Papers by Hironori NAGANO
Breeding Science
Effects of tall alleles SD1-in and SD1-ja to the dwarfing allele sd1-d originating from 'Dee-geo-... more Effects of tall alleles SD1-in and SD1-ja to the dwarfing allele sd1-d originating from 'Dee-geo-woo-gen' on yield and related traits on the genetic background of indica IR36 in rice
Agrosystems, Geosciences & Environment
Flowering behaviors (FBs) are important life‐history and agronomical traits, and their genetic ar... more Flowering behaviors (FBs) are important life‐history and agronomical traits, and their genetic architecture and evolution are of great interest to crop breeders. Flowering behavior simply indicates days to the first‐flowering time from germination (DFF) when considering only modern cultivars with small genetic variation, but flowering continuity as the result of asynchronous flowering can be relevant for the FB when an evolutionary variation is present. Evolutionary and genetic nature of asynchronous flowering has been unknown until now. Through daily observation, we recorded the first‐ and third‐flowering date of a plant, and then calculated DFF and days to the third‐flowering time from germination (DTF). Flowering asynchrony in a plant (FA) was defined as the equation, FA = DTF – DFF. Quantitative‐trait locus (QTL) analyses were performed on DFF, DTF, and FA in each of two‐density conditions in a paddy field by using 35 recombinant‐inbred lines derived from an interspecific cross ...
First flowering date of Miscanthus and sugarcane in 2014-2015 greenhouse experiment.
<i>Miscanthus</i> is a close relative of <i>Saccharum</i> and a potential... more <i>Miscanthus</i> is a close relative of <i>Saccharum</i> and a potentially valuable genetic resource for improving sugarcane.<i></i>Differences in flowering time within and between <i>Miscanthus</i> and <i>Saccharum</i> hinders intra- and interspecific hybridizations. A series of greenhouse experiments were conducted over three years to determine how to synchronize flowering time of <i>Saccharum</i> and <i>Miscanthus</i> genotypes. We found that day length was an important factor influencing when <i>Miscanthus</i> and <i>Saccharum</i> flowered<i>.</i> Sugarcane could be induced to flower in a central Illinois greenhouse using supplemental lighting to reduce the rate at which days shortened during the autumn and winter to 1 min d<sup>-1</sup>, which allowed us to synchronize the flowering of some sugarcane genotypes with <i>Miscanthus</i> genotypes primarily from low latitudes. In a complementary growth chamber experiment, we evaluated 33 <i>Miscanthus</i> genotypes, including 28 <i>M. sinensis, </i>2 <i>M. floridulus, </i>and 3<i> M. ×giganteus </i>collected from 20.9° S to 44.9° N for response to three day lengths (10 h, 12.5 h, and 15 h). High latitude-adapted <i>M. sinensis</i> flowered mainly under 15 h days, but unexpectedly, short days resulted in short, stocky plants that did not flower; in some cases, flag leaves developed under short days but heading did not occur. In contrast, for <i>M. sinensis</i> and <i>M. floridulus</i> from low latitudes, shorter day lengths typically resulted in earlier flowering, and for some low latitude genotypes, 15 h days resulted in no flowering. However, the highest ratio of reproductive shoots to total number of culms was typically observed for 12.5 h or 15 h days. Latitude of origin was significantly associated with culm length, and the shorter the days, the stronger the relationship. Nearly all entries achieved maximal culm length under the 15 h treatment, but the nearer to the equator an accession originated, the less of a difference in culm length between the short-da [...]
<b>Figure S1:</b> Scree plots showing the proportion of variation explained (percenta... more <b>Figure S1:</b> Scree plots showing the proportion of variation explained (percentage, %; Y-axis) by each principal component (PC; X-axis) in (A) <i>Miscanthus sinensis</i>, and (B) <i>Miscanthus sacchariflorus</i>. These PCs are from a principal component analysis conducted on 5,140 genome-wide markers.<b>Figure S2: </b>Phenotypic distribution of individuals in the study populations. Distributions of <i>Miscanthus sinensis</i> (blue), <i>Miscanthus sacchariflorus</i> (green), and the 09F2 population (orange) for traits Basal circumference (Bcirc; cm), Compressed circumference (Ccric; cm), Culm length (CmL; cm), Diameter of basal internode (DBI; mm), days to first heading (HD1; days), and Yield (Yld; g/plant). The median value of each population is represented in solid lines with colors corresponding to their respective populations. The trait values of the parental lines are represented in broken lines with blue corresponding to 'Cosmopolitan Revert' from <i>M. sinensis,</i> and green corresponding to 'Robustus' from <i>M. sacchariflorus</i>.<br><b>Figure S3:</b> Barplots showing the narrow-sense heritability (Y-axis) for basal circumference (Bcirc; cm), compressed circumference (Ccirc; cm), culm length (CmL; cm), days to first heading (HD1; days), and yield (Yld; g/plant) (X-axis), color coded based on the three populations considered in this study <i>Miscanthus sinensis </i>(Msi), <i>Miscanthus sacchariflorus </i>(Msa), and F<sub>2</sub> breeding population (09F2).<br><b>Figure S4: </b>Principal component (PC) analysis of <i>Miscanthus sacchariflorus</i> and <i>Miscanthus sinensis</i> diversity panels. Open circles are individuals distributed along PC1 (X-axis) and PC2 (Y-axis) in (A) <i>M. sacchariflorus</i> and (B) <i>M. sinensis</i>. These PCs are from a principal component analysis conducted on 5,140 genome-wide markers. The diamond shapes represent the parents 'Robustus' from <i>M. sacchariflorus</i> and "Cosmopolitan Revert" from <i>M. sinensis</i> that were used to develop the interspecific F<sub>2</su [...]
The study evaluates the impact of three Bayesian genotype calling methods (polyRAD, updog and EBG... more The study evaluates the impact of three Bayesian genotype calling methods (polyRAD, updog and EBG) on GWAS and genomic prediction in polyploids. We also compare the impact of continuous and discrete genotypes on the power of GWAS in a QTN simulation study. The study shows that the use of posterior mean genotypes, which are continuous genotypes that indicate the allelic dosage and level of uncertainty associated with it, is advantageous for detecting more significant association in GWAS. Continuous genotypes improve genotyping accuracy of low-depth markers, thus increasing power of GWAS.<br>
Restriction site-associated DNA sequencing (RAD-seq) data from 643 Miscanthus accessions from a d... more Restriction site-associated DNA sequencing (RAD-seq) data from 643 Miscanthus accessions from a diversity panel, including 613 Miscanthus sacchariflorus, three M. sinensis, and 27 M. xgiganteus. DNA was digested with PstI and MspI, and single-end Illumina sequencing was performed adjacent to the PstI site. Variant and genotype calling was performed with TASSEL-GBSv2, using the Miscanthus sinensis v7.1 reference genome from Phytozome 12 (https://phytozome.jgi.doe.gov). Additional ploidy-aware genotype calling was performed by polyRAD v1.1.
Genes, 2021
The optimal flowering time for bioenergy crop Miscanthus is essential for environmental adaptabil... more The optimal flowering time for bioenergy crop Miscanthus is essential for environmental adaptability and biomass accumulation. However, little is known about how genes controlling flowering in other grasses contribute to flowering regulation in Miscanthus. Here, we report on the sequence characterization and gene expression of Miscanthus sinensis Ghd8, a transcription factor encoding a HAP3/NF-YB DNA-binding domain, which has been identified as a major quantitative trait locus in rice, with pleiotropic effects on grain yield, heading date and plant height. In M. sinensis, we identified two homoeologous loci, MsiGhd8A located on chromosome 13 and MsiGhd8B on chromosome 7, with one on each of this paleo-allotetraploid species’ subgenomes. A total of 46 alleles and 28 predicted protein sequence types were identified in 12 wild-collected accessions. Several variants of MsiGhd8 showed a geographic and latitudinal distribution. Quantitative real-time PCR revealed that MsiGhd8 expressed un...
This repository contains datasets and R scripts that were used in a study of the population struc... more This repository contains datasets and R scripts that were used in a study of the population structure of Miscanthus sacchariflorus in its native range across East Asia. Notably, genotypes of 764 individuals at 34,605 SNPs, called from reduced-representation DNA sequencing using a non-reference bioinformatics pipeline, are provided. Two similar SNP datasets, used for identifying clonal duplicates and for determining the ancestry of ornamental and hybrid Miscanthus plants identified in previous studies respectively, are also provided. There is also a spreadsheet listing the provenance and ploidy of all individuals along with their plastid (chloroplast) haplotypes. Software output for Structure, Treemix, and DIYABC is also included. See README.txt for more information about individual files. Results of this study are described in a manuscript in revision in Annals of Botany by the same authors, "Population structure of Miscanthus sacchariflorus reveals two major polyploidization events, tetraploid-mediated unidirectional introgression from diploid Miscanthus sinensis, and diversity centered around the Yellow Sea."
Miscanthus is a close relative of Saccharum and a potentially valuable genetic resource for impro... more Miscanthus is a close relative of Saccharum and a potentially valuable genetic resource for improving sugarcane. Differences in flowering time within and between Miscanthus and Saccharum hinders intra- and interspecific hybridizations. A series of greenhouse experiments were conducted over three years to determine how to synchronize flowering time of Saccharum and Miscanthus genotypes. We found that day length was an important factor influencing when Miscanthus and Saccharum flowered. Sugarcane could be induced to flower in a central Illinois greenhouse using supplemental lighting to reduce the rate at which days shortened during the autumn and winter to 1 min d-1, which allowed us to synchronize the flowering of some sugarcane genotypes with Miscanthus genotypes primarily from low latitudes. In a complementary growth chamber experiment, we evaluated 33 Miscanthus genotypes, including 28 M. sinensis, 2 M. floridulus, and 3 M. ×giganteus collected from 20.9° S to 44.9° N for response...
Crop Science, 2018
ABSTRACTNicotinamide adenine dinucleotide phosphate (NADPH) oxidases catalyze the production of s... more ABSTRACTNicotinamide adenine dinucleotide phosphate (NADPH) oxidases catalyze the production of superoxide, a type of reactive oxygen species (ROS). In plants, the NADPH oxidase homologs have been identified as respiratory burst oxidase homologs (Rboh). They are involved in ROS production in response to drought stress. Three entries of tall fescue (Festuca arundinacea Schreb.) were used for analyses in the present study: tolerant (‘Isfahan’) and sensitive (‘Quchan’) accessions to drought during the germination stage, selected from 14 wild populations in Iran, as well as ‘Barvado’ as a control. Partial sequence of the Festuca respiratory burst oxidase‐D (FrbohD) gene was isolated from Barvado. We compared expression levels of the FrbohD gene as well as hydrogen peroxide (H2O2), catalase activity and some biochemical responses among the three entries. Gene expression was evaluated for leaf and shoot samples subjected to 3, 6, and 9 d without water. The transcript level of FrbohD, H2O2...
GCB Bioenergy, 2019
To breed improved biomass cultivars of Miscanthus ×giganteus, it will be necessary to select the ... more To breed improved biomass cultivars of Miscanthus ×giganteus, it will be necessary to select the highest‐yielding and best‐adapted genotypes of its parental species, Miscanthus sinensis and Miscanthus sacchariflorus. We phenotyped a diverse clonally propagated panel of 569 M. sinensis and nine natural diploid M. ×giganteus at one subtropical (Zhuji, China) and five temperate locations (Sapporo, Japan; Leamington, Ontario, Canada; Fort Collins, CO; Urbana, IL; and Chuncheon, Korea) for dry biomass yield and 14 yield‐component traits, in trials grown for 3 years. Notably, dry biomass yield of four Miscanthus accessions exceeded 80 Mg/ha in Zhuji, China, approaching the highest observed for any land plant. Additionally, six M. sinensis in Sapporo, Japan and one in Leamington, Canada also yielded more than the triploid M. ×giganteus ‘1993‐1780’ control, with values exceeding 20 Mg/ha. Diploid M. ×giganteus was the best‐yielding group at the northern sites. Genotype‐by‐environment intera...
Annals of botany, Jan 20, 2018
Miscanthus, a C4 perennial grass native to East Asia, is a promising biomass crop. Miscanthus sac... more Miscanthus, a C4 perennial grass native to East Asia, is a promising biomass crop. Miscanthus sacchariflorus has a broad geographic range, is used to produce paper in China and is one of the parents (along with Miscanthus sinensis) of the important biomass species Miscanthus × giganteus. The largest study of M. sacchariflorus population genetics to date is reported here. Collections included 764 individuals across East Asia. Samples were genotyped with 34 605 single nucleotide polymorphisms (SNPs) derived from restriction site-associated DNA sequencing (RAD-seq) and ten plastid microsatellites, and were subjected to ploidy analysis by flow cytometry. Six major genetic groups within M. sacchariflorus were identified using SNP data: three diploid groups, comprising Yangtze (M. sacchariflorus ssp. lutarioriparius), N China and Korea/NE China/Russia; and three tetraploid groups, comprising N China/Korea/Russia, S Japan and N Japan. Miscanthus sacchariflorus ssp. lutarioriparius was deri...
Journal of experimental botany, Jan 18, 2015
The genus Miscanthus is a perennial C4 grass native to eastern Asia and is a promising candidate ... more The genus Miscanthus is a perennial C4 grass native to eastern Asia and is a promising candidate bioenergy crop for cool temperate areas. Flowering time is a crucial factor governing regional and seasonal adaptation; in addition, it is also a key target trait for extending the vegetative phase to improve biomass potential. Homologues of CONSTANS (CO)/Heading date 1(Hd1) were cloned from Miscanthus sinensis and named MsiHd1. Sequences of MsiHd1 homologues were compared among 24 wild M. sinensis accessions from Japan, 14 from China, and three from South Korea. Two to five MsiHd1 alleles in each accession were identified, suggesting that MsiHd1 consists of at least three loci in the Miscanthus genome. Verifying the open reading frame in MsiHd1, they were classified as putative functional alleles without mutations or non-functional alleles caused by indels. The Neighbor-Joining tree indicated that one of the multiple MsiHd1 loci is a pseudogene locus without any functional alleles. The ...
Molecular Breeding of Forage and Turf, 2015
Cost-effective production of bioethanol and chemicals from lignocellulose, has attracted signific... more Cost-effective production of bioethanol and chemicals from lignocellulose, has attracted significant interest around the world. Rhizomatous and perennial warm-season C4 grasses such as Miscanthus spp. are potential dedicated feedstock crops, which are efficient at fixing CO2 in temperate regions and require less fertilizer for cultivation. Among Miscanthus spp., Miscanthus sinensis is the most broadly distributed in Asia. The degree of population differentiation using molecular markers, such as restriction site-associated DNA sequencing single nucleotide polymorphism (SNP) markers, Golden Gate SNPs and ten plastid microsatellite markers, has been evaluated for M. sinensis over its native range. Wide range of genetic variability in Asian Miscanthus germplasm resources was observed, and it would be valuable for the breeding programs. Targets for the improvement of grasses as feedstocks for bio-refineries are modifying biomass cell wall composition to reduce lignin concentrations to improve saccharification, regulation of flowering time for extending the vegetative phase to increase biomass potential and abiotic stresses such as cold tolerance. In this chapter, we outlined our recent research activities on molecular breeding such as candidate gene approach in Miscanthus spp.
BMC genomics, Jan 18, 2004
Plant genomes contain various kinds of repetitive sequences such as transposable elements, micros... more Plant genomes contain various kinds of repetitive sequences such as transposable elements, microsatellites, tandem repeats and virus-like sequences. Most of them, with the exception of virus-like sequences, do not allow us to trace their origins nor to follow the process of their integration into the host genome. Recent discoveries of virus-like sequences in plant genomes led us to set the objective of elucidating the origin of the repetitive sequences. Endogenous rice tungro bacilliform virus (RTBV)-like sequences (ERTBVs) have been found throughout the rice genome. Here, we reconstructed putative virus structures from RTBV-like sequences in the rice genome and characterized to understand evolutionary implication, integration manner and involvements of endogenous virus segments in the corresponding disease response. We have collected ERTBVs from the rice genomes. They contain rearranged structures and no intact ORFs. The identified ERTBV segments were shown to be phylogenetically d...
Molecular Ecology, 2009
The complex structure of a single Mendelian factor widespread in the Asian cultivated rice (Oryza... more The complex structure of a single Mendelian factor widespread in the Asian cultivated rice (Oryza sativa) and its wild progenitor (Oryza rufipogon) that caused diverse phenotypes in the timing of flowering under natural field conditions was investigated in near isogenic lines. These near isogenic lines showed differences in flowering time despite all eight accessions collected from tropical regions possessing a recessive gene allelic to the se-pat gene. Fine mapping in two of these near-isogenic lines revealed that cultivated (Patpaku) and wild (W593) accessions had three and two linked quantitative trait loci (QTL) in the candidate regions, respectively, showing that Patpaku and W593 possessed linked QTLs with different effects in addition to the commonly-observed recessive gene (se-pat). Molecular dissection suggested that the tandemly duplicated FT-like genes (Hd3a and RFT1) could be the candidate genes for these QTLs. Interestingly, the linked QTLs differed in their epistases, degree of dominance, and genotype × environment interactions. The nucleotide sequences showed that RFT1 has diverged more rapidly than Hd3a during rice evolution, suggesting phenotypic diversification of the two genes. Phylogenetic analysis implied that the se-pat + alleles might have emerged in different lineages within O. sativa. The present results strongly suggest that nucleotide divergence and shuffling of the linked QTLs by recombination might have created novel Mendelian factors that probably contribute to responding to local environments.
Uploads
Papers by Hironori NAGANO