Won Byoung Chae

A framework genetic map for Miscanthus sinensis from RNAseq-based markers shows recent tetraploidy

BackgroundMiscanthus (subtribe Saccharinae, tribe Andropogoneae, family Poaceae) is a genus of temperate perennial C4 grasses whose high biomass production makes it, along with its close relatives sugarcane and sorghum, attractive as a biofuel feedstock. The base chromosome number of Miscanthus (x = 19) is different from that of other Saccharinae and approximately twice that of the related Sorghum bicolor (x = 10), suggesting large-scale duplications may have occurred in recent ancestors of Miscanthus. Owing to the complexity of the Miscanthus genome and the complications of self-incompatibility, a complete genetic map with a high density of markers has not yet been developed.ResultsWe used deep transcriptome sequencing (RNAseq) from two M. sinensis accessions to define 1536 single nucleotide variants (SNVs) for a GoldenGate™ genotyping array, and found that simple sequence repeat (SSR) markers defined in sugarcane are often informative in M. sinensis. A total of 658 SNP and 210 SSR markers were validated via segregation in a full sibling F1 mapping population. Using 221 progeny from this mapping population, we constructed a genetic map for M. sinensis that resolves into 19 linkage groups, the haploid chromosome number expected from cytological evidence. Comparative genomic analysis documents a genome-wide duplication in Miscanthus relative to Sorghum bicolor, with subsequent insertional fusion of a pair of chromosomes. The utility of the map is confirmed by the identification of two paralogous C4-pyruvate, phosphate dikinase (C4-PPDK) loci in Miscanthus, at positions syntenic to the single orthologous gene in Sorghum.ConclusionsThe genus Miscanthus experienced an ancestral tetraploidy and chromosome fusion prior to its diversification, but after its divergence from the closely related sugarcane clade. The recent timing of this tetraploidy complicates discovery and mapping of genetic markers for Miscanthus species, since alleles and fixed differences between paralogs are comparable. These difficulties can be overcome by careful analysis of segregation patterns in a mapping population and genotyping of doubled haploids. The genetic map for Miscanthus will be useful in biological discovery and breeding efforts to improve this emerging biofuel crop, and also provide a valuable resource for understanding genomic responses to tetraploidy and chromosome fusion.

Plant morphology, genome size, and SSR markers differentiate five distinct taxonomic groups among accessions in the genus Miscanthus

Information on genome size, ploidy level, and genomic polymorphisms among accessions of the genus Miscanthus can assist in taxonomic studies, help understand the evolution of the genus, and provide valuable information to biomass crop improvement programs. Taxonomic investigation combining variation in plant morphology, genome size, chromosome numbers, and simple sequence repeat (SSR) marker polymorphisms were applied to characterize 101 Miscanthus accessions. A total of 258 amplicons generated from 17 informative SSR primer pairs was subjected to cluster and principal coordinate analysis and used to characterize genetic variation and relationships among 31 Miscanthus accessions, including four interspecific Miscanthus hybrids created from controlled pollinations, and four Saccharum, six Erianthus, and one Sorghum bicolor accessions. Miscanthus accessions were distinct from accessions in the genera Erianthus and Saccharum. Miscanthus accessions fell into five taxonomic groups, including the existing taxonomic section Miscanthus, diploid and tetraploid Miscanthus sacchariflorus, and a fourth (M. × giganteus) and fifth group (Miscanthus ‘purpurascens’); the last two being intermediate forms. In contrast to previous work, our findings suggest diploid and tetraploid M. sacchariflorus are taxonomically different, the latter more closely related to M. sacchariflorus var lutarioriparius. We also suggest that Miscanthus ‘purpurascens’ accessions are interspecific hybrids between Miscanthus sinensis and diploid M. sacchariflorus based on DNA content and SSR polymorphisms. The evolution of Miscanthus and related genera is discussed based on combined analysis and geographical origin.

Synthetic polyploid production of Miscanthus sacchariflorus, Miscanthus sinensis, and Miscanthus x giganteus

Plants from the genus Miscanthus are potential renewable sources of lignocellulosic biomass for energy production. A potential strategy for Miscanthus crop improvement involves interspecific manipulation of ploidy levels to generate superior germplasm and to circumvent reproductive barriers for the introduction of new genetic variation into core germplasm. Synthetic autotetraploid lines of Miscanthus sacchariflorus and Miscanthus sinensis, and autoallohexaploid Miscanthus x giganteus were produced in tissue culture from oryzalin treatments to seed‐ and immature inflorescence‐derived callus lines. This is the first report of the genome doubling of diploid M. sacchariflorus. Genome doubling of diploid M. sinensis, M. sacchariflorus, and triploid M. x giganteus to generate tetraploid and hexaploid lines was confirmed by stomata size, nuclear DNA content, and chromosome counts. A putative pentaploid line was also identified among the M. x giganteus synthetic polyploid lines by nuclear DNA content and chromosome counts. Comparisons of phenotypic performance of synthetic polyploid lines with their diploid and triploid progenitors in the greenhouse found species‐specific differences in plant tiller number, height, and flowering time among the doubled lines. Stem diameter tended to increase after polyploidization but there were no significant improvements in biomass traits. Under field conditions, M. x giganteus synthetic hexaploid lines showed greater phenotypic variation, in terms of plant height, stem diameter, and tiller number, than their progenitor lines. Production of synthetic autopolyploid lines displaying significant phenotypic variation suggests that ploidy manipulation can introduce useful genetic diversity in the limited Miscanthus germplasm currently available in the United States. The role of polyploidization in the evolution and breeding of the genus Miscanthus is discussed.

Mapping the genome of Miscanthus sinensis for QTL associated with biomass productivity

In light of rising energy costs, lignocellulosic ethanol has been identified as a renewable alternative to petroleum‐based transportation fuels. In an attempt to reach government mandated ethanol production levels, potential plant biofeedstock candidates have been investigated, and cold‐tolerant, perennial accessions within the C4 grass genus Miscanthus have been identified as leading contenders in the Midwestern US. To facilitate the development of improved cultivars through marker‐assisted breeding, a quantitative trait locus (QTL) study was conducted on a full‐sib, F1 mapping population segregating for flowering time, height, leaf width, and yield using a genetic map consisting of 846 segregating SNP and SSR markers. This was a 3 year study investigating the genetic architecture underlying traits important to biomass production in a population of 221 progeny from a cross between M. sinensis ‘Grosse Fountaine’ and M. sinensis ‘Undine’ established in the spring of 2010; 72 QTLs with LOD scores above the genome‐wide, permuted threshold equivalent to a P‐value of 0.05 were identified across 13 traits. Of the 36 QTLs identified in 2011, 22 were detected again the following year. Both the use of spring emergence and vigor rating as a covariate to account for variation related to differences in establishment increased the power to detect QTLs in the 2 year establishment period. Finally, a dry period in the middle of the 2012 growing season suggested that yield declines were due to a decrease in tiller diameter.

Identification of three FLOWERING LOCUS C genes responsible for vernalization response in radish (Raphanus sativus L.)

Raphanus sativus L. is grown worldwide and used as fresh vegetables. In the Brassicaceae family, the FLOWERING LOCUS C (FLC) gene is a key regulator of flowering time and explains a large part of natural flowering time variation and the vernalization response. Here we report three FLC orthologous genes RsFLC1, RsFLC2, and RsFLC3 in R. sativus identified from the de novo assembled transcriptome. The sequences of three RsFLC genes have a high similarity to Arabidopsis FLC. Overexpression of each RsFLC gene in Arabidopsis induced late flowering, suggesting that every RsFLC gene functions as a floral repressor. All RsFLC genes were highly expressed in non-vernalized plants, whereas their expression levels significantly decreased by the vernalization treatment. Furthermore, the rate of decrease in their expression was proportional to the length of cold exposure. A significant level of sequence variation exists among RsFLC alleles derived from a variety of Raphanus cultivars, suggesting that RsFLC genes have diverged considerably but still retain essential functions.

Root Glucosinolate Profiles for Screening of Radish (Raphanus sativus L.) Genetic Resources

Radish (Raphanus sativus L.), a root vegetable, is rich in glucosinolates (GLs), which are beneficial secondary metabolites for human health. To investigate the genetic variations in GL content in radish roots and the relationship with other root phenotypes, we analyzed 71 accessions from 23 different countries for GLs using HPLC. The most abundant GL in radish roots was glucoraphasatin, a GL with four-carbon aliphatic side chain. The content of glucoraphasatin represented at least 84.5% of the total GL content. Indolyl GL represented only 3.1% of the total GL at its maximum. The principal component analysis of GL profiles with various root phenotypes showed that four different genotypes exist in the 71 accessions. Although no strong correlation with GL content and root phenotype was observed, the varied GL content levels demonstrate the genetic diversity of GL content, and the amount that GLs could be potentially improved by breeding in radishes.

Influence of air temperature on yield and phytochemical content of red chicory and garland chrysanthemum grown in plant factory

This study was conducted to improve the yield and quality of red chicory (Cichorium intybus L.) and garland chrysanthemum (Chrysanthemum coronarium L.) grown in a plant factory where fluorescent lamps were used as an artificial light source. Seeds of a chicory ‘Juck’ and garland chrysanthemum ‘Joongyupssuckgot’ were sown in a peat-lite germination mix. Twenty-day old seedlings with roots being washed off were anchored on a styrofoam board and were grown in hydroponics for 30 days. Plants were exposed to one of the three different air temperature regimes (20, 25, and 30°C during the day combined with 18°C during the night) which were being monitored with a sensor at 30 cm above the plant canopy. In all treatments, light intensity was maintained at 200 ± 20 μmol·m−2·s−1, day length was 12 hours, and relative humidity was 50–80%. Electrical conductivity (EC) and pH of the nutrient solution were 2.0 ± 0.2 dS·m−1 and 6.5–7.0, respectively, in all treatments. Increase in fresh weight was observed in chicory, but not in garland chrysanthemum, in both 25 and 30°C as compared to 20°C. Photosynthetic capacity and ascorbic acid content of chicory leaves were higher at 25°C than in other temperatures. In garland chrysanthemum, photosynthetic capacity was the greatest in both 20 and 25°C, while ascorbic acid content was the greatest in 25°C. Also plants grown at 25°C had the greatest contents of total phenol and flavonoid in both chicory and garland chrysanthemum. Hence, the optimum temperature appears to be 25°C for growing both chicory and garland chrysanthemum in the plant factory with fluorescent light as the sole souse of light.

‘Redvita’: A Yellow-fleshed Kiwifruit with Red ColorAround the Core

Namhae Branch, National Institute of Horticultural and Herbal Science, Rural Development Administration, Namhae 55365, Korea Protected Horticulture Research Institute, National Institute of Horticultural and Herbal Science, Rural Development Administration, Haman 52054, Korea Apple Research Institute, National Institute of Horticultural and Herbal Science, Rural Development Administration, Gunwi 39000, Korea Department of Vegetable, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju 55365, Korea

Reproductive traits and molecular evidence related to the global distribution of cultivated radish (Raphanus sativus L.)

Reproductive characteristics frequently vary geographically, and reproductive success is critical for survival and local adaption in cultivated species. To document such variation in radish (Raphanus sativus L.), we examined reproductive traits and neutral genetic markers in 64 wild and landrace accessions varying in geographic origin. Flowering time tended to increase with latitude of origin, with southeastern Asian accessions (the lowest latitude) flowering earliest. Accessions from eastern Asia, which encompasses the greatest latitudinal range (18° and 54°N) of the regions we examined, exhibited the greatest variation in flowering time, clustering into a single group according to neutral genetic markers. Cluster analysis of genetic data divided the radish accessions into European and Asian groups. These groups were further subdivided into six, and two subgroups of Europe could be distinguished by root skin color. Although the accessions tended to cluster by geographic origin, those from central, southern, and western Asia clustered with both European and Asian accessions. Our results suggest that artificial selection of flowering time as well as root skin color has played important roles in local adaptation and increases in the genetic diversity of radish landraces in different geographic regions.

Optimum Double-Row Spacing in the Autumn Cultivation of Radish (Raphanus sativus L.)

Optimum Double-Row Spacing in the Autumn Cultivation of Radish (Raphanus sativus L.) Eun Seon Kang, Sun Mi Ha, Seoung Ryong Cheong, Myeong Whoon Seo, Su hyoung Park, Yong-Bum Kwack, Keun Jin Choi and Won Byoung Chae (Department of Vegetable, National Institute of Horticultural & Herbal Science, Rural Development Administration, Wanju 55365, Korea, Namhae Sub-Station, National Institute of Horticultural & Herbal Science, Rural Development Administration, Namhae 52430, Korea)