Effects of field high temperature on grain yield and quality of a subtropical type japonica rice—Pon-Lai rice

Typical japonica type rice is sensitive to high temperature. Pon-Lai rice is a special japonica type with adaptation to the subtropical climate in Taiwan. Facing climate change, rising temperatures would damage the yield and quality of rice production. This research was conducted using Pon-Lai rice in the field of a subtropical climate. We conducted 2 experiments, including a year-round experiment and collection of samples from different districts for building different temperature conditions. We analyzed the correlation between rising temperature and rice yield or quality. In our results, the critical period of temperature effect is 0–15 days after heading (H15). The threshold of high temperature damage in yield and appearance quality was 25–27 °C. Grain weight decreased about 2–6%, while the temperature of H15 was raised 1 °C above the thresholds. Perfect grain ratio and chalky grain ratio decreased and increased, respectively, while the temperature of H15 was raised above the thresholds. However, the high temperature in H15 affected the physicochemical characteristics. In addition, we found positive correlation between grain length to width ratio and perfect grain ratio. Grain length to width ratio could be an index of temperature effects for grain quality. In our study, when the temperature was below 30 °C, a rising temperature of H15 could damage rice yield and appearance quality, and change grain shape. Our results could provide reference for dealing with the warming future in other temperate rice-cultivated countries.     

Identification and validation of QTLs for cold tolerance at the booting stage and other agronomic traits in a rice cross of a Japanese tolerant variety,Hananomai, and a NERICA parent,WAB56-104

In Africa, cold temperatures occur in the highlands of East and Southern Africa and in some areas of the Sahel region of West Africa leading to substantial rice yield losses. Cold tolerance (CT) at booting stage on basis of spikelet fertility after cold water irrigation was evaluated using F₂ population derived from a cross between temperate japonica, Hananomai, and tropical japonica, WAB56-104. Two Quantitative trait loci (QTLs) for CT were detected on chromosome 8 and 10 with enhanced effects on the trait coming from Hananomai and WAB56-104 allele, respectively. The QTLs explained 30% and 33% of phenotypic variation in spikelet fertility, respectively. CT was negatively correlated with panicle number (r = ?0.35, p < 0.01) and positively correlated with panicle weight (r = 0.61, p < 0.001). Selected BC₁F₄ and BC₁F₅ genotypes having homozygous alleles for both CT QTLs exhibited higher spikelet fertility under cold stress. The identified QTLs will be useful in the development of cold-tolerant varieties for production in high altitude areas through marker-assisted selection.     

Species,ecotype and cultivar differences in spikelet fertility and harvest index of rice in response to high temperature stress

Spikelet fertility (seed-set) is an important component of yield that is sensitive to high temperature. The objectives of this research were (a) to quantify the effects of high temperature on spikelet fertility and harvest index of rice; (b) to determine if there were species, ecotype, and/or cultivar differences in response to high temperature; and (c) to understand the reasons for lower and/or differential spikelet fertility and harvest index of rice cultivars at high temperatures. Fourteen rice cultivars of different species (Oryza sativa and Oryza glaberrima), ecotypes (indica and japonica) and origin (temperate and tropical) were exposed to ambient and high temperature (ambient + 5 °C) at Gainesville, Florida. High temperature significantly decreased spikelet fertility across all cultivars, but effects varied among cultivars. Based on decreases in spikelet fertility at high temperature, cultivar N-22 was most tolerant, while cultivars L-204, M-202, Labelle, Italica Livorna, WAB-12, CG-14 and CG-17 were highly susceptible and cultivars M-103, S-102, Koshihikari, IR-8 and IR-72 were moderately susceptible to high temperature. There were no clear species or ecotype differences, as some cultivars in each species or within ecotypes of tropical and temperature origin were equally susceptible to high temperature (for example M-202 temperate japonica, Labelle tropical japonica, CG-14 O. glaberrima, and WAB-12 interspecific). Decreased spikelet fertility and cultivar difference at high temperature were due mainly to decreased pollen production and pollen reception (pollen numbers on stigma). Lower spikelet fertility at elevated temperature resulted in fewer filled grains, lower grain weight per panicle, and decreased harvest index. There is a potential for genetic improvement for heat tolerance, thus it is important to screen and identify heat-tolerant cultivars. Spikelet fertility at high temperature can be used as a screening tool for heat tolerance during the reproductive phase.     

Progress in varietal improvement for increasing upland rice productivity in the tropics

Enhancing rice yield in upland rice systems through genetic improvement remains a major challenge in the tropics. This review aims to provide the trends on upland rice cultivation over the last 30 years and recent distribution of upland rice in the tropics, and to report progress in studies on genetic improvement for enhancing productivity in Africa, Asia, and Latin America. While upland rice cultivation area has reduced in Asia and Latin America over the last 30 years, the area in Africa has increased. The current share of upland rice area in total rice area is related to rainfall and gross national income per capita, especially in Africa, and higher share is associated with lower rice self-sufficiency at national level. Breeding programs in Asia and Latin America have developed high-yielding varieties using indica materials as parents. In Africa, New Rice for Africa (NERICA) varieties were developed from crosses between improved tropical japonica and Oryza glaberrima. However, recent studies report that there is scope for improving existing NERICA using upland indica materials from Asia. In highlands of Africa, there are ongoing breeding programs using japonica varieties, such as the Nepalese Chhomrong Dhan. Key important plant traits used in the breeding programs are not largely different across regions, especially intermediate plant height and tillering capacity (which may be related to weed-suppressive ability), and high harvest index. In conclusion, we propose an international network for breeding upland rice with accelerating seed exchange across regions that could enhance upland rice productivity through genetic improvement.     

Ionomic Profiling of Rice Genotypes and Identification of Varieties with Elemental Covariation Effects

Ionomic profiles are primarily influenced by genetic and environmental factors. Identifying ionomic responses to varietal effects is necessary to understand the ionomic variations among species or subspecies and to potentially understand genetic effects on ionomic profiles. We cultivated 120 rice (Oryza sativa) varieties to seedling stage in identical hydroponic conditions and determined the concentrations of 26 elements (including 3 anions) in the shoots and roots of rice. Although the subspecies effects were limited by the genus Oryza pre-framework and its elemental chemical properties, we found significant differences in ionomic variations in most elements among the aus, indica and japonica subspecies. Principal component analysis of the correlations indicated that variations in the root-to-shoot ionomic transport mechanisms were the main causes of ionomic differences among the subspecies. Furthermore, the correlations were primarily associated with the screening of varieties for elemental covariation effects that can facilitate breeding biofortified rice varieties with safe concentrations of otherwise toxic elements. The japonica subspecies exhibited the strongest elemental correlations and elemental covariation effects, therefore, they showed greater advantages for biofortification than the indica and aus subspecies, whereas indica and aus subspecies were likely safer in metal(loid) polluted soils. We also found that geographical and historical distribution significantly defined the ionomic profiles. Overall, the results of this study provided a reference for further association studies to improve the nutritional status and minimize toxicity risks in rice production.     

Research Progress on Heat Stress of Rice at Flowering Stage

Global warming has caused frequent occurrence of heat stress at the flowering stage of single-season rice in the Yangtze River region of China, which results in declines of spikelet fertility and yield in rice. Rice flowering stage is the most sensitive period to high temperatures, and therefore, the key for heat stress happening is the flowering stage coinciding with high temperature, which causes spikelet fertility decreasing in heat-sensitive varieties, and is the major factor for heat injury differences among various rice planting regions. With the development of rice breeding, temperature indexes for heat stress has been converted from daily maximum temperature of 35 °C to 38 °C with the stress duration of more than 3 d. During the flowering stage, anther dehiscence inhibition and low pollen shedding onto the stigma are two main reasons for spikelet fertility reduction under high temperatures. At panicle initiation stage, high temperatures aggravate spikelet degeneration, and destroy floral organ development. Various types of rice varieties coexist in production, and indica-japonica hybrid rice demonstrates the highest heat resistance in general, followed by indica and japonica rice varieties. In production, avoiding high temperature is the main strategy of preventing heat stress, and planting suitable cultivars and adjustment of sowing date are the most effective measures. Irrigation is an effective real-time cultivation measure to decline the canopy temperature during the rice flowering stage. We suggested that further study should be focused on exploring heat injury differences among different rice variety types, and innovating rice-planting methods according to planting system changes in rice planting regions with extreme heat stress. Meanwhile, high temperature monitor and warning systems should be improved to achieve optimal heat stress management efficiencies.     

Performance of diverse upland rice cultivars in low and high soil fertility conditions in West Africa

Traditional tropical japonica (Oryza sativa) and Oryza glaberrima cultivars are typically grown in low-input, subsistence production systems in the uplands of West Africa by resource-poor farmers. In these systems, low soil fertility (LF), which is generally associated with lower organic carbon content, and N and P availability, is one of the major constraints to rice productivity. Thus, cultivars adapted to LF are needed for the food security of farmers, who would otherwise be solely reliant on nutrient inputs to increase productivity. This study evaluated the performance of six diverse cultivars grown in LF and high soil fertility (HF) conditions with supplemental irrigation over two seasons. Average grain yield across all cultivars in LF was 54% of that in HF (156 vs. 340 g m⁻²). Three improved indica rice cultivars and CG 14 (O. glaberrima) out-yielded Morobérékan (traditional tropical japonica) and WAB450-IBP-38-HB (progeny from interspecific hybridization of tropical japonica and O. glaberrima) in LF (181 vs. 105 g m⁻² on average). The high grain yield in LF was the result of large spikelet number m⁻² due to superior tillering ability and high harvest index rather than biomass production. The high-yielding cultivars in LF consistently had lower leaf chlorophyll content and higher specific leaf area during the period from the early vegetative stage through the reproductive stage. Among them, two indica cultivars (B6144F-MR-6-0-0 and IR 55423-01) were also high yielding in HF. The use of improved indica cultivars adapted to LF, but also with input-responsiveness, appears to offer an attractive and economical approach to improving upland rice productivity and widening genetic diversity in this region.     

Testing of Rice Stocks for Their Survival of Winter Cold

Rice cultivation is considered to be initiated by vegetative propagation of sprout from wild perennial stocks. To test whether any presently cultivated rice cultivar can survive the winter cold or not, rice stocks of several cultivars including indica and japonica types were placed in a shallow pool from October to April in 2015–2016 and 2016–2017. During the coldest period of the winter, the bases of the stocks were placed 5–6 cm below the surface of water, where temperatures ranged from 3 ℃ to 5 ℃, while the surface was frozen for two or three times and covered with snow for a day. Only one cultivar, Nipponbare, a japonica type, survived the winter cold and regenerated sprouts in the end of April or early May. A possibility to develop perennial cultivation of rice or perennial hybrid rice is discussed.     

Correlation and Regressive Model Between Spikelet Fertilized Rate and Temperature in Inter-Subspecific Hybrid Rice

To study the sensitivity of inter-subspecific hybrid rice to climatic conditions, the spikelet fertilized rate (SFR) of four types of rice including indica-japonica hybrid, intermediate hybrid, indica and japonica were analyzed during 2000-2004. The inter-subspecific hybrids showed lower SFR, and much higher fluctuation under various climatic conditions than indica and japonica rice, showing the inter-subspecific hybrids were sensitive to ecological conditions. Among 12 climatic factors, the key factor affecting rice SFR was temperature, with the most significant factor being the average temperature of the seven days around panicle flowering (T7). A regressive equation of SFR-temperature by T7, and a comprehensive synthetic model by four important temperature indices were put forward. The optimum temperature for inter-subspecific hybrids was estimated to be 26.1-26.6℃, and lower limit of safe temperature to be 22.5-23.3℃ for panicle flowering, showing higher by averagely 0.5℃ and 1.7℃, respectively, to be compared with indica and japonica rice. This suggested that inter-subspecific hybrids require proper climatic conditions. During panicle flowering, the suitable daily average temperature was 23.3-29.0℃, with the fittest one at 26.1-26.6℃. For an application example, optimum heading season for inter-subspecific hybrids in key rice growing areas in China was as same as common pure lines, while inferior limit for safe date of heading was about a ten-day period earlier than those of common pure lines.     

Effects of Early- and Late-Sowing on Starch Accumulation and Associated Enzyme Activities During Grain Filling Stage in Rice

The environmental temperature occurring during the grain filling stage is an important factoraffecting starch synthesis and accumulation in rice. We investigated starch accumulation, amylaseactivity and starch granule size distribution in two low-amylose japonica rice varieties, Nanjing 9108 andFujing 1606, grown in the field at different filling temperatures by manipulating sowing date. The two ricevarieties exhibited similar performances between two sowing dates. Total starch, amylose andamylopectin contents were lower at the early-filling stage of T1 treatment (Early-sowing) compared withthose at the same stage in T2 treatment (Late-sowing). In contrast, at the late-filling stage, when fieldtemperatures were generally decreasing, total starch and amylopectin contents in T1 were highercompared to those in T2. The ideal temperature for strong activity of ADP-glucose pyrophosphorylaseand soluble starch synthase was about 22℃. A higher temperature from the heading to maturity stagesin T1 increased the activities of starch branching enzyme and suppressed the activities of granule boundstarch synthetase and starch debranching enzyme. We found that rice produced larger-sized starchgranules under the T1 treatment. These results suggested that due to the early-sowing date, the hightemperature (30℃) occurring at the early-filling stage hindered starch synthesis and accumulation,however, the lower temperatures (22 ℃) at the late-filling stage allowed starch synthesis and accumulationto return to normal levels.     

Quantitative trait loci responsible for the difference in γ-oryzanol content in brown rice between japonica-type and indica-type rice cultivars

γ-Oryzanol is a main oleophilic component in rice bran oil and has been well recognized as a good dietary supplement for human health, as well as having uses in industrial materials. japonica-type rice cultivars generally showed significantly higher contents of total γ-oryzanol in brown rice compared with indica-type cultivars, although within-group variation was significant. The objective of this study was to explore quantitative trait loci (QTLs) responsible for the difference in the γ-oryzanol content between japonica-type and indica-type rice cultivars, using recombinant inbred lines (RILs), backcross inbred lines (BILs), and corresponding chromosome segment substitution lines (CSSLs) derived from crosses between japonica-type and indica-type. Results from RILs and BILs showed that eight QTLs were detected with R² from .09 to .16. Nine candidate regions for QTL were also suggested from corresponding CSSLs. These QTLs from RILs and BILs and the candidate regions from CSSLs were not overlapped, although one QTLs was mapped near the boundaries of the respective candidate region. At four QTLs and three candidate regions, alleles or segments from japonica-type caused higher contents than those from indica-type. On the other hand, at the other four QTLs and six candidate regions, alleles or segments from indica-type caused higher contents than those from japonica-type, which is a reverse result to the parental differences. This result strongly suggested that alleles with increasing effects on γ-oryzanol content could be accumulated not only from japonica-type but also from indica-type, leading to a potential for increase in γ-oryzanol content in future breeding programs.     

Genetic Diversity of Isolated Populations of Indonesian Landraces of Rice (Oryza sativa L.) Collected in East Kalimantan on the Island of Borneo

Although the genetic diversity of rice germplasm has been well characterized globally, few studies have taken an in-depth view of a large number of rice landraces on a local scale. To better understand the relationships between rice genetic diversity and associated geographic and cultural factors, we collected and characterized 183 rice landraces from 18 villages along the Bahau and Kayan rivers in the Indonesian province of East Kalimantan on the island of Borneo. A genetic diversity analysis using 30 microsatellite markers detected a clear distinction between the indica and japonica varietal groups (F _st?=?0.59), with 80% of the landraces identified as tropical japonica and 20% indica, which largely correlated with the field-level ecotypes: upland japonica and lowland indica. Indigenous knowledge from local farmers was gathered about the names, origins, and uses of the landraces, which provides a rich background to compare with the genetic relationships of these traditional varieties.     

Metabolite profiling of colored rice (Oryza sativa L.) grains

HPLC analysis of dehulled red, black and non-colored indica and japonica rice subspecies revealed significant differences in the contents of the anthocyanins cyanidin-3-glucoside and peonidin-3-glucoside. The rice materials were subjected to a comparative capillary gas chromatography-based metabolite profiling approach. The employed extraction and fractionation protocol enables the analysis of a broad spectrum of lipophilic and hydrophilic low molecular weight constituents from different chemical classes. The method covers not only primary metabolites (e.g. sugars, fatty acids) but also nutritionally relevant constituents (e.g. α-tocopherol, γ-aminobutyric acid). Statistical assessment of the data via principal component analysis and agglomerative hierarchical clustering revealed a distinct grouping of the different colored rice subspecies on the basis of their metabolite profiles. Compared to non-colored and red rice, black rice exhibited, in particular, higher levels of fatty acid methyl esters, free fatty acids, organic acids and amino acids.     

Identification of novel glutelin subunits and a comparison of glutelin composition between japonica and indica rice (Oryza sativa L.)

Glutelin, a major protein in rice grains, is encoded by a multigene family. However, its protein composition is not well characterised. Here, we identified and characterised two novel glutelin subunits, GluBX and GluC. The individual glutelin subunits of japonica cv. Nipponbare and indica cv. 93-11 rice were analysed using 2-dimensional gel electrophoresis, LC–MS/MS, and Western blotting. Comparison of the glutelin profiles between three japonica and three indica cultivars indicated two distinct subunits (GluA-1 and GluA-3 isomers) and a distinction in the subunit composition (notably GluA-3 and Lys-rich GluB-1 components) of these two subspecies. Sequence alignment revealed different nutritional (Lys residues) and functional (Cys residues) characteristics between the type-A and type-B glutelin subfamilies. We also analysed amino acid and total protein contents of the grains in thirty-five cultivars, and we demonstrated that the Lys-rich glutelin composition of indica cultivars is superior to that of japonica cultivars. The Lys-rich and Cys-poor GluBX subunit is a native protein and is a high nutritional protein in grains. Our combined approaches for the identification of glutelin subunits have revealed the nutritional characteristics of individual subunits in rice, and this knowledge will provide new insights for improving grain quality during rice breeding.     

The Endosperm Morphology of Rice and its Wild Relatives as Observed by Scanning Electron Microscopy

While cultivated rice, Oryza sativa, is arguably the world’s most important cereal crop, there is little comparative morphological information available for the grain of rice wild relatives. In this study, the endosperm of 16 rice wild relatives were compared to O. sativa subspecies indica and O. sativa subspecies japonica using scanning electron microscopy. Although the aleurone, starch granules, protein bodies and endosperm cell shapes of the cultivated and non-cultivated species were similar, several differences were observed. The starch granules of some wild species had internal channels that have not been reported in cultivated rice. Oryza longiglumis, Microlaena stipoides and Potamophila parviflora, had an aleurone that was only one-cell thick in contrast to the multiple cell layers observed in the aleurone of the remaining Oryza species. The similarity of the endosperm morphology of undomesticated species with cultivated rice suggests that some wild species may have similar functional properties. Obtaining a better understanding of the wild rice species grain ultrastructure will assist in identifying potential opportunities for development of these wild species as new cultivated crops or for their inclusion in plant improvement programmes.     

Breeding Novel Short Grain Rice for Tropical Region to Combine Important Agronomical Traits,Biotic Stress Resistance and Cooking Quality in Koshihikari Background

Breeding program strategies to develop novel short grain white rice varieties such as japonica (short grain) that introgress biotic stress resistance and high grain quality have been developed using indica rice (Pin Kaset + 4 and Riceberry) for applications in japonica rice (Koshihikari) improvement. Four breeding lines showing promising agronomic performance with short grain and low amylose content (< 20%) were obtained. In addition, sensory testing of these breeding lines showed high scores that similar to Koshihikari. Two promising lines, KP48-1-5 and KP48-1-9, which possessed a combination of four genes resistance to different biotic stresses (Bph3 + TPS + Xa21 + Pi-ta) and four genes for grain quality (GS3 + SSIIa + wx^b + badh2), were developed using marker-assisted selection (MAS) with the pedigree method. The current study clearly illustrated the successful use of MAS in combining resistance to multiple biotic stresses while maintaining a high yield potential and preferred grain quality. Moreover, the results indicated that this breeding program, which includes crossing temperate japonica with indica, can create novel short grain rice varieties adapted to a tropical environment, like the japonica type.     

Starch digestibility and the estimated glycemic score of different types of rice differing in amylose contents

Three types of rice cultivars (indica, japonica and hybrid rice) with four levels of amylose were selected for assessing variability in starch digestibility. A vitro enzymatic starch digestion method was applied to estimate the glycemic index in vivo based on the kinetics of starch hydrolysis in vitro. The results indicated that significant differences in term of glycemic response were observed in three types of rice. Amylose content had an obviously impact on the estimated glycemic score (EGS) value and resistant starch (RS) content. The contents of RS were increased with the increasing amylose in the same type of rice. Japonica rice was significantly lower in RS content compared to indica rice and hybrid rice with similar amylose. The high amylose rice cultivar ZF201, which was characterized by low major RVA parameters, i.e. peak viscosity (PKV), hot paste viscosity (HPV) and cool paste viscosity (CPV), were obviously higher in RS content and lower in EGS. The retrogradation of cooked rice led to a reduction of HI and EGS of all varieties. Starch hydrolysis tends to be more quick and complete for the waxy and low amylose rice than for the intermediate and high amylose rice.     

Rice crop duration and leaf appearance rate in a variable thermal environment. II. Comparison of genotypes

Rice crop duration in tropical-arid, irrigated environments, such as the Sahel, varies strongly among seasons and years. For rice double-cropping systems, cultivars are needed that have a stable duration under variable daylengths and temperatures. No efficient selection tools are currently available to screen for comparatively thermo- and photoperiod-insensitive cultivars, and little is known about the genetic diversity of rice in this respect. A previous study presented a model that disaggregates photothermal effects on rice phenology for the different crop development stages and the two main factors, daylength and temperature. The present study characterizes differences in the photothermal response of 18 rice lines for three major phases of their development, namely, germination, the appearance of early leaves, and the induction phase (IP) between the end of the basic vegetative phase (BVP) and panicle initiation (PI). A field experiment was conducted at Ndiaye in Senegal, using 11 staggered sowing dates at 15 day intervals. Three check cultivars were replicated four times per date, and the others were not replicated. Phenological observations included leaf tip appearance rates on a daily basis, and heading and flowering dates. Water and air temperatures were also monitored. The duration from seed soaking to the appearance of the first leaf depended linearly on water temperature, with a base temperature of about 8°C. No differences were observed among lines. The appearance rate of the first to the fourth leaf had an optimum temperature (T_opt) between 22°C and 25°C, with significant differences between lines. Lines with low T_opt had high maximal leaf appearance rates during seedling stage. The quantitatively most important component of the seasonal variability of crop duration was IP, which depended on temperature and photoperiod. Photoperiodic and temperature effects were disaggregated using an empirically based model leaf appearance (LAP), which, by way of parametrization, helped quantify genotypic differences. The photothermal differences between lines were associated with adaptation to specific seasons. Lines such as IR13240-108-2-2-3, which is adapted to several seasons, were comparatively insensitive to photoperiod and temperature. That line also had a low T_opt and a high Leaf Appearance. In conclusion, screening for temperature-insensitive leaf appearance rates may be promising for rice breeding for arid, irrigated environments. Selection for combined low thermal and photoperiod sensitivity, however, would be impractical on an experimental basis, and would therefore require genetic markers.     

Molecular Markers and Candidate Genes for Thermo-Sensitive Genic Male Sterile in Rice

The discovery of thermo-sensitive genic male sterility(TGMS) has led to development of a simple and highly efficient two-line breeding system. In this study, genetic analysis was conducted using three F_2 populations derived from crosses between IR68301 S, an indica TGMS rice line, and IR14632(tropical japonica), Supanburi 91062(indica) and IR67966-188-2-2-1(tropical japonica), respectively.Approximately 1:3 ratio between sterile and normal pollen of F_2 plants from the three populations revealed that TGMS is controlled by a single recessive gene. Bulked segregant analysis using simple sequence repeat(SSR) and insertion-deletion(InDel) markers were used to identify markers linked to the tms gene. The linkage analysis based on the three populations indicated that the tms locus was located on chromosome 2 covering the same area. Using IR68301S × IR14632 F_2 population, the results showed that the tms locus was located between SSR marker RM12676 and InDel marker 2gAP0050058. The genetic distance from the tms gene to these two flanking markers were 1.10 and 0.82 cM, respectively.InDel marker 2gAP004045 located between these two markers showed complete co-segregation with the TGMS phenotype. In addition, InDel marker vf0206114052 showed 2.94 cM linked to the tms gene using F_2 populations of IR68301S × Supanburi 91062. These markers are useful tool for developing new TGMS lines by marker-assisted selection. There were ten genes located between the two flanking markers RM12676 and 2gAP0050058. Using quantitative real-time PCR for expression analysis, 7 of the 10 genes showed expression in panicles, and response to temperatures. These genes could be the candidate gene controlling TGMS in IR68301S.     

Genome-wide association study and candidate gene analysis of rice cadmium accumulation in grain in a diverse rice collection

Background

Cadmium (Cd) accumulation in rice followed by transfer to the food chain causes severe health problems in humans. Breeding of low Cd accumulation varieties is one of the most economical ways to solve the problem. However, information on the identity of rice germplasm with low Cd accumulation is limited, particularly in indica, and the genetic basis of Cd accumulation in rice is not well understood.

Results

Screening of 312 diverse rice accessions revealed that the grain Cd concentrations of these rice accessions ranged from 0.12 to 1.23?mg/kg, with 24 accessions less than 0.20?mg/kg. Three of the 24 accessions belong to indica. Japonica accumulated significantly less Cd than indica (p < 0.001), while tropical japonica accumulated significantly less Cd than temperate japonica (p < 0.01). GWAS in all accessions identified 14 QTLs for Cd accumulation, with 7 identified in indica and 7 identified in japonica subpopulations. No common QTL was identified between indica and japonica. The previously identified genes (OsHMA3, OsNRAMP1, and OsNRAMP5) from japonica were colocalized with QTLs identified in japonica instead of indica. Expression analysis of OsNRAMP2, the candidate gene of the novel QTL (qCd3–2) identified in the present study, demonstrated that OsNRAMP2 was mainly induced in the shoots of high Cd accumulation accessions after Cd treatment. Four amino acid differences were found in the open reading frame of OsNRAMP2 between high and low Cd accumulation accessions. The allele from low Cd accumulation accessions significantly increased the Cd sensitivity and accumulation in yeast. Subcellular localization analysis demonstrated OsNRAMP2 expressed in the tonoplast of rice protoplast.

Conclusion

The results suggest that grain Cd concentrations are significantly different among subgroups, with Cd concentrations decreasing from indica to temperate japonica to tropical japonica. However, considerable variations exist within subgroups. The fact that no common QTL was identified between indica and japonica implies that there is a different genetic basis for determining Cd accumulation between indica and japonica, or that some QTLs for Cd accumulation in rice are subspecies-specific. Through further integrated analysis, it is speculated that OsNRAMP2 could be a novel functional gene associated with Cd accumulation in rice.