Whole-genome sequence of synthetically derived Brassica napus inbred cultivar Da-Ae.

Brassica napus, a globally important oilseed crop, is an allotetraploid hybrid species with two subgenomes originating from Brassica rapa and Brassica oleracea. The presence of two highly similar subgenomes has made the assembly of a complete draft genome challenging and has also resulted in natural homoeologous exchanges between the genomes, resulting in variations in gene copy number, which further complicates assigning sequences to correct chromosomes. Despite these challenges, high-quality draft genomes of this species have been released. Using third generation sequencing and assembly technologies, we generated a new genome assembly for the synthetic B. napus cultivar Da-Ae. Through the use of long reads, linked-reads, and Hi-C proximity data, we assembled a new draft genome that provides a high-quality reference genome of a synthetic B. napus. In addition, we identified potential hotspots of homoeologous exchange between subgenomes within Da-Ae, based on their presence in other independently derived lines. The occurrence of these hotspots may provide insight into the genetic rearrangements required for B. napus to be viable following the hybridization of B. rapa and B. oleracea.

Integrated QTL and eQTL Mapping Provides Insights and Candidate Genes for Fatty Acid Composition, Flowering Time, and Growth Traits in a F2 Population of a Novel Synthetic Allopolyploid Brassica napus.

Brassica napus (B. napus, AACC), is an economically important allotetraploid crop species that resulted from hybridization between two diploid species, Brassica rapa (AA) and Brassica olereacea (CC). We have created one new synthetic B. napus genotype Da-Ae (AACC) and one introgression line Da-Ol-1 (AACC), which were used to generate an F2 mapping population. Plants in this F2 mapping population varied in fatty acid content, flowering time, and growth-related traits. Using quantitative trait locus (QTL) mapping, we aimed to determine if Da-Ae and Da-Ol-1 provided novel genetic variation beyond what has already been found in B. napus. Making use of the genotyping information generated from RNA-seq data of these two lines and their F2 mapping population of 166 plants, we constructed a genetic map consisting of 2,021 single nucleotide polymorphism markers that spans 2,929 cM across 19 linkage groups. Besides the known major QTL identified, our high resolution genetic map facilitated the identification of several new QTL contributing to the different fatty acid levels, flowering time, and growth-related trait values. These new QTL probably represent novel genetic variation that existed in our new synthetic B. napus strain. By conducting genome-wide expression variation analysis in our F2 mapping population, genetic regions that potentially regulate many genes across the genome were revealed. A FLOWERING LOCUS C gene homolog, which was identified as a candidate regulating flowering time and multiple growth-related traits, was found underlying one of these regions. Integrated QTL and expression QTL analyses also helped us identified candidate causative genes associated with various biological traits through expression level change and/or possible protein function modification.

De Novo Transcriptome Analysis to Identify Anthocyanin Biosynthesis Genes Responsible for Tissue-Specific Pigmentation in Zoysiagrass (Zoysia japonica Steud.).

Zoysiagrass (Zoysia japonica Steud.) is commonly found in temperate climate regions and widely used for lawns, in part, owing to its uniform green color. However, some zoysiagrass cultivars accumulate red to purple pigments in their spike and stolon tissues, thereby decreasing the aesthetic value. Here we analyzed the anthocyanin contents of two zoysiagrass cultivars 'Anyang-jungji' (AJ) and 'Greenzoa' (GZ) that produce spikes and stolons with purple and green colors, respectively, and revealed that cyanidin and petunidin were primarily accumulated in the pigmented tissues. In parallel, we performed a de novo transcriptome assembly and identified differentially expressed genes between the two cultivars. We found that two anthocyanin biosynthesis genes encoding anthocyanidin synthase (ANS) and dihydroflavonol 4-reductase (DFR) were preferentially upregulated in the purple AJ spike upon pigmentation. Both ANS and DFR genes were also highly expressed in other zoysiagrass cultivars with purple spikes and stolons, but their expression levels were significantly low in the cultivars with green tissues. We observed that recombinant ZjDFR1 and ZjANS1 proteins successfully catalyze the conversions of dihydroflavonols into leucoanthocyanidins and leucoanthocyanidins into anthocyanidins, respectively. These findings strongly suggest that upregulation of ANS and DFR is responsible for tissue-specific anthocyanin biosynthesis and differential pigmentation in zoysiagrass. The present study also demonstrates the feasibility of a de novo transcriptome analysis to identify the key genes associated with specific traits, even in the absence of reference genome information.

Effects of high hydrostatic pressure treatment on the enhancement of functional components of germinated rough rice (Oryza sativa L.).

This study was performed to evaluate the enhancement of functional components of germinated rough rice. Rough rice was germinated at 37 °C for 6 days, and subjected to a high hydrostatic pressure treatment (HPT) at 30 MPa for 24 h (HP24) and 48 h (HP48). Germinated rough rice without HPT (HP0), HP24, and HP48 were analysed for their functional components. The highest γ-aminobutyric acid, total arabinoxylan, and tricin 4'-O-(threo-ß-guaiacylglyceryl) ether contents were 121.21 mg/100g, 10.6%, and 85.82 µg/g, respectively, after HP48 for 2 days. γ-Oryzanol contents increased from 23.19-36.20 mg/100g (at HP0) to 31.80-40.32 mg/100g (at HP48). The highest vitamin B (60.99 mg/100g) and E (4.07 mg/100g) contents were observed after HP24 for 5 and 2 days, respectively. These results suggest that a combination of HPT and germination efficiently enhances the functional characteristics of rough rice.

Cloning of genes differentially expressed during the initial stage of fruit development in melon (Cucumis melo cv. Reticulatus).

We have cloned genes involved in the initial stage of fruit development in the melon by suppression subtractive hybridization. A cDNA library of unfertilized ovules was subtracted from that of fruit 9 days after pollination (DAP); 10 of the 40 selected cDNA clones were identified by reverse Northern analysis as genes differentially expressed in fruit at 9 DAP. Seven of the ten genes were homologous to genes of known function; two were related to genes with unknown functions, and one was novel. With the exception of cucumisin, none of the cDNAs had been previously identified in melon. According to Northern analyses, six of the genes were expressed at high levels early in fruit development. Expression of cucumisin, Cmf-25, Cmf-30, and Cmf-124 was highest at 9 DAP, implying that these genes are involved in the initial stage of fruit development. Cmf-30, a seed nucellus-specific gene, was also expressed early in seed development. The other genes were expressed at a moderate level throughout fruit development, with the highest expression occurring in fruit at 9 and 18 DAP. In conclusion, nine new genes involved in early fruit development in melon were cloned, and their temporal and spatial expression patterns indicate that they are preferentially expressed during the active growing stage of fruit.