Chinese Rice Varieties Research Articles

Characterization and application of the qPL6.2 in regulating panicle length of rice (Oryza sativa L.)

Panicle length (PL) is one of the most important agronomic traits of rice; it determines panicle architecture and strongly affects grain yield and quality. Although several genes related to PL quantitative trait loci have been identified, PL has not been well characterized genetically, and its contribution to breeding and genetic improvement is unknown. Herein, we identified a novel quantitative trait locus for PL, i.e., qPL6.2, from single fragment substitution line P50, and mapped it to a region of 232.29-kb. The mapped region harbored 28 candidate genes, 7 of which were expressed more in young panicles than in other tissues. Further analysis of gene-knockout plants revealed LOC_Os06g06490 as a putative candidate gene of qPL6.2, and that the encoded protein was localized in the cell membrane. Sequence analysis of 102 modern Chinese rice varieties indicated that 3 variations at the LOC_Os06g06490 locus, among which C189G was proposed as a marker for indica-japonica differentiation, and A3259T which was specific to P50 might be as a functional variant. We hypothesize that mutations in the LOC_Os06g06490 locus affect the accumulation of indoleacetic acid, which regulates the length of young panicle. Therefore, the A3259T mutation may facilitate the breeding of better-quality high-yield japonica rice with moderate PL.

Predictive modeling of rice milling degree for three typical Chinese rice varieties using interpretative machine learning methods.

Brown rice over-milling causes high economic and nutrient loss. The rice degree of milling (DOM) detection and prediction remain a challenge for moderate processing. In this study, a self-established grain image acquisition platform was built. Degree of bran layer remaining (DOR) datasets is established with image capturing and processing (grain color, texture, and shape features extraction). The mapping relationship between DOR and the DOM is in-depth analyzed. Rice grain DOR typical machine learning and deep learning prediction models are established. The results indicate that the optimized Catboost model can be established with cross-validation and grid search method, with the best accuracy improving from 84.28% to 91.24%, achieving precision 91.31%, recall 90.89%, and F1-score 91.07%. Shapley additive explanations analysis indicates that color, texture, and shape feature affect Catboost prediction accuracy, the feature importance: color>texture>shape. The YCbCr-Cb_ske and GLCM-Contrast features make the most significant contribution to rice milling quality prediction. The feature importance provides theoretical and practical guidancefor grain DOM prediction model. PRACTICAL APPLICATION: Rice milling degree prediction and detection are valuable for rice milling process in practical application. In this paper, image processing and machine learning methods provide an automated, nondestructive, and cost-effective way to predict the quality of rice. The study may serve as a valuable reference for improving rice milling methods, retaining rice nutrition, and reducing broken rice yield.

Physiological and biochemical changes induced by Qiangdi nano-863 biological assistant growth apparatus during rice seed priming under temperature stress.

A huge amount of rice cultivation and consumption occur in Asia particularly in Pakistan and China. However, multiple abiotic stresses especially high and low-temperature proved to be a substantial threat for rice production ultimately risks for food security. To overcome various types of abiotic stress; seed priming is among the effective approaches to improve the rice seed germination and growth vigor. Therefore, the present study was planned to evaluate physiological and biochemical modifications in Chinese and Pakistani rice varieties by Qiangdi 863 biological assistant growth apparatus nano treated water (NTW), Osmopriming Calcium chloride (CaCl2), redox priming hydrogen peroxide (H2O2) and hormonal priming by Salicylic acid (SA) under temperature stress conditions. The experiment was performed with completely randomize design conditions. Five rice varieties, nomenclature as Zhongzoa 39, (Chinese rice variety) KSK 133, KS 282, Super basmati and PK 1121 aromatic (Pakistani rice variety) were sown under low temperature (LT) (17ºC), optimal temperature (OT) 27ºC and high temperature (HT) 37ºC conditions. The present study indicated that nanopriming were the most effective treatments increased Germination Energy Percentage (GEP) (96.1, 100, 100%), Speed of Germination (SG) (27.2, 35.45, 37.1), Final Germination Percentage (FGP) (98.2, 99.1, 99.4%), Seedling Dry Weight Biomass (DWB) (0.1, 0.137, 0.14g), Total Chlorophyll Content (0.502, 13.74, 15.21), antioxidant enzymes Superoxide Dismutase (SOD)(3145, 2559, 3345 µg-1FWh-1), Catalase (CAT) (300, 366, 3243 µg-1FWh-1) and decreased Malondialdehyde (MDA) (6.5, 12.2, 6.5 µmol g-1 FW) for Zhongzao 39 and KSK 133 rice varieties under low (LT+NTW), optimal temperature (OP+NTW) and high temperature (HT+NTW) stress., Therefore, nano-priming is recommended to cope with the high and low-temperature stress conditions along with improved productivity of rice.

Genome-wide selection and introgression of Chinese rice varieties during breeding

China is the largest rice-producing country, but the genomic landscape of rice diversity has not yet been clarified. In this study, we re-sequence 1070 rice varieties collected from China (400) and other regions in Asia (670). Among the six major rice groups (aus, indica-I, indica-II, aromatic, temperate japonica, and tropical japonica), almost all Chinese varieties belong to the indica-II or temperate japonica group. Most Chinese indica varieties belong to indica-II, which consists of two subgroups developed during different phases of rice breeding. The genomic segments underlying the differences between these subgroups span 36.32 Mb. The Chinese japonica rice varieties fall into the temperate japonica group, consisting of two subgroups based on their geographical distribution. The genomic segments underlying the differences between these subgroups span 27.69 Mb. These differentiated segments in the Chinese indica varieties span 45 genes with nonsynonymous mutations that are closely related to variations in plant height and grain width. Fifty-four genes with nonsynonymous mutations are associated with the differences in heading date between the two Chinese japonica subgroups. These findings provide new insights into rice diversity in China that will facilitate the molecular breeding.

An effective deep learning method with multi-feature and attention mechanism for recognition of Chinese rice variety information

An effective deep learning method with multi-feature and attention mechanism for recognition of Chinese rice variety information

Genotype and phenotype variability of BC1F1 progenies from backcross of C3 and Koshihikari

Improvement of local rice variety could be conducted by crossing it with superior varieties. C3 is improved line of Acehnese rice ‘Cantik Manis’ by crossing it with the introduced Chinese rice variety Yin Zhan to make their progenies have shorter lifespan and good productivity. Although C3 line has been improved, this variety still has lifespan for about ± 135 days. Koshihikari is Japanese rice variety with its lifespan about 80-90 days. It is though that Koshihikari has various semidwarf gene such as sd-1 or other semidwarf genes. The strategy that can be used to decrease harvesting period of C3 is by crossing this variety with Koshihikari to insert semi-dwarf gene such as sd-1. The research was conducted to analyse the existing of sd-1 gen and phenotypic performance of their progenies specially in BC1F1. The seed of BC1F1 were found by crossing 2 prospective F1 plants (T8 and T10) with C3 parent. Molecular analysis showed that the whole progenies BC1F1-T8 inherit sd-1 gene (100%). Phenotypic observation showed the whole progenies had similar architecture as their parents with average heights at 45 DAP ranged from 74-91 cm, and number of tiller range from 3-9 tillers. Whereas in BC1F1-T10 progenies, there were 11 plant from 12 plants inherit sd-1 gene (91.7%). These progenies had average heights at 45 DAP ranged from 75-88 cm, and number of tiller range from 6-13 tillers.

Identification and analysis of the structure, expression and nucleotide polymorphism of the GPAT gene family in rice

Glycerol-3-phosphate acyltransferase (GPAT), a family of membrane-bound enzymes, is involved in the initial step of glycerolipid biosynthesis in plant cells. In this study, we performed an in-silico genome-wide analysis of rice (Oryza sativa) and identified 26 GPAT genes annotated according to their chromosomal locations. Putative orthologs of the rice genes were identified in five monocot and dicot plant species. The study characterized the rice GPAT gene structures, genome localization, gene duplications, conserved motifs, and cis-elements in their promoter regions. Segmental duplication contributed to the expansion of the GPAT family in rice with purifying selection pressure. We analyzed the phylogeny between six different monocots and dicot GPAT genes and compared them with rice orthologs and their exon-intron structure to understand their evolutionary relationships. Based on RNA-seq data, we found rice GPAT genes have diverse expression patterns. Some genes had high expression in specific tissues, including; OsGPAT2,13 and 8 in the root; OsGPAT3 and 10 in the shoot; OsGPAT4 in panicle; OsGPAT25 in the leaf; OsGPAT8, 25, and 26 in the anther and OsGPAT10, and 25 in the seed. Expression analysis under salt, cold, and heat conditions showed that GPAT genes positively respond to abiotic stress conditions. Some genes demonstrated sustained up-regulation in specific stresses including; OsGPAT2, OsGPAT18, OsGPAT19, OsGPAT5, and OsGPAT12 in cold stress; OsGPAT6, 11, 13, 18, 19 and 21 in heat stress; and OsGPAT5, 14, 18, 19 and 24 during salt stress. Moreover, we used the 3000 rice genomes project (3 K RGP) data to analyze nucleotide polymorphism at each rice GPAT locus among hundred Chinese rice varieties. This study will provide a framework for future studies and further broaden our insights into the evolution and functional elucidation of GPAT genes in rice.

Food Fingerprinting: Using a Two-Tiered approach to Monitor and Mitigate Food Fraud in Rice.

Rice is an important staple food that is consumed around the world. Like many foods, the price of rice varies considerably, from very inexpensive for a low-quality product to premium pricing for highly prized varieties from specific locations. Therefore, like other foods it is vulnerable to economically motivated adulteration through substitution or misrepresentation of inferior-quality rice for more expensive varieties. In this article we describe results of a research project focused on addressing potential food fraud issues related to rice supplies in China, India, Vietnam, and Ghana. Rice fraud manifests differently in each country; therefore, tailored solutions were required. Here we describe a two-tiered testing regime of rapid screening using portable Near Infrared technology supported by second tier testing using mass spectrometry-based analysis of suspicious samples. Portable Near Infrared spectroscopy models and laboratory-based Gas Chromatography-Mass Spectrometry methods were developed to differentiate between: high-value Basmati rice varieties and their potential adulterants; six Geographic Indicated protected rice varieties from specific regions within China; various qualities of rice in Ghana and Vietnam; and locally produced and imported rice in Ghana. Furthermore, an Inductively Coupled Plasma-Mass Spectrometry method was developed to support the Chinese rice varieties methods as well as a Liquid Chromatography Quadrupole Time-of-Flight Mass Spectrometry method for quality differentiation in Vietnam. This two-tier approach can provide a substantially increased level of testing through rapid screening outside of the laboratory with the reassurance of corroborating mass spectrometry-based laboratory analysis to support decision making.

Study of pathogenicity and genetic diversity of Magnaporthe oryzae isolated from rice hybrid Wuyou 308 and detection of resistance genes

To understand the cause of loss of rice blast resistance, we studied the pathogenicity of Magnaporthe oryzae strains isolated from rice hybrid Wuyou 308 and evaluated its resistance genes. A total of 62 M. oryzae strains were isolated and tested in 7 Chinese rice varieties with varying degrees of resistance to rice blast and 30 blast-resistant monogenic lines. Fourteen physiological races of M. oryzae were identified: 8.55% belonging to the ZA group, 86.67% to the ZB group, and 5.00% to the ZC group. ZB15 was the most abundant race (45.00%). Five resistance genes, Pi-3(1), Pi-z5, Pi-k, Pi-kp(C), and Pi-k(C), conferred good resistance to the 62 strains, with resistance frequencies of 95.56, 91.11, 88.89, 82.22, and 82.22%, respectively. In contrast, Pi-a(2) had a resistance frequency of 0%. The hybrid combination Wuyou 308 was found to carry Pi-ta and Pi-b genes. Because Pi-ta and Pi-b both showed low resistance frequencies to M. oryzae isolated from Jiangxi, the hybrid rice variety Wuyou 308 could be infected by most of the 62 M. oryzae strains. The emergence and spread of rice blast disease in Wuyou 308 may thus be difficult to avoid when climatic conditions are favourable.

Using CRISPR-Cas9 to generate semi-dwarf rice lines in elite landraces

Genetic erosion refers to the loss of genetic variation in a crop. In China, only a few original landraces of rice (Oryza sativa) were used in breeding and these became the primary genetic background of modern varieties. Expanding the genetic diversity among Chinese rice varieties and cultivating high-yielding and high-quality varieties with resistance to different biotic and abiotic stresses is critical. Here, we used the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein9(Cas9) genome editing system to edit Semi-Dwarf1 (SD1) in the elite landraces Kasalath and TeTePu (TTP), which contain many desired agronomic traits such as tolerance to low phosphorous and broad-spectrum resistance to several diseases and insects. Mutations of SD1 confer shorter plant height for better resistance to lodging. Field trials demonstrated that the yield of the new Kasalath and TTP mutant lines was better than that of the wild type under modern cultivation and that the lines maintained the same desirable agronomic characteristics as their wild-type progenitors. Our results showed that breeding using available landraces in combination with genomic data of different landraces and gene-editing techniques is an effective way to relieve genetic erosion in modern rice varieties.

Physicochemical Properties of Chinese Rice Varieties

Physicochemical Properties of Chinese Rice Varieties

The Physical and Chemical Properties of the Grains of Some Chinese Rice Varieties with a Recorded Brown Rice Yield of around 1000 gm-2 in Yunnan Province, China:

The Physical and Chemical Properties of the Grains of Some Chinese Rice Varieties with a Recorded Brown Rice Yield of around 1000 gm-2 in Yunnan Province, China:

Differential regulation of proteins in rice (Oryza sativa L.) under iron deficiency.

Sixty-three proteins were identified to be differentially accumulated due to iron deficiency in shoot and root. The importance of these proteins alterations on shoot physiology is discussed. Iron (Fe) is an essential micronutrient for plant growth and its accumulation affects the quality of edible plant organs. To investigate the adaptive mechanism of a Chinese rice variety grown under iron deficiency, proteins differentially accumulated in leaves and roots of Yangdao 6, an indica cultivar, under Fe deficiency growth condition, were profiled using a two-dimensional electrophoresis (2-DE) and matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF/MS). The accumulations of seventy-three proteins were detected to be increased or decreased upon iron deficiency, and sixty-three of them were successfully identified. Among the sixty-three proteins, a total of forty proteins were identified in rice leaves, and twenty-three proteins were in roots. Most of these proteins are involved in photosynthesis, C metabolism, oxidative stress, Adenosine triphosphate synthesis, cell growth or signal transduction. The results provide a comprehensive way to understand, at the level of proteins, the adaptive mechanism used by rice shoots and roots under iron deficiency.

Functional markers developed from multiple loci in GS3 for fine marker-assisted selection of grain length in rice

The gene GS3 has major effect on grain size and plays an important role in rice breeding. The C to A mutation in the second exon of GS3 was reported to be functionally associated with enhanced grain length in rice. In the present study, besides the C-A mutation at locus SF28, three novel polymorphic loci, SR17, RGS1, and RGS2, were discovered in the second intron, the last intron and the final exon of GS3, respectively. A number of alleles at these four polymorphic loci were observed in a total of 287 accessions including Chinese rice varieties (Oryza sativa), African cultivated rice (O. glaberrima) and AA-genome wild relatives. The haplotype analysis revealed that the simple sequence repeats (AT)(n) at RGS1 and (TCC)(n) at RGS2 had differentiated in the wild rice whilst the C-A mutation occurred in the cultivated rice recently during domestication. It also indicated that A allele at SF28 was highly associated with long rice grain whilst various motifs of (AT)(n) at RGS1 and (TCC)(n) at RGS2 were mainly associated with medium to short grain in Chinese rice. The C-A mutation at SF28 explained 33.4% of the grain length variation in the whole rice population tested in this study, whereas (AT)(n) at RGS1 and (TCC)(n) at RGS2 explained 26.4 and 26.2% of the variation, respectively. These results would be helpful for better understanding domestication of GS3 and its manipulation for grain size in rice. The genic marker RGS1 based on the motifs (AT)(n) was further validated as a functional marker using two sets of backcross recombinant inbred lines. These results suggested that the functional markers developed from four different loci within GS3 could be used for fine marker-assisted selection of grain length in rice breeding.

Introduction of A Nonhost Gene Rxo1 Cloned from Maize Resistant to Rice Bacterial Leaf Streak into Rice Varieties

Bacterial leaf streak (BLS) of rice, caused by Xanthomonas oryzae pv. oryzicola (Xooc), is a destructive bacterial disease in China. Single-gene resistance to Xooc has not been found in rice germplasm. A cloned nonhost gene from maize with resistance to BLS, Rxo1, was transferred into four Chinese rice varieties through an Agrobacterium-mediated transformation system, including Zhonghua 11, 9804, C418, and Minghui 86. Polymerase chain reaction (PCR) and Southern blot analysis of the transgenic plants showed the integration of the Rxo1 gene into the rice genomes. The integrated Rxo1 gene was stably inherited, and segregated in a 3:1 (resistance: susceptible) ratio in the selfed T 1 generations derived from some T 0 plants, indicating that the Rxo1 gene is inherited as a dominate gene in rice. Transgenic T 0 plants and PCR-positive T 1 plants were resistant to Xooc on the basis of artificial inoculation

Iron, zinc and phytic acid content of selected rice varieties from China

AbstractRice is the major Chinese staple food (per capita approx 250 g day−1) and, as such, is an important source of essential minerals. However, due to a number of factors the bio‐availability of these minerals is limited. In this study, the variation of phytic acid (PA), iron (Fe) and zinc (Zn) levels in 56 varieties of Chinese rice was investigated. The samples included in this study were collected in proportion to the importance of the rice‐growing regions in China. Fe levels showed the biggest variation (9–45 mg kg−1) and were not related with PA content or grain shape although growing locations were identified yielding higher (25.2 mg kg−1) and lower (14.2 mg kg−1) Fe levels. Zn showed a moderate variability (13–39 mg kg−1), which was narrower than for Fe, while broader than for PA (7.2–11.9 g kg−1). Zn content is correlated (R2 = 0.5; P < 0.01) with PA content, and shows a relation with growing region and kernel shape. Variation of PA content is the least among the three components. Molar ratios of PA to Fe and Zn ranged from 15 to 105 and 27 to 67, respectively. The results of the mineral contents and PA content can be interpreted in terms of expected bio‐availability. This study shows that the mineral bio‐availability of Chinese rice varieties will be <4%. Despite the variation in mineral contents, in all cases the PA present is expected to render most mineral present unavailable. We conclude that there is scope for optimisation of mineral contents of rice by matching suitable varieties and growing regions, and that rice products require processing that retains minerals but results in thorough dephytinisation. Copyright © 2006 Society of Chemical Industry

Genetic characterization and fine mapping of the blast resistance locus Pigm(t) tightly linked to Pi2 and Pi9 in a broad-spectrum resistant Chinese variety

The identification and utilization of broad-spectrum resistance genes have been proven the most effective and economical approach to control rice blast disease. To understand the molecular mechanism of broad-spectrum resistance to rice blast, we conducted genetic and fine mapping analysis of the blast resistance gene in a Chinese rice variety: Gumei 4 (GM4) identified with broad-spectrum resistance and used in rice breeding for blast resistance for more than 20 years. Genetic and mapping analysis indicated that blast resistance to nine isolates of different Chinese races in GM4 was controlled by the same dominant locus designated as Pigm(t) that was finely mapped to an approximately 70-kb interval between markers C5483 and C0428 on chromosome 6, which contains five candidate NBS--LRR disease resistance genes. The allelism test showed that Pigm(t) was either tightly linked or allelic to Pi2 and Pi9, two known blast resistance genes. Mapping information also indicated that another blast resistance gene Pi26(t) might also be located at the same region. Candidate genes were identified by sequence analysis of the Nipponbare and Pi9 locus and the corresponding region in GM4. Sequence divergence of candidate genes was observed between GM4 and model varieties Nipponbare and 9311, and Pi9. Our current study provides essential information and new genetic resource for the cloning of functional resistance gene(s) and for marker-assisted selection in rice breeding for broad-spectrum blast resistance.

Introduction of a rice blight resistance gene,Xa21, into five Chinese rice varieties through anAgrobacterium-mediated system

A cloned gene, Xa21 was transferred into five widely-used Chinese rice varieties through an Agrobacterium- mediated system, and over 110 independent transgenic lines were obtained. PCR and Southern analysis of transgenic plants revealed the integration of the whole Xa21 gene into the host genomes. The integrated Xa21 gene was stably inherited, and segregated in a 3: 1 ratio in the selfed T(1) generation when one copy of the gene was integrated in the transformants. Inoculation tests displayed that transgenic T(0) plants and Xa21 PCR-positive T(1) plants were highly resistant to bacterial blight disease. The selected Xa21 homozygous resistant transgenic lines with desirable qualities may be propagated as new varieties or utilized in hybrid rice breeding.

Transgenic rice plants with a synthetic cry1Ab gene from Bacillus thuringiensis were highly resistant to eight lepidopteran rice pest species.

To fully explore the resistance potential of transgenic rice produced by Agrobacterium-mediated transformation, an elite line KMD1 was assessed for its resistance to eight lepidopteran rice pest species. KMD1 contained a synthetic cry1Ab gene from Bacillus thuringiensis under the control of a maize ubiquitin promoter. It was derived from a commercial japonica Chinese rice variety Xiushui 11, and bred true for both agronomic traits and a cry1Ab gene when the bioassays were done in 1998 in the R5 generation. The eight lepidopteran pest species were: four Pyralidae species: Chilo suppressalis (striped stem borer, SSB), Scirpophaga incertulas (yellow stem borer, YSB), Cnaphalocrocis medinalis (leaf folder), Herpitogramma licarisalis; two Noctuidae: Sesamia inferens (pink stem borer, PSB) and Naranga anescens; one Stayridae: Mycalesis gotama; and one Hesperiidae, Parnara guttata. In laboratory bioassays, 100% mortality was observed in all insect species when their newly hatched or third-instar larvae were fed KMD1 leaf tissues, whereas only 9.65% of the neonates and none of the third-instar larvae died when fed the leaf tissues of non-transgenic control. Moreover, the leaf area of control tissues consumed in four days by stem borers was 20 to 40 times higher than that of KMD1 tissues, and the area of control tissues eaten by leaf-feeding species was 120 to 180 times greater than that of the transgenic tissues. Under natural infestation, no KMD1 plant was visibly damaged by the SSB, YSB and leaf folder in field evaluation. On the other hand, 80, 9.3 and 88.7% of control plants were injured by SSB, YSB, and leaf folder, respectively. These data disclosed that the transgenic line was highly resistant to a broad spectrum of lepidopteran insect species and could be useful in insect resistance breeding programs.

Resistance to Gall Midge (GM) Orseolia oryzae in Chinese Rice Varieties Compared with Varieties From Other Countries

Resistance to Gall Midge (GM) Orseolia oryzae in Chinese Rice Varieties Compared with Varieties From Other Countries