Rice Breeding for High Grain Yield under Drought: A Strategic Solution to a Complex Problem

Drought is one of the major abiotic stresses that affect rice production in rainfed areas. Recent trends in climate change have predicted a further increase in drought intensity, making the development of new drought-tolerant rice cultivars critical to sustain rice production in this ecosystem. The use of grain yield as a selection criterion at the International Rice Research Institute (IRRI), through proper population development and precise phenotyping techniques, has allowed the development of several high-yielding rice cultivars that have been released in major rainfed rice-growing areas. This strategy has also allowed the identification of several major quantitative trait loci (QTLs) that show large effects under drought across environments and genetic backgrounds. These QTLs are being pyramided together to develop drought-tolerant versions of popular drought-susceptible varieties. The near-isogenic lines (NILs) developed can replace the popular, high-yielding but drought-susceptible varieties in rainfed areas prone to drought. Additionally, these NILs serve as suitable genetic material for the study of molecular and physiological mechanisms underlying these QTLs. This may provide a better understanding of plant functions responsible for high grain yield under drought and lead to the identification of new traits and genes

Meta-analysis of grain yield QTL identified during agricultural drought in grasses showed consensus

<p>Abstract</p> <p>Background</p> <p>In the last few years, efforts have been made to identify large effect QTL for grain yield under drought in rice. However, identification of most precise and consistent QTL across the environments and genetics backgrounds is essential for their successful use in Marker-assisted Selection. In this study, an attempt was made to locate consistent QTL regions associated with yield increase under drought by applying a genome-wide QTL meta-analysis approach.</p> <p>Results</p> <p>The integration of 15 maps resulted in a consensus map with 531 markers and a total map length of 1821 cM. Fifty-three yield QTL reported in 15 studies were projected on a consensus map and meta-analysis was performed. Fourteen meta-QTL were obtained on seven chromosomes. MQTL_1.2, MQTL_1.3, MQTL_1.4, and MQTL_12.1were around 700 kb and corresponded to a reasonably small genetic distance of 1.8 to 5 cM and they are suitable for use in marker-assisted selection (MAS). The meta-QTL for grain yield under drought coincided with at least one of the meta-QTL identified for root and leaf morphology traits under drought in earlier reports. Validation of major-effect QTL on a panel of random drought-tolerant lines revealed the presence of at least one major QTL in each line. <it>DTY</it>_{<it>12.1 </it>}was present in 85% of the lines, followed by <it>DTY</it>_{<it>4.1 </it>}in 79% and <it>DTY</it>_{<it>1.1 </it>}in 64% of the lines. Comparative genomics of meta-QTL with other cereals revealed that the homologous regions of MQTL_1.4and MQTL_3.2had QTL for grain yield under drought in maize, wheat, and barley respectively. The genes in the meta-QTL regions were analyzed by a comparative genomics approach and candidate genes were deduced for grain yield under drought. Three groups of genes such as stress-inducible genes, growth and development-related genes, and sugar transport-related genes were found in clusters in most of the meta-QTL.</p> <p>Conclusions</p> <p>Meta-QTL with small genetic and physical intervals could be useful in Marker-assisted selection individually and in combinations. Validation and comparative genomics of the major-effect QTL confirmed their consistency within and across the species. The shortlisted candidate genes can be cloned to unravel the molecular mechanism regulating grain yield under drought.</p

Understanding rice adaptation to varying agro-ecosystems: trait interactions and quantitative trait loci

Background: Interaction and genetic control for traits influencing the adaptation of the rice crop to varying environments was studied in a mapping population derived from parents (Moroberekan and Swarna) contrasting for drought tolerance, yield potential, lodging resistance, and adaptation to dry direct seeding. A BC2F3-derived mapping population for traits related to these four trait groups was phenotyped to understand the interactions among traits and to map and align QTLs using composite interval mapping (CIM). The study also aimed to identify QTLs for the four trait groups as composite traits using multivariate least square interval mapping (MLSIM) to further understand the genetic control of these traits. Results: Significant correlations between drought- and yield-related traits at seedling and reproductive stages respectively with traits for adaptation to dry direct-seeded conditions were observed. CIM and MLSIM methods were applied to identify QTLs for univariate and composite traits. QTL clusters showing alignment of QTLs for several traits within and across trait groups were detected at chromosomes 3, 4, and 7 through CIM. The largest number of QTLs related to traits belonging to all four trait groups were identified on chromosome 3 close to the qDTY3.2 locus. These included QTLs for traits such as bleeding rate, shoot biomass, stem strength, and spikelet fertility. Multivariate QTLs were identified at loci supported by univariate QTLs such as on chromosomes 3 and 4 as well as at distinctly different loci on chromosome 8 which were undetected through CIM. Conclusion: Rice requires better adaptation across a wide range of environments and cultivation practices to adjust to climate change. Understanding the genetics and trade-offs related to each of these environments and cultivation practices thus becomes highly important to develop varieties with stability of yield across them. This study provides a wider picture of the genetics and physiology of adaptation of rice to wide range of environments. With a complete understanding of the processes and relationships between traits and trait groups, marker-assisted breeding can be used more efficiently to develop plant types that can combine all or most of the beneficial traits and show high stability across environments, ecosystems, and cultivation practices

qDTY1.1, a major QTL for rice grain yield under reproductive-stage drought stress with a consistent effect in multiple elite genetic backgrounds

<p>Abstract</p> <p>Background</p> <p>Drought is one of the most important abiotic stresses causing drastic reductions in yield in rainfed rice environments. The suitability of grain yield (GY) under drought as a selection criterion has been reported in the past few years. Most of the quantitative trait loci (QTLs) for GY under drought in rice reported so far has been in the background of low-yielding susceptible varieties. Such QTLs have not shown a similar effect in multiple high- yielding drought-susceptible varieties, thus limiting their use in marker-assisted selection. Genetic control of GY under reproductive-stage drought stress (RS) in elite genetic backgrounds was studied in three F_3:4mapping populations derived from crosses of N22, a drought-tolerant <it>aus </it>cultivar, with Swarna, IR64, and MTU1010, three high-yielding popular mega-varieties, with the aim to identify QTLs for GY under RS that show a consistent effect in multiple elite genetic backgrounds. Three populations were phenotyped under RS in the dry seasons (DS) of 2009 and 2010 at IRRI. For genotyping, whole-genome scans for N22/MTU1010 and bulked segregant analysis for N22/Swarna and N22/IR64 were employed using SSR markers.</p> <p>Results</p> <p>A major QTL for GY under RS, <it>qDTY_1.1</it>, was identified on rice chromosome 1 flanked by RM11943 and RM431 in all three populations. In combined analysis over two years, <it>qDTY</it>_{<it>1.1 </it>}showed an additive effect of 29.3%, 24.3%, and 16.1% of mean yield in N22/Swarna, N22/IR64, and N22/MTU1010, respectively, under RS. <it>qDTY</it>_{<it>1.1 </it>}also showed a positive effect on GY in non-stress (NS) situations in N22/Swarna, N22/IR64 over both years, and N22/MTU1010 in DS2009.</p> <p>Conclusions</p> <p>This is the first reported QTL in rice with a major and consistent effect in multiple elite genetic backgrounds under both RS and NS situations. Consistency of the QTL effect across different genetic backgrounds makes it a suitable candidate for use in marker-assisted breeding.</p

Flood-tolerant rice for enhanced production and livelihood of smallholder farmers of Africa

Climate change has intensified food security challenges, especially in Africa, where a significant portion of produce is reliant on smallholder farmers in rainfed conditions. Prolonged flooding and droughts, driven by erratic weather patterns, have significantly elevated the risk of food scarcity. Floods, in particular, have been responsible for severe crop losses, raising concerns about increasing import costs if this issue is not mitigated. Africa is actively working to mitigate the impacts of flooding and enhance food security, although progress has been gradual. Developing flood-resilient varieties is a promising strategy to address this challenge. We explored various flood types common in the region and observed a scarcity of research on flood-resilient varieties, particularly those adapted for anaerobic germination and stagnant flooding. Conversely, varieties bred for flash flooding, such as FARO 66 and FARO 67, have seen limited distribution, primarily confined to a few West African countries, falling short of the intended impact. In contrast, deepwater tolerance research dates back to the early 1900s, but commercialization of the varieties remains limited, with scarce information regarding their cultivation, coverage, and performance. Newly developed varieties, such as Kolondieba 2 and Kadia 24, have received less attention, leaving many farmers dependent on locally adapted cultivars specific to particular areas. Remarkably, despite the limited information, both released and local stress-tolerant cultivars exhibit substantial survival rates and yield advantages. For instance, FARO 66 and FARO 67 have demonstrated 1–3 t/ha yield advantages over recurrent parents under flooding stress. Nonetheless, further efforts are required to address various forms of flooding. To this end, AfricaRice collaborates with National Rice Development Strategies, IRRI, and other partners to promote research and development. While improved flood-tolerant varieties remain limited in scope across Africa, the financial gains for farmers are significant when compared to susceptible cultivars. As the continent’s population continues to grow rapidly, there is untapped potential in African germplasms, making ongoing research and breeding strategies essential. Therefore, this review highlights the importance of intensifying efforts in screening and identifying flood-tolerant rice. Furthermore, it underscores the value of utilizing traditional flood-resilient cultivars in breeding to enhance the productivity of widely distributed and cultivated varieties

Screening of potential donors for anaerobic stress tolerance during germination in rice

The rising cost of transplanting rice has made direct seeding an affordable alternative for rice establishment, particularly in Africa. However, direct seeding, while cost-effective, faces crop establishment challenges due to flooding. Uncontrolled water, driven by erratic rains in low-lying areas or uneven fields, limit germination. Rice possesses the unique ability of anaerobic germination, enabling it to sprout and emerge in oxygen-deprived conditions. Understanding rice’s response to anaerobic stress during germination is crucial for resilience breeding. Africa, although relying on direct seeding, has made limited progress in addressing flooding during germination compared to Asia. Anaerobic stress tolerance ensures successful crop emergence even in oxygen-limited environments and can help suppress weeds, a significant challenge in direct-seeded rice cultivation. This study aims to contribute by screening for potential rice donors exhibiting anaerobic stress tolerance. We screened 200 rice genotypes at Sokoine University of Agriculture (SUA) in Morogoro, Tanzania, primarily focusing on landraces with untapped potential. Using an alpha lattice design, we conducted two anaerobic experiments in September and October 2022, adding 7 cm of standing water immediately after dry seeding for flooded and maintaining a 2 cm water level after germination in the control for duration of 21 days. We identified potential donors based on selection index computed from genomic estimated breeding values (GEBVs) using eight variables: germination at 14 DAS, germination at 21 DAS, seedling height at 14 DAS, seedling height at 21 DAS, shoot dry matter at 21 DAS, root dry matter at 21 DAS, culm diameter at 21 DAS, and root length at 21DAS. Ten genotypes emerged as the most promising, exhibiting at least 70% germination in floodwater at 21 DAS and greater selection indices. These genotypes were like: Afaa Mwanza 1/159, Rojomena 271/10, Kubwa Jinga, Wahiwahi, Magongo ya Wayungu, Mpaka wa Bibi, Mwangaza, Tarabinzona, IB126-Bug 2013A, and Kanamalia with respective percentages of 75, 74, 71, 86, 75, 80, 71, 80, 70, and 73. These findings contribute to global efforts to mitigate the impacts of flooding during germination. These donors, will be potential to enrich the gene pool for anaerobic germination, providing valuable resources for breeding for flooding tolerance

Stomatal conductance responses to evaporative demand conferred by rice drought-yield quantitative trait locus qDTY(12.1)

Rice quantitative trait locus (QTL) qDTY12.1 is a major-effect drought yield QTL that was identified from a cross of Vandana (recipient parent) and Way Rarem (donor parent) through breeding efforts to improve rice yield under upland drought stress conditions. The two main physiological effects previously observed to be related to the presence of qDTY12.1 were (i) increased lateral root growth, and (ii) increased transpiration efficiency. Since relatively more progress has thus far been made on characterising the lateral root growth response related to qDTY12.1, the present study focussed on characterising how qDTY12.1 confers higher transpiration efficiency under upland drought stress in the Vandana background. In a series of field experiments in which stomatal conductance was measured across different times of day in four qDTY12.1 near isogenic lines (NILs), the NILs and Way Rarem showed consistently higher stomatal conductance than Vandana under conditions of low vapour pressure deficit (VPD) and low photosynthetically active radiation (PAR), and consistently lower stomatal conductance than Vandana under high VPD and high PAR. Leaf δ18O was higher in the qDTY12.1 NIL than in Vandana, and although this trend was previously observed for leaf δ13C it appeared to be more consistent across measurement dates and treatments for leaf δ18O. The qDTY12.1 NILs and Way Rarem tended to show greater large vein to small vein interveinal distance and mesophyll area than Vandana, also consistent across treatments. In terms of aquaporin-related plant hydraulics, variation among NILs in terms of aquaporin inhibition of root hydraulic conductivity (Lpr) was observed, with the highest-yielding NIL showing a lack of Lpr inhibition similar to Way Rarem. The results reported here suggest that the effects of qDTY12.1 are in response not only to soil moisture, but also to atmospheric conditions. An interaction among multiple mechanisms including leaf anatomy and aquaporin function appear to confer the transpiration efficiency effect of qDTY12.1

Breeding rice for a changing climate by improving adaptations to water saving technologies

Climate change is expected to increasingly affect rice production through rising temperatures and decreasing water availability. Unlike other crops, rice is a main contributor to greenhouse gas emissions due to methane emissions from flooded paddy fields. Climate change can therefore be addressed in two ways in rice: through making the crop more climate resilient and through changes in management practices that reduce methane emissions and thereby slow global warming. In this review, we focus on two water saving technologies that reduce the periods lowland rice will be grown under fully flooded conditions, thereby improving water use efficiency and reducing methane emissions. Rice breeding over the past decades has mostly focused on developing high-yielding varieties adapted to continuously flooded conditions where seedlings were raised in a nursery and transplanted into a puddled flooded soil. Shifting cultivation to direct-seeded rice or to introducing non-flooded periods as in alternate wetting and drying gives rise to new challenges which need to be addressed in rice breeding. New adaptive traits such as rapid uniform germination even under anaerobic conditions, seedling vigor, weed competitiveness, root plasticity, and moderate drought tolerance need to be bred into the current elite germplasm and to what extent this is being addressed through trait discovery, marker-assisted selection and population improvement are reviewed

Stomatal conductance responses to evaporative demand conferred by rice drought-yield quantitative trait locus qDTY12.1

Rice quantitative trait locus (QTL) qDTY12.1 is a major-effect drought yield QTL that was identified from a cross of Vandana (recipient parent) and Way Rarem (donor parent) through breeding efforts to improve rice yield under upland drought stress conditions. The two main physiological effects previously observed to be related to the presence of qDTY12.1 were (i) increased lateral root growth, and (ii) increased transpiration efficiency. Since relatively more progress has thus far been made on characterising the lateral root growth response related to qDTY12.1, the present study focussed on characterising how qDTY12.1 confers higher transpiration efficiency under upland drought stress in the Vandana background. In a series of field experiments in which stomatal conductance was measured across different times of day in four qDTY12.1 near isogenic lines (NILs), the NILs and Way Rarem showed consistently higher stomatal conductance than Vandana under conditions of low vapour pressure deficit (VPD) and low photosynthetically active radiation (PAR), and consistently lower stomatal conductance than Vandana under highVPDand high PAR. Leaf d18Owas higher in the qDTY12.1 NIL than in Vandana, and although this trend was previously observed for leaf d13Cit appeared to be more consistent across measurement dates and treatments for leaf d18O. The qDTY12.1 NILs andWayRarem tended to show greater large vein to small vein interveinal distance and mesophyll area than Vandana, also consistent across treatments. In terms of aquaporin-related plant hydraulics, variation among NILs in terms of aquaporin inhibition of root hydraulic conductivity (Lpr) was observed, with the highest-yielding NIL showing a lack of Lpr inhibition similar toWayRarem. The results reported here suggest that the effects of qDTY12.1 are in response not only to soil moisture, but also to atmospheric conditions. Aninteraction among multiple mechanisms including leaf anatomy and aquaporin function appear to confer the transpiration efficiency effect of qDTY12.1

Grain yield and physiological traits of rice lines with the drought yield QTL qDTY12.1 showed different responses to drought and soil characteristics in upland environments

To improve yield in upland conditions, near-isogenic lines (NILs) of the major-effect drought yield quantitative trait locus qDTY12.1 in rice (Oryza sativa L.) were developed in the background of the upland variety Vandana. These NILs have shown greater water uptake a larger proportion of lateral roots, and higher transpiration efficiency under drought than Vandana, and one NIL (481-B) was selected as having the highest yield. In this study, the NILs were assessed in two greenhouse and 18 upland field trials for their response to drought and different soil textures. Performance of qDTY12.1 NILs was not affected by soil texture but showed a notable response to drought stress severity. The yield advantage of 481-B over Vandana was highest in field trials with intermittent drought stress, in which the mean trial yield was greater than 0.5 t ha–1, and in the least favourable well watered trial. The effects of qDTY12.1 on water uptake were most apparent under mild to moderate stress but not in very severe drought or well watered treatments, whereas the lateral root and transpiration efficiency responses were observed under a range of conditions. These results highlight the varying response of qDTY12.1 across upland environments and the complexity of multiple mechanisms acting together to confer an effect on rice yield under drought