Publications by authors named "Hee-Jong Koh"

77 Publications

OsCOP1 regulates embryo development and flavonoid biosynthesis in rice (Oryza sativa L.).

Theor Appl Genet 2021 May 5. Epub 2021 May 5.

Department of Agriculture, Forestry and Bioresources, Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826, Republic of Korea.

Key Message: Novel mutations of OsCOP1 were identified to be responsible for yellowish pericarp and embryo lethal phenotype, which revealed that OsCOP1 plays a crucial role in flavonoid biosynthesis and embryogenesis in rice seed. Successful production of viable seeds is a major component of plant life cycles, and seed development is a complex, highly regulated process that affects characteristics such as seed viability and color. In this study, three yellowish-pericarp embryo lethal (yel) mutants, yel-hc, yel-sk, and yel-cc, were produced from three different japonica cultivars of rice (Oryza sativa L). Mutant seeds had yellowish pericarps and exhibited embryonic lethality, with significantly reduced grain size and weight. Morphological aberrations were apparent by 5 days after pollination, with abnormal embryo development and increased flavonoid accumulation observed in the yel mutants. Genetic analysis and mapping revealed that the phenotype of the three yel mutants was controlled by a single recessive gene, LOC_Os02g53140, an ortholog of Arabidopsis thaliana CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1). The yel-hc, yel-sk, and yel-cc mutants carried mutations in the RING finger, coiled-coil, and WD40 repeat domains, respectively, of OsCOP1. CRISPR/Cas9-targeted mutagenesis was used to knock out OsCOP1 by targeting its functional domains, and transgenic seed displayed the yel mutant phenotype. Overexpression of OsCOP1 in a homozygous yel-hc mutant background restored pericarp color, and the aberrant flavonoid accumulation observed in yel-hc mutant was significantly reduced in the embryo and endosperm. These results demonstrate that OsCOP1 is associated with embryo development and flavonoid biosynthesis in rice grains. This study will facilitate a better understanding of the functional roles of OsCOP1 involved in early embryogenesis and flavonoid biosynthesis in rice seeds.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00122-021-03844-9DOI Listing
May 2021

Identification of a Candidate Gene for the Novel Cytoplasmic Male Sterility Derived from Inter-Subspecific Crosses in Rice ( L.).

Genes (Basel) 2021 Apr 17;12(4). Epub 2021 Apr 17.

Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea.

Tetep-cytoplasmic male sterility (CMS) was developed through successive backcrosses between subspecies and in rice ( L.), which showed abnormal anther dehiscence phenotypes. Whole genome sequencing and de novo assembly of the mitochondrial genome identified the chimeric gene , which possesses a transmembrane domain and overlaps with two mitotype-specific sequences (MSSs) that are unique to the Tetep-CMS line. The encoded peptide of was toxic to and inhibited cell growth compared to the control under isopropyl-β-D-1-thiogalactopyranoside (IPTG) induction. The peptide of contains COX11-interaction domains, which are thought to be a main functional domain for in the wild abortive (WA-CMS) line of rice. A QTL for (restorer-of-fertility gene(s) originating from Tetep) was identified on chromosome 10. In this region, several restorer genes, and have previously been reported. Collectively, the interactions of , a candidate gene for Tetep-CMS, and , a restorer QTL, confer male sterility and fertility restoration, respectively, which enables a hybrid rice breeding system. Further studies on and isolation of will help to identify the underlying molecular mechanism of mitochondrial ORFs with the COX11-interaction domains.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/genes12040590DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8073397PMC
April 2021

Major QTLs, and , Additively Regulate Adaxial Leaf Rolling in Rice.

Front Plant Sci 2021 19;12:626523. Epub 2021 Feb 19.

Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, South Korea.

Moderate leaf rolling is considered optimal for the ideal plant type in rice ( L.), as it improves photosynthetic efficiency and, consequently, grain yield. Determining the genetic basis of leaf rolling the identification of quantitative trait loci (QTLs) could facilitate the development of high-yielding varieties. In this study, we identified three stable rice QTLs, , , and , which control adaxial leaf rolling in a recombinant inbred line (RIL) population derived from a cross between Tong 88-7 (T887) and Milyang 23 (M23), using high-density SNP markers. These QTLs controlled the rolling phenotype of both the flag leaf (FL) and secondary leaf (SL), and different allelic combinations of these QTLs led to a wide variation in the degree of leaf rolling. Additive gene actions of and on leaf rolling were observed in a backcross population. In addition, (markers: 01id4854718 and 01asp4916781) and (markers: 09id19650402 and 09id19740436) were successfully fine-mapped to approximately 60- and 90-kb intervals on chromosomes 1 and 9, respectively. Histological analysis of near-isogenic lines (NILs) revealed that influences leaf thickness across the small vein, and affects leaf thickness in the entire leaf and bulliform cell area, thus leading to adaxial leaf rolling. The results of this study advance our understanding of the genetic and molecular bases of adaxial leaf rolling, and this information can be used for the development of rice varieties with the ideal plant type.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fpls.2021.626523DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7940999PMC
February 2021

Arachis hypogaea resveratrol synthase 3 alters the expression pattern of UDP-glycosyltransferase genes in developing rice seeds.

PLoS One 2021 14;16(1):e0245446. Epub 2021 Jan 14.

Department of Plant Science, Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul, Republic of Korea.

The resveratrol-producing rice (Oryza sativa L.) inbred lines, Iksan 515 (I.515) and Iksan 526 (I.526), developed by the expression of the groundnut (Arachis hypogaea) resveratrol synthase 3 (AhRS3) gene in the japonica rice cultivar Dongjin, accumulated both resveratrol and its glucoside, piceid, in seeds. Here, we investigated the effect of the AhRS3 transgene on the expression of endogenous piceid biosynthesis genes (UGTs) in the developing seeds of the resveratrol-producing rice inbred lines. Ultra-performance liquid chromatography (UPLC) analysis revealed that I.526 accumulates significantly higher resveratrol and piceid in seeds than those in I.515 seeds and, in I.526 seeds, the biosynthesis of resveratrol and piceid reached peak levels at 41 days after heading (DAH) and 20 DAH, respectively. Furthermore, RNA-seq analysis showed that the expression patterns of UGT genes differed significantly between the 20 DAH seeds of I.526 and those of Dongjin. Quantitative real-time PCR (RT-qPCR) analyses confirmed the data from RNA-seq analysis in seeds of Dongjin, I.515 and I.526, respectively, at 9 DAH, and in seeds of Dongjin and I.526, respectively, at 20 DAH. A total of 245 UGTs, classified into 31 UGT families, showed differential expression between Dongjin and I.526 seeds at 20 DAH. Of these, 43 UGTs showed more than 2-fold higher expression in I.526 seeds than in Dongjin seeds. In addition, the expression of resveratrol biosynthesis genes (PAL, C4H and 4CL) was also differentially expressed between Dongjin and I.526 developing seeds. Collectively, these data suggest that AhRS3 altered the expression pattern of UGT genes, and PAL, C4H and 4CL in developing rice seeds.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0245446PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7808588PMC
January 2021

Genetic Basis of Tiller Dynamics of Rice Revealed by Genome-Wide Association Studies.

Plants (Basel) 2020 Dec 2;9(12). Epub 2020 Dec 2.

Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea.

A tiller number is the key determinant of rice plant architecture and panicle number and consequently controls grain yield. Thus, it is necessary to optimize the tiller number to achieve the maximum yield in rice. However, comprehensive analyses of the genetic basis of the tiller number, considering the development stage, tiller type, and related traits, are lacking. In this study, we sequence 219 Korean rice accessions and construct a high-quality single nucleotide polymorphism (SNP) dataset. We also evaluate the tiller number at different development stages and heading traits involved in phase transitions. By genome-wide association studies (GWASs), we detected 20 significant association signals for all traits. Five signals were detected in genomic regions near known candidate genes. Most of the candidate genes were involved in the phase transition from vegetative to reproductive growth. In particular, was simultaneously associated with the productive tiller ratio and heading date, indicating that the photoperiodic heading gene directly controls the productive tiller ratio. Multiple linear regression models of lead SNPs showed coefficients of determination () of 0.49, 0.22, and 0.41 for the tiller number at the maximum tillering stage, productive tiller number, and productive tiller ratio, respectively. Furthermore, the model was validated using independent japonica rice collections, implying that the lead SNPs included in the linear regression model were generally applicable to the tiller number prediction. We revealed the genetic basis of the tiller number in rice plants during growth, By GWASs, and formulated a prediction model by linear regression. Our results improve our understanding of tillering in rice plants and provide a basis for breeding high-yield rice varieties with the optimum the tiller number.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/plants9121695DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7761586PMC
December 2020

The DROOPING LEAF (DR) gene encoding GDSL esterase is involved in silica deposition in rice (Oryza sativa L.).

PLoS One 2020 10;15(9):e0238887. Epub 2020 Sep 10.

Department of Plant Science and Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul, South Korea.

Leaf morphology is one of the most important agronomic traits in rice breeding because of its contribution to crop yield. The drooping leaf (dr) mutant was developed from the Ilpum rice cultivar by ethyl methanesulfonate (EMS) mutagenesis. Compared with the wild type, dr plants exhibited drooping leaves accompanied by a small midrib, short panicle, and reduced plant height. The phenotype of the dr plant was caused by a mutation within a single recessive gene on chromosome 2, dr (LOC_Os02g15230), which encodes a GDSL esterase. Analysis of wild-type and dr sequences revealed that the dr allele carried a single nucleotide substitution, glycine to aspartic acid. RNAi targeted to LOC_Os02g15230 produced same phenotypes to the dr mutation, confirming LOC_Os02g15230 as the dr gene. Microscopic observations and plant nutrient analysis of SiO2 revealed that silica was less abundant in dr leaves than in wild-type leaves. This study suggests that the dr gene is involved in the regulation of silica deposition and that disruption of silica processes lead to drooping leaf phenotypes.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0238887PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7482962PMC
October 2020

Identification and characterization of the stunted sterile (ss) mutant in rice.

Genes Genomics 2020 08 6;42(8):869-882. Epub 2020 Jun 6.

Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea.

Background: Proper organ development is pivotal for normal rice growth and production. Many genes are involved in this process, and these genes provide a basis for rice breeding.

Objective: To identify a novel mutation causing developmental defects in rice.

Methods: The phenotype of a rice mutant, stunted sterile (ss), identified from the japonica rice cultivar Samkwang treated with N-methyl-N-nitrosourea, was characterized, including anatomical and pollen activity analyses. A genetic analysis and fine mapping were performed to identify a candidate locus, followed by a sequence analysis to determine the causal mutation for the phenotype.

Results: Compared with wild-type plants, the mutant exhibited a 34% reduction in height, 46% reduction in flag leaf width, and complete panicle sterility. Cell proliferation in the leaf and pollen viability were significantly inhibited in the mutant. The mutant phenotypes were controlled by a single recessive gene that was fine-mapped to an 84 kb region between two SNP markers on the short arm of chromosome 5. A candidate gene analysis determined that the mutant carries an 11 bp insertion in the coding region of LOC_Os05g03550, which encodes a protein containing two SANT domains, resulting in a premature termination codon before the conserved domain.

Conclusions: We identified a novel rice gene, Stunted sterile, involved in the regulation of various developmental processes. Our findings improve our understanding of the role of chromatin remodeling in organ development and have implications for breeding owing to the broad effects of the gene on plant growth.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s13258-020-00954-4DOI Listing
August 2020

Characterization of the Common -Originated Genomic Regions in the High-Yielding Varieties Developed from Inter-Subspecific Crosses in Temperate Rice ( L.).

Genes (Basel) 2020 05 18;11(5). Epub 2020 May 18.

Department of Plant Science and Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Korea.

The inter-subspecific crossing between and subspecies in rice have been utilized to improve the yield potential of temperate rice. In this study, a comparative study of the genomic regions in the eight high-yielding varieties (HYVs) was conducted with those of the four non-HYVs. The Next-Generation Sequencing (NGS) mapping on the Nipponbare reference genome identified a total of 14 common genomic regions of -originated alleles. Interestingly, the HYVs shared -originated genomic regions on nine chromosomes, although they were developed through different breeding programs. A panel of 94 varieties was classified into four varietal groups with 38 single nucleotide polymorphism (SNP) markers from 38 genes residing in the -originated genomic regions and 16 additional trait-specific SNPs. As expected, the -originated genomic regions were only present in the (JAP) and HYV groups, except for Chr4-1 and Chr4-2. The gene, located within Chr6-1, was present in the HYV and JAP variety groups, while the yield-related genes were conserved as alleles in HYVs. The -originated genomic regions and alleles shared by HYVs can be employed in molecular breeding programs to further develop the HYVs in temperate rice.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/genes11050562DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7290844PMC
May 2020

Evaluation of Whole-Genome Sequence, Genetic Diversity, and Agronomic Traits of Basmati Rice ( L.).

Front Genet 2020 21;11:86. Epub 2020 Feb 21.

Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Science, Seoul National University, Seoul, South Korea.

Basmati is considered a unique varietal group of rice ( L.) because of its aroma and superior grain quality. Previous genetic analyses of rice showed that most of the Basmati varieties are classified into the group. Despite various efforts, genomic relationship of Basmati rice with other varietal groups and genomic variation in Basmati rice are yet to be understood. In the present study, we resequenced the whole genome of three traditional Basmati varieties at a coverage of more than 25X using Illumina HiSeq2500 and mapped the obtained sequences to the reference genome sequences of Nipponbare ( rice), Kasalath ( rice), and Zhenshan 97 ( rice). Comparison of these sequences revealed common single nucleotide polymorphisms (SNPs) in the genic regions of three Basmati varieties. Analysis of these SNPs revealed that Basmati varieties showed fewer sequence variations compared with the group than with the and groups. Gene ontology (GO) enrichment analysis indicated that SNPs were present in genes with various biological, molecular, and cellular functions. Additionally, functional annotation of the Basmati mutated gene cluster shared by Nipponbare, Kasalath, and Zhenshan 97 was found to be associated with the metabolic process involved in the cellular aromatic compound, suggesting that aroma is an important specific genomic feature of Basmati varieties. Furthermore, 30 traditional Basmati varieties were classified into three different groups, (22 varieties), (four varieties), and (four varieties), based on genome-wide SNPs. All 22 Basmati varieties harbored the fragrant-inducing allele. We also performed comparative analysis of 13 key agronomic and grain quality traits of Basmati rice and other rice varieties. Three traits including length-to-width ratio of grain (L/W ratio), panicle length (PL), and amylose content (AC) showed significant ( < 0.05 and < 0.01) differences between the and / groups. Comparative analysis of genome structure, based on genome sequence variation and GO analysis, revealed that the Basmati genome was derived mostly from the and groups. Overall, whole-genome sequence data and genetic diversity information obtained in this study will serve as an important resource for molecular breeding and genetic analysis of Basmati varieties.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fgene.2020.00086DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7046879PMC
February 2020

Analysis of evolutionary relationships provides new clues to the origins of weedy rice.

Ecol Evol 2020 Jan 20;10(2):891-900. Epub 2019 Dec 20.

Institute of Crop Sciences Chinese Academy of Agricultural Sciences Beijing China.

Weedy rice (WR) () is considered to be a pest in modern rice production systems because it competes for resources, has poor yield characteristics, and subsequently has a negative effect on rice grain yield. The evolutionary relationships among WR, landrace rice (LR), improved rice (IR) cultivars, and wild rice are largely unknown. In this study, we conducted a population genetic analysis based on neutral markers and gene haplotypes in 524 rice accessions and a comparative transcriptomic analysis using 15 representative samples. The results showed that WR populations have the highest level of genetic diversity ( = 0.8386) and can be divided into two groups (-type and -type). The -type WR accessions from Heilongjiang province (HLJ), Jilin province (JL), Liaoning province (LN), and NX provinces clustered with the landraces grown in these same provinces. The -types from Jiangsu province (JS) also clustered with the -type landraces from JS province. Comparative transcriptome analysis of WR' IR and LR from HLJ, JL, and LN provinces showed that the WR still clustered with the LR, and that the IR lines comprise a single population. Thirty-two differentially expressed genes were shared by the IR and LR groups as well as between the IR and WR groups. Using Gene ontology (GO) analysis, we identified 19 shared GO terms in the IR and LR groups as well as between the IR and WR groups. Our results suggest that WR populations in China have diverse origins, and comparative transcriptome analysis of different types of rice from HLJ, JL, and LN provinces suggests that IR populations have become a end point in the evolution of WR, which provides a new perspective for the study of WR origins and lays a solid foundation for rice breeding.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/ece3.5948DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6988545PMC
January 2020

Genomic analyses reveal selection footprints in rice landraces grown under on-farm conservation conditions during a short-term period of domestication.

Evol Appl 2020 Feb 30;13(2):290-302. Epub 2019 Sep 30.

National Key Facility for Crop Gene Resources and Genetic Improvement Institute of Crop Sciences Chinese Academy of Agricultural Sciences Beijing China.

Traditional rice landraces grown under on-farm conservation conditions by indigenous farmers are extremely important for future crop improvement. However, little is known about how the natural selection and agriculture practices of indigenous farmers interact to shape and change the population genetics of rice landraces grown under on-farm conservation conditions during the domestication. In this study, we sequenced DNA from 108 core on-farm conserved rice landraces collected from the ethnic minority regions of Yunnan, China, including 56 accessions collected in 1980 and 52 accessions collected in 2007 and obtained 2,771,245 of credible SNPs. Our findings show that most genetic diversity was retained during the 27 years of domestication by on-farm conservation. However, SNPs with marked allele frequency differences were found in some genome regions, particularly enriched in genic regions, indicating changes in genic regions may have played a much more prominent role in the short-term domestication of 27 years. We identified 186 and 183 potential selective-sweep regions in the and genomes, respectively. We propose that on-farm conserved rice landraces during the short-term domestication had a highly polygenic basis with many loci responding to selection rather than a few loci with critical changes in response to selection. Moreover, loci affecting important agronomic traits and biotic or abiotic stress responses have been particularly targeted in selection. A genome-wide association study identified 90 significant signals for six traits, 13 of which were in regions of selective sweeps. Moreover, we observed a number of significant and interesting associations between loci and environmental factors, which implies adaptation to local environment. Our results provide insights into short-term evolutionary processes and shed light on the underlying mechanisms of on-farm conservation.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/eva.12866DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6976955PMC
February 2020

Pyrophosphate-fructose 6-phosphate 1-phosphotransferase (PFP1) regulates starch biosynthesis and seed development via heterotetramer formation in rice (Oryza sativa L.).

Plant Biotechnol J 2020 01 14;18(1):83-95. Epub 2019 Jun 14.

Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China.

Pyrophosphate-fructose 6-phosphate 1-phosphotransferase (PFP1) reversibly converts fructose 6-phosphate and pyrophosphate to fructose 1, 6-bisphosphate and orthophosphate during glycolysis, and has diverse functions in plants. However, mechanisms underlying the regulation of starch metabolism by PFP1 remain elusive. This study addressed the function of PFP1 in rice floury endosperm and defective grain filling. Compared with the wild type, pfp1-3 exhibited remarkably low grain weight and starch content, significantly increased protein and lipid content, and altered starch physicochemical properties and changes in embryo development. Map-based cloning revealed that pfp1-3 is a novel allele and encodes the regulatory β-subunit of PFP1 (PFP1β). Measurement of nicotinamide adenine dinucleotide (NAD+) showed that mutation of PFP1β markedly decreased its enzyme activity. PFP1β and three of four putative catalytic α-subunits of PFP1, PFP1α1, PFP1α2, and PFP1α4, interacted with each other to form a heterotetramer. Additionally, PFP1β, PFP1α1 and PFP1α2 also formed homodimers. Furthermore, transcriptome analysis revealed that mutation of PFP1β significantly altered expression of many essential enzymes in starch biosynthesis pathways. Concentrations of multiple lipid and glycolytic intermediates and trehalose metabolites were elevated in pfp1-3 endosperm, indicating that PFP1 modulates endosperm metabolism, potentially through reversible adjustments to metabolic fluxes. Taken together, these findings provide new insights into seed endosperm development and starch biosynthesis and will help in the breeding of rice cultivars with higher grain yield and quality.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/pbi.13173DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6920184PMC
January 2020

Identification and Characterization of LARGE EMBRYO, a New Gene Controlling Embryo Size in Rice (Oryza sativa L.).

Rice (N Y) 2019 Apr 11;12(1):22. Epub 2019 Apr 11.

Department of Plant Science and Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826, South Korea.

Background: Although embryo accounts for only 2-3% of the total weight of a rice grain, it is a good source of various nutrients for human health. Because enlarged embryo size causes increase of the amount of nutrients and bioactive compounds stored within rice grain, giant embryo mutants of rice (Oryza sativa L.) are excellent genetic resources for improving the nutritional value of rice grains.

Results: Three giant embryo mutants, including large embryo (le), giant embryo (ge) and super-giant embryo (ge), with variable embryo size were used in this study. We investigated whether genes controlling embryo size in these mutants (le, ge and ge) were allelic to each other. Although ge and ge was allelic to GIANT EMBRY (GE), le was not allelic to ge and ge in allelism test. The GE gene carried a unique nucleotide substitution in each of the two mutants (ge and ge), resulting in non-synonymous mutations in exon 2 of GE in both mutants. However, the GE gene of the le mutant did not carry any mutation, suggesting that the enlarged embryo phenotype of le was governed by another gene. Using map-based cloning, we mapped the LE gene to the short arm of chromosome 3. The le mutant showed mild enlargement in embryo size, which resulted from an increase in the size of scutellar parenchyma cells. The LE encodes a C3HC4-type RING finger protein and was expressed to relatively high levels in seeds at a late developmental stage. Knockdown of LE expression using RNA interference increased the embryo size of rice grains, confirming the role of LE in determining the embryo size.

Conclusion: Overall, we identified a new gene controlling embryo size in rice. Phenotypic and molecular characterization results suggest that the le mutant will serve as a valuable resource for developing new rice cultivars with large embryos and nutrient-dense grains.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12284-019-0277-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6458227PMC
April 2019

Novel allelic variant of Lpa1 gene associated with a significant reduction in seed phytic acid content in rice (Oryza sativa L.).

PLoS One 2019 14;14(3):e0209636. Epub 2019 Mar 14.

Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Science, Seoul National University, Seoul, Republic of Korea.

In plants, myo-inositol-1,2,3,4,5,6-hexakisphosphate (InsP6), also known as phytic acid (PA), is a major component of organic phosphorus (P), and accounts for up to 85% of the total P in seeds. In rice (Oryza sativa L.), PA mainly accumulates in rice bran, and chelates mineral cations, resulting in mineral deficiencies among brown rice consumers. Therefore, considerable efforts have been focused on the development of low PA (LPA) rice cultivars. In this study, we performed genetic and molecular analyses of OsLpa1, a major PA biosynthesis gene, in Sanggol, a low PA mutant variety developed via chemical mutagenesis of Ilpum rice cultivar. Genetic segregation and sequencing analyses revealed that a recessive allele, lpa1-3, at the OsLpa1 locus (Os02g0819400) was responsible for a significant reduction in seed PA content in Sanggol. The lpa1-3 gene harboured a point mutation (C623T) in the fourth exon of the predicted coding region, resulting in threonine (Thr) to isoleucine (Ile) amino acidsubstitution at position 208 (Thr208Ile). Three-dimensional analysis of Lpa1 protein structure indicated that myo-inositol 3-monophosphate [Ins(3)P1] could bind to the active site of Lpa1, with ATP as a cofactor for catalysis. Furthermore, the presence of Thr208 in the loop adjacent to the entry site of the binding pocket suggests that Thr208Ile substitution is involved in regulating enzyme activity via phosphorylation. Therefore, we propose that Thr208Ile substitution in lpa1-3 reduces Lpa1 enzyme activity in Sanggol, resulting in reduced PA biosynthesis.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0209636PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6417671PMC
November 2019

The Rice () Encodes a Plant Spastin That Inhibits ROS Accumulation in Leaf Development and Functions in Leaf Senescence.

Front Plant Sci 2018 7;9:1925. Epub 2019 Jan 7.

Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea.

Lesion mimic mutants (LMMs) are usually controlled by single recessive mutations that cause the formation of necrotic lesions without pathogen invasion. These genetic defects are useful to reveal the regulatory mechanisms of defense-related programmed cell death in plants. Molecular evidence has been suggested that some of LMMs are closely associated with the regulation of leaf senescence in rice (). Here, we characterized the mutation underlying (), which results in lesion formation and also affects leaf senescence in rice. Map-based cloning revealed that the γ ray-induced mutant has a single base substitution in the splicing site of the locus, resulting in a 13-bp deletion within the encoded microtubule-interacting-and-transport (MIT) spastin protein containing an AAA-type ATPase domain. The T-DNA insertion mutant exhibited spontaneous lesions similar to those of the mutant, confirming that is responsible for the LMM phenotype. In addition, both mutants exhibited delayed leaf yellowing during dark-induced or natural senescence. Western blot analysis of mutant leaves suggested possible roles for SPL4 in the degradation of photosynthetic proteins. Punctate signals of SPL4-fused fluorescent proteins were detected in the cytoplasm, similar to the cellular localization of animal spastin. Based on these findings, we propose that SPL4 is a plant spastin that is involved in multiple aspects of leaf development, including senescence.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fpls.2018.01925DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6330318PMC
January 2019

Identification of a Gene Involved in Early Senescence and Defense Response in Rice.

Front Plant Sci 2018 5;9:1274. Epub 2018 Sep 5.

Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Science, Seoul National University, Seoul, South Korea.

Lesion mimic mutants (LMMs) commonly exhibit spontaneous cell death similar to the hypersensitive defense response that occurs in plants in response to pathogen infection. Several lesion mimic mutants have been isolated and characterized, but their molecular mechanisms remain largely unknown. Here, a () mutant derived from cultivar Koshihikari is described. The phenotype differed from that of other LMMs in that lesion mimic spots were observed on the leaf sheath rather than on leaves. The mutant displayed early senescence, as shown, by color loss in the mesophyll cells, a decrease in chlorophyll content, and upregulation of chlorophyll degradation-related and senescence-associated genes. ROS content was also elevated, corresponding to increased expression of genes encoding ROS-generating enzymes. Pathogenesis-related genes were also activated and showed improved resistance to pathogen infection on the leaf sheath. Genetic analysis revealed that the mutant phenotype was controlled by a single recessive nuclear gene. Genetic mapping and sequence analysis showed that a single nucleotide substitution in the sixth exon of was responsible for the mutant phenotype and this was confirmed by T-DNA insertion line. Taken together, our results revealed that was associated with the formation of lesion mimic spots on the leaf sheath resulting early senescence and defense responses. Further examination of will facilitate a better understanding of the molecular mechanisms involved in ROS homeostasis and may also provide opportunities to improve pathogen resistance in rice.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fpls.2018.01274DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6134203PMC
September 2018

Chromatin interacting factor OsVIL2 increases biomass and rice grain yield.

Plant Biotechnol J 2019 01 26;17(1):178-187. Epub 2018 Jun 26.

Crop Biotech Institute, Kyung Hee University, Yongin, Korea.

Grain number is an important agronomic trait. We investigated the roles of chromatin interacting factor Oryza sativa VIN3-LIKE 2 (OsVIL2), which controls plant biomass and yield in rice. Mutations in OsVIL2 led to shorter plants and fewer grains whereas its overexpression (OX) enhanced biomass production and grain numbers when compared with the wild type. RNA-sequencing analyses revealed that 1958 genes were up-regulated and 2096 genes were down-regulated in the region of active division within the first internodes of OX plants. Chromatin immunoprecipitation analysis showed that, among the downregulated genes, OsVIL2 was directly associated with chromatins in the promoter region of CYTOKININ OXIDASE/DEHYDROGENASE2 (OsCKX2), a gene responsible for cytokinin degradation. Likewise, active cytokinin levels were increased in the OX plants. We conclude that OsVIL2 improves the production of biomass and grain by suppressing OsCKX2 chromatin.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/pbi.12956DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6330541PMC
January 2019

Genome-wide analyses of late pollen-preferred genes conserved in various rice cultivars and functional identification of a gene involved in the key processes of late pollen development.

Rice (N Y) 2018 Apr 23;11(1):28. Epub 2018 Apr 23.

Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 446-701, South Korea.

Background: Understanding late pollen development, including the maturation and pollination process, is a key component in maintaining crop yields. Transcriptome data obtained through microarray or RNA-seq technologies can provide useful insight into those developmental processes. Six series of microarray data from a public transcriptome database, the Gene Expression Omnibus of the National Center for Biotechnology Information, are related to anther and pollen development.

Results: We performed a systematic and functional study across the rice genome of genes that are preferentially expressed in the late stages of pollen development, including maturation and germination. By comparing the transcriptomes of sporophytes and male gametes over time, we identified 627 late pollen-preferred genes that are conserved among japonica and indica rice cultivars. Functional classification analysis with a MapMan tool kit revealed a significant association between cell wall organization/metabolism and mature pollen grains. Comparative analysis of rice and Arabidopsis demonstrated that genes involved in cell wall modifications and the metabolism of major carbohydrates are unique to rice. We used the GUS reporter system to monitor the expression of eight of those genes. In addition, we evaluated the significance of our candidate genes, using T-DNA insertional mutant population and the CRISPR/Cas9 system. Mutants from T-DNA insertion and CRISPR/Cas9 systems of a rice gene encoding glycerophosphoryl diester phosphodiesterase are defective in their male gamete transfer.

Conclusion: Through the global analyses of the late pollen-preferred genes from rice, we found several biological features of these genes. First, biological process related to cell wall organization and modification is over-represented in these genes to support rapid tube growth. Second, comparative analysis of late pollen preferred genes between rice and Arabidopsis provide a significant insight on the evolutional disparateness in cell wall biogenesis and storage reserves of pollen. In addition, these candidates might be useful targets for future examinations of late pollen development, and will be a valuable resource for accelerating the understanding of molecular mechanisms for pollen maturation and germination processes in rice.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12284-018-0219-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5913055PMC
April 2018

The Rice Rolled Fine Striped (RFS) CHD3/Mi-2 Chromatin Remodeling Factor Epigenetically Regulates Genes Involved in Oxidative Stress Responses During Leaf Development.

Front Plant Sci 2018 20;9:364. Epub 2018 Mar 20.

Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea.

In rice (), moderate leaf rolling increases photosynthetic competence and raises grain yield; therefore, this important agronomic trait has attracted much attention from plant biologists and breeders. However, the relevant molecular mechanism remains unclear. Here, we isolated and characterized (), a key gene affecting rice leaf rolling, chloroplast development, and reactive oxygen species (ROS) scavenging. The gamma-ray allele and the T-DNA insertion allele of failed to complement each other and their mutants had similar phenotypes, producing extremely incurved leaves due to defective development of vascular cells on the adaxial side. Map-based cloning showed that the mutant harbors a 9-bp deletion in a gene encoding a predicted CHD3/Mi-2 chromatin remodeling factor belonging to the SNF2-ATP-dependent chromatin remodeling family. was expressed in various tissues and accumulated mainly in the vascular cells throughout leaf development. Furthermore, deficiency resulted in a cell death phenotype that was caused by ROS accumulation in developing leaves. We found that expression of five ROS-scavenging genes [encoding catalase C, ascorbate peroxidase 8, a putative copper/zinc superoxide dismutase (SOD), a putative SOD, and peroxiredoxin IIE2] decreased in mutants. Western-blot and chromatin immunoprecipitation (ChIP) assays demonstrated that mutants have reduced H3K4me3 levels in ROS-related genes. Loss-of-function in also led to multiple developmental defects, affecting pollen development, grain filling, and root development. Our results suggest that RFS is required for many aspects of plant development and its function is closely associated with epigenetic regulation of genes that modulate ROS homeostasis.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fpls.2018.00364DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5870552PMC
March 2018

Identification of a novel SPLIT-HULL (SPH) gene associated with hull splitting in rice (Oryza sativa L.).

Theor Appl Genet 2018 Jul 21;131(7):1469-1480. Epub 2018 Mar 21.

Department of Plant Science and Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826, South Korea.

Key Message: The split-hull phenotype caused by reduced lemma width and low lignin content is under control of SPH encoding a type-2 13-lipoxygenase and contributes to high dehulling efficiency. Rice hulls consist of two bract-like structures, the lemma and palea. The hull is an important organ that helps to protect seeds from environmental stress, determines seed shape, and ensures grain filling. Achieving optimal hull size and morphology is beneficial for seed development. We characterized the split-hull (sph) mutant in rice, which exhibits hull splitting in the interlocking part between lemma and palea and/or the folded part of the lemma during the grain filling stage. Morphological and chemical analysis revealed that reduction in the width of the lemma and lignin content of the hull in the sph mutant might be the cause of hull splitting. Genetic analysis indicated that the mutant phenotype was controlled by a single recessive gene, sph (Os04g0447100), which encodes a type-2 13-lipoxygenase. SPH knockout and knockdown transgenic plants displayed the same split-hull phenotype as in the mutant. The sph mutant showed significantly higher linoleic and linolenic acid (substrates of lipoxygenase) contents in spikelets compared to the wild type. It is probably due to the genetic defect of SPH and subsequent decrease in lipoxygenase activity. In dehulling experiment, the sph mutant showed high dehulling efficiency even by a weak tearing force in a dehulling machine. Collectively, the results provide a basis for understanding of the functional role of lipoxygenase in structure and maintenance of hulls, and would facilitate breeding of easy-dehulling rice.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s00122-018-3091-9DOI Listing
July 2018

Association between sequence variants in panicle development genes and the number of spikelets per panicle in rice.

BMC Genet 2018 01 15;19(1). Epub 2018 Jan 15.

Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea.

Background: Balancing panicle-related traits such as panicle length and the numbers of primary and secondary branches per panicle, is key to improving the number of spikelets per panicle in rice. Identifying genetic information contributes to a broader understanding of the roles of gene and provides candidate alleles for use as DNA markers. Discovering relations between panicle-related traits and sequence variants allows opportunity for molecular application in rice breeding to improve the number of spikelets per panicle.

Results: In total, 142 polymorphic sites, which constructed 58 haplotypes, were detected in coding regions of ten panicle development gene and 35 sequence variants in six genes were significantly associated with panicle-related traits. Rice cultivars were clustered according to their sequence variant profiles. One of the four resultant clusters, which contained only indica and tong-il varieties, exhibited the largest average number of favorable alleles and highest average number of spikelets per panicle, suggesting that the favorable allele combination found in this cluster was beneficial in increasing the number of spikelets per panicle.

Conclusions: Favorable alleles identified in this study can be used to develop functional markers for rice breeding programs. Furthermore, stacking several favorable alleles has the potential to substantially improve the number of spikelets per panicle in rice.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12863-017-0591-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5769279PMC
January 2018

The rice zebra3 (z3) mutation disrupts citrate distribution and produces transverse dark-green/green variegation in mature leaves.

Rice (N Y) 2018 Jan 5;11(1). Epub 2018 Jan 5.

Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea.

Background: Rice zebra mutants are leaf variegation mutants that exhibit transverse sectors of green/yellow or green/white in developing or mature leaves. In most cases, leaf variegation is caused by defects in chloroplast biogenesis pathways, leading to an accumulation of reactive oxygen species in a transverse pattern in the leaves. Here, we examine a new type of leaf variegation mutant in rice, zebra3 (z3), which exhibits transverse dark-green/green sectors in mature leaves and lacks the typical yellow or white sectors.

Results: Map-based cloning revealed that the Z3 locus encodes a putative citrate transporter that belongs to the citrate-metal hydrogen symport (CitMHS) family. CitMHS family members have been extensively studied in bacteria and function as secondary transporters that can transport metal-citrate complexes, but whether CitMHS family transporters exist in eukaryotes remains unknown. To investigate whether Z3 acts as a citrate transporter in rice, we measured citrate levels in wild-type leaves and in the dark-green and green sectors of the leaves of z3 mutants. The results showed that citrates accumulated to high levels in the dark-green sectors of z3 mutant leaves, but not in the green sectors as compared with the wild-type leaves.

Conclusions: These results suggest that leaf variegation in the z3 mutant is caused by an unbalanced accumulation of citrate in a transverse pattern in the leaves. Taking these results together, we propose that Z3 plays an important role in citrate transport and distribution during leaf development and is a possible candidate for a CitMHS family member in plants.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12284-017-0196-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5756232PMC
January 2018

Identification and quantification of flavonoids in yellow grain mutant of rice (Oryza sativa L.).

Food Chem 2018 Feb 30;241:154-162. Epub 2017 Aug 30.

Department of Plant Science, Research Institute for Agriculture and Life Sciences and Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Republic of Korea. Electronic address:

Flavonoids are naturally occurring phenolic compounds with potential health-promoting activities. Although anthocyanins and phenolic acids in coloured rice have been investigated, few studies have focused on flavonoids. Herein, we analysed flavonoids in a yellow grain rice mutant using UHPLC-DAD-ESI-Q-TOF-MS, and identified 19 flavonoids by comparing retention times and accurate mass measurements. Among them, six flavonoids, isoorientin, isoorientin 2″-O-glucoside, vitexin 2″-O-glucoside, isovitexin, isoscoparin 2″-O-glucoside and isoscoparin, were isolated and fully identified from the yellow grain rice mutant, and the levels were significantly higher than wild-type, with isoorientin particularly abundant in mutant embryo. Significant differences in total phenolic compounds and antioxidant activity were observed in mutant rice by DPPH, FRAP and TEAC assays. The results suggest that the representative six flavonoids may play an important role in colouration and antioxidant activity of embryo and endosperm tissue. The findings provide insight into flavonoid biosynthesis and the possibility of improving functionality in rice.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.foodchem.2017.08.089DOI Listing
February 2018

New Genetic Loci Associated with Preharvest Sprouting and Its Evaluation Based on the Model Equation in Rice.

Front Plant Sci 2017 8;8:1393. Epub 2017 Aug 8.

Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, Seoul National UniversitySeoul, South Korea.

Preharvest sprouting (PHS) in rice panicles is an important quantitative trait that causes both yield losses and the deterioration of grain quality under unpredictable moisture conditions at the ripening stage. However, the molecular mechanism underlying PHS has not yet been elucidated. Here, we explored the genetic loci associated with PHS in rice and formulated a model regression equation for rapid screening for use in breeding programs. After re-sequencing 21 representative accessions for PHS and performing enrichment analysis, we found that approximately 20,000 SNPs revealed distinct allelic distributions between PHS resistant and susceptible accessions. Of these, 39 candidate SNP loci were selected, including previously reported QTLs. We analyzed the genotypes of 144 rice accessions to determine the association between PHS and the 39 candidate SNP loci, 10 of which were identified as significantly affecting PHS based on allele type. Based on the allele types of the SNP loci, we constructed a regression equation for evaluating PHS, accounting for an value of 0.401 in rice. We validated this equation using additional accessions, which exhibited a significant value of 0.430 between the predicted values and actual measurements. The newly detected SNP loci and the model equation could facilitate marker-assisted selection to predict PHS in rice germplasm and breeding lines.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fpls.2017.01393DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5550670PMC
August 2017

Sugary Endosperm is Modulated by Starch Branching Enzyme IIa in Rice (Oryza sativa L.).

Rice (N Y) 2017 Dec 20;10(1):33. Epub 2017 Jul 20.

Department of Plant Science and Research Institute for Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826, South Korea.

Background: Starch biosynthesis is one of the most important pathways that determine both grain quality and yield in rice (Oryza sativa L.). Sugary endosperm, sugary-1 (sug-1), is a mutant trait for starch biosynthesis. Rice plants carrying sug-1 produce grains that accumulate water-soluble carbohydrates instead of starch, even after maturity. Although this trait enhances the diversity of grain quality, sugary endosperm rice has hardly been commercialized due to the severely wrinkled grains and subsequent problems in milling. This study was conducted to identify the genes responsible for the sug-h phenotype through a map-based cloning technology.

Results: We induced a mild sugary mutant, sugary-h (sug-h) through the chemical mutagenesis on the Korean japonica cultivar Hwacheong. Grains of the sug-h mutant were translucent and amber-colored, and the endosperm appeared less wrinkled than sug-1, whereas the soluble sugar content was fairly high. These characteristics confer greater marketability to the sug-h mutant. Genetic analyses indicated that the sug-h mutant phenotype was controlled by a complementary interaction of two recessive genes, Isoamylase1 (OsISA1), which was reported previously, and Starch branching enzyme IIa (OsBEIIa), which was newly identified in this study. Complementation tests indicated that OsBEIIa regulated the properties of sugary endosperm.

Conclusions: Complementary interactions between the starch biosynthesis genes OsISA1 and OsBEIIa determine the mild sugary endosperm mutant, sugary-h, in rice. Our finding may facilitate the breeding of sugaryendosperm rice for commercial benefit.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12284-017-0172-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5519516PMC
December 2017

Genetic structure and isolation by altitude in rice landraces of Yunnan, China revealed by nucleotide and microsatellite marker polymorphisms.

PLoS One 2017 19;12(4):e0175731. Epub 2017 Apr 19.

Department of Plant Science, Research Institute for Agriculture and Life Science, Seoul National University, Seoul, Republic of Korea.

Rice landraces, a genetic reservoir for varietal improvement, are developed by farmers through artificial selection during the long-term domestication process. To efficiently conserve, manage, and use such germplasm resources, an understanding of the genetic structure and differentiation of local rice landraces is required. In this study, we analyzed 188 accessions of rice landraces collected from localities across an altitudinal gradient from 425 to 2, 274 m above sea level in Yunnan Province, China using ten target genes and 48 SSR markers. We detected clear differentiation of the rice landraces into indica and japonica groups and further separation of the accessions in each group into two subgroups according to altitude, including a lower altitude subgroup and higher altitude subgroup. The AMOVA results showed significant genetic differentiation among altitude zones at SSRs and most genes, except Os1977 and STS22. We further determined that differentiation among landrace populations followed a model of isolation by altitude, in which gene flow was higher among populations at similar altitude levels than across different altitude levels. Our findings demonstrated that both adaptation to altitude and altitude-dependent gene flow played key roles in the genetic differentiation of rice landraces in Yunnan, China.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0175731PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5396909PMC
April 2017

KNOX Protein OSH15 Induces Grain Shattering by Repressing Lignin Biosynthesis Genes.

Plant Physiol 2017 May 28;174(1):312-325. Epub 2017 Mar 28.

Crop Biotech Institute and Graduate School of Biotechnology, Kyung Hee University, Yongin 446-701, Korea (J.Y., L.-H.C., H.W.A., G.A.); and Department of Plant Science, Research Institute of Agriculture and Life Sciences, and Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-921, Korea (H.-J.K.)

Seed shattering is an agronomically important trait. Two major domestication factors are responsible for this: qSH1 and SH5. Whereas qSH1 functions in cell differentiation in the abscission zone (AZ), a major role of SH5 is the repression of lignin deposition. We have determined that a KNOX protein, OSH15, also controls seed shattering. Knockdown mutations of showed reduced seed-shattering phenotypes. Coimmunoprecipitation experiments revealed that OSH15 interacts with SH5 and qSH1, two proteins in the BELL homeobox family. In transgenic plants carrying the promoter- reporter construct, the reporter gene was preferentially expressed in the AZ during young spikelet development. The RNA in situ hybridization experiment also showed that messenger RNAs were abundant in the AZ during spikelet development. Analyses of D double mutants showed that could not increase the degree of seed shattering when was absent, indicating that SH5 functions together with OSH15. In addition to the seed-shattering phenotype, mutants displayed dwarfism and accumulated a higher amount of lignin in internodes due to increased expression of the genes involved in lignin biosynthesis. Knockout mutations of , which encodes an enzyme for the last step in the monolignol biosynthesis pathway, caused an easy seed-shattering phenotype by reducing lignin deposition in the AZ This indicated that the lignin level is an important determinant of seed shattering in rice (). Chromatin immunoprecipitation assays demonstrated that both OSH15 and SH5 interact directly with chromatin. We conclude that OSH15 and SH5 form a dimer that enhances seed shattering by directly inhibiting lignin biosynthesis genes.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1104/pp.17.00298DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5411160PMC
May 2017

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

Rice (N Y) 2016 Dec 7;9(1):54. Epub 2016 Oct 7.

Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, South Korea.

View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12284-016-0128-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5055518PMC
December 2016

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

Rice (N Y) 2015 Dec 30;8(1):33. Epub 2015 Oct 30.

Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, South Korea.

Background: 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.

Results: 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.

Conclusion: 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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12284-015-0066-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4627975PMC
December 2015

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

Sci Rep 2015 Oct 28;5:15655. Epub 2015 Oct 28.

Arizona Genomics Institute, School of Plant Sciences, The University of Arizona, Tucson, Arizona, 85721, USA.

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.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/srep15655DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4623524PMC
October 2015