Indica Type Research Articles

Effect of flag leaf length of erect panicle rice on the canopy structure and biomass production after heading

ABSTRACT Increasing the yield potential of rice (Oryza sativa) is the main objective of breeders and cultivators engaged in rice improvement programs. Erect panicle (EP) rice is generally high-yielding with panicles that remain non-curved until maturation. The aim of our study was to evaluate the association of agronomic traits with rice productivity in EP rice. Here, we used the recombinant inbred lines (RILs), crosses between Liaojing5 (erect panicle japonica type) and Wanlun422 (high-yielding indica type). The yield varied among the RILs, and the flag leaf length of EP RILs was negatively correlated with the yield; however, the correlation was not significant in the non-EP RILs. The flag leaf length of the EP RILs was also negatively correlated with biomass increase during the late ripening stage. This may reflect the canopy structure of the EP RILs with short flag leaves which had a larger leaf area index in the lower strata. Additionally, the chlorophyll content in the lower leaf significantly differed among the EP RILs with flag leaves of different lengths, resulting in a higher photosynthetic ability of the lower leaf of EP RILs with short flag leaves. In the present study, an EP line, which has the shortest flag leaf, showed a higher yield than Wanlun422 in both years. EP RILs with short flag leaves might show a higher canopy photosynthetic rate in the later ripening stage; therefore, this trait could be a potential phenotypic marker for achieving high yield of EP rice.

Parental genetic distance and combining ability analyses in relation to heterosis in various rice origins

Information on parental genetic distance and combining ability is a fundamental prerequisite for hybrid rice breeding. Based on a study of genetic diversity using molecular markers, 12 parents representing various rice origins were selected to make diallel crosses, and hybrids were evaluated in tropical environments. Yield, yield heterosis and combining ability were investigated with the main objectives of (1) evaluating the genetic relationship between each type of rice by DNA marker, (2) estimating the heterosis and combining ability for yield of F1 hybrids from the crosses between indica and other types of rice, and (3) identifying hybrid parents for future hybrid rice breeding. Significant differences in yield, yield heterosis and combining ability were detected among parents and among hybrids. Results revealed that indica showed general combining ability higher than other type. Based on genetic distance identified, these rice varieties were classified into two distinct groups and seven subgroups. The varieties placed into the same cluster group were found to from the same origin. Results from the yield evaluation of hybrids and from clustering of genetic distance of the parents indicated that hybrids derived from crosses between parents with medium genetic distance (0.42) gave higher yield heterosis than those derived from crosses with extreme genetic distance (0.07 and 0.83). Heterotic performance and efficiency of breeding heterotic hybrid could be enhanced using selected parents within identified marker-based heterotic groups. This information is useful future for hybrid rice breeding.

Effects of Nano Material on Cadmium Accumulation Capacity and Grain Yield of Indica Hybrid Rice Under Wetting-drying Alternation Irrigation

Wetting-drying alternation irrigation (WDI) can harvest high grain yield under effective irrigation water saving conditions. However, the kernel cadmium (Cd) content usually exceeds the national standard of 0.20 mg Cd per kg kernel in WDI. Applying a passivating agent with high-efficient repairing capabilities could be a feasible approach to reduce Cd content lower than 0.20 mg·kg-1 in WDI. Therefore, a field experiment was conducted with different irrigation regimes and passivating agents in a mildly Cd-polluted paddy field, of which the irrigation regimes were WDI and traditional flooded irrigation (FI) and the six passivating agents treatments were CK (no passivating agent; T1), slaked lime with 1125 kg·hm-2(T2), 1125 kg slaked lime and 3000 kg biochar per hectare (T3), 1125 kg slaked lime and 3000 kg organic fertilizer per hectare (T4), 1500 kg porous Nano stupalith per hectare (T5), and 1125 kg slaked lime combined with 1500 kg porous Nano stupalith per hectare (T6). Two typical Indica hybrid rice varieties with a high accumulated capacity named cultivar Shenliangyou 1813 and a low accumulated trait named cultivar Liangyou 6206 were utilized. The main reason that Indica hybrid rice cultivars were selected was their higher absorbed and accumulated characteristics than that of Japonica rice. The results indicated that available Cd content of the soil significantly declined with 17.13%-61.01% decreasing amplitude at maturity when compared with pre-transplanting in WDI; however, the reduction was in the range of -43.45%-21.07% for the FI treatment across cultivars and passivating agents treatments. The available Cd content at maturity was significantly greater in FI than in WDI (P<0.05). In contrast, WDI had higher Cd content on stem, leaf, and kernel organs at maturity than with FI treatment of both cultivars and all of the passivating agents (P<0.05). Generally, the T1 treatment had the maximum available Cd content in the soil layer and highest accumulated Cd content on different aboveground organs, followed by the T2, T3, T4, T5, and T6 treatments considering both cultivars and irrigation regimes. The Cd kernel contents were 0.23-0.24 mg·kg-1 and 0.16-0.21 mg·kg-1 for cultivars Shenliangyou 1813 and Liangyou 6206, respectively, in the T6 treatment. The higher Cd kernel content was generally related to a larger Cd content in the stem organ. For the grain yield, no significant differences were observed among cultivars, irrigation regimes, or passivating agents treatments (P>0.05). Under WDI, the kernel Cd content was still slightly higher than 0.20 mg·kg-1 in the T6 treatment (0.24 mg·kg-1 for cultivar Shenliangyou 1813 and 0.21 mg·kg-1 for cultivar Liangyou 6206); however, there is a predictability potential to produce lower than 0.20 mg·kg-1 kernel content in the T6 treatment if a cultivar with low accumulated capacity is used. Thus, the combined mode of the WDI+T6+cultivar with accumulated low Cd content could be considered an optimized cultivation scheme to obtain no Cd contaminated kernels with high grain yield and water-use efficiency in mildly polluted paddy fields.

High-Throughput Doubled Haploid Production for Indica Rice Breeding.

Anther culture is an important biotechnological tool for quick recovery of fixed breeding lines with unique gene combinations that might otherwise disappear in the course of an extended series of segregating generations in conventional breeding methods in rice. The haploid microspores in culture or the resultant haploid plants are converted to doubled haploids (homozygotes). Variation in doubled haploid lines from F1 hybrids is due to the recovery of rare gene combinations by single round of recombination following meiosis. Androgenesis in rice is largely species- and genotype-specific. O. glaberrima responds better to anther culture than O. sativa; and japonica sub-group is more responsive to microspore embryogenesis than indica types. The author provides a detailed protocol of the anther culture technique for doubled haploid production in indica rice hybrids amenable for genetic improvement.

Identification of &amp;lt;i&amp;gt;Indica-Japonica&amp;lt;/i&amp;gt; Subspecies Rice by Duplex Fluorescence PCR Detection for Chloroplast DNA and Endogenous &amp;lt;i&amp;gt;gos&amp;lt;/i&amp;gt; Gene

Asia cultivated rice are classified into two subspecies, indica and japonica rice (hsien and keng rice called in China, separately). It is necessary to establish a convenient and effective method to identify two subspecies because of the different quality characteristics between the rice products of them, which lead to different processing uses and commodity values. The identification method of PCR based on the difference of chloroplast DNA is convenient and effective, to be attempted to establish. Based on 69 bp fragment deletion of chloroplast DNA (cpDNA) found in ORF100 region nucleotides within the cpDNA Pst I-12 fragment in indica rice but not in japonica, the primer pair and a probe located on the specific cpDNA fragment in japonica rice were designed to identify indica and japonica rice. Another primer pair and probe used to detect endogenous gene gos in rice were combined with above primer pair and probe for detecting cpDNA to establish duplex fluorescence PCR to amplify cpDNA and gos gene for improving detection accuracy, to avoid the false negative results caused by DNA extraction error. The duplex fluorescence PCR detection method was established using typical japonica rice (pearl rice) and typical indica rice (Taixian 11). The accuracy of the method was validated with 547 samples including 177 samples of rice seed and eaten rice known as conventional japonica varieties and japonica type hybrid combinations and 370 samples of rice seed and eaten rice known as conventional indica rice varieties and indica type hybrid combinations. In 177 japonica samples, 170 samples with both positive results of cpDNA marker and gos gene, a coincidence rate of 96.05% agreement japonica rice, and 7 samples with positive results of gos gene and negative of cpDNA marker, not agreement japonica rice with non-coincidence rate of 3.95%, were detected. Of the 370 samples of indica rice seed and eaten rice, with positive results of gos gene and negative of cpDNA marker were detected in 340 samples, the rate of coincidence to indica rice was 91.89%. Other 30 samples with both positive results of cpDNA marker and gos gene, were detected, and the non-coincidence rate with indica rice was 8.11%. These identification results were in good agreement with known indica and japonica varieties, and the coincidence rate of japonica varieties was higher than indica. This method can be used to identify indica and japonica subspecies rice, especially suitable to identify conventional rice varieties.

Effects of lead (Pb)-induced oxidative stress on morphological and physio-biochemical properties of rice

In rice, high concentration of lead (Pb) can cause phyto-toxicity affecting several physiological functions. Cultivation of rice varieties that are resistant to Pb-induced oxidative stress is an important management strategy in Pb-contaminated soils. In the current study, we evaluated four different rice cultivars for their response to Pb-induced stress. Three japonica type cultivars X-Jigna, Ediget, and Furat, and one Indica type cultivar Amber 33 were grown in soil containing different Pb concentrations (0 mM, 0.6 mM, and 1.2 mM). The soil was treated with 0 mM or 0.6 mM or 1.2 mM Pb solution one month prior to rice seedling transplantation. Thereafter, four-week-old rice seedlings were transplanted into the treated soil and their responses were observed until maturity. The data revealed that a highest concentration of Pb (1.2 mM) induced significant reduction in agronomic traits such as plant height, number of tillers per plant, number of panicles per plant, and number of spikelets per panicle in all the rice cultivars. However, least reduction in the agronomic traits was observed in X-Jigna, whereas the highest reduction in the agronomic traits was observed in Ediget. Antioxidant activity of catalase (CAT), peroxidase (POD), polyphenol oxidase (PPO), and superoxide dismutase (SOD), was evaluated along with the accumulation of superoxide ions (O2.-), protein, proline, chlorophyll, sucrose, glucose, and fructose contents in all the rice cultivars. A significant increase in antioxidant activity and in the accumulation of proline and sucrose contents with the least reduction in the chlorophyll and protein contents was observed in X-Jigna suggesting that X-Jigna is the most tolerant among all the rice cultivars tested against Pb-stress. On the other hand, non-significant and slightly significant increase in the antioxidant activity, less accumulation of proline and sucrose contents, and higher reduction in the chlorophyll and protein contents was observed in Ediget, which further suggest that Ediget is the most susceptible rice cultivar to Pb-stress. In addition, the other rice cultivars Furat and Amber 33, were found to be moderately tolerant to Pb-induced oxidative stress. In summary, our results suggest that tolerance to Pb-induced oxidative stress would be a result of a synergetic action of both enzymatic and non-enzymatic antioxidant systems, leading to a balanced redox status in rice.

Genetic Diversity of Selected Rice Genotypes under Water Stress Conditions.

Drought is the most challenging abiotic stress for rice production in the world. Thus, developing new rice genotype tolerance to water scarcity is one of the best strategies to achieve and maximize high yield potential with water savings. The study aims to characterize 16 rice genotypes for grain and agronomic parameters under normal and drought stress conditions, and genetic differentiation, by determining specific DNA markers related to drought tolerance using Simple Sequence Repeats (SSR) markers and grouping cultivars, establishing their genetic relationship for different traits. The experiment was conducted under irrigated (normal) and water stress conditions. Mean squares due to genotype × environment interactions were highly significant for major traits. For the number of panicles/plants, the genotypes Giza179, IET1444, Hybrid1, and Hybrid2 showed the maximum mean values. The required sterility percentage values were produced by genotypes IET1444, Giza178, Hybrid2, and Giza179, while, Sakha101, Giza179, Hybrid1, and Hybrid2 achieved the highest values of grain yield/plant. The genotypes Giza178, Giza179, Hybrid1, and Hybrid2, produced maximum values for water use efficiency. The effective number of alleles per locus ranged from 1.20 alleles to 3.0 alleles with an average of 1.28 alleles, and the He values for all SSR markers used varied from 0.94 to 1.00 with an average of 0.98. The polymorphic information content (PIC) values for the SSR were varied from 0.83 to 0.99, with an average of 0.95 along with a highly significant correlation between PIC values and the number of amplified alleles detected per locus. The highest similarity coefficient between Giza181 and Giza182 (Indica type) was observed and are susceptible to drought stress. High similarity percentage between the genotypes (japonica type; Sakha104 with Sakha102 and Sakha106 (0.45), Sakha101 with Sakha102 and Sakha106 (0.40), Sakha105 with Hybrid1 (0.40), Hybrid1 with Giza178 (0.40) and GZ1368-S-5-4 with Giza181 (0.40)) was also observed, which are also susceptible to drought stress. All genotypes are grouped into two major clusters in the dendrogram at 66% similarity based on Jaccard’s similarity index. The first cluster (A) was divided into two minor groups A1 and A2, in which A1 had two groups A1-1 and A1-2, containing drought-tolerant genotypes like IET1444, GZ1386-S-5-4 and Hybrid1. On the other hand, the A1-2 cluster divided into A1-2-1 containing Hybrid2 genotype and A1-2-2 containing Giza179 and Giza178 at coefficient 0.91, showing moderate tolerance to drought stress. The genotypes GZ1368-S-5-4, IET1444, Giza 178, and Giza179, could be included as appropriate materials for developing a drought-tolerant variety breeding program. Genetic diversity to grow new rice cultivars that combine drought tolerance with high grain yields is essential to maintaining food security.

Epistasis and Quantitative Resistance to Pyricularia oryzae Revealed by GWAS in Advanced Rice Breeding Populations

Rice blast caused by Pyricularia oryzae is a major rice disease worldwide. Despite the detailed knowledge on major resistance genes available to date, little is known about how these genes interact with quantitative blast resistance loci and with the genetic background. Knowledge on these interactions is crucial for assessing the usefulness of introgressed resistance loci in breeding germplasm. Our goal was to identify quantitative trait loci (QTL) for blast resistance in rice breeding populations and to describe how they interact among each other and with the genetic background. To that end, resistance to blast was mapped by genome-wide association study (GWAS) in two advanced rice breeding subpopulations, one made of 305 indica type inbred lines, and the other of 245 tropical japonica inbred lines. The interactions and main effects of blast resistance loci were assessed in a multilocus model. Well known, major effect blast resistance gene clusters were detected in both tropical japonica (Pii/Pi3/Pi5) and indica (Piz/Pi2/Pi9) subpopulations with the GWAS scan 1. When these major effect loci were included as fixed cofactors in subsequent GWAS scans 2 and 3, additional QTL and more complex genetic architectures were revealed. The multilocus model for the tropical japonica subpopulation showed that Pii/Pi3/Pi5 had significant interaction with two QTL in chromosome 1 and one QTL in chromosome 8, together explaining 64% of the phenotypic variance. In the indica subpopulation a significant interaction among the QTL in chromosomes 6 and 4 and the genetic background, together with Piz/Pi2/Pi9 and QTL in chromosomes 1, 4 and 7, explained 35% of the phenotypic variance. Our results suggest that epistatic interactions can play a major role modulating the response mediated by major effect blast resistance loci such as Pii/Pi3/Pi5. Furthermore, the additive and epistatic effects of multiple QTL bring additional layers of quantitative resistance with a magnitude comparable to that of major effect loci. These findings highlight the need of genetic background-specific validation of markers for molecular assisted blast resistance breeding and provide insights for developing quantitative resistance to blast disease in rice.

Dynamics of Race Structures of Pyricularia oryzae Populations Across 18 Seasons in Guangdong Province, China.

Rice blast, caused by Pyricularia oryzae, is one of the most damaging fungal diseases affecting rice. Understanding how the pathogen's race structure varies over time supports the efforts of rice breeders to develop improved cultivars. Here, the race structure of P. oryzae in Guangdong province, China, where rice is cropped twice per year, was assessed over 18 seasons from 1999 through 2008. The analysis was based on the reactions of a panel of seven differential Chinese cultivars to inoculation with a set of 1,248 isolates of P. oryzae in the province. The "total race frequency" parameter ranged from 14.7 to 39.7%, and the "race diversity index" ranged from 0.63 to 0.93. Twelve (ZA63, ZA31, ZA29, ZA21, ZA13, ZA9, ZB30, ZB17, ZB8, ZB2, ZC14, and ZC8) and two (ZD8 and ZD3) races were recognized as specific to indica and japonica rice types, respectively. Of the 59 distinct races identified, only two indica type races (ZC13 and ZC15) were identified as population-common, and nine indica type races (ZB1, ZB5, ZB6, ZB7, ZB13, ZB15, ZC5, ZC13, and ZC15) and one japonica type race (ZG1) were deemed to be population-dominant; the "total top two race isolate frequency" parameter ranged from 29.8 to 74.5%. On the host side, dynamics of resistance structures of the differential set were divided into three patterns: Both Tetep and Kanto 51 expressed the highest and most stable resistance, both Sifeng 43 and Lijiangxintuanheigu conveyed much lower and unstable resistance, and Zhenlong 13, Dongnong 363, and Heijiang 18 performed intermediate and seasonally dynamic resistance. Three interesting points distinguishing race structures of P. oryzae populations in southern and northeastern China were also discussed.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Genetic Architecture and Anthocyanin Profiling of Aromatic Rice From Manipur Reveals Divergence of Chakhao Landraces.

Aromatic rice of Manipur popularly known as Chakhao is a speciality glutinous rice, for which protection under geographical indication in India has been granted recently. The agronomic and nutraceutical variability of the Chakhao rice germplasm is yet to be genetically characterized. To address this gap, characterization of ninety-three landraces for agro-morphological traits, grain pigmentation, antioxidant properties, and molecular genetic variation was carried out to unravel their population genetic structure. Two major groups were identified based on pericarp color, namely, purple and non-purple, which showed a significant variation for plant height, panicle length, and grain yield. Molecular marker analysis revealed three subpopulations that could be associated with pericarp pigmentation. Deep purple genotypes formed POP3, japonica genotypes adapted to hill environment formed POP1, while POP2 comprised of both indica and aus types. Liquid chromatography–mass spectrometry (LC-MS) analysis revealed two major anthocyanin compounds in pigmented rices, namely, cyanidin-3-O-glucoside (C3G) and peonidin-3-O-glucoside (P3G). The total anthocyanin content among pigmented genotypes ranged from 29.8 to 275.8 mg.100g–1 DW. Total phenolics ranged from 66.5 to 700.3 mg GAE.100g–1 DW with radical scavenging activity (RSA) varying between 17.7 and 65.7%. Anthocyanins and phenolics showed a direct relationship with RSA implying the nutraceutical benefits of deep pigmented rice such as Manipur black rice. Aromatic rices from Manipur were found to be genetically diverse. Therefore, efforts need to be made for maintaining the geographic identity of these rice and utilization in breeding for region-specific cultivar improvement.

Association mapping identifies quantitative trait loci (QTL) for digestibility in rice straw

BackgroundThe conversion of lignocellulosic biomass from agricultural waste into biofuels and chemicals is considered a promising way to provide sustainable low carbon products without compromising food security. However, the use of lignocellulosic biomass for biofuel and chemical production is limited by the cost-effectiveness of the production process due to its recalcitrance to enzymatic hydrolysis and fermentable sugar release (i.e., saccharification). Rice straw is a particularly attractive feedstock because millions of tons are currently burned in the field each year for disposal. The aim of this study was to explore the underlying natural genetic variation that impacts the recalcitrance of rice (Oryza sativa) straw to enzymatic saccharification. Ultimately, we wanted to investigate whether we could identify genetic markers that could be used in rice breeding to improve commercial cultivars for this trait. Here, we describe the development and characterization of a Vietnamese rice genome-wide association panel, high-throughput analysis of rice straw saccharification and lignin content, and the results from preliminary genome-wide association studies (GWAS) of the combined data sets. We identify both QTL and plausible candidate genes that may have an impact on the saccharification of rice straw.ResultsWe assembled a diversity panel comprising 151 rice genotypes (Indica and Japonica types) from commercial, historical elite cultivars, and traditional landraces grown in Vietnam. The diversity panel was genotyped using genotype by sequencing (GBS) methods yielding a total of 328,915 single nucleotide polymorphisms (SNPs). We collected phenotypic data from stems of these 151 genotypes for biomass saccharification and lignin content. Using GWAS on the indica genotypes over 2 years we identified ten significant QTL for saccharification (digestibility) and seven significant QTL for lignin. One QTL on chromosome 11 occurred in both GWAS for digestibility and for lignin. Seven QTL for digestibility, on CH2, CH6, CH7, CH8, and CH11, were observed in both years of the study. The QTL regions for saccharification include three potential candidate genes that have been previously reported to influence digestibility: OsAT10; OsIRX9; and OsMYB58/63-L.ConclusionsDespite the difficulties associated with multi-phasic analysis of complex traits in novel germplasm, a moderate resolution GWAS successfully identified genetic associations encompassing both known and/or novel genes involved in determining the saccharification potential and lignin content of rice straw. Plausible candidates within QTL regions, in particular those with roles in cell wall biosynthesis, were identified but will require validation to confirm their value for application in rice breeding.

Physiochemical mechanisms involved in the improvement of grain-filling, rice quality mediated by related enzyme activities in the ratoon cultivation system

Abstract The grain quality of rice in the ratoon cultivation system is often higher than in the main crop (late season). To investigate the reason for that difference, a study of physiochemical factors, particularly relevant enzyme activities and their relationships with grain-filling and rice quality, was conducted with two hybrid rice cultivars, indica type Taifengyou 3301″ and indica-japonica type Yongyou 2640″. The results showed that the head rice yield of the superior and inferior grains in ratoon rice were significantly higher than those of their counterpart main crops (late season) to which rice heading time was synchronized. The degree of grain chalkiness and chalky grain percentage of both superior and inferior grains in ratoon rice were much lower than those of the late season main crop of both cultivars over two years of study. The starch RVA (Rapid Viscosity Analyzer) profile parameter analysis indicated that the maximum viscosity and setback viscosity of the superior and inferior grains of ratoon rice were higher than the late season main crop counterparts in both cultivars. We also found that the grain-filling of ratoon rice, especially for inferior grains, initiated earlier and continued longer and steadier than that of the late season main crop at the early and middle stages, which was driven by better translocation of photosynthate and the coordinated activity of enzymes including starch synthase and starch branching enzyme. These findings suggest that lower grain sink capacity and higher photosynthate remobilization ability result in fast and steady grain-filling in ratoon crops. Furthermore, coordinated enzyme activity appears to be involved in the process of starchsynthesis and dry matter translocation that drives the improvement of grain-filling and the grain quality of ratoon rice.

Effects of soluble starch synthase IIa allelic variation on rice grain quality with different Waxy backgrounds.

Soluble starch synthase IIa (ALK, SSII-3) is the major gene regulating gelatinization temperature (GT) and SSII-3 M1 is an effective marker for identifying SSIIa alleles. However, the haplotypes of SSIIa alleles amplified by SSII-3M1 and their allelic effect sunder different Waxy (Wx) background in non-glutinous rice remain unclear. By integrating the genetic background analysis and by the identification of the genotypes of Wx and SSIIa, we found that the SSIIa alleles amplified by SSII-3 M1 were haplotype 1 (G/G/GC, indica-type) and 4 (A/G/TT, japonica-type), which had a significant effect on pasting temperature (PaT), hot paste viscosity (HPV), and the alkali spreading value (ASV). There were significant effects of SSIIa alleles on HPV, cool paste viscosity (CPV), and consistency value with different Wx backgrounds. The apparent amylose content (AAC) of samples significantly affected the accuracy of GT, which was represented by the manually determined pasting temperature (PTm). The SSIIa alleles amplified by SSII-3 M1 are indica type and japonica type. Different SSIIa haplotypes significantly affect HPV, CPV, PaT, and ASV. GT, PaT, and PTm are mainly affected by SSIIa alleles. The classification of all samples with different haplotypes of SSIIa indicates that their AAC (Wx genotypes) is essentially. The effects of SSIIa alleles are themselves affected by different Wx alleles. © 2020 Society of Chemical Industry.

Physicochemical and morphological analyses on damaged rice starches

Two types of rice cultivars, indica type (Tainung Sen 19, TNuS19) and waxy (Taichung Waxy 70, TCW70) were used as samples to investigate the changes in the physicochemical properties of damaged rice starch by ball-milling treatment. Rapid Visco Analyzer (RVA) analysis indicated that onset temperature (To,η), peak viscosity (P), setback (C-H), and cold-paste viscosity (C) decreases were more pronounced in TNuS19 than in TCW70 starch during the ball-milling treatment. Similar phenomena were also found in peak temperature (Tp) and enthalpy changes (∆H) by differential scanning calorimetry (DSC), and the peak intensities measured by X-ray diffraction. However, both types of starch showed that extended treatment time resulted in higher median particle size (PS 50). Polarized light micrographs showed that damaged starch granules lost their birefringence, suggesting that the order structure of starch granule was disrupted. The morphological changes in the microstructure of rice starch during ball-milling treatment was also examined by scanning electron microscopy (SEM). The results indicated that TNuS19 starch granules may be more susceptible to mechanical action than TCW70 starch.

The impact of the indica rice SSIIa allele on the apparent high amylose starch from rice grain with downregulated japonica SBEIIb.

Catalytically active indica SSIIa allele in high amylose rice with down-regulated japonica SBEIIb can increase starch content and modify the starch structure and properties without changing its amylose content. Rice (Oryza sativa) genotypes with inactive starch synthase IIa (SSIIa) with recessive variants of starch branching enzyme IIb (SBEIIb) exhibit a range of alterations in grain phenotype, starch granule morphology, starch granule bound proteins, starch structure, and functional properties. However, the interactions between the two enzymes have not been thoroughly investigated yet. We analysed recombinant rice lines having down-regulated SBEIIb expression (SBEIIbDR) with either indica or japonica type SSIIa (SSIIaind or SSIIajap). In SBEIIbDR rice starch granules, the increased abundance of two protein bands (SSI and SSIIa) was found with eight additional protein bands not generally associated with starch granules. The amount of SSIIa was higher in SSIIaindSBEIIbDR than SSIIajapSBEIIbDR, which indicated that indica type SSIIa, possibly in the monomer form, was extensively involved in starch biosynthesis in the SBEIIbDR endosperm. Furthermore, SSIIaindSBEIIbDR grains had higher total starch content and higher starch swelling power than SSIIajapSBEIIbDR lines, but the amylopectin gelatinization temperatures and enthalpy and the apparent amylose content remained similar. In summary, this work suggests that SSIIaind can partly compensate for the alteration of starch synthesis resulting from the SBEIIb down-regulation in japonica background without reducing its amylose content. The study provides insight into the starch structural and textural improvements of high amylose starch.

Root transcriptome reveals efficient cell signaling and energy conservation key to aluminum toxicity tolerance in acidic soil adapted rice genotype

Aluminium (Al) toxicity is the single most important contributing factor constraining crop productivity in acidic soils. Hydroponics based screening of three rice genotypes, a tolerant (ARR09, AR), a susceptible (IR 1552, IR) and an acid soil adapted landrace (Theruvii, TH) revealed that AR accumulates less Al and shows minimum decrease in shoot and root biomass under Al toxicity conditions when compared with IR. Transcriptome data generated on roots (grown in presence or absence of Al) led to identification of ~1500 transcripts per genotype with percentage annotation ranging from 21.94% (AR) to 29.94% (TH). A total of 511, 804 and 912 DEGs were identified in genotypes AR, IR and TH, respectively. IR showed upregulation of transcripts involved in exergonic processes. AR appears to conserve energy by downregulating key genes of glycolysis pathway and maintaining transcript levels of key exergonic step enzymes under Al stress. The tolerance in AR appears to be as a result of novel mechanism as none of the reported Al toxicity genes or QTLs overlap with significant DEGs. Components of signal transduction and regulatory machinery like transcripts encoding zinc finger protein, calcieurin binding protein and cell wall associated transcripts are among the highly upregulated DEGs in AR, suggesting increased and better signal transduction in response to Al stress in tolerant rice. Sequencing of NRAT1 and glycine-rich protein A3 revealed distinct haplotype for indica type AR. The newly identified components of Al tolerance will help in designing molecular breeding tools to enhance rice productivity in acidic soils.

Genetic study of diversity and blast resistance in Ethiopian rice cultivars adapted to different ecosystems.

Rice (Oryza sativa L.) has been considered one of the most important crops in Ethiopia. Landraces and improved accessions in Ethiopia were characterized on the basis of polymorphism data for SSR markers, and classified into two groups: I and II. Cluster I was further divided into two sub-clusters, Ia and Ib. Cluster Ia corresponded to Japonica-like type, Cluster Ib to Japonica type, and Cluster II to Indica type with some Indica-like type. Many landraces and improved varieties belonged to Cluster Ia. Superior landraces were included in Cluster Ib. Further categorization based on blast resistance demonstrated three groups: Clusters A, B1, and B2. Cluster A comprised accessions with relatively high resistance, whereas Clusters B1 and B2 included susceptible accessions. Most of the improved varieties were found in Cluster A. Superior landraces, X-Jigna classified into Ib or DNA type tended to be susceptible in Cluster B2 for blast resistance. These results demonstrated that traditional landraces preferred by farmers should be improved for disease resistance using blast-resistant varieties. In order to avoid hybrid sterility occurring in cross-hybridizing breeding between Indica and Japonica types, desirable parental accessions can be chosen within the same DNA cluster. The clustering information among accessions may be useful in breeding schemes for selection of counterparts in cross-breeding programs.

Stingless bees and Mangifera indica: A close relationship?

Propolis is a bee product with various biological activities and phytochemical compositions. This study was aimed to identify the chemical composition and botanical origin of Indonesian stingless bees propolis produced by Tetragonula laeviceps in Banten and Heterotrigona itama in South Kalimantan, respectively. Propolis extracts were prepared using 70% ethanol and chloroform. The extracts were analysed by GC/MS after silylation. The results showed that the studied stingless bee propolis contained a relatively high amount of sugars, probably due to the harvesting method used. Furthermore, triterpenes were found as the main constituents followed by phenolic lipids. Both samples were Mangifera indica type propolis with typical compounds, including cycloartenol, isomangiferolic acid, mangiferolic acid, ambolic acid, alk(en)ylphenols, alk(en)ylresorcinols, and anacardic acids. Therefore, M. indica might be a preferred botanical source of propolis from a tropical zone. In addition, the suctioning method in harvesting the stingless bee honey could be recommended to avoid high content of sugar and sugar derivatives.

Amplified fragment length polymorphism analysis to assess genetic diversity in rice

Amplified Fragment Length polymorphism (AFLP) was studied involving 48 diverse rice genotypes, comprising of indica, japonica, and Tongil type (indica × japonica) varieties to assess the genetic diversity. Initially 64 primer pair combinations were screened of which 5 were found to be suitable producing clear fragments (35–500 bp). In total 700 amplicons (bands) were produced with an average of 140 bands per primer pair. Maximum (207) from EcoRI AC*/MseI-CAC and minimum (75) amplicons from EcoRI TG*/MseI-CTT primer pairs were observed. Minimum (0.973) and maximum (0.990) PIC values recorded for primer pair EcoRI AC*/MseI-CAC and EcoRI AC*/MseI-CAT, respectively. Pairwise genetic similarity estimates ranged in between 0.6412 and 0.943 with a mean of 0.797. Triguna, an indica high yielding variety (HYV), and a new plant type (NPT) rice, IR 7946-46-1-3-2 having indica x japonica parentage showed minimum genetic similarity coefficient (0.641) with maximum genetic divergence, whereas ADT 41 and Sasyasree, two indica HYVs displayed maximum genetic similarity coefficient—0.953 with lowest genetic distance. All accessions could be clearly identified by using five primer pairs, offers immense scope of AFLP in assessing genetic diversity in rice. The present study also identified prospective varieties for use in selective hybridization and productive progeny selection. Most of the varieties shared distinct clusters based on varietal types, race, parentage and growing area where those are cultivated traditionally albeit with a few exceptions. The dendrogram could demarcate the varieties irrespective of race with unique traits, albeit with exceptions, which warrants further experimentation involving more number of primers in future.

Evidence for selection events during domestication by extensive mitochondrial genome analysis between japonica and indica in cultivated rice

The history of the domestication of rice is controversial, as it remains unknown whether domestication processes occurred once or multiple times. To date, genetic architecture and phylogenetic studies based on the rice nuclear genome have been extensively studied, but the results are quite different. Here, we found interesting results for different selections in Oryza sativa based on comprehensive studies of the rice mitochondrial (mt) genome. In detail, 412 rice germplasms were collected from around the world for variant architecture studies. A total of 10632 variants were detected in the mt genome, including 7277 SNPs and 3355 InDels. Selection signal (πw/πc) indicated that the selection sites in Oryza sativa L. ssp. japonica were different from those of Oryza sativa L. indica rice. The fixation index (FST) was higher between indica and japonica than between indica and wild rice. Moreover, haplotype and phylogenetic analyses also revealed indica clusters and japonica clusters that were well separated from wild rice. As mentioned above, our studies indicate that the selection sites of the indica type were different from those of the japonica type. This means that indica and japonica have experienced different domestication processes. We also found that japonica may have experienced a bottleneck event during domestication.