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1.
Ionomic profiles are primarily influenced by genetic and environmental factors. Identifying ionomic responses to varietal effects is necessary to understand the ionomic variations among species or subspecies and to potentially understand genetic effects on ionomic profiles. We cultivated 120 rice (Oryza sativa) varieties to seedling stage in identical hydroponic conditions and determined the concentrations of 26 elements (including 3 anions) in the shoots and roots of rice. Although the subspecies effects were limited by the genus Oryza pre-framework and its elemental chemical properties, we found significant differences in ionomic variations in most elements among the aus, indica and japonica subspecies. Principal component analysis of the correlations indicated that variations in the root-to-shoot ionomic transport mechanisms were the main causes of ionomic differences among the subspecies. Furthermore, the correlations were primarily associated with the screening of varieties for elemental covariation effects that can facilitate breeding biofortified rice varieties with safe concentrations of otherwise toxic elements. The japonica subspecies exhibited the strongest elemental correlations and elemental covariation effects, therefore, they showed greater advantages for biofortification than the indica and aus subspecies, whereas indica and aus subspecies were likely safer in metal(loid) polluted soils. We also found that geographical and historical distribution significantly defined the ionomic profiles. Overall, the results of this study provided a reference for further association studies to improve the nutritional status and minimize toxicity risks in rice production.  相似文献   

2.
The main objectives of the “Oryza Map Alignment Project” (OMAP) are to characterize the rice genome from a comparative standpoint by establishing a genus-wide and genome-scale comparative framework from representative species. Here, we report our progress in the analyses of these datasets and emerging “comparative phylogenomics” insights into Oryza evolution at two different resolutions—chromosomal and sequence levels. We demonstrate the abundance and impact of structural variations (SV) on genome diversity using African Oryza as a model. The molecular basis of SV was inferred using three genus-wide vertical sequence datasets. Combined, these data demonstrate that a single reference genome sequence for the genus Oryza is insufficient to comprehensively capture the genomic and allelic diversity present within the genus. Towards this end, we present a strategy to generate high-quality and cost-effective de novo reference sequences of collective Oryza. The application and broader scientific impact of the OMAP resources under an international cooperative effort (I-OMAP) are discussed.  相似文献   

3.
Asian cultivated rice shows allelic variation in sodium transporter, OsHKT1;5, correlating with shoot sodium exclusion (salinity tolerance). These changes map to intra/extracellularly-oriented loops that occur between four transmembrane-P loop-transmembrane (MPM) motifs in OsHKT1;5. HKT1;5 sequences from more recently evolved Oryza species (O. sativa/O. officinalis complex species) contain two expansions that involve two intracellularly oriented loops/helical regions between MPM domains, potentially governing transport characteristics, while more ancestral HKT1;5 sequences have shorter intracellular loops. We compared homology models for homoeologous OcHKT1;5-K and OcHKT1;5-L from halophytic O. coarctata to identify complementary amino acid residues in OcHKT1;5-L that potentially enhance affinity for Na+. Using haplotyping, we showed that Asian cultivated rice accessions only have a fraction of HKT1;5 diversity available in progenitor wild rice species (O. nivara and O. rufipogon). Progenitor HKT1;5 haplotypes can thus be used as novel potential donors for enhancing cultivated rice salinity tolerance. Within Asian rice accessions, 10 non-synonymous HKT1;5 haplotypic groups occur. More HKT1;5 haplotypic diversities occur in cultivated indica gene pool compared to japonica. Predominant Haplotypes 2 and 10 occur in mutually exclusive japonica and indica groups, corresponding to haplotypes in O. sativa salt-sensitive and salt-tolerant landraces, respectively. This distinct haplotype partitioning may have originated in separate ancestral gene pools of indica and japonica, or from different haplotypes selected during domestication. Predominance of specific HKT1;5 haplotypes within the 3 000 rice dataset may relate to eco-physiological fitness in specific geo-climatic and/or edaphic contexts.  相似文献   

4.
While cultivated rice, Oryza sativa, is arguably the world’s most important cereal crop, there is little comparative morphological information available for the grain of rice wild relatives. In this study, the endosperm of 16 rice wild relatives were compared to O. sativa subspecies indica and O. sativa subspecies japonica using scanning electron microscopy. Although the aleurone, starch granules, protein bodies and endosperm cell shapes of the cultivated and non-cultivated species were similar, several differences were observed. The starch granules of some wild species had internal channels that have not been reported in cultivated rice. Oryza longiglumis, Microlaena stipoides and Potamophila parviflora, had an aleurone that was only one-cell thick in contrast to the multiple cell layers observed in the aleurone of the remaining Oryza species. The similarity of the endosperm morphology of undomesticated species with cultivated rice suggests that some wild species may have similar functional properties. Obtaining a better understanding of the wild rice species grain ultrastructure will assist in identifying potential opportunities for development of these wild species as new cultivated crops or for their inclusion in plant improvement programmes.  相似文献   

5.

Background

The rice blast resistance gene Pi54 was cloned from Oryza sativa ssp. indica cv. Tetep, which conferred broad-spectrum resistance against Magnaporthe oryzae. Pi54 allelic variants have been identified in not only domesticates but also wild rice species, but the majority of japonica and some indica cultivars lost the function.

Results

We here found that Pi54 (Os11g0639100) and its homolog Os11g0640600 (named as #11) were closely located on a 25 kbp region in japonica cv. Sasanishiki compared to a 99 kbp region in japonica cv. Nipponbare. Sasanishiki lost at least six genes containing one other R-gene cluster (Os11g0639600, Os11g0640000, and Os11g0640300). Eight AA-genome species including five wild rice species were classified into either Nipponbare or Sasanishiki type. The BB-genome wild rice species O. punctata was Sasanishiki type. The FF-genome wild rice species O. brachyantha (the basal lineage of Oryza) was neither, because Pi54 was absent and the orientation of the R-gene cluster was reversed in comparison with Nipponbare-type species. The phylogenetic analysis showed that #11gene of O. brachyantha was on the root of both Pi54 and #11 alleles. All Nipponbare-type Pi54 alleles were specifically disrupted by 143 and 37/44?bp insertions compared to Tetep and Sasanishiki type. In addition, Pi54 of japonica cv. Sasanishiki lost nucleotide-binding site and leucine-rich repeat (NBS–LRR) domains owing to additional mutations.

Conclusions

These results suggest that Pi54 might be derived from a tandem duplication of the ancestor #11 gene in progenitor FF-genome species. Two divergent structures of Pi54 locus caused by a mobile unit containing the nearby R-gene cluster could be developed before domestication. This study provides a potential genetic resource of rice breeding for blast resistance in modern cultivars sustainability.
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6.
Here, we present the results of a comprehensive study of the distribution, evolution, heterogeneity, and phylogenetic relationships of the Ty3-Gypsy Atlantys long terminal repeat retrotransposable element family in Oryza. Atlantys element-related sequences make up a significant fraction of the genomes of species from the Officinalis complex as well as the Oryza ridleyi and O. granulata genomes. The proliferation of Atlantys elements, in many cases, took place after respective speciation events occurred. Most of the retrotranspositional events occurred within the last three million years. Atlantys is an ancient and ubiquitous component of the genus Oryza and has made significant contributions to genome size variation across the genus. Its structure is unusual when compared to other Ty3-Gypsy elements and its proliferation in the different Oryza species has been rapid and differential.  相似文献   

7.
Moisture distribution in individual polished rice grains was observed during soaking by magnetic resonance (MR) imaging, and a nuclear magnetic resonance (NMR) signal intensity profile (SI-profile) was generated from the MR image. The water penetration pattern during soaking roughly showed dissimilar trends between different varieties of japonica and japonica-indica hybrid rice. NMR signal intensity at the completion of water absorption varied within each grain; high at the periphery and the central region and low in the area between the periphery and the central region. High moisture content within the central region is due to loosely packed starch granules. The SI-profile was congruent for grains of the same variety harvested in different regions and years and characterized a grain moisture distribution for each variety. Moisture distribution was compared using SI-profiles for varieties with different amylose contents and new varieties bred for specific end-uses in Japan. The NMR signal intensity, which is related to the moisture content, at the surface of soaked grain was negatively correlated to the grain amylose content. The NMR signal intensities at the surface of soaked grain negatively correlated with the overall hardness of the cooked rice grain as measured by the single-grain low-high compression test.  相似文献   

8.
Sheath blight (SB) caused by the soil borne pathogen Rhizoctonia solani is one of the most serious global rice diseases. Breeding resistant cultivar is the most economical and effective strategy to control the disease. However, no rice varieties are completely resistant to SB, and only a few reliable quantitative trait loci (QTLs) linked with SB resistance have been identified to date. In this study, we conducted a genome-wide association study (GWAS) of SB resistance using 299 varieties from the rice diversity panel 1 (RDP1) that were genotyped using 44 000 high-density single nucleotide polymorphism (SNP) markers. Through artificial inoculation, we found that only 36.5% of the tested varieties displayed resistance or moderate resistance to SB. In particular, the aromatic and aus sub-populations displayed higher SB resistance than the tropical japonica (TRJ), indica and temperate japonica sub-populations. Seven varieties showed similar resistance levels to the resistant control YSBR1. GWAS identified at least 11 SNP loci significantly associated with SB resistance in the three independent trials, leading to the identification of two reliable QTLs, qSB-3 and qSB-6, on chromosomes 3 and 6. Using favorable alleles or haplotypes of significantly associated SNP loci, we estimated that both QTLs had obvious effects on reducing SB disease severity and can be used for enhancing SB resistance, especially in improving SB resistance of TRJ sub-population rice varieties. These results provided important information and genetic materials for developing SB resistant varieties through breeding.  相似文献   

9.
Rice is a member of the genus Oryza, which has a history extending back into the Miocene. Oryza is in turn a member of the tribe Oryzeae, which along with the tribe Ehrharteae is included in the subfamily Ehrhartoideae. This paper reviews current knowledge of the genus, tribe and subfamily, and places rice in the larger evolutionary context of the entire grass family. The morphological characteristics of rice are an amalgam of characters that have originated at different times in its long evolutionary history. Increasingly, genomic characteristics are also being placed in a broad evolutionary context and it is becoming possible see which are characteristic of all grasses and which are more restricted to the genus Oryza or even to rice itself.  相似文献   

10.

Background

Although the genetic structure of rice germplasm has been characterized worldwide, few studies investigated germplasm from Thailand, the world’s largest exporter of rice. Thailand and the International Rice Research Institute (IRRI) have diverse collections of rice germplasm, which could be used to develop breeding lines with desirable traits. This study aimed to investigate the level of genetic diversity and structures of Thai and selected IRRI germplasm. Understanding the genetic structure and relationships among these germplasm will be useful for parent selection used in rice breeding programs.

Results

From the 98 InDel markers tested for single copy and polymorphism, 19 markers were used to evaluate 43 Thai and 57 IRRI germplasm, including improved cultivars, breeding lines, landraces, and 5 other Oryza species. The Thai accessions were selected from all rice ecologies such as irrigated, deep water, upland, and rainfed lowland ecosystems. The IRRI accessions were groups of germplasm having agronomic desirable traits, including temperature-sensitive genetic male sterility (TGMS), new plant type, early flowering, and biotic and abiotic stress resistances. Most of the InDel markers were genes with diverse functions. These markers produced the total of 127 alleles for all loci, with a mean of 6.68 alleles per locus, and a mean Polymorphic Information Content (PIC) of 0.440. Genetic diversity of Thai rice were 0.3665, 0.4479 and 0.3972 for improved cultivars, breeding lines, and landraces, respectively, while genetic diversity of IRRI improved and breeding lines were 0.3272 and 0.2970, respectively. Cluster, structure, and differentiation analyses showed six distinct groups: japonica, TGMS, deep-water, IRRI germplasm, Thai landraces and breeding lines, and other Oryza species.

Conclusions

Thai and IRRI germplasm were significantly different. Thus, they can be used to broaden the genetic base and trait improvements. Cluster, structure, and differentiation analyses showed concordant results having six distinct groups, in agreement with their development, and ecologies.  相似文献   

11.
Although the genetic diversity of rice germplasm has been well characterized globally, few studies have taken an in-depth view of a large number of rice landraces on a local scale. To better understand the relationships between rice genetic diversity and associated geographic and cultural factors, we collected and characterized 183 rice landraces from 18 villages along the Bahau and Kayan rivers in the Indonesian province of East Kalimantan on the island of Borneo. A genetic diversity analysis using 30 microsatellite markers detected a clear distinction between the indica and japonica varietal groups (F st?=?0.59), with 80% of the landraces identified as tropical japonica and 20% indica, which largely correlated with the field-level ecotypes: upland japonica and lowland indica. Indigenous knowledge from local farmers was gathered about the names, origins, and uses of the landraces, which provides a rich background to compare with the genetic relationships of these traditional varieties.  相似文献   

12.
Randolph Barker 《Rice》2011,4(3-4):184-186
Often overlooked is the importance of early-maturing rice varieties with their ability to escape droughts, avoid floods, and in some localities, open up the opportunity for double cropping. Most varieties grown in the tropics until the last half century matured in 150 to 180 days or longer and were photoperiod sensitive. However, non-photoperiod sensitive one-hundred-day varieties were grown in the Champa Kingdom in what is now Central Vietnam centuries ago. How these varieties moved into Song Dynasty China and the impact of the early-ripening rice on population growth in South China is well documented. However, the origin of the Champa varieties is less clear. According to a recent DNA test (see below), the Champa varieties belong to the aus sub-population. The aus have the characteristics of both indica and japonica and originated in the hill areas of what are now Eastern India, Bangladesh, and Myanmar. Because the Champa Kingdom adopted the Indian language and religion, at least in the higher courts, it seems logical that the Champa rice must have been disseminated from the hilly areas in the Indian sub-continent to Central Vietnam and eventually to China—first Fujian and later to the Yangtze region during the Song Dynasty in the eleventh century.  相似文献   

13.
Current Status of Brown Planthopper (BPH) Resistance and Genetics   总被引:4,自引:0,他引:4  
Kshirod K. Jena  Suk-Man Kim 《Rice》2010,3(2-3):161-171
Among the planthoppers of rice, the brown planthopper (BPH) is a major threat to rice production and causes significant yield loss annually. Host-plant resistance is an important strategy to reduce the damage caused by BPH and increase rice productivity. Twenty-one major genes for BPH resistance have been identified by using standard evaluation methods developed at the International Rice Research Institute (IRRI) to distinguish resistance or susceptibility of rice genotypes to BPH biotypes/populations. These genes are from diverse genetic resources such as land race cultivars and wild species of Oryza. Of the 21 resistance genes, 18 genes have been localized on specific region of six rice chromosomes using molecular genetic analysis and genomics tools. Some of these resistance genes are clustered together such as Bph1, bph2, Bph9, Bph10, Bph18, and Bph21 on the long arm of chromosome 12; Bph12, Bph15, Bph17 and Bph20 on the short arm of chromosome 4; bph11 and Bph14 on the long arm of chromosome 3 and Bph13(t) and bph19 on the short arm of chromosome 3. Six genes (Bph11, bph11, Bph12, bph12, Bph13 and Bph13) originated from wild Oryza species have either duplicate chromosome locations or wrong nomenclature. The discrepancy should be confirmed by allelism tests. Besides identification of major resistance genes, some quantitative trait loci (QTLs) associated with BPH resistance have also been identified on eight chromosomes. Most of the rice cultivars developed at IRRI possess one or two of the major resistance genes and the variety IR64 has many QTLs and confers strong resistance to BPH. More BPH resistance genes need to be identified from the wealth of gene pool available in the wild species of Oryza. Two BPH resistance genes (Bph14 and Bph18) have been cloned, and a snow drop lectin gene (GNA) has been identified and used in the development of BPH-resistant transgenic plants. Efficient introgression of resistance genes (Bph1, bph2, Bph3, Bph14, Bph15, Bph18, Bph20, and Bph21) into elite rice cultivars by marker-assisted selection together with strategic deployment of these genes can be an important approach to develop stable resistance to BPH and sustain rice production in the tropical and temperate rice growing regions.  相似文献   

14.
Australian Oryza are an understudied and underexploited genetic resource for rice improvement. Four species are indigenous: Oryza rufipogon, Oryza meridionalis, Oryza australiensis are widespread across northern Australia, whereas Oryza officinalis is known from two localities only. Molecular analysis of these wild populations is required to better define the distinctness of the taxa and the extent of any gene flow between them and rice. Limited collections of these wild populations are held in seed and DNA banks. These species have potential for domestication in some cases but also have many traits of potential value in the improvement of domesticated rice. Stress tolerance (biotic and abiotic) and grain quality characteristics in these populations may be useful.  相似文献   

15.
Accurate sequencing of the rice genome has ignited a passion for elucidating mechanism for sequence diversity among rice varieties and species, both in protein-coding regions and in genomic regions that are important for chromosome functions. Here, we have shown examples of sequence diversity in genic and non-genic regions. Sequence analysis of chromosome ends has revealed that there is diversity in both sequences and distribution in the region of telomere repeat arrays, from chromosome to chromosome, within a plant. Detailed study has allowed us to speculate the mechanism of generation of these arrays. Sequence analysis using various cultivated and wild rice of the sd1 gene, which contributed to the “Green Revolution” in rice varieties and their wild progenitors, has also demonstrated sequence diversity, which is correlated with taxonomic classification. These results indicate that detailed analysis of sequence diversity and comparison might give us a clue in elucidating mechanism of the evolution of rice genome.  相似文献   

16.
Production of Two Elite Glutinous Rice Varieties by Editing Wx Gene   总被引:1,自引:0,他引:1  
The waxy gene(Wx) in rice, which encodes the granule bound starch synthase enzyme, is responsible for amylose synthesis. Glutinous(sticky) rice has little or no amylose that can be used in various applications, such as brewing. In this study, knockout of the Wx gene with CRISPR/Cas9 technology was conducted in two elite japonica rice lines, Huaidao 5(HD5) and Suken 118(SK118), aiming to develop elite sticky rice varieties. We achieved six homozygous T_0 plants with more than 200 bp deletion in the Wx gene, as well as 36 wx-HD5 and 18 wx-SK118 homozygous transgene-free plants in the T_1 generation. The seeds of all the mutants were white and opaque, similar to those of sticky rice, and contained only 2.6%–3.2% amylose. Results of scanning electron microscopy showed that the quality of rice did not change. In conclusion, we successfully developed two elite sticky rice varieties.  相似文献   

17.
Breeding program strategies to develop novel short grain white rice varieties such as japonica (short grain) that introgress biotic stress resistance and high grain quality have been developed using indica rice (Pin Kaset + 4 and Riceberry) for applications in japonica rice (Koshihikari) improvement. Four breeding lines showing promising agronomic performance with short grain and low amylose content (< 20%) were obtained. In addition, sensory testing of these breeding lines showed high scores that similar to Koshihikari. Two promising lines, KP48-1-5 and KP48-1-9, which possessed a combination of four genes resistance to different biotic stresses (Bph3 + TPS + Xa21 + Pi-ta) and four genes for grain quality (GS3 + SSIIa + wxb + badh2), were developed using marker-assisted selection (MAS) with the pedigree method. The current study clearly illustrated the successful use of MAS in combining resistance to multiple biotic stresses while maintaining a high yield potential and preferred grain quality. Moreover, the results indicated that this breeding program, which includes crossing temperate japonica with indica, can create novel short grain rice varieties adapted to a tropical environment, like the japonica type.  相似文献   

18.
An extreme high temperature during grain filling is an important environmental factor that reduce the yield and quality of rice. In this study, we compared the grain appearance, composition and starch structure of four rice varieties response to high temperature during grain filling. The results obviously revealed that two indica AUS varieties Halwa and Jamir showed more tolerance to high temperature during grain filling than either the japonica Nipponbare or another AUS rice DJ24. The data showed that Halwa and Jamir presented less chalkiness, less grain weight loss, less change of endosperm components as well as starch structure than Nipponbare and DJ24 under high temperature treatment. Hence, the results implied that Halwa and Jamir might be useful targets to further identify genetic mechanism response to high temperature, at least during grain filling and endosperm development. Moreover, these AUS varieties have potential application value in further breeding of rice with good quality and heat tolerance.  相似文献   

19.

Background

Fixed arrays of single nucleotide polymorphism (SNP) markers have advantages over reduced representation sequencing in their ease of data analysis, consistently higher call rates, and rapid turnaround times. A 6 K SNP array represents a cost-benefit “sweet spot” for routine genetics and breeding applications in rice. Selection of informative SNPs across species and subpopulations during chip design is essential to obtain useful polymorphism rates for target germplasm groups. This paper summarizes results from large-scale deployment of an Illumina 6 K SNP array for rice.

Results

Design of the Illumina Infinium 6 K SNP chip for rice, referred to as the Cornell_6K_Array_Infinium_Rice (C6AIR), includes 4429 SNPs from re-sequencing data and 1571 SNP markers from previous BeadXpress 384-SNP sets, selected based on polymorphism rate and allele frequency within and between target germplasm groups. Of the 6000 attempted bead types, 5274 passed Illumina’s production quality control. The C6AIR was widely deployed at the International Rice Research Institute (IRRI) for genetic diversity analysis, QTL mapping, and tracking introgressions and was intensively used at Cornell University for QTL analysis and developing libraries of interspecific chromosome segment substitution lines (CSSLs) between O. sativa and diverse accessions of O. rufipogon or O. meridionalis. Collectively, the array was used to genotype over 40,000 rice samples. A set of 4606 SNP markers was used to provide high quality data for O. sativa germplasm, while a slightly expanded set of 4940 SNPs was used for O. sativa X O. rufipogon populations. Biparental polymorphism rates were generally between 1900 and 2500 well-distributed SNP markers for indica x japonica or interspecific populations and between 1300 and 1500 markers for crosses within indica, while polymorphism rates were lower for pairwise crosses within U.S. tropical japonica germplasm. Recently, a second-generation array containing ~7000 SNP markers, referred to as the C7AIR, was designed by removing poor-performing SNPs from the C6AIR and adding markers selected to increase the utility of the array for elite tropical japonica material.

Conclusions

The C6AIR has been successfully used to generate rapid and high-quality genotype data for diverse genetics and breeding applications in rice, and provides the basis for an optimized design in the C7AIR.
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20.
Global warming has caused frequent occurrence of heat stress at the flowering stage of single-season rice in the Yangtze River region of China, which results in declines of spikelet fertility and yield in rice. Rice flowering stage is the most sensitive period to high temperatures, and therefore, the key for heat stress happening is the flowering stage coinciding with high temperature, which causes spikelet fertility decreasing in heat-sensitive varieties, and is the major factor for heat injury differences among various rice planting regions. With the development of rice breeding, temperature indexes for heat stress has been converted from daily maximum temperature of 35 °C to 38 °C with the stress duration of more than 3 d. During the flowering stage, anther dehiscence inhibition and low pollen shedding onto the stigma are two main reasons for spikelet fertility reduction under high temperatures. At panicle initiation stage, high temperatures aggravate spikelet degeneration, and destroy floral organ development. Various types of rice varieties coexist in production, and indica-japonica hybrid rice demonstrates the highest heat resistance in general, followed by indica and japonica rice varieties. In production, avoiding high temperature is the main strategy of preventing heat stress, and planting suitable cultivars and adjustment of sowing date are the most effective measures. Irrigation is an effective real-time cultivation measure to decline the canopy temperature during the rice flowering stage. We suggested that further study should be focused on exploring heat injury differences among different rice variety types, and innovating rice-planting methods according to planting system changes in rice planting regions with extreme heat stress. Meanwhile, high temperature monitor and warning systems should be improved to achieve optimal heat stress management efficiencies.  相似文献   

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