The comparison of forecasting performance of historical volatility versus realized volatility

When forecasting stock market volatility with a standard volatility method (GARCH), it is common that the forecast evaluation criteria often suggests that the realized volatility (the sum of squared high-frequency returns) has a better prediction performance compared to the historical volatility (extracted from the close-to-close return). Since many extensions of the GARCH model have been developed, we follow the previous works to compare the historical volatility with many new GARCH family models (i.e., EGARCH, TGARCH, and APARCH model) and realized volatility with the ARMA model. Our analysis is based on the S&P 500 index from August 1st, 2018 to February 1st, 2019 (127 trading days), and the data has been separated into an estimation period (90 trading days) and an evaluation period (37 trading days). In the evaluation period, by taking realized volatility as the proxy of the true volatility, our empirical result shows that the realized volatility with ARMA model provides more accurate predictions, compared to the historical volatility with the GARCH family models

Genetic Maps of Diploid Orchardgrass (\u3cem\u3eDactylis glomerata\u3c/em\u3e L.)

Orchardgrass (Dactylis glomerata L.) is indigenous to Eurasia and northern Africa. It has been naturalized on nearly every continent and is one of the top four economically important perennial forage grasses grown worldwide (Stewart and Ellison 2010). It has been used widely as forage due to its quality, biomass production and good shade tolerance. Despite its various agricultural uses, little information is available for functional and comparative genetic analysis and concomitant genetic improvement of this species. To date, a number of linkage maps have been constructed for forage grasses such as perennial ryegrass (Lolium perenne L.) (Jones et al. 2002), tall fescue (Lolium arundinaceum (Schreb.) Darbysh.) (Saha et al. 2005), and Zoysiagrass (Zoysia japonica) (Cai et al. 2005). Until recently, there have been no reports of genetic linkage studies in orchardgrass. In the present study, a genetic linkage map of diploid orchardgrass based on two-way pseudo-testcross mapping strategy was constructed using SRAP and SSR markers. This is the first step towards genomic mapping for this species

Phylogenetic Relationships in the Festuca-Lolium Complex (Loliinae; Poaceae): New Insights from Chloroplast Sequences

The species within the Lolium/Festuca grass complex have dispersed and colonized large areas of temperate global grasslands both naturally and by human intervention. The species within this grass complex represent some of the most important grass species both for amenity and agricultural use worldwide. There has been renewed interest by grass breeders in producing hybrid combinations between these species and several countries now market Festulolium varieties as a combination of genes from both genera. The two genera have been differentiated by their inflorescence structure, but controversy has surrounded the taxonomic classification of the Lolium-Festuca complex species for several decades. In order to better understand the complexities within the Lolium/Festuca complex and their genetic background, the phylogeny of important examplers from the Lolium-Festuca complex were reconstructed. In total 40 taxa representing the Festuca and Lolium species with Vulpia myuros and Brachypodium distachyon as outgroups were sampled, using two noncoding intergenic spacers (trnQ-rps16, trnH-psbA) and one coding gene (rbcL). Maximum parsimony (MP), Bayesian inference (BI) analyses based on each partition and combined plastid DNA dataset, and median-jointing network analysis were employed. The outcomes strongly suggested that the subgen. Schedonorus has a close relationship to Lolium, and it is also proposed to move the sect. Leucopoa from subgen. Leucopoa to Subgen. Schedonorus and to separate sect. Breviaristatae from the subgen. Leucopoa. We found that F. californica could be a lineage of hybrid origin because of its intermediate placement between the broad-leaved and fine-leaved clade

Enriching Genomic Resources and Transcriptional Profile Analysis of Miscanthus sinensis

Miscanthus × giganteus is wildly cultivated as a potential biofuel feedstock around the world; however, the narrow genetic basis and sterile characteristics have become a limitation for its utilization. As a progenitor of M. × giganteus, M. sinensis is widely distributed around East Asia providing well abiotic stress tolerance. To enrich the M. sinensis genomic databases and resources, we sequenced and annotated the transcriptome of M. sinensis by using an Illumina HiSeq 2000 platform. Approximately 316 million high-quality trimmed reads were generated from 349 million raw reads, and a total of 114,747 unigenes were obtained after de novo assembly. Furthermore, 95,897 (83.57%) unigenes were annotated to at least one database including NR, Swiss-Prot, KEGG, COG, GO, and NT, supporting that the sequences obtained were annotated properly. Differentially expressed gene analysis indicates that drought stress 15 days could be a critical period for M. sinensis response to drought stress. The high-throughput transcriptome sequencing of M. sinensis under drought stress has greatly enriched the current genomic available resources. The comparison of DEGs under different periods of drought stress identified a wealth of candidate genes involved in drought tolerance regulatory networks, which will facilitate further genetic improvement and molecular studies of the M. sinensis

Genome-Wide Analysis of the PvHsp20 Family in Switchgrass: Motif, Genomic Organization, and Identification of Stress or Developmental-Related Hsp20s

Hsp20 proteins exist in all plant species and represent the most abundant small heat shock proteins (sHSPs) in plants. Hsp20s were known as chaperones maintaining cellular homeostasis during heat or other kinds of abiotic stresses. The objective of this study was to understand the phylogenetic relationship, genomic organization, diversification of motif modules, genome localization, expression profiles, and interaction networks of switchgrass (Panicum virgatum L.) Hsp20s (PvHsp20s). A total of 63 PvHsp20s were identified with their consensus as well as unique ACD motifs and gene structures analyzed. Most PvHsp20s (87%) were responsive to heat and other kinds of abiotic stresses. When under optimum growth condition, 38 of them displayed relative higher expression levels in inflorescence and seeds, suggesting their protective roles in the stress-sensitive reproductive organs. An in silico analysis of interaction network of PvHsp20 proteins further revealed potential interactive proteins, including stress-inducible ones in the network. Furthermore, PvHsp20 genes unevenly distributed in two sets of homeologous chromosomes, and only segmental duplication was found among the paralogous gene pairs, reflecting that the allotetraploidization of switchgrass allowed the accumulation of PvHsp20s that in turn facilitated its successful adaptation in hot and dry plateaus of North America. The present results provided an insight into PvHsp20s with an emphasis on the uniqueness of this gene family in switchgrass. Such information shall also be useful in functional studies of PvHsp20 genes and molecular breeding of switchgrass

Genetic diversity and association of EST-SSR and SCoT markers with rust traits in orchardgrass (Dactylis glomerata L.)

This article belongs to the Section Molecular Diversity.Orchardgrass (Dactylis glomerata L.), is a well-known perennial forage species; however, rust diseases have caused a noticeable reduction in the quality and production of orchardgrass. In this study, genetic diversity was assessed and the marker-trait associations for rust were examined using 18 EST-SSR and 21 SCoT markers in 75 orchardgrass accessions. A high level of genetic diversity was detected in orchardgrass with an average genetic diversity index of 0.369. For the EST-SSR and SCoT markers, 164 and 289 total bands were obtained, of which 148 (90.24%) and 272 (94.12%) were polymorphic, respectively. Results from an AMOVA analysis showed that more genetic variance existed within populations (87.57%) than among populations (12.43%). Using a parameter marker index, the efficiencies of the EST-SSR and SCoT markers were compared to show that SCoTs have higher marker efficiency (8.07) than EST-SSRs (4.82). The results of a UPGMA cluster analysis and a STRUCTURE analysis were both correlated with the geographic distribution of the orchardgrass accessions. Linkage disequilibrium analysis revealed an average r2 of 0.1627 across all band pairs, indicating a high extent of linkage disequilibrium in the material. An association analysis between the rust trait and 410 bands from the EST-SSR and SCoT markers using TASSEL software revealed 20 band panels were associated with the rust trait in both 2011 and 2012. The 20 bands obtained from association analysis could be used in breeding programs for lineage selection to prevent great losses of orchardgrass caused by rust, and provide valuable information for further association mapping using this collection of orchardgrass.This work was supported by the National Basic Research Program of China (973 Program) (2014CB138705) and the National Natural Science Foundation of China, NSFC (31101760).Peer reviewe

Influence of radiation on Hemarthria compressa's genetic variations

Using the material of Hemarthria compressa (L.F.) R.Br. cv. YA’AN, we carried out this research to study the influence of radiation on the genetic variation of plants. Genetic difference was analyzed with expressed sequence tag-simple sequence repeat (EST-SSR) molecular marker through the comparison of 60Co-γ radiation on H. compressa seed stems and original variety. By using 20 primer pairs, 176 polymerase chain reaction (PCR)-amplifications with clear and consistent bands were obtained. The results showed that 155 of 176 bands were polymorphic, which indicating an 88.07% polymorphism rate, and each pair of primers had 8.8 amplified bands on average; the amplitude of polymorphism information content was 0.4709–0.6952 with an average value 0.6081. The genetic similarity coefficient of H. compressa and its mutants ranged from 0.4318 to 0.8239 with an average of 0.6671. As a consequence, existence of genetic differences between the mutants and the basic material was proved.We gratefully acknowledge financial support from the Modern Agro-industry Technology Research System (CARS-34) and the Sichuan Province Breeding Research grant (2016NZ0098-11).Peer reviewe

Identification of the Valid Reference Genes for Quantitative RT-PCR in Annual Ryegrass (Lolium multiflorum) under Salt Stress

Annual ryegrass (Lolium multiflorum) is a cool-season annual grass cultivated worldwide for its high yield and quality. With the areas of saline soil increasing, investigation of the molecular mechanisms of annual ryegrass tolerance under salt stress has become a significant topic. qRT-PCR has been a predominant assay for determination of the gene expression, in which selecting a valid internal reference gene is a crucial step. The objective of present study was to evaluate and identify suitable reference genes for qRT-PCR in annual ryegrass under salt stress. The results calculated by RefFinder indicated that eEF1A(s) was the most stable reference gene in leaves, whereas EF1-a was the least stable; meanwhile, TBP-1 was the most optimal in roots and in all samples, and the eIF-5A shouldn’t be utilized for normalization of the gene expression. eEF1A(s) is more suitable than TBP-1 as reference gene in leaves when verified with P5CS1 and Cyt-Cu/Zn SOD genes. We should choose optimal reference genes in specific tissues instead of the most stable one selected from different conditions and tissues