Agro-morphological characterization and assessment of variability,heritability, genetic advance and divergence in bacterial blight resistant rice genotypes

Genetic based knowledge of different growth traits including morphological, physiological and developmental plays fundamental role in the improvement of rice. Genetic divergence allows superior recombinants which are essential in any crop development project. Forty-one rice genotypes including bacterial blight (BB) resistant and susceptible checks were assessed for 13 morphological traits. Among the genotypes, almost all the traits exhibited highly significant variation. The higher extent of genotypic (GCV) as well as phenotypic coefficients of variation (PCV) were noticed for number of tillers hill^− 1, total number of spikelets panicle^− 1, number of filled grains panicle^− 1, and yield hill^− 1. High heritability together with high genetic advance was observed for total number of spikelets panicle^− 1, number of filled grains panicle^− 1, and yield hill^− 1 indicating dominant role of additive gene action in the expression of these traits. Number of filled grains panicle^− 1 exhibited positive correlation with most of the traits. Yield hill^− 1 showed a good number of highly significant positive correlations with number of filled grain panicle^− 1, total number of spikelets panicle^− 1, 1000 grain weight hill^− 1, number of panicle hill^− 1, and panicle length. The UPGMA dendrogram divided all the genotypes in to six major clusters. The PCA showed 13 morphological traits generated about 71% of total variation among all the genotypes under this study. On the basis of 13 morphological traits, genotypes such as IRBB2, IRBB4, IRBB13, IRBB21, and MR263 could be hybridized with genotypes MR84, MR159, MRQ50, MRQ74, PH9 and IR8 in order to develop suitable BB resistant rice genotypes.     

The Endosperm-Specific Expression of <i>YUCCA</i> Genes Enhances Rice Grain Filling

Grain filling is a crucial process that affects yield in rice (Oryza sativa L.). Auxin biosynthesis and signaling are closely related to rice yield; therefore, it is important to understand the effects of auxin biosynthesis on rice grain filling to improve crop yield. In this study, we used physiological and molecular strategies to identify the roles of auxin in rice grain filling. Exogenous application of auxin (IAA) or auxin analogues (2, 4-D) to young spikelets and flag leaves improved the seed-setting rate and yield per spike. Furthermore, real-time quantitative PCR assays confirmed that nine members of the OsYUCCA family of auxin biosynthetic genes were upregulated during grain filling, implication that auxin biosynthesis plays a major role in grain development. The specific expression of either Arabidopsis AtYUCCA1 or OsYUCCA2 in the endosperm or leaves resulted in increased expression of OsIAA genes and auxin content of seeds, as well as increased grain filling and seed-setting rate. This result establishes that the auxin content in grains and leaves is important for grain development. Our findings further highlight the potential applications for improving rice yield by elevating targeted gene expression in specific tissues.     

Effect of weedy rice at different densities on photosynthetic characteristics and yield of cultivated rice

In order to evaluate effect of weedy rice on the photosynthesis and grain filling of cultivated rice, cultivated rice ‘Nanjing 44’ was planted in the field under different densities of weedy rice ‘JS-Y1’ for two years. The results showed that net photosynthetic rate (P_N), net assimilation rate, grain filling rate, and the grain yield of cultivated rice all decreased with increasing weedy rice density. Furthermore, yield component analysis revealed that increasing weedy rice density had the most significant effect on the percentage of filled grains and the number of rice panicles. The correlation analyses indicated that the yield of cultivated rice was highly correlated with the net photosynthetic rate and the net assimilation rate. Our results illustrated that high density of weedy rice might cause yield losses in cultivated rice by inhibition of photosynthesis and grain filling.     

Amylose Content and Starch Granule Size in Rice Grains are Affected By Growing Season

Amylose content and starch granule size in grains influence rice quality, which differs between the early (ES) and late season (LS). The objective of this study was to determine the variation of amylose content and starch granule size between seasons and find the main reasons (e.g., temperature and solar radiation) for the observed variation. Field experiments with six rice varieties (three high and three low amylose content rice) planted in the ES and LS were conducted in 2016 and 2017, respectively. The mean temperatures during the filling stage were higher in ES, however, the daily temperatures at 7-10 days after flowering (DAF) in 2016, and at 5-10, 13-14 DAF in 2017 were higher in LS. The results showed that amylose content in LS was lower than in ES with high amylose content rice varieties (HACV); the opposite trend occurred with low amylose content rice varieties (LACV). The mean starch granule diameter was higher in LS than ES in 2016, but the opposite result occurred in 2017 with all rice. Our results suggest that higher temperatures increased and decreased the amylose content in HACV and LACV, respectively. Temperatures at 5-15 DAF were important for the formation of starch granules: lower temperatures during 10-14 DAF increased the proportion of larger starch granules (d＞6.21 μm, some with d＞13.3 μm), and higher temperatures at 5-6 DAF increased the proportion of starch granules with diameter 4.24-6.21 μm.     

Dynamic proteomic analysis reveals a switch between central carbon metabolism and alcoholic fermentation in rice filling grains

Accumulation of reserve materials in filling grains involves the coordination of different metabolic and cellular processes, and understanding the molecular mechanisms underlying the interconnections remains a major challenge for proteomics. Rice (Oryza sativa) is an excellent model for studying grain filling because of its importance as a staple food and the available genome sequence database. Our observations showed that embryo differentiation and endosperm cellularization in developing rice seeds were completed approximately 6 d after flowering (DAF); thereafter, the immature seeds mainly underwent cell enlargement and reached the size of mature seeds at 12 DAF. Grain filling began at 6 DAF and lasted until 20 DAF. Dynamic proteomic analyses revealed 396 protein spots differentially expressed throughout eight sequential developmental stages from 6 to 20 DAF and determined 345 identities. These proteins were involved in different cellular and metabolic processes with a prominently functional skew toward metabolism (45%) and protein synthesis/destination (20%). Expression analyses of protein groups associated with different functional categories/subcategories showed that substantially up-regulated proteins were involved in starch synthesis and alcoholic fermentation, whereas the down-regulated proteins in the process were involved in central carbon metabolism and most of the other functional categories/subcategories such as cell growth/division, protein synthesis, proteolysis, and signal transduction. The coordinated changes were consistent with the transition from cell growth and differentiation to starch synthesis and clearly indicated that a switch from central carbon metabolism to alcoholic fermentation may be important for starch synthesis and accumulation in the developmental process.     

Identification of quantitative trait loci for grain quality in an advanced backcross population derived from the<Emphasis Type="Italic"> Oryza sativa</Emphasis> variety IR64 and the wild relative<Emphasis Type="Italic"> O. rufipogon</Emphasis>

The objective of this study was to identify quantitative trait loci (QTLs) associated with grain quality in rice. Two hundred eighty-five BC₂F₂ families developed from an interspecific cross between cv IR64 and Oryza rufipogon (IRGC 105491) were evaluated for 14 seed quality traits. A total of 165 markers consisting of 131 single sequence repeats and 34 restriction fragment length polymorphism markers were used to create a genetic linkage map spanning the 12 rice chromosomes. Twenty-three independent QTLs were identified using single point analysis, interval mapping, and composite interval mapping. These loci consisted of one QTL for filled rough/total rough rice ratio, two for grain density, one for percentage of de-husked rice grains, two for percentage of green rice grains, three for percentage of damaged-yellow rice grains, two for percentage of red rice grains, one for milled rice recovery, three for head rice recovery, four for broken rice grains, two for crushed rice grains, one for amylose content, and one for gel consistency. For most of the QTLs identified in this study, the O. rufipogon-derived allele contributed an undesirable effect. For amylose content and gel consistency, the O. rufipogon allele may be useful in an IR64 background, depending on the cultural preferences of the consumer. Careful selection against the regions associated with negative effects will be required to avoid unwanted grain quality characteristics during the development of improved varieties for yield and yield components using introgressions from O. rufipogon.Communicated by D. Mackill     

Responses of the antioxidative enzymes in Malaysian rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.) cultivars under submergence condition

The potential involvement of activated oxygen species by submergence stress was studied in two Malaysian rice cultivars, MR219-4 and MR219-9, and cultivar FR13A that is known to be tolerant to submergence. Seedlings of these three rice cultivars were subjected to different submergence periods (4, 8, and 12 days). Under 8 days of complete submergence, FR13A cultivar showed higher lipid peroxidation in terms of malondialdehyde level and activities of antioxidative enzymes, superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidase (APX), and glutathione reductase (GR) when compared to the MR219-4 and MR219-9 cultivars. MR219-9 showed higher SOD, APX, and GR activities after 12 days of submergence. The levels of SOD activity indicated that detoxification of O₂^·− to H₂O₂ was maintained at a stable level throughout the submergence stress until up to 8 days and increased rapidly at 12 days of submergence. The results indicated that tolerance to submergence in rice is associated until 8 days submergence for MR219-4 and FR13A cultivars. These findings suggested that tolerance to submergence stress in rice might be proven by increased the capacity of antioxidative system. In addition, CAT activity has much higher affinity for scavenges H₂O₂ than APX. Therefore, ascorbate glutathione cycle might be more efficient to scavenge H₂O₂.     

Studies on the nature of relationships between grain size,spikelet number,grain yield and spikelet filling in late duration varieties of rice (Oryza sativa L.)

Summary Studies on the nature of relationship between grain size (in terms of thousand grain weight), grain number, rate of filling and yield have been worked out with late duration (140–150 days) rice varieties. Grain number per m², grains per panicle and yield showed a negative relationship with grain size. There was no compensatory balance between grain size and grain number within a range of thousand grain weight of 15 to 30 g. Based on the peaks in grain filling activity, the varieties were classified into four groups. There was no relationship between grain size and rate of grain filling thereby suggesting that grain filling is determined by inherent endogenous factors.     

Efficient plant regeneration of Malaysian <Emphasis Type="Italic">indica</Emphasis> rice MR 219 and 232 via somatic embryogenesis system

Improvement on rice plant regeneration system from an embryogenic callus using two Malaysian indica rice MR 219 and MR 232 was developed in this study. Different stages of rice explants (zygotic embryos) were tested for callus induction and regeneration using various carbon sources and amino acids. The present study shows that dough stage of zygotic embryos was the best stage of explants for the embryogenic callus induction and regeneration of both rice cultivars. The embryogenic callus nature with the compact structure was confirmed by scanning electron microscopy (SEM) analysis. Inclusion of maltose at the concentration between 10 and 20 mg/L shown higher responsive for the development of green somatic embryos and initiation of rice regeneration with an average of 29–37 (87–91%) regenerated plantlets, respectively. All in vitro regenerated rice plantlets were green, morphological and physiologically healthy condition. Rice plantlets were hardened in acclimatization room for 3 weeks and later transferred into soil with 95% survival in both varieties were recorded. Hence, regeneration system from zygotic rice embryos via somatic embryogenesis system was carried out successfully by using 10 g/L of maltose and combinations of glutamine, asparagine and arginine amino acids.     

Comparative proteomic analysis of indica and japonica rice varieties

Indica and japonica are two main subspecies of Asian cultivated rice (Oryza sativa L.) that differ clearly in morphological and agronomic traits, in physiological and biochemical characteristics and in their genomic structure. However, the proteins and genes responsible for these differences remain poorly characterized. In this study, proteomic tools, including two-dimensional electrophoresis and mass spectrometry, were used to globally identify proteins that differed between two sequenced rice varieties (93–11 and Nipponbare). In all, 47 proteins that differed significantly between 93–11 and Nipponbare were identified using mass spectrometry and database searches. Interestingly, seven proteins were expressed only in Nipponbare and one protein was expressed specifically in 93–11; these differences were confirmed by quantitative real-time PCR and proteomic analysis of other indica and japonica rice varieties. This is the first report to successfully demonstrate differences in the protein composition of indica and japonica rice varieties and to identify candidate proteins and genes for future investigation of their roles in the differentiation of indica and japonica rice.     

Comparison of gene expression measurements from cDNA and 60-mer oligonucleotide microarrays

As the data generated by microarray technology continue to amass, it is necessary to compare and combine gene expression data from different platforms. To evaluate the performance of cDNA and long oligonucleotide (60-mer) arrays, we generated gene expression profiles for two cancer cell lines and compared the data between the two platforms. All 6182 unique genes represented on both platforms were included in the analysis. A limited correlation (r = 0.4708) was obtained and the difference in measurement of low-expression genes was considered to contribute to the limited correlation. Further restriction of the data set to differentially expressed genes detected in cDNA microarrays (1205 genes) and oligonucleotide arrays (1325 genes) showed modest correlations of 0.7076 and 0.6441 between the two platforms. Quantitative real-time PCR measurements of a set of 10 genes showed better correlation with oligonucleotide arrays. Our results demonstrate that there is substantial variation in the data generated from cDNA and 60-mer oligonucleotide arrays. Although general agreement was observed in measurements of differentially expressed genes, we suggest that data from different platforms could not be directly amassed.     

Roles of FERONIA-like receptor genes in regulating grain size and quality in rice

Grain yield and quality are critical factors that determine the value of grain crops. In this study, we analyzed the functions of 12 FERONIA-like receptor(FLR) family members in rice and investigated their effects on grain size and quality. We found that FLR1, FLR2 and FLR8 negatively regulated grain size, and FLR15 positively regulated grain size. flr1 mutants had a higher cell number and an accelerated rate of grain filling compared to wild-type plants, which led to grains with greater widths. A mechanism underlying the regulation of grain size by FLR1 is that FLR1 is associated with OsRac1 Rho-like GTPase, a positive regulator of grain size. Regarding grain quality, the flr1 mutant had a higher percentage of chalkiness compared with wild-type plants, and seeds carrying mutations in flr3 and flr14 had endosperms with white floury cores. To elucidate the possible mechanism underlying this phenomenon, we found that FLR1 was constitutively expressed during endosperm development.RNA-seq analysis identified 2,367 genes that were differentially expressed in the flr1 mutant, including genes involved in starch and sucrose metabolism and carbon fixation. In this study, we identified the roles played by several FLR genes in regulating grain size and quality in rice and provided insights into the molecular mechanism governing the FLR1-mediated regulation of grain size.     

Response of antioxidant systems in oxygen deprived suspension cultures of rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.)

The effect of oxygen deprivation (anoxia) on the antioxidant system in suspension culture of anoxia-intolerant Malaysian rice mutants cells was examined. Abiotic stresses have been reported to adversely affect cell division, damage cellular and organelle membranes. The signaling defense mechanisms, such as molecular and biochemical aspects responding to stress have been proven to be very complex, and still largely untapped. The objective of this study was to determine the potential involvement of activated oxygen species, such as superoxide dismutase, catalase (CAT), ascorbate peroxidase (APX), and glutathione reductase which occur in cells of rice plants exposed to anoxia stress in two Malaysian rice mutants, MR219-4 and MR219-9, and rice cultivar FR13A which is known to be tolerant to anoxia stress during 5–30 days of exposure. The antioxidative enzymes were decreased for MR219-4 and MR219-9 mutants for CAT and APX activities, and increased in FR13A cultivar starting at 20 days in suspension culture compared to that of control. CAT and APX activities were maintained higher in anoxia condition for all mutants and cultivar. These findings suggested that anoxia stress in suspension cultures induced the level of H₂O₂ to toxic levels.     

Assessment of Real-time PCR Based Methods for Quantification of Pollen-mediated Gene Flow from GM to Conventional Maize in a Field Study

Maize is one of the main crops worldwide and an increasing number of genetically modified (GM) maize varieties are cultivated and commercialized in many countries in parallel to conventional crops. Given the labeling rules established e.g. in the European Union and the necessary coexistence between GM and non-GM crops, it is important to determine the extent of pollen dissemination from transgenic maize to other cultivars under field conditions. The most widely used methods for quantitative detection of GMO are based on real-time PCR, which implies the results are expressed in genome percentages (in contrast to seed or grain percentages). Our objective was to assess the accuracy of real-time PCR based assays to accurately quantify the contents of transgenic grains in non-GM fields in comparison with the real cross-fertilization rate as determined by phenotypical analysis. We performed this study in a region where both GM and conventional maize are normally cultivated and used the predominant transgenic maize Mon810 in combination with a conventional maize variety which displays the characteristic of white grains (therefore allowing cross-pollination quantification as percentage of yellow grains). Our results indicated an excellent correlation between real-time PCR results and number of cross-fertilized grains at Mon810 levels of 0.1–10%. In contrast, Mon810 percentage estimated by weight of grains produced less accurate results. Finally, we present and discuss the pattern of pollen-mediated gene flow from GM to conventional maize in an example case under field conditions.     

Opportunities of marker‐assisted selection for rice fragrance through marker–trait association analysis of microsatellites and gene‐based markers

Developing fragrant rice through marker‐assisted/aided selection (MAS) is an economical and profitable approach worldwide for the enrichment of an elite genetic background with a pleasant aroma. The PCR‐based DNA markers that distinguish the alleles of major fragrance genes in rice have been synthesised to develop rice scent biofortification through MAS. Thus, the present study examined the aroma biofortification potential of these co‐dominant markers in a germplasm panel of 189 F₂ progeny developed from crosses between a non‐aromatic variety (MR84) and a highly aromatic but low‐yielding variety (MRQ74) to determine the most influential diagnostic markers for fragrance biofortification. The SSRs and functional DNA markers RM5633 (on chromosome 4), RM515, RM223, L06, NKSbad2, FMbadh2‐E7, BADEX7‐5, Aro7 and SCU015RM (on chromosome 8) were highly associated with the 2AP (2‐acetyl‐1‐pyrroline) content across the population. The alleles traced via these markers were also in high linkage disequilibrium (R² > 0.70) and explained approximately 12.1, 27.05, 27.05, 27.05, 25.42, 25.42, 20.53, 20.43 and 20.18% of the total phenotypic variation observed for these biomarkers, respectively. F₂ plants harbouring the favourable alleles of these effective markers produced higher levels of fragrance. Hence, these rice plants can be used as donor parents to increase the development of fragrance‐biofortified tropical rice varieties adapted to growing conditions and consumer preferences, thus contributing to the global rice market.     

水稻籽粒灌浆过程中蛋白质表达特性及其对氮肥运筹的响应

采用大田栽培的方式,研究了大穗型水稻金辉809籽粒灌浆过程中蛋白质的差异表达变化模式以及同一施氮量下不同的氮肥施用比例(总施氮量225 kg/hm2,基蘖肥:穗粒肥分别为7∶3和6∶4)对强弱势粒灌浆影响的分子机制。获得了水稻不同灌浆时段籽粒总蛋白的表达图谱,共发现32个在灌浆过程中发生显著差异表达的蛋白点,涉及籽粒的淀粉合成,能量代谢,激素信号转导,基因表达调节和抗逆响应等。在此基础上,进一步构建了不同灌浆发育时段水稻强弱势籽粒响应不同氮肥比例调控的蛋白表达图谱,结果发现强势籽粒响应氮肥调控出现差异表达的蛋白点有8个,而弱势籽粒有26个,可见强势籽粒灌浆具有更强的环境稳定性,相对地,弱势籽粒灌浆则易被环境所调节。在总施氮量不变的情况下,适当增加生育后期氮肥的施用量,有利于增强弱势籽粒中信号转导,促进相关基因的表达,提高物质调运与能量代谢速率,增强抗逆性,增强弱势籽粒的代谢水平,延长其灌浆时期,提升弱势籽粒活性和灌浆强度,增加结实率和千粒重,最终实现高产高效。研究结果对于进一步明确氮素调控水稻强弱势粒灌浆的分子生态特性具有重要的理论与实际意义。