Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

Identification of grain shape determining genes can facilitate breeding of rice cultivars with optimal grain shape and appearance quality. Here, we identify GS9 (Grain Shape Gene on Chromosome 9) gene by map-based cloning. The gs9 null mutant has slender grains, while overexpression GS9 results in round grains. GS9 encodes a protein without known conserved functional domain. It regulates grain shape by altering cell division. The interaction of GS9 and ovate family proteins OsOFP14 and OsOFP8 is modulated by OsGSK2 kinase, a key regulator of the brassinosteroids signaling pathway. Genetic interaction analysis reveals that GS9 functions independently from other previously identified grain size genes. Introducing the gs9 allele into elite rice cultivars significantly improves grain shape and appearance quality. It suggests potential application of gs9, alone or in combination with other grain size determining genes, in breeding of rice varieties with optimized grain shape.

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GS9 acts as a transcriptional activator to regulate rice grain shape and appearance quality

Cytoplasmic chloroplast (cp) genomes and nuclear ribosomal DNA (nR) are the primary sequences used to understand plant diversity and evolution. We introduce a high-throughput method to simultaneously obtain complete cp and nR sequences using Illumina platform whole-genome sequence. We applied the method to 30 rice specimens belonging to nine Oryza species. Concurrent phylogenomic analysis using cp and nR of several of specimens of the same Oryza AA genome species provides insight into the evolution and domestication of cultivated rice, clarifying three ambiguous but important issues in the evolution of wild Oryza species. First, cp-based trees clearly classify each lineage but can be biased by inter-subspecies cross-hybridization events during speciation. Second, O. glumaepatula, a South American wild rice, includes two cytoplasm types, one of which is derived from a recent interspecies hybridization with O. longistminata. Third, the Australian O. rufipogan-type rice is a perennial form of O. meridionalis.

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Complete chloroplast and ribosomal sequences for 30 accessions elucidate evolution of Oryza AA genome species

Rice Variation Map (RiceVarMap, http:/ricevarmap.ncpgr.cn) is a database of rice genomic variations. The database provides comprehensive information of 6 551 358 single nucleotide polymorphisms (SNPs) and 1 214 627 insertions/deletions (INDELs) identified from sequencing data of 1479 rice accessions. The SNP genotypes of all accessions were imputed and evaluated, resulting in an overall missing data rate of 0.42% and an estimated accuracy greater than 99%. The SNP/INDEL genotypes of all accessions are available for online query and download. Users can search SNPs/INDELs by identifiers of the SNPs/INDELs, genomic regions, gene identifiers and keywords of gene annotation. Allele frequencies within various subpopulations and the effects of the variation that may alter the protein sequence of a gene are also listed for each SNP/INDEL. The database also provides geographical details and phenotype images for various rice accessions. In particular, the database provides tools to construct haplotype networks and design PCR-primers by taking into account surrounding known genomic variations. These data and tools are highly useful for exploring genetic variations and evolution studies of rice and other species.

RiceVarMap: A Comprehensive Database of Rice Genomic Variations

Significant yield increase has been achieved by simultaneous introduction of three trait-related QTLs in three rice varieties with multiplex editing by CRISPR–Cas9. Using traditional breeding approaches to develop new elite rice varieties with high yield and superior quality is challenging. It usually requires introduction of multiple trait-related quantitative trait loci (QTLs) into an elite background through multiple rounds of crossing and selection. CRISPR–Cas9-based multiplex editing of QTLs represents a new breeding strategy that is straightforward and cost effective. To test this approach, we simultaneously targeted three yield-related QTLs for editing in three elite rice varieties, namely J809, L237 and CNXJ. The chosen yield-related QTL genes are OsGS3, OsGW2 and OsGn1a, which have been identified to negatively regulate the grain size, width and weight, and number, respectively. Our approach rapidly generated all seven combinations of single, double and triple mutants for the target genes in elite backgrounds. Detailed analysis of these mutants revealed differential contributions of QTL mutations to yield performance such as grain length, width, number and 1000-grain weight. Overall, the contributions are additive, resulting in 68 and 30% yield per panicle increase in triple mutants of J809 and L237, respectively. Our data hence demonstrates a promising genome editing approach for rapid breeding of QTLs in elite crop varieties.

Multiplex QTL editing of grain-related genes improves yield in elite rice varieties

Grain size is one of the key factors determining yield and quality in rice. A large number of genes are involved in the regulation of grain size parameters such as grain length and grain width. Different alleles of these genes have different impacts on the grain size traits under their control. However, the combined influence of multiple alleles of different genes on grain size remains to be investigated. Six key genes known to influence grain size were investigated in this study: GS3, GS5, GS6, GW2, qSW5/GW5, and GW8/OsSPL16. Allele and grain measurement data were used to develop a regression equation model that can be used for molecular breeding of rice with desired grain characteristics. A total of 215 diverse rice germplasms, which originated from or were developed in 28 rice-consuming countries, were used in this study. Genotyping analysis demonstrated that a relatively small number of allele combinations were preserved in the diverse population and that these allele combinations were significantly associated with differences in grain size. Furthermore, in several cases, variation at a single gene was sufficient to influence grain size, even when the alleles of other genes remained constant. The data were used to develop a regression equation model for prediction of rice grain size, and this was tested using data from a further 34 germplasms. The model was significantly correlated with three of the four grain size-related traits examined in this study. Rice grain size is strongly influenced by specific combinations of alleles from six different genes. A regression equation model developed from allele and grain measurement data can be used in rice breeding programs for the development of new rice varieties with desired grain size and shape.

/pdf/influence-of-multi-gene-allele-combinations-on-grain-size-of-vbqu6wv6rp.pdf

Influence of Multi-Gene Allele Combinations on Grain Size of Rice and Development of a Regression Equation Model to Predict Grain Parameters

Summary form only given, as follows. In plasma spraying, higher temperature and velocity of thermal plasma jets are preferable for producing high qualities of protective coatings for their industrial uses, because the sprayed coating powders are melted and accelerated in the plasma flame ejected from a non-transferred DC arc torch through an ambient air toward a substrate. In the typical plasma spray process operated under an atmospheric-pressure condition, the entrainment, of ambient air into the thermal plasma jet is inevitable. An air inflow to the flame alters chemical compositions of the plasma species, cools the thermal plasma flame, and decreases the jet velocity. Furthermore, the dissociation of entrained air enhances the specific heat of plasma, and then the plasma temperatures decrease even when operation power level of the plasma torch is not changed. Consequently, the gradients of temperature and velocity in the plasma jet increase with the degree of air entrainment. Therefore, the ambient air entrainment should be controlled to the lower degree for getting the better quality of coating products with higher purity, density and bond strength. In this experimental work, the geometrical effects of anode nozzle of the non-transferred plasma torch on the air entrainment are examined by measurements using a quadruple mass spectrometer. Two different types of anode nozzle, i.e., tubular and stepped nozzles are employed for the torch. For each nozzle, air contents in the thermal plasma are measured to find the effects of nozzle geometry on the ambient air mixing with the plasma species. The radial and axial distributions of plasma temperature and velocity are also measured. By analyzing the measured results of the thermal plasma characteristics and the geometrical effects of nozzle shape on the air entrainment, the suitable design requirements of the nozzle are determined for optimal processes of plasma spraying.

/pdf/effects-of-anode-nozzle-geometry-on-ambient-air-entrainment-fogvnfzmh6.pdf

Effects of anode nozzle geometry on ambient air entrainment into thermal plasma jets generated by a non-transferred plasma torch

Molecular markers are efficient and essential genotyping tools for molecular breeding and genetic analysis of rice. We developed two 96-plex indica–japonica single nucleotide polymorphism (SNP) genotyping sets for genetic analysis and molecular breeding in rice using the Fluidigm platform. Informative SNPs between indica and japonica were selected from SNP data of the Rice Diversity database, HapRice world SNP data of the Q-TARO database, and our 40 rice cultivar resequencing dataset. SNPs in set 1 were evenly distributed across all 12 rice chromosomes at a spacing of 4–5 Mb between adjacent SNPs. SNPs in set 2 mapped to the long genetic intervals in set 1 and included 14 functional or linked SNPs in genes previously cloned and associated with agronomic traits. Additionally, we used the SNP sets developed in this study to perform genetic diversity analysis of various cultivated and wild rice accessions, construction and validation of a subspecies diagnostic subset, linkage map construction and quantitative trait locus (QTL) analysis of a japonica × indica F2 population, and background profiling during marker-assisted backcrossing. Furthermore, we identified subspecies-specific SNPs and discuss their distribution and association with agronomic traits and subspecies differentiation. Our results indicate that these subspecies-specific SNPs were present in wild rice prior to domestication. This genotyping system will serve as an efficient and quick tool for genetic analysis and molecular breeding in rice.

/pdf/development-and-application-of-indica-japonica-snp-assays-p138fb1lgv.pdf

Development and application of indica – japonica SNP assays using the Fluidigm platform for rice genetic analysis and molecular breeding

Tongil (IR667-98-1-2) rice, developed in 1972, is a high-yield rice variety derived from a three-way cross between indica and japonica varieties. Tongil contributed to the self-sufficiency of staple food production in Korea during a period known as the `Korean Green Revolution'. We analyzed the nucleotide-level genome structure of Tongil rice and compared it to those of the parental varieties. A total of 17.3 billion Illumina Hiseq reads, 47× genome coverage, were generated for Tongil rice. Three parental accessions of Tongil rice, two indica types and one japonica type, were also sequenced at approximately 30x genome coverage. A total of 2,149,991 SNPs were detected between Tongil and Nipponbare varieties. The average SNP frequency of Tongil was 5.77 per kb. Genome composition was determined based on SNP data by comparing Tongil with three parental genome sequences using the sliding window approach. Analyses revealed that 91.8% of the Tongil genome originated from the indica parents and 7.9% from the japonica parent. Copy numbers of SSR motifs, ORF gene distribution throughout the whole genome, gene ontology (GO) annotation, and some yield-related QTLs or gene locations were also comparatively analyzed between Tongil and parental varieties using sequence-based tools. Each genetic factor was transferred from the parents into Tongil rice in amounts that were in proportion to the whole genome composition. Tongil was derived from a three-way cross among two indica and one japonica varieties. Defining the genome structure of Tongil rice demonstrates that the Tongil genome is derived primarily from the indica genome with a small proportion of japonica genome introgression. Comparative gene distribution, SSR, GO, and yield-related gene analysis support the finding that the Tongil genome is primarily made up of the indica genome.

/pdf/defining-the-genome-structure-of-tongil-rice-an-important-3h4m2u2179.pdf

Defining the genome structure of ‘Tongil’ rice, an important cultivar in the Korean “Green Revolution”

Kim, Backki; Kim, Dong-Gwan; Lee, Gileung; Seo, Jeonghwan; Choi, Ik-Young; Choi, Beom-Soon; Yang, Tae-Jin; Kim, Kwang Soo; Lee, Joohyun; Chin, Joong Hyoun; Koh, Hee-Jong.September, 2014.Defining the genome structure of `Tongil' rice, an important cultivar in the Korean ʺGreen Revolutionʺ,Articles,Berlin, GermanySpringer Nature,9

Jeonghwan Seo

Papers

Influence of Multi-Gene Allele Combinations on Grain Size of Rice and Development of a Regression Equation Model to Predict Grain Parameters

Effects of anode nozzle geometry on ambient air entrainment into thermal plasma jets generated by a non-transferred plasma torch

Development and application of indica – japonica SNP assays using the Fluidigm platform for rice genetic analysis and molecular breeding

Defining the genome structure of ‘Tongil’ rice, an important cultivar in the Korean “Green Revolution”

Defining the genome structure of `Tongil' rice, an important cultivar in the Korean ʺGreen Revolutionʺ