Analysis of Erect-Panicle Japonica Rice in Northern China: Yield, Quality Status, and Quality Improvement Directions

China is the only country that extensively cultivates the indica and japonica rice varieties, with the largest japonica rice production area being in northeast China. A study of the relationship between the yield and quality of japonica rice and the effect of nitrogen fertilizer application on this relationship is important. In this paper, we aimed to assess the current yield and quality of japonica rice in northeast China. We selected erect-panicle varieties as the test materials. Field experiments were conducted using different nitrogen fertilizer levels for two consecutive years to analyze the rice varieties' yield, quality, interrelationship, and nitrogen fertilizer response. The average yield following high- and low-nitrogen treatments exceeded 10,000.00 kg/hm2, with a maximum of 12,285.63 kg/hm2. The high-yield-high-nitrogen treatment group had more panicles, a higher seed-setting rate, and a higher 1000-grain weight than the other groups. The high-yield-low-nitrogen group had a higher number of panicles and seed-setting rate than the other groups. The low-yield-high-nitrogen group had a lower number of whole grains, grain length-to-width ratio, and taste value than the other groups. The low-yield-low-nitrogen group had fewer primary branches than the other groups; excluding the primary branch-setting rate and 1000-grain weight, the values of the other panicle traits of the group were significantly higher than those of the other groups. The high-nitrogen-high-flavor group had lower panicle and spikelet numbers and higher spikelet fertility rates than the other groups. The low-nitrogen-high-flavor group had higher spikelet fertility rates and 1000-grain weight than the other groups. Compared to the other groups, the low-nitrogen-high-flavor group had a higher head rice yield, and the high-nitrogen-high-flavor group had a lower chalkiness rate. The main goal of the breeding and cultivation of high-yield and high-quality erect-panicle japonica rice in northern China is to achieve "dual high, dual low, and one high and one low" conditions, signifying a high yield with high or low nitrogen levels, low protein and amylose contents, high head rice rates, and low chalkiness. This study provides a new technique for enhancing the taste of northern erect-panicle japonica rice to promote the sustainable, high-yield, and high-quality development of japonica rice in northern China.

A Novel Allele in the Promoter of Wx Decreases Gene Expression and Confers Lower Apparent Amylose Contents in Japonica Rice (Oryza sativa L.)

Wx is the key gene that controls amylose content (AC), and various alleles have been found in rice populations. Wxb is the major allele in japonica and produces moderate AC (15~18%). It was recently found that editing the promoter of Wx could produce a series of alleles that have different Wx activities. Although some studies have edited the promoter, few studies have focused on the natural variations in Wx. Here, we used the Rice3K database to investigate variations in the Wx promoter and found that the allele Wx1764178 (A/G) has a higher LD (linkage disequilibrium) with the two key SNPs (1765751, T/G; 1768006, A/C), which could produce different Wx alleles and influence AC, as reported previously. Further study showed that the Wx1764178 allele (A/G) is functional and influences the expression of Wx positively. Editing the A allele using CRISPR‒Cas9 produced 36 and 3 bp deletions and caused a decrease in the expression of Wx. The apparent amylose content (AAC) in the edited lines was decreased by 7.09% and 11.50% compared with that of the wild type, which was the japonica variety Nipponbare with Wxb and the A allele at 1764178, while a complementary line with the G allele showed a lower AAC than the A allele with no effect on other agronomic traits. The AAC of the edited lines showed a higher increase than that of the wild type (Nipponbare, Wxb) in low-nitrogen conditions relative to high-nitrogen conditions. We also developed a dCAPS marker to identify the allele and found that the G allele has widely been used (82.95%) in japonica-bred varieties from Jiangsu Province, China. Overall, we found a functional allele (Wx1764178, A/G) in the Wx promoter that could affect AAC in japonica cultivars and be developed as markers for quality improvement in rice breeding programs.

A comparative study of grain quality and physicochemical properties of premium japonica rice from three typical production regions

Grain quality indicates rice commodity value. This research compared grain quality and physicochemical properties of premium japonica rice from three production regions, Yangtze River downstream of China (YRDCN), Northeast region of China (NECN) and Japan. Results showed that there were distinct quality and physicochemical characteristics variance among the three groups of japonica rice, while CVs of most quality parameters from low to high was Japan, YRDCN and NECN. YRDCN rice presented obvious lower apparent amylose content (AAC) and ratio of each chain-length sections of amylopectin, and showed higher protein contents especially glutelin and ratio in short and intermediate amylopectin molecules. Among three rice groups, YRDCN rice presented weaker appearance, whereas did not show inferior cooking and eating properties, which was primarily linked to lower AAC. Rice AAC and starch fine structure significantly correlated with pasting parameters, swelling power and solubility, while protein content had close relation with taste analyzer parameters. Results of this study indicated improvement direction for japonica rice of YRDCN, and also provided reference for consumers' rice purchasing selection in accordance with individual taste preference.

Effects of Lactic Acid Bacteria Fermentation on the Physicochemical Properties of Rice Flour and Rice Starch and on the Anti-Staling of Rice Bread

In this study, Lactococcus lactis lactis subspecies 1.2472, Streptococcus thermophilus 1.2718, and thermostable Lactobacillus rhamnosus HCUL 1.1901-1912 were used to ferment rice flour for preparing rice bread. The characteristics of fermented rice bread were studied to elucidate the mechanism by which fermentation improves the anti-staling ability of rice bread. The amylose content of rice flour increased after fermentation. The peak viscosity, attenuation value, final viscosity, recovery value, and gelatinization temperature decreased. Amylopectin was partially hydrolyzed, and the amylose content decreased. The crystallinity of starch decreased, and the minimum crystallinity of Lactococcus lactis subsp. lactis fermented rice starch (LRS) was 11.64%. The thermal characteristics of fermented rice starch, including To, Tp, Tc, and ΔH, were lower than RS (rice starch), and the △H of LRS was the lowest. Meanwhile, LRS exhibited the best anti-staling ability, and with a staling degree of 43.22%. The T22 of the LRF rice flour dough was lower, and its moisture fluidity was the weakest, indicating that moisture was more closely combined with other components. The texture characteristics of fermented rice bread were improved; among these, LRF was the best: the hardness change value was 1.421 times, the elasticity decrease was 2.35%, and the chewability change was 47.07%. There, it provides a theoretical basis for improving the shelf life of bread.

Effects of three patterns of elevated CO2 in single and multiple generations on photosynthesis and stomatal features in rice

BACKGROUND AND AIMS

Effects of elevated CO2 (E) within a generation on photosynthesis and stomatal features have been well documented in crops; however, long-term responses to gradually elevated CO2 (Eg) and abruptly elevated CO2 (Ea) over multiple generations remain scarce.

METHODS

Japonica rice plants grown in open-top chambers were tested in the first generation (F1) under Ea and in the fifth generation (F5) under Eg and Ea, as follows: Ea in F1: ambient CO2 (A) + 200 μmol mol-1; Eg in F5: an increase of A + 40 μmol mol-1 year-1 until A + 200 μmol mol-1 from 2016 to 2020; Ea in F5: A + 200 μmol mol-1 from 2016 to 2020. For multigenerational tests, the harvested seeds were grown continuously in the following year in the respective CO2 environments.

KEY RESULTS

The responses to Ea in F1 were consistent with the previous consensus, such as the occurrence of photosynthetic acclimation, stimulation of photosynthesis, and downregulation of photosynthetic physiological parameters and stomatal area. In contrast, multigenerational exposure to both Eg and Ea did not induce photosynthetic acclimation, but stimulated greater photosynthesis and had little effect on the photosynthetic physiology and stomatal traits. This suggests that E retained intergenerational effects on photosynthesis and stomatal features and that there were no multigenerational differences in the effects of Eg and Ea.

CONCLUSIONS

The present study demonstrated that projecting future changes induced by E based on the physiological responses of contemporary plants could be misleading. Thus, responses of plants to large and rapid environmental changes within a generation cannot predict the long-term response of plants to natural environmental changes over multiple generations, especially in annual herbs with short life cycles.

Generation of new rice germplasms with low amylose content by CRISPR/CAS9-targeted mutagenesis of the FLOURY ENDOSPERM 2 gene

FLOURY ENDOSPERM 2 (FLO2), encoding a tetratricopeptide repeat domain (TPR)-containing protein located in the nucleus, is considered to be a regulatory protein that controls the biosynthesis of seed storage substances. The diversity of flo2 allele is attributable for the variations in grain appearance, amylose content (AC), and physicochemical properties, influencing the eating and cooking quality (ECQ) of rice. In this study, we used CRISPR/Cas9 to introduce loss-of-function mutations into the FLOURY ENDOSPERM 2 gene in Suken118 (SK118), a widely cultivated elite japonica rice variety in Jiangsu, China. Physiochemical analyses of the flo2 mutants were congruent with previous studies, exhibiting lowered AC and viscosity, risen gel consistency (GC) and gelatinization temperature (GT) values, which were all instrumental to the improvement of ECQ. However, the wrinkled opaque appearance and the decrease in grain width, grain thickness and grain weight imply trade-offs in grain yield. Despite the ex-ante estimation for low yielding, the superior ECQ in these novel genotypes generated by using genome editing approach may have the potential for formulating high value specialty food.

OsBBX11 on qSTS4 links to salt tolerance at the seeding stage in Oryza sativa L. ssp. Japonica

Rice has been reported to be highly sensitive to salt stress at the seedling stage. However, the lack of target genes that can be used for improving salt tolerance has resulted in several saline soils unsuitable for cultivation and planting. To characterize new salt-tolerant genes, we used 1,002 F_2:3 populations derived from Teng-Xi144 and Long-Dao19 crosses as the phenotypic source to systematically characterize seedlings' survival days and ion concentration under salt stress. Utilizing QTL-seq resequencing technology and a high-density linkage map based on 4,326 SNP markers, we identified qSTS4 as a major QTL influencing seedling salt tolerance, which accounted for 33.14% of the phenotypic variation. Through functional annotation, variation detection and qRT-PCR analysis of genes within 46.9 Kb of qSTS4, it was revealed that there was one SNP in the promoter region of OsBBX11, which resulted in a significant response difference between the two parents to salt stress. Transgenic plants using knockout-based technology and demonstrated that Na⁺ and K⁺ in the roots of the functional-loss-type OsBBX11 were translocated largely to the leaves under 120 mmol/L NaCl compared with the wild-type, causing osbbx11 leaves to die after 12 days of salt stress due to an imbalance in osmotic pressure. In conclusion, this study identified OsBBX11 as a salt-tolerance gene, and one SNPs in the OsBBX11 promoter region can be used to identify its interacting transcription factors. This provides a theoretical basis for finding the molecular mechanism of OsBBX11 upstream and downstream regulation of salt tolerance and molecular design breeding in the future.

Comprehensive Evaluation of Rice Qualities under Different Nitrogen Levels in South China

There is a need to comprehensively evaluate the rice quality of different rice varieties under different nitrogen treatments. Therefore, in this study, we used twenty-one hybrid indica rice varieties and twenty-three inbred japonica rice varieties with three nitrogen fertilizer levels to investigate differences in rice qualities. As compared with hybrid indica rice, inbred japonica rice had lower coefficient of variation values for grain shape, mild rice percentage, and head rice percentage, but relatively higher coefficient of variation values for chalkiness traits, appearance, and taste value of cooked rice. A principal component analysis and membership function method were used to comprehensively evaluate the qualities of rice. The overall eating quality value by sensory evaluation and head rice percentage explained 61.3% and 67.9% of the variations in comprehensive quality of hybrid indica rice and inbred japonica rice across different nitrogen levels, respectively. We also found that rice comprehensive quality was better under low nitrogen levels for hybrid indica rice, while for inbred japonica rice, properly increasing nitrogen application could improve the comprehensive quality.

Polyphenol Composition and Antioxidant Activity of Japonica Rice Cultivars and Intake Status

Japonica rice is produced mainly in northeast China, Japan, and the Korean Peninsula. Polyphenols and flavonoids are the main antioxidants in japonica rice. This study reported the polyphenol content and antioxidant activity of nine brown and white japonica rice cultivars. The total phenolic and flavonoid contents of brown rice were in the ranges of 241.98-296.76 GAE mg/100 g, and 225.30-276.80 RE mg/100 g, respectively. These values were significantly higher than that of white rice by 118.98-206.06% and 135.0-217%, respectively. The bound fraction from phenolics and flavonoids contributed 41.1-63.6% and 62.22-78.19% of the total phenolic and flavonoid content in brown rice, respectively, while these ranges were 55.5-73.5% and 46.07-66.83% in white rice, respectively. p-Hydroxybenzonic acid was the predominant phenolic acid in japonica rice. All four antioxidant capacities of brown rice (DPPH, ABTS, OH, FRAP) were higher by up to 1.68-2.85 times than those of white rice. The PZ21 (Yanfeng 47) japonica rice variety has outstanding antioxidant capacity based on the weights of each antioxidant index. According to the differences of functional substances among varieties, it can provide guidance for consumers and theoretical basis for the production of healthy food.

[Comparison of three α-glucosidases from different sources in the synthesis of L-ascorbic acid 2-glucoside]

_L-ascorbic acid 2-glucoside (AA-2G) is a derivative of _L-ascorbic acid (_L-AA). Compared with _L-AA, it has good stability and is easily decomposed by enzyme in the human body. α-Glucosidase (AG) was the first enzyme found capable of producing AA-2G. However, researches on this enzyme is still in infancy. We took AG derived from Aspergillus niger (AAG), Japanese rice (JrAG) and Rattus rattus (RAG), and compared their specific enzymatic activity and transglycosidation rate, with the aim to improve the synthesis of AA-2G by the transglycosidation of AG. The genes encoding these three different AG were cloned and expressed in engineered yeast. The conditions for the transglycosidation reaction of these three enzymes were optimized and the transglycosidation efficiency and yield of AA-2G under the optimized conditions were compared. The specific activity of AAG reached 1.0 U/mg, while the yield of AA-2G reached 153.1 mg/L with a transglycosidation rate of 0.5%. The specific activity of RAG reached 0.4 U/mg, while the yield of AA-2G reached 861.0 mg/L with a transglycosidation rate of 2.5%. JrAG showed the highest specific activity and transglycosidation rate. The enzyme specific activity of JrAG reached 1.9 U/mg, while the yield of AA-2G reached 2 577.2 mg/L with a transglycosidation rate of 7.6%, much higher than that of the other two glucosidases. JrAG may thus have potential to improve the synthesis of AA-2G.

Early Austronesians Cultivated Rice and Millet Together: Tracing Taiwan's First Neolithic Crops

This study presents the first directly dated physical evidence of crop remains from the Early Neolithic archaeological layers in Taiwan. Systematic sampling and analysis of macro-plant remains suggested that Neolithic farmers at the Zhiwuyuan (Botanical Garden) site in Taipei, northern Taiwan, had cultivated rice and foxtail millet together at least 4,500 years ago. A more comprehensive review of all related radiocarbon dates suggests that agriculture emerged in Taiwan around 4,800-4,600 cal. BP, instead of the previous claim of 5,000 cal. BP. According to the rice grain metrics from three study sites of Zhiwuyuan, Dalongdong, and Anhe, the rice cultivated in northern and western-central Taiwan was mainly a short-grained type of the japonica subspecies, similar to the discoveries from the southeast coast of mainland China and the middle Yangtze valley. These new findings support the hypothesis that the southeast coast of mainland China was the origin of proto-Austronesian people who brought their crops and other cultural traditions across the Taiwan Strait 4,800 years ago and eventually farther into Island Southeast Asia.

ITRAQ-based quantitative proteomic analysis of japonica rice seedling during cold stress

Low temperature is one of the important environmental factors that affect rice growth and yield. To better understand the japonica rice responses to cold stress, isobaric tags for a relative and absolute quantification (iTRAQ) labeling-based quantitative proteomics approach was used to detected changes in protein levels. Two-week-old seedlings of the cold tolerant rice variety Kongyu131 were treated at 8°C for 24, 48 and 72 h, then the total proteins were extracted from tissues and used for quantitative proteomics analysis. A total of 5082 proteins were detected for quantitative analysis, of which 289 proteins were significantly regulated, consisting of 169 uniquely up-regulated proteins and 125 uniquely down-regulated proteins in cold stress groups relative to the control group. Functional analysis revealed that most of the regulated proteins are involved in photosynthesis, metabolic pathway, biosynthesis of secondary metabolites and carbon metabolism. Western blot analysis showed that protein regulation was consistent with the iTRAQ data. The corresponding genes of 25 regulated proteins were used for quantitative real time PCR analysis, and the results showed that the mRNA level was not always parallel to the corresponding protein level. The importance of our study is that it provides new insights into cold stress responses in rice with respect to proteomics and provides candidate genes for cold-tolerance rice breeding.

Differences in Eating Quality Attributes between Japonica Rice from the Northeast Region and Semiglutinous Japonica Rice from the Yangtze River Delta of China

Differences in cooked rice and starch and protein physicochemical properties of three japonica rice were compared systematically. Cultivars of japonica rice, Daohuaxiang2, from Northeast China (NR) and two semiglutinous japonica rice (SGJR), Nangeng46 and Nangeng2728, from the Yangtze River Delta (YRD) were investigated. Both Daohuaxiang2 and Nangeng46 achieved high taste values, but there were great differences in starch and protein physicochemical properties. Daohuaxiang2 showed higher apparent amylose content (AAC), lower protein content (PC), and longer amylopectin (especially fb2 and fb3) and amylose chain lengths, resulting in thicker starch lamellae and larger starch granule size. Its cooked rice absorbed more water and expanded to larger sizes. All of these differences created a more compact gel network and harder but more elastic cooked rice for Daohuaxiang2. Nangeng46 produced a lower AAC, a higher PC, shorter amylopectin and amylose chain lengths, thinner starch lamellae, and smaller starch granule sizes, creating a looser gel network and softer cooked rice. The two SGJR, Nangeng46 and Nangeng2728, had similar low AACs but great differences in taste values. The better-tasting Nangeng46 had a lower PC (especially glutelin content) and higher proportion of amylopectin fa chains, which likely reduced the hardness, improved the appearance, and increased the adhesiveness of its cooked rice. Overall, both types of japonica rice from the NR and YRD could potentially have good eating qualities where Nangeng46's cooked rice was comparable to that of Daohuaxiang2 because of its lower AC. Moreover, its lower PC and higher proportion of amylopectin fa chains likely improved its eating quality over the inferior-tasting SGJR, Nangeng2728. This research lays a foundation for the improvement of the taste of japonica rice in rice breeding.

Novel Sources of Pre-Harvest Sprouting Resistance for Japonica Rice Improvement

Pre-harvest sprouting (PHS), induced by unexpected weather events, such as typhoons, at the late seed maturity stage, is becoming a serious threat to rice production, especially in the state of California, USA, Japan, and the Republic of Korea, where japonica varieties (mostly susceptible to PHS) are mainly cultivated. A projected economic loss by severe PHS in these three countries could range between 8-10 billion USD per year during the next 10 years. Here, we present promising rice germplasm with strong resistance to PHS that were selected from a diverse rice panel of accessions held in the International Rice Genebank (IRG) at the International Rice Research Institute (IRRI). To induce PHS, three panicle samples per accession were harvested at 20 and 30 days after flowering (DAF), respectively, and incubated at 100% relative humidity (RH), 30 °C in a growth chamber for 15 days. A genome-wide association (GWA) analysis using a 4.8 million single nucleotide polymorphisms (SNP) marker set was performed to identify loci and candidate genes conferring PHS resistance. Interestingly, two tropical japonica and four temperate japonica accessions showed outstanding PHS resistance as compared to tolerant indica accessions. Two major loci on chromosomes 1 and 4 were associated with PHS resistance. A priori candidate genes interactions with rice gene networks, which are based on the gene ontology (GO), co-expression, and other evidence, suggested that a key resistance mechanism is related to abscisic acid (ABA), gibberellic acid (GA), and auxin mediated signaling pathways.

Candidate Gene Analysis for Nitrogen Absorption and Utilization in Japonica Rice at the Seedling Stage Based on a Genome-Wide Association Study

Over-application of nitrogen (N) fertilizer in fields has had a negative impact on both environment and human health. Domesticated rice varieties with high N use efficiency (NUE) reduce fertilizer requirements, enabling sustainable agriculture. Genome-wide association study (GWAS) analysis of N absorption and utilization traits under low and high N conditions was performed to obtain 12 quantitative trait loci (QTLs) based on genotypic data including 151,202 single-nucleotide polymorphisms (SNPs) developed by re-sequencing 267 japonica rice varieties. Eighteen candidate genes were obtained by integrating GWAS and transcriptome analyses; among them, the functions of OsNRT2.4, OsAMT1.2, and OsAlaAT genes in N transport and assimilation have been identified, and OsJAZ12 and OsJAZ13 also play important roles in rice adaptation to abiotic stresses. A NUE-related candidate gene, OsNAC68, was identified by quantitative real-time PCR (qRT-PCR) analyses. OsNAC68 encodes a NAC transcription factor and has been shown to be a positive regulator of the drought stress response in rice. Overexpression of OsNAC68 significantly increased rice NUE and grain yield under deficient N conditions, but the difference was not significant under sufficient N conditions. NUE and grain yield significantly decreased under both N supply conditions in the osbnac68 mutant. This study provides crucial insights into the genetic basis of N absorption and utilization in rice, and a NUE-related gene, OsNAC68, was cloned to provide important resources for rice breeding with high NUE and grain yield.

Inheritance and breeding of japonica rice with good eating quality in Jiangsu province

In order to develop a variety of japonica rice with good eating quality suitable for planting in Jiangsu Province, the genetic basis of high quality, disease resistance and high yield japonica rice varieties in Jiangsu Province was systematically studied. The relationship among different rice qualities of cooking, nutrition, and eating was studied by association analysis. It was clear that amylose content was the key factor affecting eating quality. The semi waxy rice with amylose content of 10%~14% has bright surface, soft texture, and elasticity, combining the softness of glutinous rice and the elasticity of japonica rice. The cold rice is not hard, and the taste is excellent. It meets the taste requirements of people in Yangtze River Delta region who like to eat soft fragrant japonica rice. The semi waxy japonica rice variety "Kantou 194" with a low expression of amylose content gene Wx ^mp and an amylose content of about 10% was selected as the core germplasm for improving eating quality. Pyramiding breeding of japonica rice variety with good eating quality, disease resistance and high yield was carried out by examining the development of Wx ^mp gene molecular markers and the use of closely linked molecular markers with disease resistance and high yield genes. A series of new japonica rice varieties with good taste such as Nanjing 46, Nanjing 5055, Nanjing 9108, and Nanjing 5718, suitable for different rice areas of Jiangsu Province, have been bred and approved by Jiangsu Provincial Variety Approval Committee. The layout of japonica rice varieties with good taste covering different rice areas in Jiangsu Province has been formed. These varieties have been planted with an accumulated area of more than 5.3 million hectares, which has effectively promoted the development of high quality rice industry in Jiangsu Province and its surrounding areas, and made important contributions to the structural adjustment of the supply side of rice industry, improving quality and efficiency, and ensuring food security.

Grain quality evaluation of japonica rice effected by cultivars, environment, and their interactions based on appearance and processing characteristics

Appearance and processing characteristics of 45 japonica rice samples, collected from different regions in Jiangsu province, were investigated and evaluated in this study. Specifically, the chalkiness degree had been presented significant differences among different cultivars and regions. The average chalkiness degree varied from 6.81% to 15.34% for different regions and from 1.93% to 28.31% for different cultivars. The minimum head rice rate of cultivars from four regions, NJ9108 (HA), was 80.5%. The AC of CNG10, HD5, and PJ surpassed 13.68% and lower than 11.33% for the others. The protein content ranged from 6.1% to 11%, and the taste value was significantly different among cultivars. In addition, the RVA curves of the samples were similar, but the peak viscosities of NG8 and NJ5055 were higher than others, and there were significant differences in RVA traits among regions. Cultivars were the main reasons for the difference in appearance and processing quality of japonica rice, while environmental factors had leaded to the change of rice composition, texture, and gelatinization.

Effects of vacuum soaking on the hydration, steaming, and physiochemical properties of japonica rice

Soaking is an essential step in the processing of various rice products. In this study, the influences of vacuum soaking on hydration, steaming, and physiochemical properties of rice were investigated. Results showed that vacuum soaking accelerated water absorption as well as affected the mobility and density of water protons inside rice during soaking. Vacuum soaking could considerably shorten the optimal steaming time from 58 to 32 min and reduce the adhesiveness of steamed rice. Microstructure analysis of rice revealed that porous structure was formed on rice surface and the arrangement of starch granules became loosened after vacuum soaking. Moreover, vacuum soaking slightly reduced the relative crystallinity of rice starches without altering the crystalline type. The gelatinization temperature as well as the peak and trough viscosity was also decreased after vacuum soaking. Our study suggested that vacuum soaking was conducive to improve the soaking and steaming properties of rice.

In-Frame and Frame-Shift Editing of the Ehd1 Gene to Develop Japonica Rice With Prolonged Basic Vegetative Growth Periods

Japonica rice has become increasingly popular in China owing to its superior grain quality. Over the past decades, "indica to japonica" projects have been proposed to promote cultivation of japonica rice in low latitudes in China. Traditionally, japonica varieties were planted mainly in mid latitudes in the northeast plain and Yangtze River region. The key obstacle for introducing elite mid-latitude japonica varieties to low latitudes is the severe shortening of growth period of the japonica varieties due to their sensitivity to low-latitude short photoperiod and high temperature. Here we report development of new japonica rice with prolonged basic vegetative growth (BVG) periods for low latitudes by targeted editing the Early heading date 1 (Ehd1) gene. Using CRISPR/Cas9 system, we generated both frame-shift and/or in-frame deletion mutants in four japonica varieties, Nipponbare, Longdao16, Longdao24, and Xiushui134. When planting at low-latitude stations, the frame-shift homozygous lines exhibited significantly longer BVG periods compared with wild-types. Interestingly, we observed that minor deletion of the first few residues within the receiver domain could quantitatively impair the function of Ehd1 on activation of Hd3a and RFT1, resulting in an intermediate-long BVG period phenotype in the homozygous in-frame deletion ehd1 lines. Field investigation further showed that, both the in-frame and frame-shift lines exhibited significantly improved yield potential compared with wild-types. Our study demonstrates an effective approach to rapid breeding of elite japonica varieties with intermediate-long and long BVG periods for flexible cropping systems in diverse areas or under different seasons in southern China, and other low-latitude regions.

Genetic Dissection of Germinability under Low Temperature by Building a Resequencing Linkage Map in japonica Rice

Among all cereals, rice is highly sensitive to cold stress, especially at the germination stage, which adversely impacts its germination ability, seed vigor, crop stand establishment, and, ultimately, grain yield. The dissection of novel quantitative trait loci (QTLs) or genes conferring a low-temperature germination (LTG) ability can significantly accelerate cold-tolerant rice breeding to ensure the wide application of rice cultivation through the direct seeding method. In this study, we identified 11 QTLs for LTG using 144 recombinant inbred lines (RILs) derived from a cross between a cold-tolerant variety, Lijiangxintuanheigu (LTH), and a cold-sensitive variety, Shennong265 (SN265). By resequencing two parents and RIL lines, a high-density bin map, including 2,828 bin markers, was constructed using 123,859 single-nucleotide polymorphisms (SNPs) between two parents. The total genetic distance corresponding to all 12 chromosome linkage maps was 2,840.12 cm. Adjacent markers were marked by an average genetic distance of 1.01 cm, corresponding to a 128.80 kb physical distance. Eight and three QTL alleles had positive effects inherited from LTH and SN265, respectively. Moreover, a pleiotropic QTL was identified for a higher number of erected panicles and a higher grain number on Chr-9 near the previously cloned DEP1 gene. Among the LTG QTLs, qLTG3 and qLTG7b were also located at relatively small genetic intervals that define two known LTG genes, qLTG3-1 and OsSAP16. Sequencing comparisons between the two parents demonstrated that LTH possesses qLTG3-1 and OsSAP16 genes, and SN-265 owns the DEP1 gene. These comparison results strengthen the accuracy and mapping resolution power of the bin map and population. Later, fine mapping was done for qLTG6 at 45.80 kb through four key homozygous recombinant lines derived from a population with 1569 segregating plants. Finally, LOC_Os06g01320 was identified as the most possible candidate gene for qLTG6, which contains a missense mutation and a 32-bp deletion/insertion at the promoter between the two parents. LTH was observed to have lower expression levels in comparison with SN265 and was commonly detected at low temperatures. In conclusion, these results strengthen our understanding of the impacts of cold temperature stress on seed vigor and germination abilities and help improve the mechanisms of rice breeding programs to breed cold-tolerant varieties.

Colchicine and osmotic stress for improving anther culture efficiency on long grain temperate and tropical japonica rice genotypes

Anther culture is a fast tool to obtain double haploid plant lines for breeding purposes. In rice, this procedure is commonly performed in two steps: i) induction of calli from anthers and ii) regeneration of plantlets from calli. It has been stated that genotype highly influences the anther culture efficiency, so the media used in each step should be optimized for each variety. In this study, we tested different media modifications of an efficient protocol optimized for a medium sized grain temperate japonica NRVC980385, used as a control, in a long grain temperate japonica rice variety (NRVC20120346), and two long grain tropical japonica varieties (303012 and 303013). We found that the addition of 150 mg l^-1 colchicine to the induction medium worked best for all genotypes except for NRVC20120346, whose best induction was obtained with the colchicine-free medium. Referring to regeneration, increased gelling agent in the medium provided the best rates in NRVC980385, improving our former NRVC980385-optimized anther culture protocol. Sorbitol fortified regeneration medium worked the best in the case of the long grain varieties. The presence of colchicine in the induction medium was also related to a higher obtention of double haploid plantlets. This study highlights that genotype is a key factor in the performance of rice anther culture. It has set a first anther culture study on long grain japonica varieties and optimizes the anther culture protocol for temperate japonica medium grain NRVC980385 with the use of colchicine and other additives that increase osmotic stress.

Differential Uptake and Utilization of Two Forms of Nitrogen in Japonica Rice Cultivars From North-Eastern China

Japonica rice is widely planted in north-eastern China because of its superior food quality and stable grain yields. Nitrogen (N) is an essential element for rice growth, and development and its availability directly impacts on rice yields. The knowledge of N uptake and its utilization characteristics in japonica are thus important areas of research. Three japonica rice cultivars, SN265, SN1401, and SN9816, which are planted across large areas of north-eastern China, were used here to evaluate the uptake and utilization along the life cycle of both ammonium( N H 4 + ) and nitrate( N O 3 - ) in hydroponically grown plants. The plants were grown in one of three different solutions with varying N H 4 + : N O 3 - ratios: 1:0, 0:1, and 1:1 (The total N content was 40 mg L-1 for each treatment). At the tillering stage, when only N O 3 - was provided, lower rates of N uptake and enzyme activities of three rice plants resulted in reduced tiller numbers. During the reproductive stage, the N H 4 + and( N H 4 + ) uptake rates in SN1401 were consistently maintained at high levels, whereas the rates in SN265 and SN9816 were significantly lower, across all three treatments. At the booting stage, when only N O 3 - was provided, SN1401 plants had significantly higher expression levels of OsNRT2.1 and OsNRT2.2, higher activity of nitrate reductase in the roots, and higher activity levels of glutamine synthetase and glutamate synthase in the leaves, compared with the SN265 and SN9816 plants. The higher enzyme activity was beneficial to the secondary assimilation of N, which ultimately promoted panicle development in SN1401. Consequently, the grain yield per plant of SN1401 was the highest with solutions of both N H 4 + and N O 3 - . These results indicate that selecting a rice cultivar with higher utilization of N O 3 - is beneficial for increasing the number of grains per panicle, grain yield, and N use efficiency.

[Study on quality standard of rice as excipients during rice stir-frying method]

Commercially available japonica rice and indica rice with different trade names were collected,and then based on the method of rice stir-frying,their many indexes were evaluated,for example the physical and chemical properties such as appearance color,grain type,broken kernel ratio,length-width ratio,1 000-grain weight,specific heat capacity,moisture content,amylose content,and protein content. The discriminant function analysis was used to determine the effective factors affecting the quality of rice as excipients. The results showed that two types of rice could be distinguished by rice color parameter a*,grain parameter circularity,1 000-grain weight and amylose content. These four effective factors can be used as the quality evaluation indexes for fried rice as excipients.Protein is one of the main components of rice,and its content affects the quality of rice. There is a significant difference in the protein content between japonica rice and indica rice. Therefore,protein content should be used as one of the evaluation indexes for rice quality. After comprehensive consideration,it is suggested that the red-green value a*shall not be less than 0. 50; the circularity not less than 53. 0,the 1 000-grain weight not less than 16. 0 g,the amylose content not less than 12. 0% and the protein content not less than4. 0% in the japonica rice; the red-green value a*shall not be lower than-1. 0,the circularity not less than 41. 0,the 1 000-grain weight not less than 13. 0 g,the amylose content not less than 9. 0% and the protein content not less than 3. 5% in the indica rice. In this study,the quality evaluation standards for rice as excipients( japonica rice,indica rice) were supplemented and improved,laying foundation for the development of quality standards for rice as excipients with the rice stir-frying method.

Coexistence of Multiple Endemic and Pandemic Lineages of the Rice Blast Pathogen

The rice blast fungus Magnaporthe oryzae (syn., Pyricularia oryzae) is both a threat to global food security and a model for plant pathology. Molecular pathologists need an accurate understanding of the origins and line of descent of M. oryzae populations in order to identify the genetic and functional bases of pathogen adaptation and to guide the development of more effective control strategies. We used a whole-genome sequence analysis of samples from different times and places to infer details about the genetic makeup of M. oryzae from a global collection of isolates. Analyses of population structure identified six lineages within M. oryzae, including two pandemic on japonica and indica rice, respectively, and four lineages with more restricted distributions. Tip-dating calibration indicated that M. oryzae lineages separated about a millennium ago, long after the initial domestication of rice. The major lineage endemic to continental Southeast Asia displayed signatures of sexual recombination and evidence of DNA acquisition from multiple lineages. Tests for weak natural selection revealed that the pandemic spread of clonal lineages entailed an evolutionary “cost,” in terms of the accumulation of deleterious mutations. Our findings reveal the coexistence of multiple endemic and pandemic lineages with contrasting population and genetic characteristics within a widely distributed pathogen.

The rice blast fungus Magnaporthe oryzae (syn., Pyricularia oryzae) is a textbook example of a rapidly adapting pathogen, and it is responsible for one of the most damaging diseases of rice. Improvements in our understanding of Magnaporthe oryzae’s diversity and evolution are required to guide the development of more effective control strategies. We used genome sequencing data for samples from around the world to infer the evolutionary history of M. oryzae. We found that M. oryzae diversified about 1,000 years ago, separating into six main lineages: two pandemic on japonica and indica rice, respectively, and four with more restricted distributions. We also found that a lineage endemic to continental Southeast Asia displayed signatures of sexual recombination and the acquisition of genetic material from multiple lineages. This work provides a population-level genomic framework for defining molecular markers for the control of rice blast and investigations of the molecular basis of differences in pathogenicity between M. oryzae lineages.

Divergent Hd1, Ghd7, and DTH7 Alleles Control Heading Date and Yield Potential of Japonica Rice in Northeast China

The heading date is a vital factor in achieving a full rice yield. Cultivars with particular flowering behaviors have been artificially selected to survive in the long-day and low-temperature conditions of Northeast China. To dissect the genetic mechanism responsible for heading date in rice populations from Northeast China, association mapping was performed to identify major controlling loci. A genome-wide association study (GWAS) identified three genetic loci, Hd1, Ghd7, and DTH7, using general and mixed linear models. The three genes were sequenced to analyze natural variations and identify their functions. Loss-of-function alleles of these genes contributed to early rice heading dates in the northern regions of Northeast China, while functional alleles promoted late rice heading dates in the southern regions of Northeast China. Selecting environmentally appropriate allele combinations in new varieties is recommended during breeding. Introducing the early indica rice's genetic background into Northeast japonica rice is a reasonable strategy for improving genetic diversity.

Changes in mineral elements and starch quality of grains during the improvement of japonica rice cultivars

BACKGROUND

The improvement of rice cultivars plays an important role in yield increase. However, little is known about the changes in starch quality and mineral elements during the improvement of rice cultivars. This study was conducted to investigate the changes in starch quality and mineral elements in japonica rice cultivars.

RESULTS

Twelve typical rice cultivars, applied in the production in Jiangsu province during the last 60 years, were grown in the paddy fields. These cultivars were classified into six types according to their application times, plant types and genotypes. The nitrogen (N), phosphorus (P) and, and potassium (K) were mainly distributed in endosperm, bran and bran, respectively. Secondary and micromineral nutrients were distributed throughout grains. With the improvement of cultivars, total N contents gradually decreased, while total P, K and magnesium contents increased in grains. Total copper and zinc contents in type 80'S in grains were highest. The improvement of cultivars enhanced palatability (better gelatinisation enthalpy and amylose content), taste (better protein content) and protein quality (better protein components and essential amino acids). Correlation analysis indicated the close relationship between mineral elements and starch quality.

CONCLUSION

The mineral elements and starch quality of grains during the improvement of japonica rice cultivars are improved. © 2017 Society of Chemical Industry.

Differences in Viscosity of Superior and Inferior Spikelets of Japonica Rice with Various Percentages of Apparent Amylose Content

Viscosity, a crucial characteristic for rice palatability, is affected by endosperm characters. We compared correlations between differences in viscosity of japonica rice with various palatability and endosperm characters. Changes in apparent amylose and protein contents (AAC% and PC%, respectively) and amylopectin side-chain distribution and the relationship of these traits with palatability were investigated in superior and inferior spikelets of good cultivars with low amylose content from Hokkaido and common cultivars from northeastern Japan, using rapid visco analyzer characteristics and rice-grain microstructures. Significant differences occurred in PC%, AAC%, breakdown, setback, peak time, and pasting temperature of different cultivars and grain positions. Amylopectin components showed remarkable differences in grain surfaces, surface layers, and section structure between the grain varieties. Hokkaido cultivars showed better viscosity than northeastern cultivars, particularly initial stage grains. Correlation analysis indicated viscosity was mainly AAC%-dependent, whereas differences in endosperm characteristics between spikelet positions were mainly due to grain-filling temperature.

Assessment of Five Chilling Tolerance Traits and GWAS Mapping in Rice Using the USDA Mini-Core Collection

Rice (Oryza sativa L.) is often exposed to cool temperatures during spring planting in temperate climates. A better understanding of genetic pathways regulating chilling tolerance will enable breeders to develop varieties with improved tolerance during germination and young seedling stages. To dissect chilling tolerance, five assays were developed; one assay for the germination stage, one assay for the germination and seedling stage, and three for the seedling stage. Based on these assays, five chilling tolerance indices were calculated and assessed using 202 O. sativa accessions from the Rice Mini-Core (RMC) collection. Significant differences between RMC accessions made the five indices suitable for genome-wide association study (GWAS) based quantitative trait loci (QTL) mapping. For young seedling stage indices, japonica and indica subspecies clustered into chilling tolerant and chilling sensitive accessions, respectively, while both subspecies had similar low temperature germinability distributions. Indica subspecies were shown to have chilling acclimation potential. GWAS mapping uncovered 48 QTL at 39 chromosome regions distributed across all 12 rice chromosomes. Interestingly, there was no overlap between the germination and seedling stage QTL. Also, 18 QTL and 32 QTL were in regions discovered in previously reported bi-parental and GWAS based QTL mapping studies, respectively. Two novel low temperature seedling survivability (LTSS)-QTL, qLTSS3-4 and qLTSS4-1, were not in a previously reported QTL region. QTL with strong effect alleles identified in this study will be useful for marker assisted breeding efforts to improve chilling tolerance in rice cultivars and enhance gene discovery for chilling tolerance.

Effects of Surface Charge and Functional Groups on the Adsorption and Binding Forms of Cu and Cd on Roots of indica and japonica Rice Cultivars

This work was designed to understand the mechanisms of adsorption of copper (Cu) and cadmium (Cd) on roots of indica and japonica varieties of rice. Six varieties each of indica and japonica rice were grown in hydroponics and the chemical properties of the root surface were analyzed, including surface charges and functional groups (-COO- groups) as measured by the streaming potential and attenuated total reflectance-Fourier transform infrared spectroscopy (ATR-FTIR). Binding forms of heavy metals adsorbed on rice roots were identified using sequential extraction methods. In rice roots exposed to Cu and Cd solutions, Cu existed mainly in both exchangeable and complexed forms, whereas Cd existed mainly in the exchangeable form. The amounts of exchangeable Cu and Cd and total adsorbed metal cations on the roots of indica varieties were significantly greater than those on the roots of japonica varieties, and the higher negative charges and the larger number of functional groups on the roots of indica varieties were responsible for their higher adsorption capacity and greater binding strength for Cu and Cd. Surface charge and functional groups on roots play an important role in the adsorption of Cu and Cd on the rice roots.

Genetic diversity and genetic relationships of japonica rice varieties in Northeast Asia based on SSR markers

Genetic diversity and the relationship among nine japonica rice groups consisting of 288 landraces and varieties in different geographical origins of Northeast Asia (China, Japan, Korea, Democratic People's Republic of Korea) and the Russian Far East district of the Russian Federation were evaluated with 154 simple sequence repeat (SSR) markers. A total of 823 alleles were detected. The observed allele numbers (Na) per locus, Nei's gene diversity (He) and the polymorphism information content (PIC) ranged from 2 to 9, 0.061 to 0.869 and 0.060 to 0.856, with an average of 5.344, 0.624 and 0.586, respectively. Five SSR loci, RM1350, RM1369, RM257, RM336 and RM1374, provided the highest PIC values and are potential for exploring the genetic diversity of rice cultivars in Northeast Asia. Molecular variance analysis showed that a significant difference existed both among groups (91.6%) and within each group (8.4%). The low genetic variation within each group indicated that the gene pool is narrow and alien genetic variation should be introduced into the rice breeding program in Northeast Asia. Based on the He and PIC values, the nine groups were ranked in a descending order: Heilongjiang landraces, Jilin landraces, Japanese improved varieties, Heilongjiang improved varieties, Russian Far East district of the Russian Federation improved varieties, Liaoning improved varieties, Jilin improved varieties, Korean improved varieties and Democratic People's Republic of Korea improved varieties. The nine groups were further divided into three subgroups and the 288 varieties into five clusters. This study provided information for parent selection in order to broaden the gene pool of the japonica rice germplasm in Northeast Asia.