Nitika Sandhu

Rice Root Architectural Plasticity Traits and Genetic Regions for Adaptability to Variable Cultivation and Stress Conditions.

Rice root genetic regions determining root architectural plasticity can be used for selection of improved adaptability to variable conditions. Future rice (Oryza sativa) crops will likely experience a range of growth conditions, and root architectural plasticity will be an important characteristic to confer adaptability across variable environments. In this study, the relationship between root architectural plasticity and adaptability (i.e. yield stability) was evaluated in two traditional × improved rice populations (Aus 276 × MTU1010 and Kali Aus × MTU1010). Forty contrasting genotypes were grown in direct-seeded upland and transplanted lowland conditions with drought and drought + rewatered stress treatments in lysimeter and field studies and a low-phosphorus stress treatment in a Rhizoscope study. Relationships among root architectural plasticity for root dry weight, root length density, and percentage lateral roots with yield stability were identified. Selected genotypes that showed high yield stability also showed a high degree of root plasticity in response to both drought and low phosphorus. The two populations varied in the soil depth effect on root architectural plasticity traits, none of which resulted in reduced grain yield. Root architectural plasticity traits were related to 13 (Aus 276 population) and 21 (Kali Aus population) genetic loci, which were contributed by both the traditional donor parents and MTU1010. Three genomic loci were identified as hot spots with multiple root architectural plasticity traits in both populations, and one locus for both root architectural plasticity and grain yield was detected. These results suggest an important role of root architectural plasticity across future rice crop conditions and provide a starting point for marker-assisted selection for plasticity.

Traits and QTLs for development of dry direct-seeded rainfed rice varieties

Highlight text Characterization and QTL identification of seedling-stage traits revealed relationships with nutrient uptake and grain yield; these traits may improve the adaptation and productivity of rice under direct-seeded conditions.

Root Traits Enhancing Rice Grain Yield under Alternate Wetting and Drying Condition

Reducing water requirements and lowering environmental footprints require attention to minimize risks to food security. The present study was conducted with the aim to identify appropriate root traits enhancing rice grain yield under alternate wetting and drying conditions (AWD) and identify stable, high-yielding genotypes better suited to the AWD across variable ecosystems. Advanced breeding lines, popular rice varieties and drought-tolerant lines were evaluated in a series of 23 experiments conducted in the Philippines, India, Bangladesh, Nepal and Cambodia in 2015 and 2016. A large variation in grain yield under AWD conditions enabled the selection of high-yielding and stable genotypes across locations, seasons and years. Water savings of 5.7–23.4% were achieved without significant yield penalty across different ecosystems. The mean grain yield of genotypes across locations ranged from 3.5 to 5.6 t/ha and the mean environment grain yields ranged from 3.7 (Cambodia) to 6.6 (India) t/ha. The best-fitting Finlay-Wilkinson regression model identified eight stable genotypes with mean grain yield of more than 5.0 t/ha across locations. Multidimensional preference analysis represented the strong association of root traits (nodal root number, root dry weight at 22 and 30 days after transplanting) with grain yield. The genotype IR14L253 outperformed in terms of root traits and high mean grain yield across seasons and six locations. The 1.0 t/ha yield advantage of IR14L253 over the popular cultivar IR64 under AWD shall encourage farmers to cultivate IR14L253 and also adopt AWD. The results suggest an important role of root architectural traits in term of more number of nodal roots and root dry weight at 10–20 cm depth on 22–30 days after transplanting (DAT) in providing yield stability and preventing yield reduction under AWD compared to continuous flooded conditions. Genotypes possessing increased number of nodal roots provided higher yield over IR64 as well as no yield reduction under AWD compared to flooded irrigation. The identification of appropriate root architecture traits at specific depth and specific growth stage shall help breeding programs develop better rice varieties for AWD conditions.

Positive interactions of major-effect QTLs with genetic background that enhances rice yield under drought

To improve the grain yield of the lowland-adapted popular rice variety Samba Mahsuri under reproductive-stage drought (RS) and to understand the interactions between drought QTLs, two mapping populations were developed using marker-assisted selection (MAS) and marker-assisted recurrent selection (MARS). The mean grain yield of pyramided lines (PLs) with qDTY2.2 + qDTY4.1 in MAS is significantly higher under RS and irrigated control than lines with single QTLs. Among MARS PLs, lines with four qDTYs (qDTY1.1 + qDTY2.1 + qDTY3.1 + qDTY11.1) and two QTLs (qDTY1.1 + qDTY11.1) yielded higher than PLs with other qDTY combinations. The selected PLs showed a yield advantage of 0.3–2.0 t ha−1 under RS. An allelic profile of MAS PLs having same qDTY combination but with different yields under drought was studied. Hierarchical clustering grouped together the selected lines with high yield under drought. Epistasis test showed the interaction of qDTY4.1 and qDTY9.1 loci with qDTY7.1 significantly increased yield under drought and all the lines with higher yield under drought possessed the conserved region of qDTY7.1 on chromosome 7. The positive interactions among QTLs, effectiveness of QTLs in different backgrounds, introgression of DTY QTLs together with resistance to biotic stresses shall help enhance grain yield under RS.

Combining drought and submergence tolerance in rice: marker-assisted breeding and QTL combination effects

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.

Genetic loci governing grain yield and root development under variable rice cultivation conditions

Drought is the major abiotic stress to rice grain yield under unpredictable changing climatic scenarios. The widely grown, high yielding but drought susceptible rice varieties need to be improved by unraveling the genomic regions controlling traits enhancing drought tolerance. The present study was conducted with the aim to identify quantitative trait loci (QTLs) for grain yield and root development traits under irrigated non-stress and reproductive-stage drought stress in both lowland and upland situations. A mapping population consisting of 480 lines derived from a cross between Dular (drought-tolerant) and IR64-21 (drought susceptible) was used. QTL analysis revealed three major consistent-effect QTLs for grain yield (qDTY1.1, qDTY1.3, and qDTY8.1) under non-stress and reproductive-stage drought stress conditions, and 2 QTLs for root traits (qRT9.1 for root-growth angle and qRT5.1 for multiple root traits, i.e., seedling-stage root length, root dry weight and crown root number). The genetic locus qDTY1.1 was identified as hotspot for grain yield and yield-related agronomic and root traits. The study identified significant positive correlations among numbers of crown roots and mesocotyl length at the seedling stage and root length and root dry weight at depth at later stages with grain yield and yield-related traits. Under reproductive stage drought stress, the grain yield advantage of the lines with QTLs ranged from 24.1 to 108.9% under upland and 3.0–22.7% under lowland conditions over the lines without QTLs. The lines with QTL combinations qDTY1.3+qDTY8.1 showed the highest mean grain yield advantage followed by lines having qDTY1.1+qDTY8.1 and qDTY1.1+qDTY8.1+qDTY1.3, across upland/lowland reproductive-stage drought stress. The identified QTLs for root traits, mesocotyl length, grain yield and yield-related traits can be immediately deployed in marker-assisted breeding to develop drought tolerant high yielding rice varieties.

Molecular Mapping of QTLs Associated with Lodging Resistance in Dry Direct-Seeded Rice (Oryza sativa L.)

Dry direct-seeded rice (DSR) is an alternative crop establishment method with less water and labor requirement through mechanization. It provides better opportunities for a second crop during the cropping season and therefore, a feasible alternative system to transplanted lowland rice. However, lodging is one of the major constraints in attaining high yield in DSR. Identification of QTLs for lodging resistance and their subsequent use in improving varieties under DSR will be an efficient breeding strategy to address the problem. In order to map the QTLs associated with lodging resistance, a set of 253 BC3F4 lines derived from a backcross between Swarna and Moroberekan were evaluated in two consecutive years. A total of 12 QTLs associated with lodging resistance traits [culm length (qCL), culm diameter (qCD), and culm strength (qCS)] were mapped on chromosomes 1, 2, 6, and 7 using 193 polymorphic SNP markers. Two major and consistent effect QTLs, namely qCD1.1 (with R2 of 10%) and qCS1.1 (with R2 of 14%) on chromosome 1 with id1003559 being the peak SNP marker (flanking markers; id1001973-id1006772) were identified as a common genomic region associated with important lodging resistance traits. In silico analysis revealed the presence of Gibberellic Acid 3 beta-hydroxylase along with 34 other putative candidate genes in the marker interval region of id1001973-id1006772. The positive alleles for culm length, culm diameter, and culm strength were contributed by the upland adaptive parent Moroberekan. Our results identified significant positive correlation between lodging related traits (culm length diameter and strength) and grain yield under DSR, indicating the role of lodging resistant traits in grain yield improvement under DSR. Deployment of the identified alleles influencing the culm strength and culm diameter in marker assisted introgression program may facilitate the lodging resistance under DSR.

Cold and Water Deficit Regulatory Mechanisms in Rice: Optimizing Stress Tolerance Potential by Pathway Integration and Network Engineering

The responses of rice to cold and water deficit are multidimensional. A holistic approach to maximize tolerance potential requires the optimization of ideal combinations of multiple interacting entities in a genetic network. This chapter presents a modern view for engineering stress-resilient rice cultivars. The first section summarizes the physiological and biochemical aspects of cold and water deficit at the whole-plant and cellular levels. The second part summarizes the major hubs of signaling and transcriptional regulation that lead to biochemical and physiological changes as validated by functional genomics. The rapidly emerging area of investigation on epigenetic regulatory mechanisms as critical layer of control for fine-tuning is presented in brief in the third section. And finally, the last section summarizes the large-effect QTL for cold tolerance and yield stability under drought. By integrating these four layers of information, this chapter should inspire a holistic approach for stress tolerance engineering with strategies illuminated by systems-level biology.

Developing Climate Smart Aerobic Rice Varieties for Addressing the Problems of Water Scarcity and Global Warming

Growing population, rising demand for food, looming water crisis, climate change and global warming, reduced nutrient availability, higher cost of irrigation, and poor availability of labor have threatened the puddled transplanted system of rice (PTR). Rice needs two to three times more water than other cereals. Due to water scarcity, farmers may not be in a state to use the same amount of water for cultivation of rice and there is an urgent need to find out long-term effective and reliable methods to grow rice more efficiently. Use of machines, new technologies, coping strategies, genes for a range of agro-ecologies varying in edaphic and water regimes, and novel genomic techniques will allow us to move toward resource (labor, water, and energy) efficient and climate smart agriculture, especially in the case of rice. The identification of suitable traits and use of correlated genetic regions for seedling establishment and root traits that can potentially improve the nutrient uptake and grain yield under water-deficient conditions and pyramiding of these regions in a breeding program may lead to higher yield and adaptability of rainfed rice under aerobic conditions. Understanding of molecular mechanisms and successful exploitation of major effect genetic regions in various genetic backgrounds under variable environment and subsequent selection of lines with desired traits may result in development of novel water-efficient aerobic rice varieties. This chapter reviews the research including the development and use of innovative technologies and identification of useful traits and genetic regions associated with aerobic adaptation to achieve resource efficient cultivation of rice and to combat the effects of climate shift, water scarcity, and global warming.

Marker-assisted selection and QTL mapping for yield, root morphology and agronomic traits using MASARB25 (aerobic) × Pusa Basmati 1460 F3 mapping populations

Increasing scarcity of water has threatened the sustainability of the irrigated rice production system and hence the food security and livelihood of rice producers. Experiments were conducted to study the correlation and QTL mapping for yield, root-related and agronomic traits under aerobic conditions using MASARB25 × Pusa Basmati 1460 F3 mapping population. Yield of aerobic rice variety MASARB25 was 9–12.3% higher than Basmati rice variety Pusa Basmati 1460. MASARB25 had 9.32% higher root length, 11.76% higher fresh root weight, 19.98% higher dry root weight as compared to Pusa Basmati 1460. A total of 15 QTLs associated with 10 traits were mapped on chromosomes 2, 4, 6, 8, 9, and 11. qGY8.1 with an R2 value of 36.3% and qGY2.1 with an R2 value of 29% and qRL8.1 with an R2 value of 27.2% were identified for root length indicating the role of root traits in improving grain yield under water limited conditions. A positive correlation was found between root traits and yield under aerobic conditions. Breeding lines with higher yield per plant, root length, dry root biomass, length-breadth ratio, and with Pusa Basmati 1460-specific alleles in a homozygous or heterozygous condition at the BAD2 locus were identified that will serve as novel material for the selection of stable aerobic Basmati rice breeding lines.