Heat Stress Tolerance in Rice (Oryza sativa L.): Identification of Quantitative Trait Loci and Candidate Genes for Seedling Growth Under Heat Stress

Productivity of rice, world's most important cereal is threatened by high temperature stress, intensified by climate change. Development of heat stress-tolerant varieties is one of the best strategies to maintain its productivity. However, heat stress tolerance is a multigenic trait and the candidate genes are poorly known. Therefore, we aimed to identify quantitative trait loci (QTL) for vegetative stage tolerance to heat stress in rice and the corresponding candidate genes. We used genotyping-by-sequencing to generate single nucleotide polymorphic (SNP) markers and genotype 150 F8 recombinant inbred lines (RILs) obtained by crossing heat tolerant “N22” and heat susceptible “IR64” varieties. A linkage map was constructed using 4,074 high quality SNP markers that corresponded to 1,638 recombinationally unique events in this mapping population. Six QTL for root length and two for shoot length under control conditions with 2.1–12% effect were identified. One QTL rlht5.1 was identified for “root length under heat stress,” with 20.4% effect. Four QTL were identified for “root length under heat stress as percent of control” that explained the total phenotypic variation from 5.2 to 8.6%. Three QTL with 5.3–10.2% effect were identified for “shoot length under heat stress,” and seven QTL with 6.6–19% effect were identified for “shoot length under heat stress expressed as percentage of control.” Among the QTL identified six were overlapping between those identified using shoot traits and root traits: two were overlapping between QTL identified for “shoot length under heat stress” and “root length expressed as percentage of control” and two QTL for “shoot length as percentage of control” were overlapping a QTL each for “root length as percentage of control” and “shoot length under heat stress.” Genes coding 1,037 potential transcripts were identified based on their location in 10 QTL regions for vegetative stage heat stress tolerance. Among these, 213 transcript annotations were reported to be connected to stress tolerance in previous research in the literature. These putative candidate genes included transcription factors, chaperone proteins (e.g., alpha-crystallin family heat shock protein 20 and DNAJ homolog heat shock protein), proteases, protein kinases, phospholipases, and proteins related to disease resistance and defense and several novel proteins currently annotated as expressed and hypothetical proteins

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

Comparison of Selection Indices for Tolerance to Water Stress in Common Beans(Phaseolus Vulgaris L) for the Dry Environment of Tanzania

Beans are an important crop in Tanzania grown by a wide range of farming communities. Its production, however, is very low due to various factors of which drought is becoming very important due to its frequency in the recent past. Provision of bean varieties that would withstand drought is important to contribute to food security in the farming communities. This study was conducted with the overall aim of selecting a simple selection index for drought tolerance. Performance of the bean genotypes under water stress conditions was assessed and drought tolerant varieties were identified. Fourteen genotypes, MN 14059-4-4P, RWR 109, MR 14000-2-IP, MR 14144, MMS 243, MN 14059-4-4P, MRl4000-2-1 OP, MR 14140-45-4P, MR 14215-9-8P, MR13944-14-9P, MR 14153-3-2P, MR 14198-13-lP, CNF5547 (Control), MR 13095-6-IP and DOR 390 were planted in a Split-Plot design with water stress period as main plot and bean genotypes as subplots at Sokoine University of Agriculture horticulture unit in Tanzania. Grain yield, seeds/pod; pods/plant, 100-seed weight, root length, root weight, days to physiological maturity, days to 50% flowering and dry matter content were determined. Drought Susceptibility Index (DSI), Sensitivity Index (SI) and Drought Intensity Index (DII) were derived from the grain yield data under the three water stress treatments. The water stress imposed at different periods of plant growth and development significantly influenced the phenotypic expression of the bean line in morphological traits and grain yield and its components. Days to 50% flowering dropped from 43 in the no water stress treatment to 41 days when water stress was imposed from flowering to mid-pod filling. The early maturing lines however showed less sensitivity to water stress with regards to days to 50% flowering. Root weight and dry matter weight were reduced under water stress while root elongation was enhanced from 27 cm to 29 cm when stress was early. Water stress imposed during any period of growth and development negatively affected grain yield. In this study yields dropped from 1188 kg/ha (stress O) to 720 kg/ha (stress I) and 432 kg/ha (stress II). Yields of early maturing genotypes were relatively less affected by water stress at any of the periods due to the earlier flowering, thereby escaped the full effects of the stress. Medium maturing lines, gave the lowest yield reduction from stress 0 to stress I and this was associated with relatively high retention of root weight, dry matter accumulation and enhanced root elongation under water stress. DSI was found to be the most reliable index to identify the drought tolerant genotypes because it identified specific drought tolerant genotypes while DII and SI related intensity of drought at a location and grouping of drought tolerant genotypes, respectively. In this regards the current study recommends DSI to be used further in breeding programme. Based on DSI MR 14154-4-6P, MR 14153-4-2P, MR 14000-2-1 OP and MR 14144-11-5 were the most tolerant genotype

Identification of Drought Tolerant Rice (<i>Oryza Sativa</i> L.) Genotypes with Asian and African Backgrounds

Drought is among the major abiotic stresses on rice production that can cause yield losses of up to 100% under severe drought conditions. Neither of the rice varieties currently grown in Burundi can withstand very low and irregular precipitation. This study identified genotypes that have putative quantitative trait loci (QTLs) associated with drought tolerance and determined their performance in the field. Two hundred and fifteen genotypes were grown in the field under both drought and irrigated conditions. Genomic deoxyribonucleic acid (DNA) was extracted from rice leaves for further genotypic screening. The results revealed the presence of the QTLs qDTY12.1, qDTY3.1, qDTY2-2_1, and qDTY1.1 in 90%, 85%, 53%, and 22% of the evaluated genotypes, respectively. The results of the phenotypic evaluation showed a significant yield reduction due to drought stress. Yield components and other agronomic traits were also negatively affected by drought. Genotypes having high yield best linear unbiased predictions (BLUPs) with two or more major QTLs for drought tolerance, including IR 108044-B-B-B-3-B-B, IR 92522-45-3-1-4, and BRRI DHAN 55 are of great interest for breeding programs to improve the drought tolerance of lines or varieties with other preferred traits