Knockout of the sugar transporter OsSTP15 enhances grain yield by improving tiller number due to increased sugar content in the shoot base of rice (Oryza sativa L.).

Sugar transporter proteins (STPs) play critical roles in regulating plant stress tolerance, growth, and development. However, the role of STPs in regulating crop yield is poorly understood. This study elucidates the mechanism by which knockout of the sugar transporter OsSTP15 enhances grain yield via increasing the tiller number in rice. We found that OsSTP15 is specifically expressed in the shoot base and vascular bundle sheath of seedlings and encodes a plasma membrane-localized high-affinity glucose efflux transporter. OsSTP15 knockout enhanced sucrose and trehalose-6-phosphate (Tre6P) synthesis in leaves and improved sucrose transport to the shoot base by inducing the expression of sucrose transporters. Higher glucose, sucrose, and Tre6P contents were observed at the shoot base of stp15 plants. Transcriptome and metabolome analyses of the shoot base demonstrated that OsSTP15 knockout upregulated the expression of cytokinin (CK) synthesis- and signaling pathway-related genes and increased CK levels. These findings suggest that OsSTP15 knockout represses glucose export from the cytoplasm and simultaneously enhances sugar transport from source leaves to the shoot base by promoting the synthesis of sucrose and Tre6P in leaves. Subsequent accumulation of glucose, sucrose, and Tre6P in the shoot base promotes tillering by stimulating the CK signaling pathway.

Nitrogen form-mediated ethylene signal regulates root-to-shoot K+ translocation via NRT1.5.

Nitrogen-potassium synergistic and antagonistic interactions are the typical case of nutrient interactions. However, the underlying mechanism for the integration of the external N form into K+ homeostasis remains unclear. Here, we show that opposite effects of NO3- and NH4+ on root-shoot K+ translocation were due to differential regulation of an ethylene signalling pathway targeting the NRT1.5 transporter. NH4+ upregulated the transcriptional activity of EIN3, but repressed the expression of NRT1.5. However, the addition of NO3- strongly suppressed the activity of EIN3, whereas its addition upregulated the expression of AtNRT1.5 and shoot K+ concentration. The 35S:EIN3/ein3eil1 plants, nrt1.5 mutants and nrt1.5/skor double mutants displayed a low K+ chlorosis phenotype, especially under NH4+ conditions with low K+ supply. Ion content analyses indicate that root-to-shoot K+ translocation was significantly reduced in these mutants. A Y1H assay, an EMSA and a transient expression assay confirmed that AtEIN3 protein could directly bind to the promoter of NRT1.5 to repress its expression. Furthermore, grafted plants with the roots of 35S:EIN3 and ein3eil1/nrt1.5 mutants displayed marked leaf chlorosis with a low K+ concentration. Collectively, our findings reveal that the interaction between N form and K+ was achieved by modulating root-derived ethylene signals to regulate root-to-shoot K+ translocation via NRT1.5.

Increasing flooding tolerance in rice: combining tolerance of submergence and of stagnant flooding.

BACKGROUND AND AIMS: Rice ecosystems in the tropical coastal areas are subject to two types of flooding stress: transient complete submergence and long-term water stagnation (stagnant flooding). Here, we aimed to dissect the mechanisms for stagnant flooding tolerance of rice genotypes carrying SUB1, a quantitative trait locus for submergence tolerance. METHODS: We screened 80 elite genotypes under stagnant flooding stress in the lowland rice fields in the wet and dry seasons, and examined the tolerance mechanisms of promising genotypes for the two following seasons. KEY RESULTS: Yield reduction under stagnant flooding averaged 48 % in the dry season and 89 % in the wet season. Elite genotypes carrying SUB1 showed 49 % lower yield than those without SUB1 under stagnant flooding, with no differences under shallow water conditions. However, we identified a few high-yielding Sub1 genotypes that were as tolerant of stagnant flooding as a reference genotype that lacked SUB1. These genotypes had intermediate stature with more shoot elongation in response to rising water than a moderately tolerant Sub1 reference variety, resulting in greater canopy expansion and higher yield. It was important to increase lodging resistance, since plant height >140 cm increased lodging under stagnant flooding. The culm diameter was closely associated with culm strength; reduced aerenchyma formation and increased lignin accumulation in the culm should increase lodging resistance. CONCLUSIONS: The study demonstrated a successful combination of submergence and stagnant flooding tolerance in a rice breeding programme, and identified elite Sub1 genotypes that also tolerate stagnant flooding. Our results will support genetic improvement of Sub1 varieties for stagnant flooding tolerance.

A GWAS approach to find SNPs associated with salt removal in rice leaf sheath.

BACKGROUND AND AIMS: The ability for salt removal at the leaf sheath level is considered to be one of the major mechanisms associated with salt tolerance in rice. Thus, understanding the genetic control of the salt removal capacity in leaf sheaths will help improve the molecular breeding of salt-tolerant rice varieties and speed up future varietal development to increase productivity in salt-affected areas. We report a genome-wide association study (GWAS) conducted to find single nucleotide polymorphisms (SNPs) associated with salt removal in leaf sheaths of rice. METHODS: In this study, 296 accessions of a rice (Oryza sativa) diversity panel were used to identify salt removal-related traits and conduct GWAS using 36 901 SNPs. The sheath:blade ratio of Na+ and Cl- concentrations was used to determine the salt removal ability in leaf sheaths. Candidate genes were further narrowed via Gene Ontology and RNA-seq analysis to those whose putative function was likely to be associated with salt transport and were up-regulated in response to salt stress. KEY RESULTS: For the association signals of the Na+ sheath:blade ratio, significant SNPs were found only in the indica sub-population on chromosome 5. Within candidate genes found in the GWAS study, five genes were upregulated and eight genes were downregulated in the internal leaf sheath tissues in the presence of salt stress. CONCLUSIONS: These GWAS data imply that rice accessions in the indica variety group are the main source of genes and alleles associated with Na+ removal in leaf sheaths of rice under salt stress.

NRT1.1-Related NH4 + Toxicity Is Associated with a Disturbed Balance between NH4 + Uptake and Assimilation.

A high concentration of ammonium (NH4 +) as the sole source of nitrogen in the growth medium often is toxic to plants. The nitrate transporter NRT1.1 is involved in mediating the effects of NH4 + toxicity; however, the mechanism remains undefined. In this study, wild-type Arabidopsis (Arabidopsis thaliana Columbia-0 [Col-0]) and NRT1.1 mutants (chl1-1 and chl1-5) were grown hydroponically in NH4NO3 and (NH4)2SO4 media to assess the function of NRT1.1 in NH4 + stress responses. All the plants grew normally in medium containing mixed nitrogen sources, but Col-0 displayed more chlorosis and lower biomass and photosynthesis than the NRT1.1 mutants in (NH4)2SO4 medium. Grafting experiments between Col-0 and chl1-5 further confirmed that NH4 + toxicity is influenced by NRT1.1. In (NH4)2SO4 medium, NRT1.1 induced the expression of NH4 + transporters, increasing NH4 + uptake. Additionally, the activities of glutamine synthetase and glutamate synthetase in roots of Col-0 plants decreased and soluble sugar accumulated significantly, whereas pyruvate kinase-mediated glycolysis was not affected, all of which contributed to NH4 + accumulation. By contrast, the NRT1.1 mutants showed reduced NH4 + accumulation and enhanced NH4 + assimilation through glutamine synthetase, glutamate synthetase, and glutamate dehydrogenase. Moreover, the up-regulation of genes involved in ethylene synthesis and senescence in Col-0 plants treated with (NH4)2SO4 suggests that ethylene is involved in NH4 + toxicity responses. This study showed that NH4 + toxicity is related to a nitrate-independent signaling function of NRT1.1 in Arabidopsis, characterized by enhanced NH4 + accumulation and altered NH4 + metabolism, which stimulates ethylene synthesis, leading to plant senescence.

QTL mapping for tolerance to anaerobic germination in rice from IR64 and the aus landrace Kharsu 80A.

Direct seeding of rice often results in poor crop establishment due to unlevelled fields, unpredicted heavy rains after sowing, and weed and pest invasion. Thus, it is important to develop varieties able to tolerate flooding during germination, also known as anaerobic germination (AG), to address these constraints. A study was conducted to identify QTLs associated with AG tolerance from an IR64/Kharsu 80A F2:3 mapping population using 190 lines phenotyped for seedling survival under the stress. Genotyping was performed using a genomewide 384-plex Indica/Indica SNP set. Four QTLs derived from Kharsu 80A providing increased tolerance to anaerobic germination were identified: three on chromosome 7 (qAG7.1, qAG7.2 and qAG7.3) and one on chromosome 3 (qAG3), with LOD values ranging from 5.7 to 7.7, and phenotypic variance explained (R2) from 8.1% to 12.6%. The QTLs identified in this study can be further investigated to better understand the genetic bases of AG tolerance in rice, and used for marker-assisted selection to develop more robust direct-seeded rice varieties.

Describing the physiological responses of different rice genotypes to salt stress using sigmoid and piecewise linear functions.

Rice is the staple food for almost half of the world population. In South and South East Asia, about 40% of rice production is from deltaic regions that are vulnerable to salt stress. A quantitative approach was developed for characterizing genotypic variability in biomass production, leaf transpiration rate and leaf net photosynthesis responses to salinity during the vegetative stage, with the aim of developing efficient screening protocols to accelerate breeding varieties adapted to salt-affected areas. Three varieties were evaluated in pots under greenhouse conditions and in the field, with average soil salinity ranging from 2 to 12 dS m-1. Plant biomass, net photosynthesis rate, leaf transpiration rate and leaf conductance were measured at regular intervals. Crop responses were fitted using a logistic function with three parameters: 1) maximum rate under control conditions (Ymax), 2) salinity level for 50% of reduction (b), and 3) rate of reduction (a). Variation in the three parameters correlated significantly with variation in plant biomass production under increasing salinity. Salt stress levels that caused 50% reduction in net leaf photosynthesis and transpiration rates were higher in the tolerant genotype BRRI Dhan47 (16.5 dS m-1 and 14.3 dS m-1, respectively) than the sensitive genotype IR29 (11.1 dS m-1 and 6.8 dS m-1). In BRRI Dhan47, the threshold beyond which growth was significantly reduced was above 5 dS m-1 and the rate of growth reduction beyond this threshold was as low as 4% per unit increase in salinity. This quantitative approach to screening for salinity tolerance in rice offers a means to better understand rice growth under salt stress and, using simulation modelling, can provide an improved tool for varietal characterization.

Participatory evaluation guides the development and selection of farmers' preferred rice varieties for salt- and flood-affected coastal deltas of South and Southeast Asia.

Rice is the staple food and provides livelihood for smallholder farmers in the coastal delta regions of South and Southeast Asia. However, its productivity is often low because of several abiotic stresses including high soil salinity and waterlogging during the wet (monsoon) season and high soil and water salinity during the dry season. Development and dissemination of suitable rice varieties tolerant of these multiple stresses encountered in coastal zones are of prime importance for increasing and stabilizing rice productivity, however adoption of new varieties has been slow in this region. Here we implemented participatory varietal selection (PVS) processes to identify and understand smallholder farmers' criteria for selection and adoption of new rice varieties in coastal zones. New breeding lines together with released rice varieties were evaluated in on-station and on-farm trials (researcher-managed) during the wet and dry seasons of 2008-2014 in the Indian Sundarbans region. Significant correlations between preferences of male and female farmers in most trials indicated that both groups have similar criteria for selection of rice varieties. However, farmers' preference criteria were different from researchers' criteria. Grain yield was important, but not the sole reason for variety selection by farmers. Several other factors also governed preferences and were strikingly different when compared across wet and dry seasons. For the wet season, farmers preferred tall (140-170 cm), long duration (160-170 d), lodging resistant and high yielding rice varieties because these traits are required in lowlands where water stagnates in the field for about four months (July to October). For the dry season, farmers' preferences were for high yielding, salt tolerant, early maturing (115-130 d) varieties with long slender grains and good quality for better market value. Pest and disease resistance was important in both seasons but did not rank high. When farmers ranked the two most preferred varieties, the ranking order was sometimes variable between locations and years, but when the top four varieties that consistently ranked high were considered, the variability was low. This indicates that at least 3-4 of the best-performing entries should be considered in succeeding multi-location and multi-year trials, thereby increasing the chances that the most stable varieties are selected. These findings will help improve breeding programs by providing information on critical traits. Selected varieties through PVS are also more likely to be adopted by farmers and will ensure higher and more stable productivity in the salt- and flood-affected coastal deltas of South and Southeast Asia.

Nitrogen Use Efficiency Is Mediated by Vacuolar Nitrate Sequestration Capacity in Roots of Brassica napus.

Enhancing nitrogen use efficiency (NUE) in crop plants is an important breeding target to reduce excessive use of chemical fertilizers, with substantial benefits to farmers and the environment. In Arabidopsis (Arabidopsis thaliana), allocation of more NO3 (-) to shoots was associated with higher NUE; however, the commonality of this process across plant species have not been sufficiently studied. Two Brassica napus genotypes were identified with high and low NUE. We found that activities of V-ATPase and V-PPase, the two tonoplast proton-pumps, were significantly lower in roots of the high-NUE genotype (Xiangyou15) than in the low-NUE genotype (814); and consequently, less vacuolar NO3 (-) was retained in roots of Xiangyou15. Moreover, NO3 (-) concentration in xylem sap, [(15)N] shoot:root (S:R) and [NO3 (-)] S:R ratios were significantly higher in Xiangyou15. BnNRT1.5 expression was higher in roots of Xiangyou15 compared with 814, while BnNRT1.8 expression was lower. In both B. napus treated with proton pump inhibitors or Arabidopsis mutants impaired in proton pump activity, vacuolar sequestration capacity (VSC) of NO3 (-) in roots substantially decreased. Expression of NRT1.5 was up-regulated, but NRT1.8 was down-regulated, driving greater NO3 (-) long-distance transport from roots to shoots. NUE in Arabidopsis mutants impaired in proton pumps was also significantly higher than in the wild type col-0. Taken together, these data suggest that decrease in VSC of NO3 (-) in roots will enhance transport to shoot and essentially contribute to higher NUE by promoting NO3 (-) allocation to aerial parts, likely through coordinated regulation of NRT1.5 and NRT1.8.

Genetic dissection for zinc deficiency tolerance in rice using bi-parental mapping and association analysis.

KEY MESSAGE: Zinc deficiency is a widespread soil constraint in rice production. Here, we present QTL/candidate genes associated with Zn deficiency tolerance identified through bi-parental QTL mapping and genome-wide association analysis. Zinc (Zn) deficiency is a widespread soil constraint in rice production. Despite several physiological studies elucidating Zn deficiency tolerance mechanisms, little is known about genetic factors conferring tolerance. To identify QTL associated with root development, biomass accumulation, and grain yield under Zn deficiency, we combined bi-parental QTL mapping in a population of 200 backcross inbred (BC1F6) lines and genome-wide association analysis using 247 k SNP markers across 140 accessions of an indica diversity panel. Three QTLs for Zn deficiency tolerance on chromosomes 3, 6, and 12 co-localized in both approaches and the association analysis detected two additional strong QTL on chromosomes 1 and 9 not present in the bi-parental population. Based on haplotype analysis of the indica panel, biomass consistently increased due to the minor 'tolerance' haplotypes, which had frequencies between 13 and 34%. By utilizing the previous transcript data collected from the same Zn-deficient field, we identified one putative candidate gene within the chromosome 6-QTL, which was associated with all traits in both analyses. Gene Os06g44220 was barely expressed under +Zn conditions but strongly upregulated in both root and shoot under stress and consistently more so in the tolerant genotype. Os06g44220 is an uncharacterized gene with expression previously detected only under salinity stress. Four SNP alterations within the promoter region distinguish the two alleles identified and a genotype tolerant to Zn deficiency shares the same allele as salinity tolerant varieties, lending support to the hypothesis that this gene may confer tolerance to both stresses.

Biochemical indicators of root damage in rice (Oryza sativa) genotypes under zinc deficiency stress.

Zn deficiency is one of the major soil constraints currently limiting rice production. Although recent studies demonstrated that higher antioxidant activity in leaf tissue effectively protects against Zn deficiency stress, little is known about whether similar tolerance mechanisms operate in root tissue. In this study we explored root-specific responses of different rice genotypes to Zn deficiency. Root solute leakage and biomass reduction, antioxidant activity, and metabolic changes were measured using plants grown in Zn-deficient soil and hydroponics. Solute leakage from roots was higher in sensitive genotypes and linked to membrane damage caused by Zn deficiency-induced oxidative stress. However, total root antioxidant activity was four-fold lower than in leaves and did not differ between sensitive and tolerant genotypes. Root metabolite analysis using gas chromatography-mass spectrometry and high performance liquid chromatography indicated that Zn deficiency triggered the accumulation of glycerol-3-phosphate and acetate in sensitive genotypes, while less or no accumulation was seen in tolerant genotypes. We suggest that these metabolites may serve as biochemical indicators of root damage under Zn deficiency.

Exploring novel genetic sources of salinity tolerance in rice through molecular and physiological characterization.

BACKGROUND AND AIMS: Agricultural productivity is increasingly being affected by the build-up of salinity in soils and water worldwide. The genetic base of salt-tolerant rice donors being used in breeding is relatively narrow and needs broadening to breed varieties with wider adaptation to salt-affected areas. This study evaluated a large set of rice accessions of diverse origins to identify and characterize novel sources of salt tolerance. METHODS: Diversity analysis was performed on 107 germplasm accessions using a genome-wide set of 376 single-nucleotide polymorphism (SNP) markers, along with characterization of allelic diversity at the major quantitative trait locus Saltol Sixty-nine accessions were further evaluated for physiological traits likely associated with responses to salt stress during the seedling stage. KEY RESULTS: Three major clusters corresponding to the indica, aus and aromatic subgroups were identified. The largest group was indica, with the salt-tolerant Pokkali accessions in one sub-cluster, while a set of Bangladeshi landraces, including Akundi, Ashfal, Capsule, Chikirampatnai and Kutipatnai, were in a different sub-cluster. A distinct aus group close to indica contained the salt-tolerant landrace Kalarata, while a separate aromatic group closer to japonica rice contained a number of traditional, but salt-sensitive Bangladeshi landraces. These accessions have different alleles at the Saltol locus. Seven landraces - Akundi, Ashfal, Capsule, Chikirampatnai, Jatai Balam, Kalarata and Kutipatnai - accumulated less Na and relatively more K, maintaining a lower Na/K ratio in leaves. They effectively limit sodium transport to the shoot. CONCLUSIONS: New salt-tolerant landraces were identified that are genetically and physiologically distinct from known donors. These landraces can be used to develop better salt-tolerant varieties and could provide new sources of quantitative trait loci/alleles for salt tolerance for use in molecular breeding. The diversity observed within this set and in other donors suggests multiple mechanisms that can be combined for higher salt tolerance.

Gas film retention and underwater photosynthesis during field submergence of four contrasting rice genotypes.

Floods can completely submerge some rice (Oryza sativa L.) fields. Leaves of rice have gas films that aid O2 and CO2 exchange under water. The present study explored the relationship between gas film persistence and underwater net photosynthesis (PN) as influenced by genotype and submergence duration. Four contrasting genotypes (FR13A, IR42, Swarna, and Swarna-Sub1) were submerged for 13 days in the field and leaf gas films, chlorophyll, and the capacity for underwater PN at near ambient and high CO2 were assessed with time of submergence. At high CO2 during the PN assay, all genotypes initially showed high rates of underwater PN, and this rate was not affected by time of submergence in FR13A. This superior photosynthetic performance of FR13A was not evident in Swarna-Sub1 (carrying the SUB1 QTL) and the declines in underwater PN in both Swarna-Sub1 and Swarna were equal to that in IR42. At near ambient CO2 concentration, underwater PN declined in all four genotypes and this corresponded with loss of leaf gas films with time of submergence. FR13A retained leaf gas films moderately longer than the other genotypes, but gas film retention was not linked to SUB1. Diverse rice germplasm should be screened for gas film persistence during submergence, as this trait could potentially increase carbohydrate status and internal aeration owing to increased underwater PN, which contributes to submergence tolerance in rice.

Salinity tolerance, Na+ exclusion and allele mining of HKT1;5 in Oryza sativa and O. glaberrima: many sources, many genes, one mechanism?

BACKGROUND: Cultivated rice species (Oryza sativa L. and O. glaberrima Steud.) are generally considered among the crop species most sensitive to salt stress. A handful of lines are known to be tolerant, and a small number of these have been used extensively as donors in breeding programs. However, these donors use many of the same genes and physiological mechanisms to confer tolerance. Little information is available on the diversity of mechanisms used by these species to cope with salt stress, and there is a strong need to identify varieties displaying additional physiological and/or genetic mechanisms to confer higher tolerance. RESULTS: Here we present data on 103 accessions from O. sativa and 12 accessions from O. glaberrima, many of which are identified as salt tolerant for the first time, showing moderate to high tolerance of high salinity. The correlation of salinity-induced senescence (as judged by the Standard Evaluation System for Rice, or SES, score) with whole-plant and leaf blade Na+ concentrations was high across nearly all accessions, and was almost identical in both O. sativa and O. glaberrima. The association of leaf Na+ concentrations with cultivar-groups was very weak, but association with the OsHKT1;5 allele was generally strong. Seven major and three minor alleles of OsHKT1;5 were identified, and their comparisons with the leaf Na+ concentration showed that the Aromatic allele conferred the highest exclusion and the Japonica allele the least. A number of exceptions to this association with the Oryza HKT1;5 allele were identified; these probably indicate the existence of additional highly effective exclusion mechanisms. In addition, two landraces were identified, one from Thailand and the other from Senegal, that show high tissue tolerance. CONCLUSIONS: Significant variation in salinity tolerance exists within both cultivated Oryza species, and this is the first report of significant tolerance in O. glaberrima. The majority of accessions display a strong quantitative relationship between tolerance and leaf blade Na+ concentration, and thus the major tolerance mechanisms found in these species are those contributing to limiting sodium uptake and accumulation in active leaves. However, there appears to be genetic variation for several mechanisms that affect leaf Na+ concentration, and rare cases of accessions displaying different mechanisms also occur. These mechanisms show great promise for improving salt tolerance in rice over that available from current donors.

Internal aeration of paddy field rice (Oryza sativa) during complete submergence---importance of light and floodwater O2.

Flash floods can submerge paddy field rice (Oryza sativa), with adverse effects on internal aeration, sugar status and survival. Here, we investigated the in situ aeration of roots of rice during complete submergence, and elucidated how underwater photosynthesis and floodwater pO(2) influence root aeration in anoxic soil. In the field, root pO(2) was measured using microelectrodes during 2 d of complete submergence. Leaf gas films that formed on the superhydrophobic leaves were left intact, or experimentally removed, to elucidate their effect on internal aeration. In darkness, root pO(2) declined to very low concentrations (0.24 kPa) and was strongly correlated with floodwater pO(2). In light, root pO(2) was high (14 kPa) and primarily a function of the incident light determining the rates of underwater net photosynthesis. Plants with intact leaf gas films maintained higher underwater net photosynthesis relative to plants without gas films when the submerged shoots were in light. During complete submergence, internal aeration of rice in the field relies on underwater photosynthesis during the day and entry of O(2) from the floodwater during the night. Leaf gas films enhance photosynthesis during submergence leading to improved O(2) production and sugar status, and therefore contribute to the submergence tolerance of rice.

Zn uptake, translocation and grain Zn loading in rice (Oryza sativa L.) genotypes selected for Zn deficiency tolerance and high grain Zn.

Zn deficiency is a widespread problem in rice (Oryza sativa L.) grown under flooded conditions, limiting growth and grain Zn accumulation. Genotypes with Zn deficiency tolerance or high grain Zn have been identified in breeding programmes, but little is known about the physiological mechanisms conferring these traits. A protocol was developed for growing rice to maturity in agar nutrient solution (ANS), with optimum Zn-sufficient growth achieved at 1.5 µM ZnSO4.7H2O. The redox potential in ANS showed a decrease from +350 mV to -200 mV, mimicking the reduced conditions of flooded paddy soils. In subsequent experiments, rice genotypes contrasting for Zn deficiency tolerance and grain Zn were grown in ANS with sufficient and deficient Zn to assess differences in root uptake of Zn, root-to-shoot Zn translocation, and in the predominant sources of Zn accumulation in the grain. Zn efficiency of a genotype was highly influenced by root-to-shoot translocation of Zn and total Zn uptake. Translocation of Zn from root to shoot was more limiting at later growth stages than at the vegetative stage. Under Zn-sufficient conditions, continued root uptake during the grain-filling stage was the predominant source of grain Zn loading in rice, whereas, under Zn-deficient conditions, some genotypes demonstrated remobilization of Zn from shoot and root to grain in addition to root uptake. Understanding the mechanisms of grain Zn loading in rice is crucial in selecting high grain Zn donors for target-specific breeding and also to establish fertilizer and water management strategies for achieving high grain Zn.

QTL mapping and confirmation for tolerance of anaerobic conditions during germination derived from the rice landrace Ma-Zhan Red.

Wide adoption of direct-seeded rice practices has been hindered by poorly leveled fields, heavy rainfall and poor drainage, which cause accumulation of water in the fields shortly after sowing, leading to poor crop establishment. This is due to the inability of most rice varieties to germinate and reach the water surface under complete submergence. Hence, tolerance of anaerobic conditions during germination is an essential trait for direct-seeded rice cultivation in both rainfed and irrigated ecosystems. A QTL study was conducted to unravel the genetic basis of tolerance of anaerobic conditions during germination using a population derived from a cross between IR42, a susceptible variety, and Ma-Zhan Red, a tolerant landrace from China. Phenotypic data was collected based on the survival rates of the seedlings at 21 days after sowing of dry seeds under 10 cm of water. QTL analysis of the mapping population consisting of 175 F2:3 families genotyped with 118 SSR markers identified six significant QTLs on chromosomes 2, 5, 6, and 7, and in all cases the tolerant alleles were contributed by Ma-Zhan Red. The largest QTL on chromosome 7, having a LOD score of 14.5 and an R (2) of 31.7 %, was confirmed using a BC2F3 population. The QTLs detected in this study provide promising targets for further genetic characterization and for use in marker-assisted selection to rapidly develop varieties with improved tolerance to anaerobic condition during germination. Ultimately, this trait can be combined with other abiotic stress tolerance QTLs to provide resilient varieties for direct-seeded systems.