY3.3, qDTY6.3, and qDTY11.2) for grain yield under drought stress. Two BC1F3 mapping populations – Swarna*2/Dular and IR11N121*2/Aus 196 – were phenotyped in 2016 and 2017 under reproductive stage drought stress and non-stress conditions. Genotyping was performed using the next generation sequencing (NGS)-based approach called genotyping by sequencing (GBS) using the DNA of these two mapping populations through MACROGEN, Korea. A total of 3,929 polymorphic SNP markers well distributed on all 12 chromosomes were identified from the GBS data of Swarna*2/Dular to identify the QTLs for reproductive stage drought tolerance.