Climate change is affecting rice production in many countries. Developing new rice varieties with heat tolerance is an essential way to sustain rice production in future global warming. We have previously reported four quantitative trait loci (QTLs) responsible for rice spikelet fertility under high temperature at flowering stage from an IR64/N22 population. To further explore additional QTL from other varieties, two bi-parental F2 populations and one three-way F2 population derived from heat tolerant variety Giza178 were used for indentifying and confirming QTLs for heat tolerance at flowering stage. Four QTLs (qHTSF1.2, qHTSF2.1, qHTSF3.1 and qHTSF4.1) were identified in the IR64/Giza178 population, and two other QTLs (qHTSF6.1 and qHTSF11.2) were identified in the Milyang23/Giza178 population. To confirm the identified QTLs, another three-way-cross population derived from IR64//Milyang23/Giza178 was genotyped using 6K SNP chips. Five QTLs were identified in the three-way-cross population, and three of those QTLs (qHTSF1.2, qHTSF4.1 and qHTSF6.1) were overlapped with the QTLs identified in the bi-parental populations. The tolerance alleles of these QTLs were from the tolerant parent Giza178 except for qHTSF3.1. The QTL on chromosome 4 (qHTSF4.1) is the same QTL previously identified in the IR64/N22 population. The results from different populations suggest that heat tolerance in rice at flowering stage is controlled by several QTLs with small effects and stronger heat tolerance could be attained through pyramiding validated heat tolerance QTLs. QTL qHTSF4.1 was consistently detected across different genetic backgrounds and could be an important source for enhancing heat tolerance in rice at flowering stage. Polymorphic SNP markers in these QTL regions can be used for future fine mapping and developing SNP chips for marker-assisted breeding.

Extreme temperatures are considered one of the main constraints that limit the growth and development of rice. We elucidated the root and shoot developmental plasticity of 64 rice genotypes during early seedling establishment, using the sunlit plant growth chambers at 22/14 (low), 30/22 (optimum), and 38/30 °C (high) day/night temperatures. Low temperature severely inhibited 23 traits, such as shoot (68%), root (57%), and physiological (35%) attributes. On the contrary, the high temperature positively affected most of the shoot (48%) and root (31%) traits, except root diameter and root/shoot ratio, compared with the optimum. Alternatively, leaf chlorophyll fluorescence-associated parameters declined under low (34%) and high (8%) temperatures. A weak correlation between cumulative high-temperature response index (CHTRI) and cumulative low-temperature response index (CLTRI) indicates the operation of different low- and high-temperature tolerance mechanisms at the early seedling stage. Groups of distinct rice genotypes associated with low or high-temperature tolerance were selected based on CHTRI and CLTRI. The genotypes that commonly performed well under low and high temperatures (IR65600-81-5-2-3, CT18593-1-7-2-2-5, RU1504114, RU1504122, Bowman, and INIA Tacuari) will be valuable genetic resources for breeders in developing early-season high- and low-temperature-tolerant genotypes for a broad range of both tropical and temperate rice-growing environments.

Drought is a major abiotic stress factor affecting the growth and development of plants at all stages. Developing a screening tool for identifying drought stress tolerance during seedling establishment is important in the deployment of rice varieties suited to water-limited growing environments. An experiment was conducted to evaluate 100 rice genotypes, mostly belonging to the tropical japonica subspecies, for drought stress tolerance using low-cost, pre-fabricated mini-hoop structures. The rice seedlings were subjected to two different soil moisture regimes- control pots managed at 100% and drought pots at 50% field capacity, from 12 to 30 days after sowing (DAS). Several morpho-physiological parameters including root traits were measured to assess the response of genotypes to drought stress. Significant moisture stress × genotype interactions were found for most of the parameters measured. A cumulative drought stress response index (CDSRI) was developed by adding the individual response indices of all cultivars. Based on CDSRI and standard deviation values, 5 and 28 genotypes were identified as highly sensitive and sensitive to drought, respectively, and 45 as moderately sensitive. On the other hand, 16 and 6 genotypes were classified as tolerant and highly tolerant to drought, respectively. Cheniere, a released cultivar, and RU1402174, an experimental breeding line, were identified as the least and most tolerant to drought among the 100 genotypes tested. Significant linear correlation coefficients were obtained between CDSRI and root growth parameters (R² = 0.91, n = 100) and CDSRI with shoot growth parameters (R² = 0.48, n = 100), revealing the importance of root traits in studying and identifying drought tolerant lines during the seedling establishment stages in rice. The tolerant rice genotypes identified will be valuable for rice scientists in studying the mechanism for early season drought as well as for rice breeders for developing new genotypes best suited under growing environments prone to early-season drought.

Extreme weather events, especially heat waves, have become more frequent with global warming. High temperature significantly affects world food security by decreasing crop yield. Rice is intensively planted in tropical and subtropical areas in Asia, where high temperature has become a major factor affecting rice production. Rice is sensitive to high temperature, especially at booting and flowering stages. Rice varieties tolerant of high temperature are rare, and only a few heat-tolerant rice varieties have been identified. High temperature at booting and flowering stages causes sterile pollen, decreased pollen shedding, and poor pollen germination, which finally lead to a yield decrease. Heat-tolerant QTLs have been identified in different studies, but new breeding lines with considerable heat tolerance have not been bred using identified heat-tolerance donors and QTLs. Research on heat-tolerant donor identification, QTL mapping, gene cloning, and large-scale phenotyping technology is important for developing heat-tolerant rice varieties.

Drought stress is one of the most devastating abiotic factors limiting plant growth and development. Devising an efficient and rapid screening method at the seedling stage is vital in identifying genotypes best suited under drought conditions. An experiment was conducted to assess 74 rice genotypes for drought tolerance using specially designed mini-hoop structures. Two treatments were imposed on rice seedlings, including 100% moisture and a 50% moisture regime. Several shoot morpho-physiological traits and root traits were measured and analyzed. The genotypes exhibited a wide range of variability for the measured traits, with the leaf area showing the most significant variation, followed by plant height, tiller number, and shoot dry weight. In contrast, the drought did not significantly affect most root traits. The germplasm was classified into different categories using cumulative drought stress response indices (CDSRI); 19 genotypes (26%) were identified as drought sensitive, and 33 (45%), 15 (20%), and 7 (9%) were determined as low, moderately, and highly drought-tolerant, respectively. Genotypes IR86638 and IR49830 were the most and least drought-tolerant, respectively. Overall, a poor correlation was observed between CDSRI, total shoot traits (R² = 0.36), and physiological parameters (R² = 0.10). A strong linear correlation was found between CDSRI and root traits (R² = 0.81), suggesting that root traits are more crucial and better descriptors in screening for drought tolerance. This study can help rice breeders and scientists to accelerate breeding by adopting a mini-hoop rapid screening method. The tolerant genotypes could serve as appropriate donor parents, progenies, and potential genotypes for developing drought-tolerant commercial cultivars.

Increasing agricultural productivity is indispensable to meet future food demand. Crop improvement programs rely heavily on genetic diversity. The success of weeds in the ecosystem can be attributed to genetic diversity and plasticity. Weedy rice, a major weed of rice, has diverse morphology and phenology, implying wide genetic diversity. Study was conducted to genotype weedy rice accessions (n = 54) previously phenotyped for herbicide tolerance and allelopathic potential using 30 SSR markers. Cultivated rice (CL163, REX) and allelopathic rice (RONDO, PI312777, PI338047) were also included in the study. Nei’s genetic diversity among weedy rice (0.45) was found to be higher than cultivated rice (0.24) but less than allelopathic rice (0.56). The genetic relationship and population structure based on herbicide tolerance and allelopathic potential were evaluated. Herbicide-tolerant and susceptible accessions formed distinct clusters in the dendrogram, indicating their genetic variation, whereas no distinction was observed between allelopathic and non-allelopathic weedy rice accessions. Weedy rice accession B2, which was previously reported to have high allelopathy and herbicide tolerance, was genetically distinct from other weedy rice. Results from the study will help leverage weedy rice for rice improvement programs as both rice and weedy rice are closely related, thus having a low breeding barrier.